@article{
 title = {Capital Breeding in a Diapausing Copepod: A Transcriptomics Analysis},
 type = {article},
 year = {2020},
 keywords = {Energy resources,Gene Expression,Neocalanus flemingeri,Oogenesis,RNA-Seq},
 pages = {56},
 volume = {7},
 websites = {https://www.frontiersin.org/article/10.3389/fmars.2020.00056/full},
 month = {3},
 publisher = {Frontiers},
 day = {6},
 id = {6bfc10a6-4435-3ef4-9aae-951c94ee2a93},
 created = {2020-04-29T21:57:54.675Z},
 accessed = {2020-03-06},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.732Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Capital breeders must balance the energetic requirements of cellular function and the cost of reproduction in organisms. The subarctic copepod Neocalanus flemingeri, a small planktonic crustacean, depends on a short annual phytoplankton bloom to acquire the energy needed to support a non-feeding female adult that enters a period of diapause prior to spawning five to seven months later. After emergence from diapause, the reproductive program takes two-months starting with germline development. The relationships between energy utilization, cellular maintenance and oogenesis were investigated through gene expression profiling. The sequential up- and down-regulation of genes involved in cellular maintenance and metabolic pathways coincided with four developmental groups: diapause, emergence from diapause and early oogenesis, mid to late oogenesis, and finally spawning and end-of-life. Up-regulation of genes involved in cellular homeostasis, glycolysis and lipid catabolism as well as germline development characterized the transition from diapause to post-diapause. The down-regulation of genes involved in cellular homeostasis coincided with the up-regulation of genes related to mid-late oogenesis and protein degradation. As females started to spawn, genes involved in protein ubiquitination and programmed cell death became up-regulated. Energy allocation and utilization is highly dynamic in N. flemingeri during the non-feeding period and it is linked to the provisioning and maturation of eggs through lipid catabolism and autophagy. The data suggest the presence of a mechanism that regulates fecundity to match the availability of stored resources. Such a mechanism would minimize reproductive failure when resources and contribute to the resilience of the species.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Cieslak, Matthew C. and Hopcroft, Russell R. and Lenz, Petra H.},
 doi = {10.3389/fmars.2020.00056},
 journal = {Frontiers in Marine Science}
}

Capital breeders must balance the energetic requirements of cellular function and the cost of reproduction in organisms. The subarctic copepod Neocalanus flemingeri, a small planktonic crustacean, depends on a short annual phytoplankton bloom to acquire the energy needed to support a non-feeding female adult that enters a period of diapause prior to spawning five to seven months later. After emergence from diapause, the reproductive program takes two-months starting with germline development. The relationships between energy utilization, cellular maintenance and oogenesis were investigated through gene expression profiling. The sequential up- and down-regulation of genes involved in cellular maintenance and metabolic pathways coincided with four developmental groups: diapause, emergence from diapause and early oogenesis, mid to late oogenesis, and finally spawning and end-of-life. Up-regulation of genes involved in cellular homeostasis, glycolysis and lipid catabolism as well as germline development characterized the transition from diapause to post-diapause. The down-regulation of genes involved in cellular homeostasis coincided with the up-regulation of genes related to mid-late oogenesis and protein degradation. As females started to spawn, genes involved in protein ubiquitination and programmed cell death became up-regulated. Energy allocation and utilization is highly dynamic in N. flemingeri during the non-feeding period and it is linked to the provisioning and maturation of eggs through lipid catabolism and autophagy. The data suggest the presence of a mechanism that regulates fecundity to match the availability of stored resources. Such a mechanism would minimize reproductive failure when resources and contribute to the resilience of the species.

@article{
 title = {Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus},
 type = {article},
 year = {2019},
 keywords = {Cave,De novo transcriptome,Differential expression,Regressive evolution,Troglomorphy},
 pages = {42},
 volume = {11},
 websites = {https://www.mdpi.com/2073-4425/11/1/42},
 month = {12},
 publisher = {MDPI AG},
 day = {29},
 id = {1eeab3b4-5f35-350b-934f-a111a928def2},
 created = {2020-04-29T21:57:54.627Z},
 accessed = {2020-02-10},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.720Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {<p>Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.</p>},
 bibtype = {article},
 author = {Gross, Joshua B. and Sun, Dennis A. and Carlson, Brian M. and Brodo-Abo, Sivan and Protas, Meredith E.},
 doi = {10.3390/genes11010042},
 journal = {Genes},
 number = {1}
}

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.

@article{
 title = {Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum},
 type = {article},
 year = {2019},
 keywords = {Differential gene expression,Flowering,Metabolome,Rhododendron arboreum,Transcriptome,Winter adaptation},
 pages = {1-10},
 volume = {690},
 month = {3},
 publisher = {Elsevier B.V.},
 day = {30},
 id = {27f37b1f-0e1b-321d-a02f-5df0023ff4b6},
 created = {2020-04-29T21:57:54.764Z},
 accessed = {2019-08-12},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.835Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Rhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responses.},
 bibtype = {article},
 author = {Choudhary, Shruti and Thakur, Sapna and Jaitak, Vikas and Bhardwaj, Pankaj},
 doi = {10.1016/j.gene.2018.12.035},
 journal = {Gene}
}

Rhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responses.

@article{
 title = {Gene and metabolite profiling reveals flowering and survival strategies in Himalayan Rhododendron arboreum},
 type = {article},
 year = {2019},
 keywords = {Differential gene expression,Flowering,Metabolome,Rhododendron arboreum,Transcriptome,Winter adaptation},
 pages = {1-10},
 volume = {690},
 id = {57f3246b-e7bd-3838-b696-ec69396ccdaf},
 created = {2020-04-29T21:57:55.065Z},
 accessed = {2019-08-06},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.157Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Rhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responses.},
 bibtype = {article},
 author = {Choudhary, Shruti and Thakur, Sapna and Jaitak, Vikas and Bhardwaj, Pankaj},
 doi = {10.1016/j.gene.2018.12.035},
 journal = {Gene}
}

Rhododendron arboreum inhabits the Himalayan climate otherwise detrimental to many species, though the underlying survival mechanism remains unclear. Such temperate species have an inherent endurance towards freezing temperature which is prerequisite for an initiation and transition to flowering phase. Orchestrating the molecular architecture is vital towards managing distinct abiotic signals. To determine the molecular factors directing growth, development, and tolerance under environmental extremes in the species, the high-throughput transcriptome and metabolome data from vegetative as well as cold-acclimatized flowering season tissues were generated. Firstly, the de novo assembly pertaining to the foliar and floral tissues comprising of 157,427 unigenes was examined for a comparative analysis. 4149 of 12,577 transcripts observed with a significant fluctuating expression corresponded to seasonal retorts. Following the interactive network, 525 genes were distinguished as the epicenters of sense, response, and tolerance. Secondly, liquid chromatography coupled to mass spectrometry was adopted to profile the extent of metabolite richness across the tissues of two seasons. Taking into account the formula-based mappings offered by MetaboSearch tool, 421 unique ions obtained were annotated to 173 KEGG compounds, especially secondary metabolites. Moreover, by integrating the transcript and metabolite annotations, it was found that right from active metabolism, signaling, development, and their regulations, supplementary response to abiotic/biotic stimuli was induced. A multifaceted response displayed during flowering not only sponsored the climatic encounters but brought the shift from vegetative to reproductive growth. Overall, this comprehensive approach following transcriptome and non-targeted metabolome elucidated the contribution of genetic and metabolic factors in environmental responses.

@article{
 title = {Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2,517 ultraconserved element loci},
 type = {article},
 year = {2019},
 pages = {ukz012},
 volume = {136},
 id = {f9012880-0585-3567-885a-b3cf01cd8ea6},
 created = {2020-04-29T21:57:55.095Z},
 accessed = {2019-08-06},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.192Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Winker, Kevin and Glenn, Travis and Withrow, Jack and Sealy, Spencer and Faircloth, Brant},
 doi = {10.1093/auk/ukz012},
 journal = {The Auk: Ornithological Advances},
 number = {2}
}

@article{
 title = {Multiple plasticity regulators reveal targets specifying an induced predatory form in nematodes},
 type = {article},
 year = {2019},
 keywords = {Pristionchus pacificus,alternative splicing,developmental plasticity,differential expression,phenotypic variation,switch mechanism},
 volume = {msz171},
 websites = {https://academic.oup.com/mbe/advance-article-abstract/doi/10.1093/molbev/msz171/5541796},
 id = {1e190e53-6dfd-3f62-88cf-4f026f3f9767},
 created = {2020-04-29T21:57:55.146Z},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.207Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 private_publication = {false},
 abstract = {The ability to translate a single genome into multiple phenotypes, or developmental plasticity, defines how phenotype derives from more than just genes. However, to study the evolutionary targets of plasticity and their evolutionary fates, we need to understand how genetic regulators of plasticity control downstream gene expression. Here, we have identified a transcriptional response specific to polyphenism (i.e., discrete plasticity) in the nematode Pristionchus pacificus. This species produces alternative resource-use morphs-microbivorous and predatory forms, differing in the form of their teeth, a morphological novelty-as influenced by resource availability. Transcriptional profiles common to multiple polyphenism-controlling genes in P. pacificus reveal a suite of environmentally sensitive loci, or ultimate target genes, that make up an induced developmental response. Additionally, in vitro assays show that one polyphenism regulator, the nuclear receptor (NR) NHR-40, physically binds to promoters with putative HNF4⍺ (the NR class including NHR-40) binding sites, suggesting this receptor may directly regulate genes that describe alternative morphs. Among differentially expressed genes were morph-limited genes, highlighting factors with putative "on-off" function in plasticity regulation. Further, predatory morph-biased genes included candidates-namely, all four P. pacificus homologs of Hsp70, which have HNF4⍺ motifs-whose natural variation in expression matches phenotypic differences among P. pacificus wild isolates. In summary, our study links polyphenism regulatory loci to the transcription producing alternative forms of a morphological novelty. Consequently, our findings establish a platform for determining how specific regulators of morph-biased genes may influence selection on plastic phenotypes.},
 bibtype = {article},
 author = {Bui, Linh T and Ragsdale, Erik J},
 doi = {10.1093/molbev/msz171/5541796},
 journal = {Molecular Biology and Evolution}
}

The ability to translate a single genome into multiple phenotypes, or developmental plasticity, defines how phenotype derives from more than just genes. However, to study the evolutionary targets of plasticity and their evolutionary fates, we need to understand how genetic regulators of plasticity control downstream gene expression. Here, we have identified a transcriptional response specific to polyphenism (i.e., discrete plasticity) in the nematode Pristionchus pacificus. This species produces alternative resource-use morphs-microbivorous and predatory forms, differing in the form of their teeth, a morphological novelty-as influenced by resource availability. Transcriptional profiles common to multiple polyphenism-controlling genes in P. pacificus reveal a suite of environmentally sensitive loci, or ultimate target genes, that make up an induced developmental response. Additionally, in vitro assays show that one polyphenism regulator, the nuclear receptor (NR) NHR-40, physically binds to promoters with putative HNF4⍺ (the NR class including NHR-40) binding sites, suggesting this receptor may directly regulate genes that describe alternative morphs. Among differentially expressed genes were morph-limited genes, highlighting factors with putative "on-off" function in plasticity regulation. Further, predatory morph-biased genes included candidates-namely, all four P. pacificus homologs of Hsp70, which have HNF4⍺ motifs-whose natural variation in expression matches phenotypic differences among P. pacificus wild isolates. In summary, our study links polyphenism regulatory loci to the transcription producing alternative forms of a morphological novelty. Consequently, our findings establish a platform for determining how specific regulators of morph-biased genes may influence selection on plastic phenotypes.

@article{
 title = {Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny},
 type = {article},
 year = {2019},
 keywords = {Free-living,Nematoda,Parasitism,Phylogenomic},
 volume = {19},
 id = {b8acc90c-571c-3162-861b-dc5414694c16},
 created = {2020-04-29T21:57:55.163Z},
 accessed = {2019-08-06},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.261Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {article},
 author = {Smythe, Ashleigh B. and Holovachov, Oleksandr and Kocot, Kevin M.},
 doi = {10.1186/s12862-019-1444-x},
 journal = {BMC Evolutionary Biology},
 number = {121}
}

@article{
 title = {Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics},
 type = {article},
 year = {2019},
 keywords = {Aureococcus anophagefferens,Brown tide,Nutrient physiology,harmful  algal  bloom,metatranscirptomics,pelagophyte},
 pages = {136},
 volume = {10},
 websites = {https://www.frontiersin.org/article/10.3389/fmicb.2019.00136/full},
 month = {2},
 publisher = {Frontiers},
 day = {12},
 id = {c036f981-4a71-33d7-b719-7cb7b848c3a3},
 created = {2020-04-29T21:57:57.536Z},
 accessed = {2019-06-27},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.618Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy. However, defining best nutrient management practices is a long-standing challenge, in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data highlight the role of phosphorus in brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.},
 bibtype = {article},
 author = {Wurch, Louie L. and Alexander, Harriet and Frischkorn, Kyle R. and Haley, Sheean T. and Gobler, Christopher J. and Dyhrman, Sonya T.},
 doi = {10.3389/fmicb.2019.00136},
 journal = {Frontiers in Microbiology}
}

Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy. However, defining best nutrient management practices is a long-standing challenge, in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data highlight the role of phosphorus in brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.

@article{
 title = {Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata},
 type = {article},
 year = {2018},
 pages = {e0006730},
 volume = {12},
 month = {10},
 publisher = {NLM (Medline)},
 day = {1},
 id = {6559325e-f82c-3648-964d-c70e2f424dac},
 created = {2020-04-29T21:57:54.865Z},
 accessed = {2019-08-12},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.921Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.},
 bibtype = {article},
 author = {Orantes, Lucia C. and Monroy, Carlota and Dorn, Patricia L. and Stevens, Lori and Rizzo, Donna M. and Morrissey, Leslie and Hanley, John P. and Rodas, Antonieta Guadalupe and Richards, Bethany and Wallin, Kimberly F. and Helms Cahan, Sara},
 doi = {10.1371/journal.pntd.0006730},
 journal = {PLoS neglected tropical diseases},
 number = {10}
}

Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.

@article{
 title = {De novo transcriptome assembly of the calanoid copepod Neocalanus flemingeri: A new resource for emergence from diapause},
 type = {article},
 year = {2018},
 keywords = {CAP3 assembly program,Dormancy,Illumina,Sub Artic Pacific Ocean,Trinity},
 id = {07f48277-03d8-3b43-ace8-202df8d6e45f},
 created = {2020-04-29T21:57:54.899Z},
 accessed = {2019-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.961Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Cieslak, Matthew C. and Sommer, Stephanie A. and Hopcroft, Russell R. and Lenz, Petra H.},
 doi = {10.1016/j.margen.2017.09.002},
 journal = {Marine Genomics}
}

Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.

@article{
 title = {Differentially expressed genes in hemocytes of Litopenaeus vannamei challenged with Vibrio parahaemolyticus AHPND (VPAHPND) and VPAHPND toxin},
 type = {article},
 year = {2018},
 keywords = {Early mortality syndrome,Hemocyte,Immune system,Shrimp,Transcriptome},
 id = {5b672441-9c7d-35ee-8f9e-6a3e1737bbfb},
 created = {2020-04-29T21:57:54.984Z},
 accessed = {2019-08-06},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.070Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {While toxin-harboring Vibrio parahaemolyticus has been previously established as the causative agent of early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimp, information on the mechanistic processes that happen in the host during infection is still lacking. Here, we examined the expression responses of the shrimp hemocyte transcriptome to V. parahaemolyticus AHPND (VPAHPND) by RNA sequencing (RNA-seq). Using libraries (SRA accession number SRP137285) prepared from shrimp hemocytes under experimental conditions, a reference library was de novo assembled for gene expression analysis of VPAHPND-challenged samples at 0, 3/6, and 48 h post infection (hpi). Using the library from 0-hpi as the control, 359 transcripts were found to be differentially expressed in the 3/6-hpi library, while 429 were differentially expressed in the 48-hpi library. The expression patterns reported in the RNA-seq of 9 representative genes such as anti-lipopolysaccharide factor (LvALF), crustin p (CRU), serpin 3 (SER), C-type lectin 3 (CTL), clottable protein 2 (CLO), mitogen-activated protein kinase kinase 4 (MKK4), P38 mitogen-activated protein kinase (P38), protein kinase A regulatory subunit 1 (PKA) and DNAJ homolog subfamily C member 1-like (DNJ) were validated by qRT-PCR. The expression of these genes was also analyzed in shrimp that were injected with the partially purified VPAHPND toxin. A VPAHPND toxin-responsive gene, LvALF was identified, and its function was characterized by RNA interference. LvALF knockdown resulted in significantly rapid increase of shrimp mortality caused by toxin injection. Protein-protein interaction analysis by molecular docking suggested that LvALF possibly neutralizes VPAHPND toxin through its LPS-binding domain. The data generated in this study provide preliminary insights into the differences in the immune response of shrimp to the bacterial and toxic aspect of VPAHPND as a disease.},
 bibtype = {article},
 author = {Maralit, Benedict A. and Jaree, Phattarunda and Boonchuen, Pakpoom and Tassanakajon, Anchalee and Somboonwiwat, Kunlaya},
 doi = {10.1016/j.fsi.2018.06.054},
 journal = {Fish and Shellfish Immunology}
}

While toxin-harboring Vibrio parahaemolyticus has been previously established as the causative agent of early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimp, information on the mechanistic processes that happen in the host during infection is still lacking. Here, we examined the expression responses of the shrimp hemocyte transcriptome to V. parahaemolyticus AHPND (VPAHPND) by RNA sequencing (RNA-seq). Using libraries (SRA accession number SRP137285) prepared from shrimp hemocytes under experimental conditions, a reference library was de novo assembled for gene expression analysis of VPAHPND-challenged samples at 0, 3/6, and 48 h post infection (hpi). Using the library from 0-hpi as the control, 359 transcripts were found to be differentially expressed in the 3/6-hpi library, while 429 were differentially expressed in the 48-hpi library. The expression patterns reported in the RNA-seq of 9 representative genes such as anti-lipopolysaccharide factor (LvALF), crustin p (CRU), serpin 3 (SER), C-type lectin 3 (CTL), clottable protein 2 (CLO), mitogen-activated protein kinase kinase 4 (MKK4), P38 mitogen-activated protein kinase (P38), protein kinase A regulatory subunit 1 (PKA) and DNAJ homolog subfamily C member 1-like (DNJ) were validated by qRT-PCR. The expression of these genes was also analyzed in shrimp that were injected with the partially purified VPAHPND toxin. A VPAHPND toxin-responsive gene, LvALF was identified, and its function was characterized by RNA interference. LvALF knockdown resulted in significantly rapid increase of shrimp mortality caused by toxin injection. Protein-protein interaction analysis by molecular docking suggested that LvALF possibly neutralizes VPAHPND toxin through its LPS-binding domain. The data generated in this study provide preliminary insights into the differences in the immune response of shrimp to the bacterial and toxic aspect of VPAHPND as a disease.

@techreport{
 title = {Big Data Science Training Program at a Minority Serving Institution: Processes and Initial Outcomes},
 type = {techreport},
 year = {2018},
 source = {Californian Journal of Health Promotion},
 keywords = {Big Data,Data Science,Education,Training},
 pages = {1-5},
 volume = {16},
 issue = {1},
 websites = {www.UseGalaxy.org},
 id = {ab9ac866-fd76-3f57-9f8f-0f267ae8346f},
 created = {2020-04-29T21:57:55.054Z},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.127Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 bibtype = {techreport},
 author = {Mceligot, A J and Cuajungco, M P and Behseta, S and Chandler, L and Chauhan, H and Mitra, S and Rusmevichientong, P and Charles, S}
}

@article{
 title = {Transcriptional patterns identify resource controls on the diazotroph Trichodesmium in the Atlantic and Pacific oceans},
 type = {article},
 year = {2018},
 pages = {1486-1495},
 volume = {12},
 websites = {https://doi.org/10.1038/s41396-018-0087-z},
 id = {8a8a5054-f92a-3bae-b8ec-81cdcb2239ff},
 created = {2020-04-29T21:57:55.317Z},
 accessed = {2019-06-27},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.421Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {The N 2-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.},
 bibtype = {article},
 author = {Rouco, Mónica and Frischkorn, Kyle R and Haley, Sheean T and Alexander, Harriet and Dyhrman, Sonya T},
 doi = {10.1038/s41396-018-0087-z},
 journal = {The ISME Journal}
}

The N 2-fixing cyanobacterium Trichodesmium is intensely studied because of the control this organism exerts over the cycling of carbon and nitrogen in the low nutrient ocean gyres. Although iron (Fe) and phosphorus (P) bioavailability are thought to be major drivers of Trichodesmium distributions and activities, identifying resource controls on Trichodesmium is challenging, as Fe and P are often organically complexed and their bioavailability to a single species in a mixed community is difficult to constrain. Further, Fe and P geochemistries are linked through the activities of metalloenzymes, such as the alkaline phosphatases (APs) PhoX and PhoA, which are used by microbes to access dissolved organic P (DOP). Here we identified significant correlations between Trichodesmium-specific transcriptional patterns in the North Atlantic (NASG) and North Pacific Subtropical Gyres (NPSG) and patterns in Fe and P biogeochemistry, with the relative enrichment of Fe stress markers in the NPSG, and P stress markers in the NASG. We also observed the differential enrichment of Fe-requiring PhoX transcripts in the NASG and Fe-insensitive PhoA transcripts in the NPSG, suggesting that metalloenzyme switching may be used to mitigate Fe limitation of DOP metabolism in Trichodesmium. This trait may underpin Trichodesmium success across disparate ecosystems.

@article{
 title = {Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods},
 type = {article},
 year = {2018},
 pages = {330-342},
 volume = {118},
 websites = {https://www.sciencedirect.com/science/article/pii/S1055790317301112?via%3Dihub},
 month = {1},
 publisher = {Academic Press},
 day = {1},
 id = {6920c530-45c8-3c31-9350-e305c8dfe880},
 created = {2020-04-29T21:57:55.395Z},
 accessed = {2018-09-19},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.468Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life.},
 bibtype = {article},
 author = {Lindgren, Annie R. and Anderson, Frank E.},
 doi = {10.1016/J.YMPEV.2017.10.004},
 journal = {Molecular Phylogenetics and Evolution}
}

Historically, deep-level relationships within the molluscan class Cephalopoda (squids, cuttlefishes, octopods and their relatives) have remained elusive due in part to the considerable morphological diversity of extant taxa, a limited fossil record for species that lack a calcareous shell and difficulties in sampling open ocean taxa. Many conflicts identified by morphologists in the early 1900s remain unresolved today in spite of advances in morphological, molecular and analytical methods. In this study we assess the utility of transcriptome data for resolving cephalopod phylogeny, with special focus on the orders of Decapodiformes (open-eye squids, bobtail squids, cuttlefishes and relatives). To do so, we took new and previously published transcriptome data and used a unique cephalopod core ortholog set to generate a dataset that was subjected to an array of filtering and analytical methods to assess the impacts of: taxon sampling, ortholog number, compositional and rate heterogeneity and incongruence across loci. Analyses indicated that datasets that maximized taxonomic coverage but included fewer orthologs were less stable than datasets that sacrificed taxon sampling to increase the number of orthologs. Clades recovered irrespective of dataset, filtering or analytical method included Octopodiformes (Vampyroteuthis infernalis + octopods), Decapodiformes (squids, cuttlefishes and their relatives), and orders Oegopsida (open-eyed squids) and Myopsida (e.g., loliginid squids). Ordinal-level relationships within Decapodiformes were the most susceptible to dataset perturbation, further emphasizing the challenges associated with uncovering relationships at deep nodes in the cephalopod tree of life.

@article{
 title = {Periodic and coordinated gene expression between a diazotroph and its diatom host},
 type = {article},
 year = {2018},
 websites = {http://www.nature.com/articles/s41396-018-0262-2},
 month = {8},
 day = {16},
 id = {33e0b1cb-537e-3022-8278-68d29cc6a511},
 created = {2020-04-29T21:57:55.444Z},
 accessed = {2018-08-23},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.540Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Harke2018},
 private_publication = {false},
 abstract = {In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom–diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day–night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont–host physiological ecology is strongly interconnected in the NPSG.},
 bibtype = {article},
 author = {Harke, Matthew J. and Frischkorn, Kyle R. and Haley, Sheean T. and Aylward, Frank O. and Zehr, Jonathan P. and Dyhrman, Sonya T.},
 doi = {10.1038/s41396-018-0262-2},
 journal = {The ISME Journal},
 keywords = {PY8}
}

In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom–diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day–night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont–host physiological ecology is strongly interconnected in the NPSG.

@article{
 title = {De novo transcriptome assembly of the calanoid copepod Neocalanus flemingeri: A new resource for emergence from diapause},
 type = {article},
 year = {2018},
 keywords = {PY8},
 pages = {114-119},
 volume = {37},
 websites = {https://www.sciencedirect.com/science/article/pii/S1874778717302155?via%3Dihub},
 month = {2},
 publisher = {Elsevier},
 day = {1},
 id = {ae97b1d1-4510-396e-9077-e7284fe01a1a},
 created = {2020-04-29T21:57:55.488Z},
 accessed = {2018-08-22},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.550Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Roncalli2018},
 private_publication = {false},
 abstract = {Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Cieslak, Matthew C. and Sommer, Stephanie A. and Hopcroft, Russell R. and Lenz, Petra H.},
 doi = {10.1016/j.margen.2017.09.002},
 journal = {Marine Genomics}
}

Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.

@article{
 title = {Surgical necrotizing enterocolitis in extremely premature neonates is associated with genetic variations in an intergenic region of chromosome 8},
 type = {article},
 year = {2018},
 pages = {943-953},
 volume = {83},
 websites = {http://www.nature.com/doifinder/10.1038/pr.2018.33},
 month = {5},
 publisher = {Nature Publishing Group},
 day = {16},
 id = {598440e5-5c94-3eef-bc32-610437bb51eb},
 created = {2020-04-29T21:57:55.606Z},
 accessed = {2018-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.688Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Jilling2018},
 private_publication = {false},
 abstract = {Surgical necrotizing enterocolitis in extremely premature neonates is associated with genetic variations in an intergenic region of chromosome 8},
 bibtype = {article},
 author = {Jilling, Tamas and Ambalavanan, Namasivayam and Cotten, C. Michael and Martin, Colin A. and Maheshwari, Akhil and Schibler, Kurt and Levy, Joshua and Page, Grier P.},
 doi = {10.1038/pr.2018.33},
 journal = {Pediatric Research},
 number = {5},
 keywords = {PY8}
}

Surgical necrotizing enterocolitis in extremely premature neonates is associated with genetic variations in an intergenic region of chromosome 8

@article{
 title = {Ultraconserved elements ( UCEs ) illuminate the population genomics of a recent , high-latitude avian speciation event},
 type = {article},
 year = {2018},
 keywords = {PY8},
 websites = {https://peerj.com/preprints/27035/},
 month = {7},
 publisher = {PeerJ Inc.},
 day = {13},
 id = {c03d17f1-35ea-3660-aad1-706b23e2a721},
 created = {2020-04-29T21:57:55.618Z},
 accessed = {2018-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.724Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Winker2018},
 private_publication = {false},
 abstract = {Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8- 5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.},
 bibtype = {article},
 author = {Winker, Kevin and Glenn, Travis C and Faircloth, Brant C},
 doi = {https://doi.org/10.7287/peerj.preprints.27035v1},
 journal = {PeerJ PrePrints}
}

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8- 5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

@article{
 title = {Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species ( Rhododendron arboreum )},
 type = {article},
 year = {2018},
 keywords = {PY8},
 pages = {417-428},
 volume = {61},
 websites = {http://www.nrcresearchpress.com/doi/10.1139/gen-2017-0143},
 month = {6},
 publisher = {NRC Research Press},
 id = {be848dc9-3f02-3dbc-9308-fbc4a1b6c10c},
 created = {2020-04-29T21:57:55.774Z},
 accessed = {2018-08-09},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.828Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Choudhary2018},
 private_publication = {false},
 abstract = {Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710...},
 bibtype = {article},
 author = {Choudhary, Shruti and Thakur, Sapna and Najar, Raoof Ahmad and Majeed, Aasim and Singh, Amandeep and Bhardwaj, Pankaj},
 editor = {Crease, T.},
 doi = {10.1139/gen-2017-0143},
 journal = {Genome},
 number = {6}
}

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710...

@article{
 title = {Prediction of a peptidome for the ecotoxicological model Hyalella azteca (Crustacea; Amphipoda) using a de novo assembled transcriptome},
 type = {article},
 year = {2018},
 keywords = {PY8},
 pages = {67-88},
 volume = {38},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/29395622,http://linkinghub.elsevier.com/retrieve/pii/S1874778717303252},
 month = {4},
 id = {4b84e6d5-497e-3206-92a3-9dbb851b0f0b},
 created = {2020-04-29T21:57:56.166Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.245Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Christie2018},
 private_publication = {false},
 abstract = {Due to its sensitivity to many environmental and anthropogenic stressors, including a wide range of chemical compounds, Hyalella azteca, a freshwater amphipod, has emerged as one of the most commonly used invertebrates for ecotoxicological assessment.Peptidergic signaling systems are key components in the control of organism-environment interactions, and there is a growing literature suggesting that they are targets of a number of aquatic toxicants.Interestingly, and despite its model species status in the field of ecotoxicology, little is known about the peptide hormones of H. azteca.Here, a transcriptome was produced for this species using the de novo assembler Trinity and mined for sequences encoding putative peptide precursors; the transcriptome was assembled from 460,291,636 raw reads and consists of 133,486 unique transcripts.Seventy-six sequences encoding peptide pre/preprohormones were identified from this transcriptome, allowing for the prediction of 202 distinct peptides, which included members of the allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, ecdysis-triggering hormone, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone, GSEFLamide, inotocin, leucokinin, myosuppressin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families.These peptides expand the known peptidome for H. azteca approximately nine-fold, forming a strong foundation for future studies of peptidergic control, including disruption by aquatic toxicants, in this important ecotoxicological model.},
 bibtype = {article},
 author = {Christie, Andrew E. and Cieslak, Matthew C. and Roncalli, Vittoria and Lenz, Petra H. and Major, Kaley M. and Poynton, Helen C.},
 doi = {10.1016/j.margen.2017.12.003},
 journal = {Marine Genomics}
}

Due to its sensitivity to many environmental and anthropogenic stressors, including a wide range of chemical compounds, Hyalella azteca, a freshwater amphipod, has emerged as one of the most commonly used invertebrates for ecotoxicological assessment.Peptidergic signaling systems are key components in the control of organism-environment interactions, and there is a growing literature suggesting that they are targets of a number of aquatic toxicants.Interestingly, and despite its model species status in the field of ecotoxicology, little is known about the peptide hormones of H. azteca.Here, a transcriptome was produced for this species using the de novo assembler Trinity and mined for sequences encoding putative peptide precursors; the transcriptome was assembled from 460,291,636 raw reads and consists of 133,486 unique transcripts.Seventy-six sequences encoding peptide pre/preprohormones were identified from this transcriptome, allowing for the prediction of 202 distinct peptides, which included members of the allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, ecdysis-triggering hormone, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone, GSEFLamide, inotocin, leucokinin, myosuppressin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families.These peptides expand the known peptidome for H. azteca approximately nine-fold, forming a strong foundation for future studies of peptidergic control, including disruption by aquatic toxicants, in this important ecotoxicological model.

@article{
 title = {Vectors of diversity: Genome wide diversity across the geographic range of the Chagas disease vector Triatoma dimidiata sensu lato (Hemiptera: Reduviidae)},
 type = {article},
 year = {2018},
 keywords = {Biogeography,Chagas disease,Insect vector,Phylogeny,Species delimitation,Triatoma dimidiata},
 pages = {144-150},
 volume = {120},
 month = {3},
 publisher = {Academic Press Inc.},
 day = {1},
 id = {dbabf380-53fe-3e7b-b5f2-d52a55033714},
 created = {2020-04-29T21:57:57.129Z},
 accessed = {2019-08-12},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.221Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {To date, the phylogeny of Triatoma dimidiata sensu lato (s. l.) (Hemiptera: Reduviidae: Triatominae), the epidemiologically most important Chagas disease vector in Central America and a secondary vector in Mexico and northern South America, has only been investigated by one multi-copy nuclear gene (Internal Transcribed Spacer – 2) and a few mitochondrial genes. We examined 450 specimens sampled across most of its native range from Mexico to Ecuador using reduced representation next-generation sequencing encompassing over 16,000 single nucleotide polymorphisms (SNPs). Using a combined phylogenetic and species delimitation approach we uncovered two distinct species, as well as a well-defined third group that may contain multiple species. The findings are discussed with respect to possible drivers of diversification and the epidemiological importance of the distinct species and groups.},
 bibtype = {article},
 author = {Justi, Silvia A. and Cahan, Sara and Stevens, Lori and Monroy, Carlota and Lima-Cordón, Raquel and Dorn, Patricia L.},
 doi = {10.1016/j.ympev.2017.12.016},
 journal = {Molecular Phylogenetics and Evolution}
}

To date, the phylogeny of Triatoma dimidiata sensu lato (s. l.) (Hemiptera: Reduviidae: Triatominae), the epidemiologically most important Chagas disease vector in Central America and a secondary vector in Mexico and northern South America, has only been investigated by one multi-copy nuclear gene (Internal Transcribed Spacer – 2) and a few mitochondrial genes. We examined 450 specimens sampled across most of its native range from Mexico to Ecuador using reduced representation next-generation sequencing encompassing over 16,000 single nucleotide polymorphisms (SNPs). Using a combined phylogenetic and species delimitation approach we uncovered two distinct species, as well as a well-defined third group that may contain multiple species. The findings are discussed with respect to possible drivers of diversification and the epidemiological importance of the distinct species and groups.

@article{
 title = {Physiological characterization of the emergence from diapause: A transcriptomics approach},
 type = {article},
 year = {2018},
 pages = {12577},
 volume = {8},
 id = {f38b49da-6ab6-3911-bd51-667c280bd533},
 created = {2020-04-29T21:57:57.188Z},
 accessed = {2019-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.299Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {© 2018, The Author(s). Organisms inhabiting high-latitude environments have evolved adaptations, such as diapause to time reproduction and growth to optimize their survival. However, the physiological regulation of the timing of complex life histories is poorly understood, particularly for marine copepods, that diapause at depth. A member of the pelagic community of the sub-Arctic Pacific Ocean, Neocalanus flemingeri enters diapause in June. Egg production occurs in winter/spring. In order to characterize the transition from diapause to egg release, females were collected in late September from 400–700 m depth, incubated in the dark at 4–5 °C and sampled for RNASeq at weekly intervals. The diapause phenotype showed down-regulation of protein turnover and up-regulation of stress genes. Activation of the reproductive program was marked by the up-regulation of genes involved in germline development. Thereafter, progress through phases of oocyte development could be linked to changes in gene expression. At 5 weeks, females showed up-regulation of spermatogenesis, indicating that stored sperm had been in a quiescent stage and completed their maturation inside the female. Gene expression profiles provide a framework to stage field-collected females. The 7-week progression from diapause to late oogenesis suggests that females typically spawning in January initiated the reproductive program in November.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Sommer, Stephanie A. and Cieslak, Matthew C. and Clarke, Cheryl and Hopcroft, Russell R. and Lenz, Petra H.},
 doi = {10.1038/s41598-018-30873-0},
 journal = {Scientific Reports}
}

© 2018, The Author(s). Organisms inhabiting high-latitude environments have evolved adaptations, such as diapause to time reproduction and growth to optimize their survival. However, the physiological regulation of the timing of complex life histories is poorly understood, particularly for marine copepods, that diapause at depth. A member of the pelagic community of the sub-Arctic Pacific Ocean, Neocalanus flemingeri enters diapause in June. Egg production occurs in winter/spring. In order to characterize the transition from diapause to egg release, females were collected in late September from 400–700 m depth, incubated in the dark at 4–5 °C and sampled for RNASeq at weekly intervals. The diapause phenotype showed down-regulation of protein turnover and up-regulation of stress genes. Activation of the reproductive program was marked by the up-regulation of genes involved in germline development. Thereafter, progress through phases of oocyte development could be linked to changes in gene expression. At 5 weeks, females showed up-regulation of spermatogenesis, indicating that stored sperm had been in a quiescent stage and completed their maturation inside the female. Gene expression profiles provide a framework to stage field-collected females. The 7-week progression from diapause to late oogenesis suggests that females typically spawning in January initiated the reproductive program in November.

@article{
 title = {The impact of elevated CO2 on Prochlorococcus and microbial interactions with ‘helper’ bacterium Alteromonas},
 type = {article},
 year = {2018},
 keywords = {Climate,Marine microbiology,Photosynthesis,Water microbiology,change ecology,change impacts},
 pages = {520-531},
 volume = {12},
 websites = {http://www.nature.com/articles/ismej2017189},
 month = {2},
 publisher = {Nature Publishing Group},
 day = {31},
 id = {107ef2ab-caed-35ca-bd81-c060a0f00513},
 created = {2020-04-29T21:57:57.399Z},
 accessed = {2019-06-27},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.473Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {The impact of elevated CO<sub>2</sub> on <i>Prochlorococcus</i> and microbial interactions with ‘helper’ bacterium Alteromonas},
 bibtype = {article},
 author = {Hennon, Gwenn MM and Morris, J Jeffrey and Haley, Sheean T and Zinser, Erik R and Durrant, Alexander R and Entwistle, Elizabeth and Dokland, Terje and Dyhrman, Sonya T},
 doi = {10.1038/ismej.2017.189},
 journal = {The ISME Journal},
 number = {2}
}

The impact of elevated CO₂ on Prochlorococcus and microbial interactions with ‘helper’ bacterium Alteromonas

@article{
 title = {Modulation of the heat shock response is associated with acclimation to novel temperatures but not adaptation to climatic variation in the ants Aphaenogaster picea and A. rudis},
 type = {article},
 year = {2017},
 keywords = {Ants,Heat shock proteins,Heat shock response,Hsc70-4,Hsp40,Hsp70,Hsp90},
 pages = {113-120},
 volume = {204},
 month = {2},
 publisher = {Elsevier Inc.},
 day = {1},
 id = {39a40960-3179-31c7-892b-8612a0457766},
 created = {2020-04-29T21:57:54.621Z},
 accessed = {2019-08-12},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.685Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Ecological diversification into thermally divergent habitats can push species toward their physiological limits, requiring them to accommodate temperature extremes through plastic or evolutionary changes that increase persistence under the local thermal regime. One way to withstand thermal stress is to increase production of heat shock proteins, either by maintaining higher baseline abundance within cells or by increasing the magnitude of induction in response to heat stress. We evaluated whether environmental variation was associated with expression of three heat shock protein genes in two closely-related species of woodland ant, Aphaenogaster picea and A. rudis. We compared adult workers from colonies collected from 25 sites across their geographic ranges. Colonies were maintained at two different laboratory temperatures, and tested for the independent effects of environment, phylogeny, and acclimation temperature on baseline and heat-induced gene expression. The annual maximum temperature at each collection site (Tmax) was not a significant predictor of either baseline expression or magnitude of induction of any of the heat shock protein genes tested. A phylogenetic effect was detected only for basal expression of Hsp40, which was lower in the most southern populations of A. rudis and higher in a mid-range population of possible hybrid ancestry. In contrast, a higher acclimation temperature significantly increased baseline expression of Hsc70-4, and increased induction of Hsp40 and Hsp83. Thus, physiological acclimation to temperature variation appears to involve modulation of the heat shock response, whereas other mechanisms are likely to be responsible for evolutionary shifts in thermal performance associated with large-scale climate gradients.},
 bibtype = {article},
 author = {Helms Cahan, Sara and Nguyen, Andrew D. and Stanton-Geddes, John and Penick, Clint A. and Hernáiz-Hernández, Yainna and DeMarco, Bernice B. and Gotelli, Nicholas J.},
 doi = {10.1016/j.cbpa.2016.11.017},
 journal = {Comparative Biochemistry and Physiology -Part A : Molecular and Integrative Physiology}
}

Ecological diversification into thermally divergent habitats can push species toward their physiological limits, requiring them to accommodate temperature extremes through plastic or evolutionary changes that increase persistence under the local thermal regime. One way to withstand thermal stress is to increase production of heat shock proteins, either by maintaining higher baseline abundance within cells or by increasing the magnitude of induction in response to heat stress. We evaluated whether environmental variation was associated with expression of three heat shock protein genes in two closely-related species of woodland ant, Aphaenogaster picea and A. rudis. We compared adult workers from colonies collected from 25 sites across their geographic ranges. Colonies were maintained at two different laboratory temperatures, and tested for the independent effects of environment, phylogeny, and acclimation temperature on baseline and heat-induced gene expression. The annual maximum temperature at each collection site (Tmax) was not a significant predictor of either baseline expression or magnitude of induction of any of the heat shock protein genes tested. A phylogenetic effect was detected only for basal expression of Hsp40, which was lower in the most southern populations of A. rudis and higher in a mid-range population of possible hybrid ancestry. In contrast, a higher acclimation temperature significantly increased baseline expression of Hsc70-4, and increased induction of Hsp40 and Hsp83. Thus, physiological acclimation to temperature variation appears to involve modulation of the heat shock response, whereas other mechanisms are likely to be responsible for evolutionary shifts in thermal performance associated with large-scale climate gradients.

@article{
 title = {Evolutionary transition from blood feeding to obligate nonbiting in a mosquito},
 type = {article},
 year = {2017},
 keywords = {PY8},
 pages = {201717502},
 volume = {115},
 websites = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717502115},
 publisher = {National Academy of Sciences},
 day = {30},
 id = {6f929fe4-11a7-34eb-96d7-a73932aab078},
 created = {2020-04-29T21:57:55.737Z},
 accessed = {2018-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.843Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bradshaw2017},
 private_publication = {false},
 abstract = {The spread of blood-borne pathogens by mosquitoes relies on their taking a blood meal; if there is no bite, there is no disease transmission. Although many species of mosquitoes never take a blood meal, identifying genes that distinguish blood feeding from obligate nonbiting is hampered by the fact that these different lifestyles occur in separate, genetically incompatible species. There is, however, one unique extant species with populations that share a common genetic background but blood feed in one region and are obligate nonbiters in the rest of their range: Wyeomyia smithii Contemporary blood-feeding and obligate nonbiting populations represent end points of divergence between fully interfertile southern and northern populations. This divergence has undoubtedly resulted in genetic changes that are unrelated to blood feeding, and the challenge is to winnow out the unrelated genetic factors to identify those related specifically to the evolutionary transition from blood feeding to obligate nonbiting. Herein, we determine differential gene expression resulting from directional selection on blood feeding within a polymorphic population to isolate genetic differences between blood feeding and obligate nonbiting. We show that the evolution of nonbiting has resulted in a greatly reduced metabolic investment compared with biting populations, a greater reliance on opportunistic metabolic pathways, and greater reliance on visual rather than olfactory sensory input. W. smithii provides a unique starting point to determine if there are universal nonbiting genes in mosquitoes that could be manipulated as a means to control vector-borne disease.},
 bibtype = {article},
 author = {Bradshaw, William E. and Burkhart, Joshua and Colbourne, John K. and Borowczak, Rudyard and Lopez, Jacqueline and Denlinger, David L. and Reynolds, Julie A. and Pfrender, Michael E. and Holzapfel, Christina M.},
 doi = {10.1073/pnas.1717502115},
 journal = {Proceedings of the National Academy of Sciences},
 number = {5}
}

The spread of blood-borne pathogens by mosquitoes relies on their taking a blood meal; if there is no bite, there is no disease transmission. Although many species of mosquitoes never take a blood meal, identifying genes that distinguish blood feeding from obligate nonbiting is hampered by the fact that these different lifestyles occur in separate, genetically incompatible species. There is, however, one unique extant species with populations that share a common genetic background but blood feed in one region and are obligate nonbiters in the rest of their range: Wyeomyia smithii Contemporary blood-feeding and obligate nonbiting populations represent end points of divergence between fully interfertile southern and northern populations. This divergence has undoubtedly resulted in genetic changes that are unrelated to blood feeding, and the challenge is to winnow out the unrelated genetic factors to identify those related specifically to the evolutionary transition from blood feeding to obligate nonbiting. Herein, we determine differential gene expression resulting from directional selection on blood feeding within a polymorphic population to isolate genetic differences between blood feeding and obligate nonbiting. We show that the evolution of nonbiting has resulted in a greatly reduced metabolic investment compared with biting populations, a greater reliance on opportunistic metabolic pathways, and greater reliance on visual rather than olfactory sensory input. W. smithii provides a unique starting point to determine if there are universal nonbiting genes in mosquitoes that could be manipulated as a means to control vector-borne disease.

@article{
 title = {Complex modular architecture around a simple toolkit of wing pattern genes.},
 type = {article},
 year = {2017},
 pages = {52},
 volume = {1},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/28523290,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5432014},
 publisher = {NIH Public Access},
 id = {351f755c-85f5-37ed-9804-f5a392bc8019},
 created = {2020-04-29T21:57:55.766Z},
 accessed = {2018-06-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.869Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification.},
 bibtype = {article},
 author = {Van Belleghem, Steven M and Rastas, Pasi and Papanicolaou, Alexie and Martin, Simon H and Arias, Carlos F and Supple, Megan A and Hanly, Joseph J and Mallet, James and Lewis, James J and Hines, Heather M and Ruiz, Mayte and Salazar, Camilo and Linares, Mauricio and Moreira, Gilson R P and Jiggins, Chris D and Counterman, Brian A and McMillan, W Owen and Papa, Riccardo},
 doi = {10.1038/s41559-016-0052},
 journal = {Nature ecology & evolution},
 number = {3},
 keywords = {PY7}
}

Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification.

@article{
 title = {A deep transcriptomic resource for the copepod crustacean Labidocera madurae: A potential indicator species for assessing near shore ecosystem health},
 type = {article},
 year = {2017},
 pages = {e0186794},
 volume = {12},
 websites = {http://dx.plos.org/10.1371/journal.pone.0186794},
 month = {10},
 publisher = {Public Library of Science},
 day = {24},
 id = {73023f88-7871-3920-a246-00763e8ee462},
 created = {2020-04-29T21:57:56.034Z},
 accessed = {2018-05-29},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.105Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Roncalli2017},
 private_publication = {false},
 abstract = {Coral reef ecosystems of many sub-tropical and tropical marine coastal environments have suffered significant degradation from anthropogenic sources. Research to inform management strategies that mitigate stressors and promote a healthy ecosystem has focused on the ecology and physiology of coral reefs and associated organisms. Few studies focus on the surrounding pelagic communities, which are equally important to ecosystem function. Zooplankton, often dominated by small crustaceans such as copepods, is an important food source for invertebrates and fishes, especially larval fishes. The reef-associated zooplankton includes a sub-neustonic copepod family that could serve as an indicator species for the community. Here, we describe the generation of a de novo transcriptome for one such copepod, Labidocera madurae, a pontellid from an intensively-studied coral reef ecosystem, Kāne‘ohe Bay, Oahu, Hawai‘i. The transcriptome was assembled using high-throughput sequence data obtained from whole organisms. It comprised 211,002 unique transcripts, including 72,391 with coding regions. It was assessed for quality and completeness using multiple workflows. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified transcripts for 88% of expected eukaryotic core proteins. Targeted gene-discovery analyses included searches for transcripts coding full-length “giant” proteins (>4,000 amino acids), proteins and splice variants of voltage-gated sodium channels, and proteins involved in the circadian signaling pathway. Four different reference transcriptomes were generated and compared for the detection of differential gene expression between copepodites and adult females; 6,229 genes were consistently identified as differentially expressed between the two regardless of reference. Automated bioinformatics analyses and targeted manual gene curation suggest that the de novo assembled L. madurae transcriptome is of high quality and completeness. This transcriptome provides a new resource for assessing the global physiological status of a planktonic species inhabiting a coral reef ecosystem that is subjected to multiple anthropogenic stressors. The workflows provide a template for generating and assessing transcriptomes in other non-model species.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Christie, Andrew E. and Sommer, Stephanie A. and Cieslak, Matthew C. and Hartline, Daniel K. and Lenz, Petra H.},
 editor = {Ianora, Adrianna},
 doi = {10.1371/journal.pone.0186794},
 journal = {PLoS ONE},
 number = {10},
 keywords = {PY8}
}

Coral reef ecosystems of many sub-tropical and tropical marine coastal environments have suffered significant degradation from anthropogenic sources. Research to inform management strategies that mitigate stressors and promote a healthy ecosystem has focused on the ecology and physiology of coral reefs and associated organisms. Few studies focus on the surrounding pelagic communities, which are equally important to ecosystem function. Zooplankton, often dominated by small crustaceans such as copepods, is an important food source for invertebrates and fishes, especially larval fishes. The reef-associated zooplankton includes a sub-neustonic copepod family that could serve as an indicator species for the community. Here, we describe the generation of a de novo transcriptome for one such copepod, Labidocera madurae, a pontellid from an intensively-studied coral reef ecosystem, Kāne‘ohe Bay, Oahu, Hawai‘i. The transcriptome was assembled using high-throughput sequence data obtained from whole organisms. It comprised 211,002 unique transcripts, including 72,391 with coding regions. It was assessed for quality and completeness using multiple workflows. Bench-marking-universal-single-copy-orthologs (BUSCO) analysis identified transcripts for 88% of expected eukaryotic core proteins. Targeted gene-discovery analyses included searches for transcripts coding full-length “giant” proteins (>4,000 amino acids), proteins and splice variants of voltage-gated sodium channels, and proteins involved in the circadian signaling pathway. Four different reference transcriptomes were generated and compared for the detection of differential gene expression between copepodites and adult females; 6,229 genes were consistently identified as differentially expressed between the two regardless of reference. Automated bioinformatics analyses and targeted manual gene curation suggest that the de novo assembled L. madurae transcriptome is of high quality and completeness. This transcriptome provides a new resource for assessing the global physiological status of a planktonic species inhabiting a coral reef ecosystem that is subjected to multiple anthropogenic stressors. The workflows provide a template for generating and assessing transcriptomes in other non-model species.

@article{
 title = {Molecular Characterization of Copepod Photoreception.},
 type = {article},
 year = {2017},
 keywords = {PY7},
 pages = {96-110},
 volume = {233},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/29182504},
 month = {8},
 id = {90990a42-1910-32ce-93ae-ada909e21e5a},
 created = {2020-04-29T21:57:56.050Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.139Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Copepod crustaceans are an abundant and ecologically significant group whose basic biology is guided by numerous visually guided behaviors. These behaviors are driven by copepod eyes, including naupliar eyes and Gicklhorn's organs, which vary widely in structure and function among species. Yet little is known about the molecular aspects of copepod vision. In this study we present a general overview of the molecular aspects of copepod vision by identifying phototransduction genes from newly generated and publicly available RNA-sequencing data and assemblies from 12 taxonomically diverse copepod species. We identify a set of 10 expressed transcripts that serve as a set of target genes for future studies of copepod phototransduction. Our more detailed evolutionary analyses of the opsin gene responsible for forming visual pigments found that all of the copepod species investigated express two main groups of opsins: middle-wavelength-sensitive (MWS) opsins and pteropsins. Additionally, there is evidence from a few species (e.g., Calanus finmarchicus, Eurytemora affinis, Paracyclopina nana, and Lernaea cyprinacea) for the expression of two additional groups of opsins-the peropsins and rhodopsin 7 (Rh7) opsins-at low levels or distinct developmental stages. An ontogenetic analysis of opsin expression in Calanus finmarchicus found the expression of a single dominant MWS opsin, as well as evidence for differences in expression across development in some MWS, pteropsin, and Rh7 opsins, with expression peaking in early naupliar through early copepodite stages.},
 bibtype = {article},
 author = {Porter, Megan L and Steck, Mireille and Roncalli, Vittoria and Lenz, Petra H},
 doi = {10.1086/694564},
 journal = {The Biological bulletin},
 number = {1}
}

Copepod crustaceans are an abundant and ecologically significant group whose basic biology is guided by numerous visually guided behaviors. These behaviors are driven by copepod eyes, including naupliar eyes and Gicklhorn's organs, which vary widely in structure and function among species. Yet little is known about the molecular aspects of copepod vision. In this study we present a general overview of the molecular aspects of copepod vision by identifying phototransduction genes from newly generated and publicly available RNA-sequencing data and assemblies from 12 taxonomically diverse copepod species. We identify a set of 10 expressed transcripts that serve as a set of target genes for future studies of copepod phototransduction. Our more detailed evolutionary analyses of the opsin gene responsible for forming visual pigments found that all of the copepod species investigated express two main groups of opsins: middle-wavelength-sensitive (MWS) opsins and pteropsins. Additionally, there is evidence from a few species (e.g., Calanus finmarchicus, Eurytemora affinis, Paracyclopina nana, and Lernaea cyprinacea) for the expression of two additional groups of opsins-the peropsins and rhodopsin 7 (Rh7) opsins-at low levels or distinct developmental stages. An ontogenetic analysis of opsin expression in Calanus finmarchicus found the expression of a single dominant MWS opsin, as well as evidence for differences in expression across development in some MWS, pteropsin, and Rh7 opsins, with expression peaking in early naupliar through early copepodite stages.

@article{
 title = {Unexplained Early Infantile Epileptic Encephalopathy in Han Chinese Children: Next-Generation Sequencing and Phenotype Enriching},
 type = {article},
 year = {2017},
 keywords = {PY8},
 pages = {46227},
 volume = {7},
 websites = {https://www.nature.com/articles/srep46227.pdf,http://view.ncbi.nlm.nih.gov/pubmed/28387369,http://www.ncbi.nlm.nih.gov/pubmed/28387369,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5384237,http://www.nature.com/articles/srep46227},
 month = {4},
 day = {7},
 id = {40727339-aa12-3658-82af-291fc1019c32},
 created = {2020-04-29T21:57:56.271Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.347Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {citeulike:14367006},
 source_type = {article},
 private_publication = {false},
 abstract = {Early Infantile Epileptic Encephalopathy (EIEE) presents shortly after birth with frequent, severe seizures and progressive disturbance of cerebral function. This study was to investigate a cohort of Chinese children with unexplained EIEE, infants with previous genetic diagnoses, causative brain malformations, or inborn errors of metabolism were excluded. We used targeted next-generation sequencing to identify potential pathogenic variants of 308 genes in 68 Han Chinese patients with unexplained EIEE. A filter process was performed to prioritize rare variants of potential functional significance. In all cases where parental testing was accessible, Sanger sequencing confirmed the variants and determined the parental origin. In 15% of patients (n = 10/68), we identified nine de novo pathogenic variants, and one assumed de novo pathogenic variant in the following genes: CDKL5 (n = 2), STXBP1 (n = 2), SCN1A (n = 3), KCNQ2 (n = 2), SCN8A (n = 1), four of the variants are novel variants. In 4% patients (n = 3/68), we identified three likely pathogenic variants; two assumed de novo and one X-linked in the following genes: SCN1A (n = 2) and ARX (n = 1), two of these variants are novel. Variants were assumed de novo when parental testing was not available. Our findings were first reported in Han Chinese patients with unexplained EIEE, enriching the EIEE mutation spectrum bank.},
 bibtype = {article},
 author = {Arafat, Ahmed and Jing, Peng and Ma, Yuping and Pu, Miao and Nan, Gai and Fang, He and Chen, Chen and Fei, Yin},
 doi = {10.1038/srep46227},
 journal = {Scientific Reports}
}

Early Infantile Epileptic Encephalopathy (EIEE) presents shortly after birth with frequent, severe seizures and progressive disturbance of cerebral function. This study was to investigate a cohort of Chinese children with unexplained EIEE, infants with previous genetic diagnoses, causative brain malformations, or inborn errors of metabolism were excluded. We used targeted next-generation sequencing to identify potential pathogenic variants of 308 genes in 68 Han Chinese patients with unexplained EIEE. A filter process was performed to prioritize rare variants of potential functional significance. In all cases where parental testing was accessible, Sanger sequencing confirmed the variants and determined the parental origin. In 15% of patients (n = 10/68), we identified nine de novo pathogenic variants, and one assumed de novo pathogenic variant in the following genes: CDKL5 (n = 2), STXBP1 (n = 2), SCN1A (n = 3), KCNQ2 (n = 2), SCN8A (n = 1), four of the variants are novel variants. In 4% patients (n = 3/68), we identified three likely pathogenic variants; two assumed de novo and one X-linked in the following genes: SCN1A (n = 2) and ARX (n = 1), two of these variants are novel. Variants were assumed de novo when parental testing was not available. Our findings were first reported in Han Chinese patients with unexplained EIEE, enriching the EIEE mutation spectrum bank.

@article{
 title = {A de novo loss-of-function GRIN2A mutation associated with childhood focal epilepsy and acquired epileptic aphasia},
 type = {article},
 year = {2017},
 keywords = {PY7},
 pages = {e0170818+},
 volume = {12},
 websites = {http://dx.plos.org/10.1371/journal.pone.0170818,http://dx.doi.org/10.1371/journal.pone.0170818},
 month = {2},
 publisher = {Public Library of Science},
 day = {9},
 id = {aa029353-f6e4-3d04-89de-9d20b3ec6cb9},
 created = {2020-04-29T21:57:56.336Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.454Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {citeulike:14367013},
 source_type = {article},
 private_publication = {false},
 abstract = {N-methyl-D-aspartate receptors (NMDAR) subunit GRIN2A/GluN2A mutations have been identified in patients with various neurological diseases, such as epilepsy and intellectual disability / developmental delay (ID/DD). In this study, we investigated the phenotype and underlying molecular mechanism of a GRIN2A missense mutation identified by next generation sequencing on idiopathic focal epilepsy using in vitro electrophysiology. Genomic DNA of patients with epilepsy and ID/DD were sequenced by targeted next-generation sequencing within 300 genes related to epilepsy and ID/DD. The effects of one missense GRIN2A mutation on NMDAR function were evaluated by two-electrode voltage clamp current recordings and whole cell voltage clamp current recordings. We identified one de novo missense GRIN2A mutation (Asp731Asn, GluN2A(D731N)) in a child with unexplained epilepsy and DD. The D731N mutation is located in a portion of the agonist-binding domain (ABD) in the GluN2A subunit, which is the binding pocket for agonist glutamate. This residue in the ABD is conserved among vertebrate species and all other NMDAR subunits, suggesting an important role in receptor function. The proband shows developmental delay as well as EEG-confirmed seizure activity. Functional analyses reveal that the GluN2A(D731N) mutation decreases glutamate potency by over 3,000-fold, reduces amplitude of current response, shortens synaptic-like response time course, and decreases channel open probability, while enhancing sensitivity to negative allosteric modulators, including extracellular proton and zinc inhibition. The combined effects reduce NMDAR function. We identified a de novo missense mutation in the GRIN2A gene in a patient with childhood focal epilepsy and acquired epileptic aphasia. The mutant decreases NMDAR activation suggesting NMDAR hypofunction may contribute to the epilepsy pathogenesis.},
 bibtype = {article},
 author = {Gao, Kai and Tankovic, Anel and Zhang, Yujia and Kusumoto, Hirofumi and Zhang, Jin and Chen, Wenjuan and XiangWei, Wenshu and Shaulsky, Gil H. and Hu, Chun and Traynelis, Stephen F. and Yuan, Hongjie and Jiang, Yuwu},
 editor = {Mothet, Jean-Pierre},
 doi = {10.1371/journal.pone.0170818},
 journal = {PLOS ONE},
 number = {2}
}

N-methyl-D-aspartate receptors (NMDAR) subunit GRIN2A/GluN2A mutations have been identified in patients with various neurological diseases, such as epilepsy and intellectual disability / developmental delay (ID/DD). In this study, we investigated the phenotype and underlying molecular mechanism of a GRIN2A missense mutation identified by next generation sequencing on idiopathic focal epilepsy using in vitro electrophysiology. Genomic DNA of patients with epilepsy and ID/DD were sequenced by targeted next-generation sequencing within 300 genes related to epilepsy and ID/DD. The effects of one missense GRIN2A mutation on NMDAR function were evaluated by two-electrode voltage clamp current recordings and whole cell voltage clamp current recordings. We identified one de novo missense GRIN2A mutation (Asp731Asn, GluN2A(D731N)) in a child with unexplained epilepsy and DD. The D731N mutation is located in a portion of the agonist-binding domain (ABD) in the GluN2A subunit, which is the binding pocket for agonist glutamate. This residue in the ABD is conserved among vertebrate species and all other NMDAR subunits, suggesting an important role in receptor function. The proband shows developmental delay as well as EEG-confirmed seizure activity. Functional analyses reveal that the GluN2A(D731N) mutation decreases glutamate potency by over 3,000-fold, reduces amplitude of current response, shortens synaptic-like response time course, and decreases channel open probability, while enhancing sensitivity to negative allosteric modulators, including extracellular proton and zinc inhibition. The combined effects reduce NMDAR function. We identified a de novo missense mutation in the GRIN2A gene in a patient with childhood focal epilepsy and acquired epileptic aphasia. The mutant decreases NMDAR activation suggesting NMDAR hypofunction may contribute to the epilepsy pathogenesis.

@article{
 title = {Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae},
 type = {article},
 year = {2017},
 keywords = {PY7},
 pages = {1279},
 volume = {8},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/28769884,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5513979,http://journal.frontiersin.org/article/10.3389/fmicb.2017.01279/full},
 month = {7},
 day = {18},
 id = {8c54442a-bcd8-3292-8ae7-56490995f05b},
 created = {2020-04-29T21:57:57.604Z},
 accessed = {2018-08-23},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.713Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.},
 bibtype = {article},
 author = {Harke, Matthew J. and Juhl, Andrew R. and Haley, Sheean T. and Alexander, Harriet and Dyhrman, Sonya T.},
 doi = {10.3389/fmicb.2017.01279},
 journal = {Frontiers in Microbiology}
}

The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.

@article{
 title = {High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans},
 type = {article},
 year = {2016},
 keywords = {PY5},
 pages = {288-308},
 volume = {524},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/26132897,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4685035,http://doi.wiley.com/10.1002/cne.23843},
 month = {2},
 day = {1},
 id = {43ede0e4-3620-3389-9463-5f6c69a81794},
 created = {2020-04-29T21:57:56.307Z},
 accessed = {2017-09-05},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.414Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Lipovich2016},
 private_publication = {false},
 abstract = {The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes.},
 bibtype = {article},
 author = {Lipovich, Leonard and Hou, Zhuo-Cheng and Jia, Hui and Sinkler, Christopher and McGowen, Michael and Sterner, Kirstin N. and Weckle, Amy and Sugalski, Amara B. and Pipes, Lenore and Gatti, Domenico L. and Mason, Christopher E. and Sherwood, Chet C. and Hof, Patrick R. and Kuzawa, Christopher W. and Grossman, Lawrence I. and Goodman, Morris and Wildman, Derek E.},
 doi = {10.1002/cne.23843},
 journal = {Journal of Comparative Neurology},
 number = {2}
}

The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes.

@article{
 title = {Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis},
 type = {article},
 year = {2016},
 keywords = {PY6},
 pages = {1092},
 volume = {56},
 websites = {+,http://dx.doi.org/10.1093/icb/icw043,https://academic.oup.com/icb/article-lookup/doi/10.1093/icb/icw043,https://watermark.silverchair.com/api/watermark?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAfwwggH4BgkqhkiG9w0BBwagggHpMIIB5QIBADCCAd4},
 month = {12},
 publisher = {NCBI,},
 day = {1},
 id = {9573aebd-62a6-3143-bf19-71a21329eef3},
 created = {2020-04-29T21:57:56.405Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.499Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {doi:10.1093/icb/icw043},
 source_type = {article},
 private_publication = {false},
 bibtype = {article},
 author = {Armstrong, Eric J. and Stillman, Jonathon H.},
 doi = {10.1093/icb/icw043},
 journal = {Integrative and Comparative Biology},
 number = {6}
}

@article{
 title = {Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance.},
 type = {article},
 year = {2016},
 keywords = {PY5},
 pages = {784-792},
 volume = {65},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/27259867,http://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.000289,http://view.ncbi.nlm.nih.gov/pubmed/27259867},
 month = {8},
 day = {1},
 id = {0ab187cf-8771-3613-849f-df43ec52e663},
 created = {2020-04-29T21:57:56.418Z},
 accessed = {2017-09-05},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.492Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {citeulike:14366765},
 source_type = {article},
 private_publication = {false},
 abstract = {Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Pseudomonas aeruginosa isolates associated with transposon Tn4401 commonly located in plasmids. Acinetobacter baumannii has become an important multidrug-resistant nosocomial pathogen. KPC-producing A. baumannii has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing A. baumannii in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the blaKPC and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The blaKPC-2 was identified on a novel truncated version of Tn4401e (tentatively named Tn4401h), located in the chromosome within an IncA/C plasmid fragment derived from an Enterobacteriaceae, probably owing to insertion sequence IS26. A chromosomally located truncated Tn1 transposon harbouring a blaTEM-1 was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In439 and the novel In1252, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the blaKPC in an already globally disseminated A. baumannii ST2 presents a serious threat of further dissemination.},
 bibtype = {article},
 author = {Martinez, Teresa and Aquino, Edna E. and Robledo, Iraida E. and Martinez, Idali and Vazquez, Guillermo J. and Aquino, Edna E. and Robledo, Iraida E.},
 doi = {10.1099/jmm.0.000289},
 journal = {Journal of medical microbiology},
 number = {8}
}

Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Pseudomonas aeruginosa isolates associated with transposon Tn4401 commonly located in plasmids. Acinetobacter baumannii has become an important multidrug-resistant nosocomial pathogen. KPC-producing A. baumannii has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing A. baumannii in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the blaKPC and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The blaKPC-2 was identified on a novel truncated version of Tn4401e (tentatively named Tn4401h), located in the chromosome within an IncA/C plasmid fragment derived from an Enterobacteriaceae, probably owing to insertion sequence IS26. A chromosomally located truncated Tn1 transposon harbouring a blaTEM-1 was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In439 and the novel In1252, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the blaKPC in an already globally disseminated A. baumannii ST2 presents a serious threat of further dissemination.

@article{
 title = {Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors.},
 type = {article},
 year = {2016},
 keywords = {PY5},
 pages = {127},
 volume = {17},
 websites = {https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-016-2454-3?site=bmcgenomics.biomedcentral.com},
 month = {2},
 id = {d6210485-5ece-35af-b930-b797733d951a},
 created = {2020-04-29T21:57:56.531Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.701Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Huth2016},
 source_type = {Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.},
 language = {eng},
 country = {England},
 patent_owner = {NLM},
 private_publication = {false},
 abstract = {BACKGROUND: As global climate change progresses, the Southern Ocean surrounding Antarctica is poised to undergo potentially rapid and substantial changes in temperature and pCO2. To survive in this challenging environment, the highly cold adapted endemic fauna of these waters must demonstrate sufficient plasticity to accommodate these changing conditions or face inexorable decline. Previous studies of notothenioids have focused upon the short-term response to heat stress; and more recently the longer-term physiological response to the combined stress of increasing temperatures and pCO2. This inquiry explores the transcriptomic response of Trematomus bernacchii to increased temperatures and pCO2 at 7, 28 and 56 days, in an attempt to discern the innate plasticity of T. bernacchii available to cope with a changing Southern Ocean. RESULTS: Differential gene expression analysis supported previous research in that T. bernacchii exhibits no inducible heat shock response to stress conditions. However, T. bernacchii did demonstrate a strong stress response to the multi-stressor condition in the form of metabolic shifts, DNA damage repair, immune system processes, and activation of apoptotic pathways combined with negative regulation of cell proliferation. This response declined in magnitude over time, but aspects of this response remained detectable throughout the acclimation period. CONCLUSIONS: When exposed to the multi-stressor condition, T. bernacchii demonstrates a cellular stress response that persists for a minimum of 7 days before returning to near basal levels of expression at longer acclimation times. However, subtle changes in expression persist in fish acclimated for 56 days that may significantly affect the fitness T. bernacchii over time.},
 bibtype = {article},
 author = {Huth, Troy J and Place, Sean P},
 doi = {10.1186/s12864-016-2454-3},
 journal = {BMC genomics}
}

BACKGROUND: As global climate change progresses, the Southern Ocean surrounding Antarctica is poised to undergo potentially rapid and substantial changes in temperature and pCO2. To survive in this challenging environment, the highly cold adapted endemic fauna of these waters must demonstrate sufficient plasticity to accommodate these changing conditions or face inexorable decline. Previous studies of notothenioids have focused upon the short-term response to heat stress; and more recently the longer-term physiological response to the combined stress of increasing temperatures and pCO2. This inquiry explores the transcriptomic response of Trematomus bernacchii to increased temperatures and pCO2 at 7, 28 and 56 days, in an attempt to discern the innate plasticity of T. bernacchii available to cope with a changing Southern Ocean. RESULTS: Differential gene expression analysis supported previous research in that T. bernacchii exhibits no inducible heat shock response to stress conditions. However, T. bernacchii did demonstrate a strong stress response to the multi-stressor condition in the form of metabolic shifts, DNA damage repair, immune system processes, and activation of apoptotic pathways combined with negative regulation of cell proliferation. This response declined in magnitude over time, but aspects of this response remained detectable throughout the acclimation period. CONCLUSIONS: When exposed to the multi-stressor condition, T. bernacchii demonstrates a cellular stress response that persists for a minimum of 7 days before returning to near basal levels of expression at longer acclimation times. However, subtle changes in expression persist in fish acclimated for 56 days that may significantly affect the fitness T. bernacchii over time.

@article{
 title = {Non-coding single nucleotide variants affecting estrogen receptor binding and activity.},
 type = {article},
 year = {2016},
 keywords = {PY6},
 pages = {128},
 volume = {8},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/27964748,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5154163,http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0382-0,http://view.ncbi.nlm.nih.gov/pubmed/27964748,https://genomemedicine},
 month = {12},
 day = {13},
 id = {5d2412ed-6eb2-3152-a394-662bc1e08334},
 created = {2020-04-29T21:57:56.647Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.756Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {citeulike:14366768},
 source_type = {article},
 private_publication = {false},
 abstract = {Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic changes in different breast cancer models. We investigated whether single nucleotide variants (SNVs) in ER binding sites (regSNVs) contribute to ER action through changes in the ER cistrome, thereby affecting disease progression. Here we developed a computational pipeline to identify SNVs in ER binding sites using chromatin immunoprecipitation sequencing (ChIP-seq) data from ER+ breast cancer models. ER ChIP-seq data were downloaded from the Gene Expression Omnibus (GEO). GATK pipeline was used to identify SNVs and the MACS algorithm was employed to call DNA-binding sites. Determination of the potential effect of a given SNV in a binding site was inferred using reimplementation of the is-rSNP algorithm. The Cancer Genome Atlas (TCGA) data were integrated to correlate the regSNVs and gene expression in breast tumors. ChIP and luciferase assays were used to assess the allele-specific binding. Analysis of ER ChIP-seq data from MCF7 cells identified an intronic SNV in the IGF1R gene, rs62022087, predicted to increase ER binding. Functional studies confirmed that ER binds preferentially to rs62022087 versus the wild-type allele. By integrating 43 ER ChIP-seq datasets, multi-omics, and clinical data, we identified 17 regSNVs associated with altered expression of adjacent genes in ER+ disease. Of these, the top candidate was in the promoter of the GSTM1 gene and was associated with higher expression of GSTM1 in breast tumors. Survival analysis of patients with ER+ tumors revealed that higher expression of GSTM1, responsible for detoxifying carcinogens, was correlated with better outcome. In conclusion, we have developed a computational approach that is capable of identifying putative regSNVs in ER ChIP-binding sites. These non-coding variants could potentially regulate target genes and may contribute to clinical prognosis in breast cancer.},
 bibtype = {article},
 author = {Bahreini, Amir and Levine, Kevin and Santana-Santos, Lucas and Benos, Panayiotis V. and Wang, Peilu and Andersen, Courtney and Oesterreich, Steffi and Lee, Adrian V.},
 doi = {10.1186/s13073-016-0382-0},
 journal = {Genome medicine},
 number = {1}
}

Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic changes in different breast cancer models. We investigated whether single nucleotide variants (SNVs) in ER binding sites (regSNVs) contribute to ER action through changes in the ER cistrome, thereby affecting disease progression. Here we developed a computational pipeline to identify SNVs in ER binding sites using chromatin immunoprecipitation sequencing (ChIP-seq) data from ER+ breast cancer models. ER ChIP-seq data were downloaded from the Gene Expression Omnibus (GEO). GATK pipeline was used to identify SNVs and the MACS algorithm was employed to call DNA-binding sites. Determination of the potential effect of a given SNV in a binding site was inferred using reimplementation of the is-rSNP algorithm. The Cancer Genome Atlas (TCGA) data were integrated to correlate the regSNVs and gene expression in breast tumors. ChIP and luciferase assays were used to assess the allele-specific binding. Analysis of ER ChIP-seq data from MCF7 cells identified an intronic SNV in the IGF1R gene, rs62022087, predicted to increase ER binding. Functional studies confirmed that ER binds preferentially to rs62022087 versus the wild-type allele. By integrating 43 ER ChIP-seq datasets, multi-omics, and clinical data, we identified 17 regSNVs associated with altered expression of adjacent genes in ER+ disease. Of these, the top candidate was in the promoter of the GSTM1 gene and was associated with higher expression of GSTM1 in breast tumors. Survival analysis of patients with ER+ tumors revealed that higher expression of GSTM1, responsible for detoxifying carcinogens, was correlated with better outcome. In conclusion, we have developed a computational approach that is capable of identifying putative regSNVs in ER ChIP-binding sites. These non-coding variants could potentially regulate target genes and may contribute to clinical prognosis in breast cancer.

@article{
 title = {Vibrio elicits targeted transcriptional responses from copepod hosts.},
 type = {article},
 year = {2016},
 keywords = {PY5},
 pages = {72},
 volume = {92},
 websites = {https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw072},
 month = {6},
 publisher = {Massachusetts Institute of Technology,},
 day = {1},
 id = {b892284d-1457-3cd0-9c89-d3d686418bf7},
 created = {2020-04-29T21:57:56.660Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.740Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Almada2016},
 source_type = {Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.},
 language = {eng},
 country = {England},
 patent_owner = {NLM},
 private_publication = {false},
 abstract = {Copepods are abundant crustaceans that harbor diverse bacterial communities, yet the nature of their interactions with microbiota are poorly understood. Here, we report that Vibrio elicits targeted transcriptional responses in the estuarine copepod Eurytemora affinis We pre-treated E. affinis with an antibiotic cocktail and exposed them to either a zooplankton specialist (Vibrio sp. F10 9ZB36) or a free-living species (Vibrio ordalii 12B09) for 24 h. We then identified via RNA-Seq a total of 78 genes that were differentially expressed following Vibrio exposure, including homologs of C-type lectins, chitin-binding proteins and saposins. The response differed between the two Vibrio treatments, with the greatest changes elicited upon inoculation with V. sp. F10 We suggest that these differentially regulated genes play important roles in cuticle integrity, the innate immune response, and general stress response, and that their expression may enable E. affinis to recognize and regulate symbiotic vibrios. We further report that V. sp. F10 culturability is specifically altered upon colonization of E. affinis These findings suggest that rather than acting as passive environmental vectors, copepods discriminately interact with vibrios, which may ultimately impact the abundance and activity of copepod-associated bacteria.},
 bibtype = {article},
 author = {Almada, Amalia A. and Tarrant, Ann M.},
 doi = {10.1093/femsec/fiw072},
 journal = {FEMS microbiology ecology},
 number = {6}
}

Copepods are abundant crustaceans that harbor diverse bacterial communities, yet the nature of their interactions with microbiota are poorly understood. Here, we report that Vibrio elicits targeted transcriptional responses in the estuarine copepod Eurytemora affinis We pre-treated E. affinis with an antibiotic cocktail and exposed them to either a zooplankton specialist (Vibrio sp. F10 9ZB36) or a free-living species (Vibrio ordalii 12B09) for 24 h. We then identified via RNA-Seq a total of 78 genes that were differentially expressed following Vibrio exposure, including homologs of C-type lectins, chitin-binding proteins and saposins. The response differed between the two Vibrio treatments, with the greatest changes elicited upon inoculation with V. sp. F10 We suggest that these differentially regulated genes play important roles in cuticle integrity, the innate immune response, and general stress response, and that their expression may enable E. affinis to recognize and regulate symbiotic vibrios. We further report that V. sp. F10 culturability is specifically altered upon colonization of E. affinis These findings suggest that rather than acting as passive environmental vectors, copepods discriminately interact with vibrios, which may ultimately impact the abundance and activity of copepod-associated bacteria.

@article{
 title = {A pilot study on the prevalence of DNA palindromes in breast cancer genomes.},
 type = {article},
 year = {2016},
 keywords = {PY5},
 pages = {73},
 volume = {9},
 websites = {https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-016-0232-3?site=bmcmedgenomics.biomedcentral.com,http://view.ncbi.nlm.nih.gov/pubmed/28117658,http://www.ncbi.nlm.nih.gov/pubmed/28117658,http://www.pubmedcentral.nih.gov/articlerender.fcgi},
 month = {12},
 day = {5},
 id = {3a8ceea3-314c-3090-aaa9-775cc40aba9e},
 created = {2020-04-29T21:57:56.888Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.995Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {citeulike:14366763},
 source_type = {article},
 private_publication = {false},
 abstract = {DNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in human cancers by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of breast cancer genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and cancer genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of cancer genomes to identify computationally the differentially occurring palindromes. We processed 69 breast cancer genomes from The Cancer Genome Atlas including serum-normal and tumor genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes. We carried out a pilot study on chr 8 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in cancer genomes, 38% of what were near breast cancer genes happened to be the most differentiated palindromes in tumor (i.e. they ranked among the top 25% by our heuristic measure). These results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and breast cancer progression.},
 bibtype = {article},
 author = {Subramanian, Sandeep and Chaparala, Srilakshmi and Avali, Viji and Ganapathiraju, Madhavi K.},
 doi = {10.1186/s12920-016-0232-3},
 journal = {BMC medical genomics},
 number = {Suppl 3}
}

DNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in human cancers by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of breast cancer genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and cancer genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of cancer genomes to identify computationally the differentially occurring palindromes. We processed 69 breast cancer genomes from The Cancer Genome Atlas including serum-normal and tumor genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes. We carried out a pilot study on chr 8 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in cancer genomes, 38% of what were near breast cancer genes happened to be the most differentiated palindromes in tumor (i.e. they ranked among the top 25% by our heuristic measure). These results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and breast cancer progression.

@article{
 title = {Glutathione S-Transferase Regulation in Calanus finmarchicus Feeding on the Toxic Dinoflagellate Alexandrium fundyense},
 type = {article},
 year = {2016},
 pages = {e0159563},
 volume = {11},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/27427938,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4948837,http://dx.plos.org/10.1371/journal.pone.0159563},
 month = {7},
 day = {18},
 id = {3a0f5622-4b84-3277-ab42-2cf42412aed9},
 created = {2020-04-29T21:57:57.937Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:58.006Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {The effect of the dinoflagellate, Alexandrium fundyense, on relative expression of glutathione S-transferase (GST) transcripts was examined in the copepod Calanus finmarchicus. Adult females were fed for 5-days on one of three experimental diets: control (100% Rhodomonas spp.), low dose of A. fundyense (25% by volume, 75% Rhodomonas spp.), and high dose (100% A. fundyense). Relative expression of three GST genes was measured using RT-qPCR on days 0.5, 1, 2 and 5 in two independent experiments. Differential regulation was found for the Delta and the Sigma GSTs between 0.5 to 2 days, but not on day 5 in both experiments. The third GST, a microsomal, was not differentially expressed in either treatment or day. RT-qPCR results from the two experiments were similar, even though experimental females were collected from the Gulf of Maine on different dates and their reproductive output differed. In the second experiment, expression of 39 GSTs was determined on days 2 and 5 using RNA-Seq. Global gene expression analyses agreed with the RT-qPCR results. Furthermore, the RNA-Seq measurements indicated that only four GSTs were differentially expressed under the experimental conditions, and the response was small in amplitude. In summary, the A. fundyense diet led to a rapid and transient response in C. finmarchicus in three cytosolic GSTs, while a fourth GST (Omega I) was significantly up-regulated on day 5. Although there was some regulation of GSTs in response the toxic dinoflagellate, the tolerance to A. fundyense by C. finmarchicus is not dependent on the long-term up-regulation of specific GSTs.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Jungbluth, Michelle J. and Lenz, Petra H.},
 editor = {Ianora, Adrianna},
 doi = {10.1371/journal.pone.0159563},
 journal = {PLOS ONE},
 number = {7},
 keywords = {PY5}
}

The effect of the dinoflagellate, Alexandrium fundyense, on relative expression of glutathione S-transferase (GST) transcripts was examined in the copepod Calanus finmarchicus. Adult females were fed for 5-days on one of three experimental diets: control (100% Rhodomonas spp.), low dose of A. fundyense (25% by volume, 75% Rhodomonas spp.), and high dose (100% A. fundyense). Relative expression of three GST genes was measured using RT-qPCR on days 0.5, 1, 2 and 5 in two independent experiments. Differential regulation was found for the Delta and the Sigma GSTs between 0.5 to 2 days, but not on day 5 in both experiments. The third GST, a microsomal, was not differentially expressed in either treatment or day. RT-qPCR results from the two experiments were similar, even though experimental females were collected from the Gulf of Maine on different dates and their reproductive output differed. In the second experiment, expression of 39 GSTs was determined on days 2 and 5 using RNA-Seq. Global gene expression analyses agreed with the RT-qPCR results. Furthermore, the RNA-Seq measurements indicated that only four GSTs were differentially expressed under the experimental conditions, and the response was small in amplitude. In summary, the A. fundyense diet led to a rapid and transient response in C. finmarchicus in three cytosolic GSTs, while a fourth GST (Omega I) was significantly up-regulated on day 5. Although there was some regulation of GSTs in response the toxic dinoflagellate, the tolerance to A. fundyense by C. finmarchicus is not dependent on the long-term up-regulation of specific GSTs.

@article{
 title = {Molecular tools to support metabolic and immune function research in the Guinea Fowl (Numida meleagris)},
 type = {article},
 year = {2015},
 keywords = {De novo assembly,Guinea fowl,Immune function,Metabolic function,RNA-seq},
 id = {9ba861a7-1824-3554-b3bd-542f7ffee4bc},
 created = {2020-04-29T21:57:54.898Z},
 accessed = {2019-08-09},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.981Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {BACKGROUND Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000. RESULTS 74 million sequences were generated and assembled into 96,492 contigs using the Trinity software suite. Over 39,000 of these transcripts were found to have in silico translated protein sequences that are homologous to chicken protein sequences. Gene ontology analysis uncovered 416 transcripts with metabolic functions and 703 with immune function. CONCLUSION The transcriptome information presented here will support the development of molecular approaches to improve production efficiency of the guinea fowl and other avian species.},
 bibtype = {article},
 author = {Darris, Carl E. and Tyus, James E. and Kelley, Gary and Ropelewski, Alexander J. and Nicholas, Hugh B. and Wang, Xiaofei and Nahashon, Samuel},
 doi = {10.1186/s12864-015-1520-6},
 journal = {BMC Genomics}
}

BACKGROUND Guinea fowl (Numidia meleagris) production as an alternative source of meat and poultry has shown potential for economic viability. However, there has been little progress in characterizing the transcriptome of the guinea fowl. In this study RNA-sequencing and de novo transcriptome assembly of several Guinea fowl tissues (pancreas, hypothalamus, liver, bone marrow and bursa) which play key roles in regulating feed intake, satiety, and immune function was performed using Illumina's Hi-Seq 2000. RESULTS 74 million sequences were generated and assembled into 96,492 contigs using the Trinity software suite. Over 39,000 of these transcripts were found to have in silico translated protein sequences that are homologous to chicken protein sequences. Gene ontology analysis uncovered 416 transcripts with metabolic functions and 703 with immune function. CONCLUSION The transcriptome information presented here will support the development of molecular approaches to improve production efficiency of the guinea fowl and other avian species.

@article{
 title = {Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus – Contributors to Cellular Detoxification},
 type = {article},
 year = {2015},
 pages = {e0123322},
 volume = {10},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/25945801,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4422733,http://dx.plos.org/10.1371/journal.pone.0123322},
 month = {5},
 day = {6},
 id = {857db555-2770-3ccc-8a09-3ddf4fdd024b},
 created = {2020-04-29T21:57:56.030Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.116Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.},
 bibtype = {article},
 author = {Roncalli, Vittoria and Cieslak, Matthew C. and Passamaneck, Yale and Christie, Andrew E. and Lenz, Petra H.},
 editor = {Uversky, Vladimir N.},
 doi = {10.1371/journal.pone.0123322},
 journal = {PLOS ONE},
 number = {5},
 keywords = {PY4}
}

Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.

@article{
 title = {Describing and predicting developmental profiles of externalizing problems from childhood to adulthood},
 type = {article},
 year = {2015},
 pages = {791-818},
 volume = {27},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/25166430,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4344932,http://www.journals.cambridge.org/abstract_S0954579414000789},
 month = {8},
 day = {28},
 id = {56bd41b4-6abc-3bb4-9838-772d0c89b49e},
 created = {2020-04-29T21:57:56.167Z},
 accessed = {2017-09-08},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.240Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {This longitudinal study considers externalizing behavior problems from ages 5 to 27 ( N = 585). Externalizing problem ratings by mothers, fathers, teachers, peers, and self-report were modeled with growth curves. Risk and protective factors across many different domains and time frames were included as predictors of the trajectories. A major contribution of the study is in demonstrating how heterotypic continuity and changing measures can be handled in modeling changes in externalizing behavior over long developmental periods. On average, externalizing problems decreased from early childhood to preadolescence, increased during adolescence, and decreased from late adolescence to adulthood. There was strong nonlinear continuity in externalizing problems over time. Family process, peer process, stress, and individual characteristics predicted externalizing problems beyond the strong continuity of externalizing problems. The model accounted for 70% of the variability in the development of externalizing problems. The model's predicted values showed moderate sensitivity and specificity in prediction of arrests, illegal drug use, and drunk driving. Overall, the study showed that by using changing, developmentally relevant measures and simultaneously taking into account numerous characteristics of children and their living situations, research can model lengthy spans of development and improve predictions of the development of later, severe externalizing problems.},
 bibtype = {article},
 author = {Petersen, Isaac T. and Bates, John E. and Dodge, Kenneth A. and Lansford, Jennifer E. and Pettit, Gregory S.},
 doi = {10.1017/S0954579414000789},
 journal = {Development and Psychopathology},
 number = {03},
 keywords = {DvlFinal,PY5}
}

This longitudinal study considers externalizing behavior problems from ages 5 to 27 ( N = 585). Externalizing problem ratings by mothers, fathers, teachers, peers, and self-report were modeled with growth curves. Risk and protective factors across many different domains and time frames were included as predictors of the trajectories. A major contribution of the study is in demonstrating how heterotypic continuity and changing measures can be handled in modeling changes in externalizing behavior over long developmental periods. On average, externalizing problems decreased from early childhood to preadolescence, increased during adolescence, and decreased from late adolescence to adulthood. There was strong nonlinear continuity in externalizing problems over time. Family process, peer process, stress, and individual characteristics predicted externalizing problems beyond the strong continuity of externalizing problems. The model accounted for 70% of the variability in the development of externalizing problems. The model's predicted values showed moderate sensitivity and specificity in prediction of arrests, illegal drug use, and drunk driving. Overall, the study showed that by using changing, developmentally relevant measures and simultaneously taking into account numerous characteristics of children and their living situations, research can model lengthy spans of development and improve predictions of the development of later, severe externalizing problems.

@article{
 title = {Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities},
 type = {article},
 year = {2015},
 pages = {e0141782},
 volume = {10},
 websites = {http://dx.plos.org/10.1371/journal.pone.0141782,http://www.ncbi.nlm.nih.gov/pubmed/26544041,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4636363},
 month = {11},
 publisher = {Public Library of Science},
 day = {6},
 id = {73a933f6-aaaa-31a7-9206-9f9b9bf3e5e2},
 created = {2020-04-29T21:57:56.531Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.727Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zhang2015},
 private_publication = {false},
 abstract = {OBJECTIVE Epilepsy and intellectual/developmental disabilities (ID/DD) have a high rate of co-occurrence. Here, we investigated gene mutations in Chinese children with unexplained epilepsy and ID/DD. METHODS We used targeted next-generation sequencing to detect mutations within 300 genes related to epilepsy and ID/DD in 253 Chinese children with unexplained epilepsy and ID/DD. A series of filtering criteria was used to find the possible pathogenic variations. Validation and parental origin analyses were performed by Sanger sequencing. We reviewed the phenotypes of patients with each mutated gene. RESULTS We identified 32 novel and 16 reported mutations within 24 genes in 46 patients. The detection rate was 18% (46/253) in the whole group and 26% (17/65) in the early-onset (before three months after birth) epilepsy group. To our knowledge, we are the first to report KCNAB1 is a disease-causing gene of epilepsy by identifying a novel de novo mutation (c.1062dupCA p.Leu355HisfsTer5) within this gene in one patient with early infantile epileptic encephalopathy (EIEE). Patients with an SCN1A mutation accounted for the largest proportion, 17% (8/46). A total of 38% (9/24) of the mutated genes re-occurred at least 2 times and 63% (15/24) occurred only one time. Ion channel genes are the most common (8/24) and genes related to synapse are the next most common to occur (5/24). SIGNIFICANCE We have established genetic diagnosis for 46 patients of our cohort. Early-onset epilepsy had the highest detection rate. KCNAB1 mutation was first identified in EIEE patient. We expanded the phenotype and mutation spectrum of the genes we identified. The mutated genes in this cohort are mostly isolated. This suggests that epilepsy and ID/DD phenotypes occur as a consequence of brain dysfunction caused by a highly diverse population of mutated genes. Ion channel genes and genes related to synapse were more common mutated in this patient cohort.},
 bibtype = {article},
 author = {Zhang, Yujia Yuehua and Kong, Weijing and Gao, Yang and Liu, Xiaoyan and Gao, Kai and Xie, Han and Wu, Ye and Zhang, Yujia Yuehua and Wang, Jingmin and Gao, Feng and Wu, Xiru and Jiang, Yuwu},
 editor = {Shapiro, Mark S.},
 doi = {10.1371/journal.pone.0141782},
 journal = {PLOS ONE},
 number = {11},
 keywords = {PY5}
}

OBJECTIVE Epilepsy and intellectual/developmental disabilities (ID/DD) have a high rate of co-occurrence. Here, we investigated gene mutations in Chinese children with unexplained epilepsy and ID/DD. METHODS We used targeted next-generation sequencing to detect mutations within 300 genes related to epilepsy and ID/DD in 253 Chinese children with unexplained epilepsy and ID/DD. A series of filtering criteria was used to find the possible pathogenic variations. Validation and parental origin analyses were performed by Sanger sequencing. We reviewed the phenotypes of patients with each mutated gene. RESULTS We identified 32 novel and 16 reported mutations within 24 genes in 46 patients. The detection rate was 18% (46/253) in the whole group and 26% (17/65) in the early-onset (before three months after birth) epilepsy group. To our knowledge, we are the first to report KCNAB1 is a disease-causing gene of epilepsy by identifying a novel de novo mutation (c.1062dupCA p.Leu355HisfsTer5) within this gene in one patient with early infantile epileptic encephalopathy (EIEE). Patients with an SCN1A mutation accounted for the largest proportion, 17% (8/46). A total of 38% (9/24) of the mutated genes re-occurred at least 2 times and 63% (15/24) occurred only one time. Ion channel genes are the most common (8/24) and genes related to synapse are the next most common to occur (5/24). SIGNIFICANCE We have established genetic diagnosis for 46 patients of our cohort. Early-onset epilepsy had the highest detection rate. KCNAB1 mutation was first identified in EIEE patient. We expanded the phenotype and mutation spectrum of the genes we identified. The mutated genes in this cohort are mostly isolated. This suggests that epilepsy and ID/DD phenotypes occur as a consequence of brain dysfunction caused by a highly diverse population of mutated genes. Ion channel genes and genes related to synapse were more common mutated in this patient cohort.

@article{
 title = {Gene expression underlying enhanced, steroid-dependent auditory sensitivity of hair cell epithelium in a vocal fish},
 type = {article},
 year = {2015},
 pages = {782},
 volume = {16},
 websites = {https://doi.org/10.1186/s12864-015-1940-3,http://www.ncbi.nlm.nih.gov/pubmed/26466782,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4607102},
 month = {10},
 publisher = {BioMed Central},
 day = {14},
 id = {5614830b-6f7c-357d-9fe0-8c9d6a972ad8},
 created = {2020-04-29T21:57:56.872Z},
 accessed = {2017-09-05},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.930Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Fergus2015},
 source_type = {JOUR},
 private_publication = {false},
 abstract = {Successful animal communication depends on a receiver’s ability to detect a sender’s signal. Exemplars of adaptive sender-receiver coupling include acoustic communication, often important in the context of seasonal reproduction. During the reproductive summer season, both male and female midshipman fish (Porichthys notatus) exhibit similar increases in the steroid-dependent frequency sensitivity of the saccule, the main auditory division of the inner ear. This form of auditory plasticity enhances detection of the higher frequency components of the multi-harmonic, long-duration advertisement calls produced repetitively by males during summer nights of peak vocal and spawning activity. The molecular basis of this seasonal auditory plasticity has not been fully resolved. Here, we utilize an unbiased transcriptomic RNA sequencing approach to identify differentially expressed transcripts within the saccule’s hair cell epithelium of reproductive summer and non-reproductive winter fish.},
 bibtype = {article},
 author = {Fergus, Daniel J and Feng, Ni Y and Bass, Andrew H},
 doi = {10.1186/s12864-015-1940-3},
 journal = {BMC Genomics},
 number = {1},
 keywords = {PY5}
}

Successful animal communication depends on a receiver’s ability to detect a sender’s signal. Exemplars of adaptive sender-receiver coupling include acoustic communication, often important in the context of seasonal reproduction. During the reproductive summer season, both male and female midshipman fish (Porichthys notatus) exhibit similar increases in the steroid-dependent frequency sensitivity of the saccule, the main auditory division of the inner ear. This form of auditory plasticity enhances detection of the higher frequency components of the multi-harmonic, long-duration advertisement calls produced repetitively by males during summer nights of peak vocal and spawning activity. The molecular basis of this seasonal auditory plasticity has not been fully resolved. Here, we utilize an unbiased transcriptomic RNA sequencing approach to identify differentially expressed transcripts within the saccule’s hair cell epithelium of reproductive summer and non-reproductive winter fish.

@article{
 title = {Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus.},
 type = {article},
 year = {2014},
 pages = {975},
 volume = {15},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/25404257,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4251933},
 month = {11},
 publisher = {BioMed Central},
 day = {17},
 id = {b2de3314-65f1-3fe2-9938-c8d99d8f620a},
 created = {2020-04-29T21:57:55.506Z},
 accessed = {2018-08-10},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.578Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {BACKGROUND Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-determination gene. Once established, the clonal inheritance of sex-linked inversions leads to the accumulation of deleterious alleles, repetitive elements and a gradual decay of sex-linked genes. This in turn creates selective pressures for the evolution of mechanisms that compensate for the unequal dosage of gene expression. Here we use whole genome sequencing to characterize the structure of a young sex chromosome and quantify sex-specific gene expression in the developing gonad. RESULTS We found an 8.8 Mb block of strong differentiation between males and females that corresponds to the location of a previously mapped sex-determiner on linkage group 1 of Oreochromis niloticus. Putatively disruptive mutations are found in many of the genes within this region. We also found a significant female-bias in the expression of genes within the block of differentiation compared to those outside the block of differentiation. Eight candidate sex-determination genes were identified within this region. CONCLUSIONS This study demonstrates a block of differentiation on linkage group 1, suggestive of an 8.8 Mb inversion encompassing the sex-determining locus. The enrichment of female-biased gene expression inside the proposed inversion suggests incomplete dosage compensation. This study helps establish a model for studying the early-to-intermediate stages of sex chromosome evolution.},
 bibtype = {article},
 author = {Gammerdinger, William J and Conte, Matthew A and Acquah, Enoch A and Roberts, Reade B and Kocher, Thomas D},
 doi = {10.1186/1471-2164-15-975},
 journal = {BMC genomics},
 number = {1},
 keywords = {PY4}
}

BACKGROUND Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-determination gene. Once established, the clonal inheritance of sex-linked inversions leads to the accumulation of deleterious alleles, repetitive elements and a gradual decay of sex-linked genes. This in turn creates selective pressures for the evolution of mechanisms that compensate for the unequal dosage of gene expression. Here we use whole genome sequencing to characterize the structure of a young sex chromosome and quantify sex-specific gene expression in the developing gonad. RESULTS We found an 8.8 Mb block of strong differentiation between males and females that corresponds to the location of a previously mapped sex-determiner on linkage group 1 of Oreochromis niloticus. Putatively disruptive mutations are found in many of the genes within this region. We also found a significant female-bias in the expression of genes within the block of differentiation compared to those outside the block of differentiation. Eight candidate sex-determination genes were identified within this region. CONCLUSIONS This study demonstrates a block of differentiation on linkage group 1, suggestive of an 8.8 Mb inversion encompassing the sex-determining locus. The enrichment of female-biased gene expression inside the proposed inversion suggests incomplete dosage compensation. This study helps establish a model for studying the early-to-intermediate stages of sex chromosome evolution.

@article{
 title = {Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus},
 type = {article},
 year = {2014},
 keywords = {PY3},
 pages = {28-39},
 volume = {195},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/24148657,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3872210,http://linkinghub.elsevier.com/retrieve/pii/S001664801300405X},
 month = {1},
 day = {1},
 id = {88972c79-e893-3ef5-b373-f2c215e4d815},
 created = {2020-04-29T21:57:55.757Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.851Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Neurochemicals are likely to play key roles in physiological/behavioral control in the copepod crustacean Calanus finmarchicus, the biomass dominant zooplankton for much of the North Atlantic Ocean. Previously, a de novo assembled transcriptome consisting of 206,041 unique sequences was used to characterize the peptidergic signaling systems of Calanus. Here, this assembly was mined for transcripts encoding enzymes involved in amine biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Calanus homologs of tryptophan-phenylalanine hydroxylase (dopamine, octopamine and serotonin biosynthesis), tyrosine hydroxylase (dopamine biosynthesis), DOPA decarboxylase (dopamine and serotonin biosynthesis), histidine decarboxylase (histamine biosynthesis), tyrosine decarboxylase (octopamine biosynthesis), tyramine β-hydroxylase (octopamine biosynthesis) and tryptophan hydroxylase (serotonin biosynthesis) were identified. Reverse BLAST and domain analyses show that the proteins deduced from these transcripts possess sequence homology to and the structural hallmarks of their respective enzyme families. Developmental profiling revealed a remarkably consistent pattern of expression for all transcripts, with the highest levels of expression typically seen in the early nauplius and early copepodite. These expression patterns suggest roles for amines during development, particularly in the metamorphic transitions from embryo to nauplius and from nauplius to copepodite. Taken collectively, the data presented here lay a strong foundation for future gene-based studies of aminergic signaling in this and other copepod species, in particular assessment of the roles they may play in developmental control.},
 bibtype = {article},
 author = {Christie, Andrew E. and Fontanilla, Tiana M. and Roncalli, Vittoria and Cieslak, Matthew C. and Lenz, Petra H.},
 doi = {10.1016/j.ygcen.2013.10.003},
 journal = {General and Comparative Endocrinology}
}

Neurochemicals are likely to play key roles in physiological/behavioral control in the copepod crustacean Calanus finmarchicus, the biomass dominant zooplankton for much of the North Atlantic Ocean. Previously, a de novo assembled transcriptome consisting of 206,041 unique sequences was used to characterize the peptidergic signaling systems of Calanus. Here, this assembly was mined for transcripts encoding enzymes involved in amine biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Calanus homologs of tryptophan-phenylalanine hydroxylase (dopamine, octopamine and serotonin biosynthesis), tyrosine hydroxylase (dopamine biosynthesis), DOPA decarboxylase (dopamine and serotonin biosynthesis), histidine decarboxylase (histamine biosynthesis), tyrosine decarboxylase (octopamine biosynthesis), tyramine β-hydroxylase (octopamine biosynthesis) and tryptophan hydroxylase (serotonin biosynthesis) were identified. Reverse BLAST and domain analyses show that the proteins deduced from these transcripts possess sequence homology to and the structural hallmarks of their respective enzyme families. Developmental profiling revealed a remarkably consistent pattern of expression for all transcripts, with the highest levels of expression typically seen in the early nauplius and early copepodite. These expression patterns suggest roles for amines during development, particularly in the metamorphic transitions from embryo to nauplius and from nauplius to copepodite. Taken collectively, the data presented here lay a strong foundation for future gene-based studies of aminergic signaling in this and other copepod species, in particular assessment of the roles they may play in developmental control.

@article{
 title = {De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean},
 type = {article},
 year = {2014},
 pages = {e88589},
 volume = {9},
 websites = {http://dx.plos.org/10.1371/journal.pone.0088589},
 month = {2},
 publisher = {Public Library of Science},
 day = {19},
 id = {ac92a020-f21a-3730-9d84-81a97bc30a99},
 created = {2020-04-29T21:57:55.911Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:55.993Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components (“comps”) was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is “silent” at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter.},
 bibtype = {article},
 author = {Lenz, Petra H. and Roncalli, Vittoria and Hassett, R. Patrick and Wu, Le-Shin and Cieslak, Matthew C. and Hartline, Daniel K. and Christie, Andrew E.},
 editor = {Ianora, Adrianna},
 doi = {10.1371/journal.pone.0088589},
 journal = {PLoS ONE},
 number = {2},
 keywords = {PY3}
}

Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components (“comps”) was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is “silent” at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and physiology of this environmentally important zooplankter.

@article{
 title = {Diffusible gas transmitter signaling in the copepod crustacean Calanus finmarchicus: Identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome},
 type = {article},
 year = {2014},
 keywords = {PY3},
 pages = {76-86},
 volume = {202},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/24747481,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4041660,http://linkinghub.elsevier.com/retrieve/pii/S0016648014001233},
 month = {6},
 day = {1},
 id = {b4ed2b4e-94ee-32d0-a517-ababec185403},
 created = {2020-04-29T21:57:57.893Z},
 accessed = {2018-05-29},
 file_attached = {false},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:57.947Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Neurochemical signaling is a major component of physiological/behavioral control throughout the animal kingdom. Gas transmitters are perhaps the most ancient class of molecules used by nervous systems for chemical communication. Three gases are generally recognized as being produced by neurons: nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S). As part of an ongoing effort to identify and characterize the neurochemical signaling systems of the copepod Calanus finmarchicus, the biomass dominant zooplankton in much of the North Atlantic Ocean, we have mined a de novo assembled transcriptome for sequences encoding the neuronal biosynthetic enzymes of these gases, i.e. nitric oxide synthase (NOS), heme oxygenase (HO) and cystathionine β-synthase (CBS), respectively. Using Drosophila proteins as queries, two NOS-, one HO-, and one CBS-encoding transcripts were identified. Reverse BLAST and structural analyses of the deduced proteins suggest that each is a true member of its respective enzyme family. RNA-Seq data collected from embryos, early nauplii, late nauplii, early copepodites, late copepodites and adults revealed the expression of each transcript to be stage specific: one NOS restricted primarily to the embryo and the other was absent in the embryo but expressed in all other stages, no CBS expression in the embryo, but present in all other stages, and HO expressed across all developmental stages. Given the importance of gas transmitters in the regulatory control of a number of physiological processes, these data open opportunities for investigating the roles these proteins play under different life-stage and environmental conditions in this ecologically important species.},
 bibtype = {article},
 author = {Christie, Andrew E. and Fontanilla, Tiana M. and Roncalli, Vittoria and Cieslak, Matthew C. and Lenz, Petra H.},
 doi = {10.1016/j.ygcen.2014.04.003},
 journal = {General and Comparative Endocrinology}
}

Neurochemical signaling is a major component of physiological/behavioral control throughout the animal kingdom. Gas transmitters are perhaps the most ancient class of molecules used by nervous systems for chemical communication. Three gases are generally recognized as being produced by neurons: nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S). As part of an ongoing effort to identify and characterize the neurochemical signaling systems of the copepod Calanus finmarchicus, the biomass dominant zooplankton in much of the North Atlantic Ocean, we have mined a de novo assembled transcriptome for sequences encoding the neuronal biosynthetic enzymes of these gases, i.e. nitric oxide synthase (NOS), heme oxygenase (HO) and cystathionine β-synthase (CBS), respectively. Using Drosophila proteins as queries, two NOS-, one HO-, and one CBS-encoding transcripts were identified. Reverse BLAST and structural analyses of the deduced proteins suggest that each is a true member of its respective enzyme family. RNA-Seq data collected from embryos, early nauplii, late nauplii, early copepodites, late copepodites and adults revealed the expression of each transcript to be stage specific: one NOS restricted primarily to the embryo and the other was absent in the embryo but expressed in all other stages, no CBS expression in the embryo, but present in all other stages, and HO expressed across all developmental stages. Given the importance of gas transmitters in the regulatory control of a number of physiological processes, these data open opportunities for investigating the roles these proteins play under different life-stage and environmental conditions in this ecologically important species.

@article{
 title = {Rapid SNP discovery and genetic mapping using sequenced RAD markers},
 type = {article},
 year = {2008},
 volume = {3},
 month = {10},
 day = {13},
 id = {27858770-ef73-3e65-a4a6-503c3680cef4},
 created = {2020-04-29T21:57:54.624Z},
 accessed = {2019-08-12},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:54.696Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F(2) individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.},
 bibtype = {article},
 author = {Baird, Nathan A. and Etter, Paul D. and Atwood, Tressa S. and Currey, Mark C. and Shiver, Anthony L. and Lewis, Zachary A. and Selker, Eric U. and Cresko, William A. and Johnson, Eric A.},
 doi = {10.1371/journal.pone.0003376},
 journal = {PLoS ONE},
 number = {10}
}

Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F(2) individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.

@article{
 title = {Dynamics of a methanol-fed marine denitrifying biofilm: 2-impact of environmental changes on the microbial community},
 type = {article},
 websites = {http://doi.org/10.7717/peerj.7467},
 id = {abaf8f63-257e-3061-a6ac-ad35aea2d941},
 created = {2020-04-29T21:57:56.911Z},
 file_attached = {true},
 profile_id = {5db6d3e7-562f-3ec2-a249-16ecf1e747e4},
 group_id = {bbf8f605-d7c8-3b07-85eb-dbce5212cc00},
 last_modified = {2020-04-29T21:57:56.995Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {false},
 hidden = {false},
 private_publication = {false},
 abstract = {Background. The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm. Methods. The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59. Results. High proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0-1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures. Conclusions. These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The},
 bibtype = {article},
 author = {Villemur, Richard and Payette, Geneviève and Geoffroy, Valérie and Mauffrey, Florian and Martineau, Christine},
 doi = {10.7717/peerj.7467}
}

Background. The biofilm of a methanol-fed, marine denitrification system is composed of a multi-species microbial community, among which Hyphomicrobium nitrativorans and Methylophaga nitratireducenticrescens are the principal bacteria involved in the denitrifying activities. To assess its resilience to environmental changes, the biofilm was cultivated in artificial seawater (ASW) under anoxic conditions and exposed to a range of specific environmental conditions. We previously reported the impact of these changes on the denitrifying activities and the co-occurrence of H. nitrativorans strain NL23 and M. nitratireducenticrescens in the biofilm cultures. Here, we report the impact of these changes on the dynamics of the overall microbial community of the denitrifying biofilm. Methods. The original biofilm (OB) taken from the denitrification system was cultivated in ASW under anoxic conditions with a range of NaCl concentrations, and with four combinations of nitrate/methanol concentrations and temperatures. The OB was also cultivated in the commercial Instant Ocean seawater (IO). The bacterial diversity of the biofilm cultures and the OB was determined by 16S ribosomal RNA gene sequences. Culture approach was used to isolate other denitrifying bacteria from the biofilm cultures. The metatranscriptomes of selected biofilm cultures were derived, along with the transcriptomes of planktonic pure cultures of H. nitrativorans strain NL23 and M. nitratireducenticrescens strain GP59. Results. High proportions of M. nitratireducenticrescens occurred in the biofilm cultures. H. nitrativorans strain NL23 was found in high proportion in the OB, but was absent in the biofilm cultures cultivated in the ASW medium at 2.75% NaCl. It was found however in low proportions in the biofilm cultures cultivated in the ASW medium at 0-1% NaCl and in the IO biofilm cultures. Denitrifying bacterial isolates affiliated to Marinobacter spp. and Paracoccus spp. were isolated. Up regulation of the denitrification genes of strains GP59 and NL23 occurred in the biofilm cultures compared to the planktonic pure cultures. Denitrifying bacteria affiliated to the Stappia spp. were metabolically active in the biofilm cultures. Conclusions. These results illustrate the dynamics of the microbial community in the denitrifying biofilm cultures in adapting to different environmental conditions. The