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Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed Mar 2018

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal ...


Mitochondrial Dna Sequence Alignments And Raw Fastq Files For The Population Genetic Analysis Of The Deep Sea Isopod, Bathynomus Giganteus, Laura Timm, Barbara Moahamed Jan 2018

Mitochondrial Dna Sequence Alignments And Raw Fastq Files For The Population Genetic Analysis Of The Deep Sea Isopod, Bathynomus Giganteus, Laura Timm, Barbara Moahamed

DEEPEND Datasets

This data set includes three alignments (12S, 16S, COI) of mitochondrial DNA sequences, as well as two raw fastq files generated through the next-generation sequencing (NGS) method ddRADseq. This data was collected from Bathynomus giganteus specimens collected from throughout the northeastern Gulf of Mexico.


16s And Coi Barcoding Sequences For Crustaceans Collected From The Northern Gulf Of Mexico For Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Heather Bracken-Grissom Dr. Jan 2018

16s And Coi Barcoding Sequences For Crustaceans Collected From The Northern Gulf Of Mexico For Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Heather Bracken-Grissom Dr.

DEEPEND Datasets

These are the 16S and COI barcoding sequences for crustaceans collected on cruises DP02, DP03, and DP04. These barcodes, obtained from the species we collected, will be used to aid in species identification efforts, evolutionary relationships analyses, adult-larval linkages, and new species discoveries. Samples were taken from animals collected during cruises that took place in the northern Gulf of Mexico from August 2015 - August 2016.


Complete Bacterial Symbiont Genome Sequences From Anglerfish Cryptopsaras Couesii And Melanocetus Johnsonii, Lindsay L. Freed, Dana Fadera, Dante Fenolio, Tracey Sutton, Jose V. Lopez Nov 2017

Complete Bacterial Symbiont Genome Sequences From Anglerfish Cryptopsaras Couesii And Melanocetus Johnsonii, Lindsay L. Freed, Dana Fadera, Dante Fenolio, Tracey Sutton, Jose V. Lopez

DEEPEND Datasets

These are the complete bacterial symbiont genome sequences from anglerfish Cryptopsaras couesii (individual CC26) and one individual Melanocetus johnsonii. These data were generated and analyzed by the laboratory of Dr Tory Hendry (Cornell University). The full sequences of two symbiotic bacterial genomes have been submitted to public DDBJ/ENA/GenBank repositories under the accessions CP020660- CP020663 (CC26 Cryptopsaras couesii) and NBYY01000001-NBYY01000039 (Melanocetus johnsonii). The total genome size for each of the symbiont species is about 2-2.6 Mb.


Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan May 2017

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf ...


Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez Feb 2017

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp01 And Dp02 From May 2015 - August 2015, Cole Easson, Jose V. Lopez

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 ...


Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest Jan 2017

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381


High And Dry: Post-Fire Tree Seedlingestablishment In Subalpine Forestsdecreases With Post-Fire Drought Andlarge Stand-Replacing Burn Patches, Brian J. Harvey, Daniel C. Donato, Monica G. Turner Jan 2016

High And Dry: Post-Fire Tree Seedlingestablishment In Subalpine Forestsdecreases With Post-Fire Drought Andlarge Stand-Replacing Burn Patches, Brian J. Harvey, Daniel C. Donato, Monica G. Turner

Aspen Bibliography

Aim: Climate warming and increased wildfire activity are hypothesized to catalyse biogeographical shifts, reducing the resilience of fire-prone forests world-wide. Two key mechanisms underpinning hypotheses are: (1) reduced seed availability in large stand-replacing burn patches, and (2) reduced seedling establishment/survival after post-fire drought. We tested for regional evidence consistent with these mechanisms in an extensive fire-prone forest biome by assessing post-fire tree seedling establishment, a key indicator of forest resilience.

Location: Subalpine forests, US Rocky Mountains.

Methods: We analysed post-fire tree seedling establishment from 184 field plots where stand-replacing forest fires were followed by varying post-fire climate conditions. Generalized ...


Understanding The Physical Properties That Control Protein Crystallization By Analysis Of Largescale Experimental Data, W. Nicholson Price Ii, Yang Chen, Samuel K. Handelman, Helen Neely, Philip Manor, Richard Karlin, Rajesh Nair, Jinfeng Liu, Michael Baran, John Everett, Saichiu N. Tong, Farhad Forouhar, Swarup S. Swaminathan, Thomas Acton, Rong Xiao, Joseph R. Luft, Angela Lauricella, George T. Detitta, Burkhard Rost, Gaetano T. Montelione, John T. Hunt Jan 2009

Understanding The Physical Properties That Control Protein Crystallization By Analysis Of Largescale Experimental Data, W. Nicholson Price Ii, Yang Chen, Samuel K. Handelman, Helen Neely, Philip Manor, Richard Karlin, Rajesh Nair, Jinfeng Liu, Michael Baran, John Everett, Saichiu N. Tong, Farhad Forouhar, Swarup S. Swaminathan, Thomas Acton, Rong Xiao, Joseph R. Luft, Angela Lauricella, George T. Detitta, Burkhard Rost, Gaetano T. Montelione, John T. Hunt

Law Faculty Scholarship

Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of ...