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Articles 1 - 9 of 9
Full-Text Articles in Genetics and Genomics
Red Fox Genome Assembly Identifies Genomic Regions Associated With Tame And Aggressive Behaviours, Anna V. Kukekova, Jennifer L. Johnson, Xueyan Xiang, Shaohong Feng, Shiping Liu, Halie M. Rando, Anastasiya V. Kharlamova, Yury Herbeck, Natalya A. Serdyukova, Zijun Xiong, Violetta Beklemischeva, Klaus Peter Koepfli, Rimma G. Gulevich, Anastasiya V. Vladimirova, Jessica P. Hekman, Polina L. Perelman, Aleksander S. Graphodatsky, Stephen J. O’Brien, Xu Wang, Andrew G. Clark, Gregory M. Acland, Lyudmila N. Trut, Guojie Zhang
Red Fox Genome Assembly Identifies Genomic Regions Associated With Tame And Aggressive Behaviours, Anna V. Kukekova, Jennifer L. Johnson, Xueyan Xiang, Shaohong Feng, Shiping Liu, Halie M. Rando, Anastasiya V. Kharlamova, Yury Herbeck, Natalya A. Serdyukova, Zijun Xiong, Violetta Beklemischeva, Klaus Peter Koepfli, Rimma G. Gulevich, Anastasiya V. Vladimirova, Jessica P. Hekman, Polina L. Perelman, Aleksander S. Graphodatsky, Stephen J. O’Brien, Xu Wang, Andrew G. Clark, Gregory M. Acland, Lyudmila N. Trut, Guojie Zhang
Biology Faculty Articles
Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes …
The Complete Phylogeny Of Pangolins: Scaling Up Resources For The Molecular Tracing Of The Most Trafficked Mammals On Earth, Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T. Stanley, Stephen J. O'Brien, Warren E. Johnson, Shu Jin Luo
The Complete Phylogeny Of Pangolins: Scaling Up Resources For The Molecular Tracing Of The Most Trafficked Mammals On Earth, Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T. Stanley, Stephen J. O'Brien, Warren E. Johnson, Shu Jin Luo
Biology Faculty Articles
Pangolins, considered the most-traffcked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here, we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and 9 nuclear genes. We confrm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca. 23 million years ago (Ma) (95% HPD = 18.7-27.2), limited fossil evidence suggesting dispersals from Europe. We recognize 3 genera including Manis (Asian pangolins), Smutsia (large African pangolins), and Phataginus …
Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng
Marker Of Proliferation Ki-67 Expression Is Associated With Transforming Growth Factor Beta 1 And Can Predict The Prognosis Of Patients With Hepatic B Virus-Related Hepatocellular Carcinoma, Chengkun Yang, Hao Su, Xiwen Liao, Chuangye Han, Tingdong Yu, Guangzhi Zhu, Xiangkun Wang, Cheryl Ann Winkler, Stephen J. O’Brien, Tao Peng
Biology Faculty Articles
Hepatocellular carcinoma (HCC) is the most frequent malignancy of the liver. Transforming growth factor beta 1 (TGFB1) and marker of proliferation Ki-67 (MKI67) regulate cell proliferation, differentiation, and growth. The association between MKI67 and TGFB1 expression and its clinical implications in HCC remain unknown. Methods: Public databases were used to analyze TGFB1 and MKI67 expression in different pathologic grades/stages and tissue types of HCC. The association between MKI67 and TGFB1 expression was explored using pathway analysis and in a HepG2 cell line treated with TGFB1. Survival analysis was performed to evaluate the prognostic value of TGFB1 and MKI67 expression in …
Salvinia Radseq, Carol A. Rowe, Donald Hauber, Paul G. Wolf
Salvinia Radseq, Carol A. Rowe, Donald Hauber, Paul G. Wolf
Browse all Datasets
No abstract provided.
Genetic Differentiation Between Two Species Of Buckwheat (Eriogonum), Paul G. Wolf, Jenessa B. Lemon
Genetic Differentiation Between Two Species Of Buckwheat (Eriogonum), Paul G. Wolf, Jenessa B. Lemon
Browse all Datasets
Discovering the extent of genetic differentiation between closely related taxa facilitates decisions regarding species protection under the Endangered Species Act. Here, we analyze genotype data to explore the relatedness of two buckwheat species: Eriogonum soredium Reveal- a narrow endemic under consideration for protection, and a widespread close relative, Eriogonum shockleyi S. Watson. Eriogonum soredium grows only on Ordovician limestone outcroppings in west central Utah, whereas the range of E. shockleyi is broad, spanning the western United States from Colorado to California, and Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with other buckwheats throughout this range. We detected higher …
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
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 …
Whole-Genome Analysis Of Mycobacterium Tuberculosis From Patients With Tuberculous Spondylitis, Russia, Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Andrey Yurchenko, Anna Vyazovaya, Igor Mokrousov, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O’Brien
Whole-Genome Analysis Of Mycobacterium Tuberculosis From Patients With Tuberculous Spondylitis, Russia, Ekaterina Chernyaeva, Mikhail Rotkevich, Ksenia Krasheninnikova, Andrey Yurchenko, Anna Vyazovaya, Igor Mokrousov, Natalia Solovieva, Viacheslav Zhuravlev, Piotr Yablonsky, Stephen J. O’Brien
Biology Faculty Articles
Whole-genome analysis of Mycobacterium tuberculosis isolates collected in Russia (N = 71) from patients with tuberculous spondylitis supports a detailed characterization of pathogen strain distributions and drug resistance phenotype, plus distinguished occurrence and association of known resistance mutations. We identify known and novel genome determinants related to bacterial virulence, patho-genicity, and drug resistance.
Mitochondrial Dna Sequence Alignments And Raw Fastq Files For The Population Genetic Analysis Of The Deep Sea Isopod, Bathynomus Giganteus, Laura Timm, Barbara Moahamed
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.
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.