Read by QxMD icon Read


Zuyi Chen, Yaling Jing, Qiang Wen, Xianping Ding, Shun Zhang, Tao Wang, Yiwen Zhang, Jianhui Zhang
BACKGROUND: Cervical cancer is associated with infection by certain subtypes of human papillomavirus (HPV). The L1 protein comprising HPV vaccine formulations elicits high-titre neutralizing antibodies and confers protection against specific HPV subtypes. HPV L2 protein is an attractive candidate for cross-protective vaccines. HPV-33 and HPV-58 are very prevalent among Chinese women. METHODS: To study the gene intratypic variations and polymorphisms of HPV-33 and HPV-58 L1/L2 in Sichuan China, HPV-33 and HPV-58 L1 and L2 genes were sequenced and compared with other genes submitted to GenBank...
October 7, 2016: Virology Journal
Xinxin Du, Yuezhong Liu, Jinxiang Liu, Quanqi Zhang, Xubo Wang
Following the two rounds of whole-genome duplication (WGD) during deuterosome evolution, a third genome duplication occurred in the ray-fined fish lineage and is considered to be responsible for the teleost-specific lineage diversification and regulation mechanisms. As a receptor-regulated SMAD (R-SMAD), the function of SMAD3 was widely studied in mammals. However, limited information of its role or putative paralogs is available in ray-finned fishes. In this study, two SMAD3 paralogs were first identified in the transcriptome and genome of Japanese flounder (Paralichthys olivaceus)...
2016: PeerJ
Kevin N Chesmore, Jacquelaine Bartlett, Chao Cheng, Scott M Williams
Pleiotropy has been claimed to constrain gene evolution but specific mechanism and extent of these constraints have been difficult to demonstrate. The expansion of molecular data makes it possible to investigate these pleiotropic effects. Few classes of genes have been characterized as intensely as human transcription factors (TF). We therefore analyzed the evolutionary rates of full TF proteins, along with their DNA binding domains and protein-protein interacting domains in light of the degree of pleiotropy, measured by the number of TF-TF interaction, or the number of DNA binding targets...
September 15, 2016: Genome Biology and Evolution
N K Jue, P G Batta-Lona, S Trusiak, C Obergfell, A Bucklin, M J O'Neill, R J O'Neill
A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely-related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936 bp genome sequence, covering more than 50% of the estimated 602 MB (±173 MB) genome size for S...
September 13, 2016: Genome Biology and Evolution
Moses Okpeku, Ali Esmailizadeh, Adeniyi C Adeola, Liping Shu, Yesheng Zhang, Yangzi Wang, Timothy M Sanni, Ikhide G Imumorin, Sunday O Peters, Jiajin Zhang, Yang Dong, Wen Wang
The immune systems are fundamentally vital for evolution and survival of species; as such, selection patterns in innate immune loci are of special interest in molecular evolutionary research. The interferon regulatory factor (IRF) gene family control many different aspects of the innate and adaptive immune responses in vertebrates. Among these, IRF3 is known to take active part in very many biological processes. We assembled and evaluated 1356 base pairs of the IRF3 gene coding region in domesticated goats from Africa (Nigeria, Ethiopia and South Africa) and Asia (Iran and China) and the wild goat (Capra aegagrus)...
2016: PloS One
Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vitor Vasconcelos, Agostinho Antunes
BACKGROUND: Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the efficiency to pinpoint genes involved in the adaptive evolution of phenotypes. Reliability of such findings is most often examined with statistical and computational methods using Maximum Likelihood codon-based models (i.e., site, branch, branch-site and clade models), such as those available in codeml from the Phylogenetic Analysis by Maximum Likelihood (PAML) package...
2016: BMC Bioinformatics
Jennifer B Permuth, Ailith Pirie, Y Ann Chen, Hui-Yi Lin, Brett M Reid, Zhihua Chen, Alvaro Monteiro, Joe Dennis, Gustavo Mendoza-Fandino, Hoda Anton-Culver, Elisa V Bandera, Maria Bisogna, Louise Brinton, Angela Brooks-Wilson, Michael E Carney, Georgia Chenevix-Trench, Linda S Cook, Daniel W Cramer, Julie M Cunningham, Cezary Cybulski, Aimee A D'Aloisio, Jennifer Anne Doherty, Madalene Earp, Robert P Edwards, Brooke L Fridley, Simon A Gayther, Aleksandra Gentry-Maharaj, Marc T Goodman, Jacek Gronwald, Estrid Hogdall, Edwin S Iversen, Anna Jakubowska, Allan Jensen, Beth Y Karlan, Linda E Kelemen, Suzanne K Kjaer, Peter Kraft, Nhu D Le, Douglas A Levine, Jolanta Lissowska, Jan Lubinski, Keitaro Matsuo, Usha Menon, Rosemary Modugno, Kirsten B Moysich, Toru Nakanishi, Roberta B Ness, Sara Olson, Irene Orlow, Celeste L Pearce, Tanja Pejovic, Elizabeth M Poole, Susan J Ramus, Mary Anne Rossing, Dale P Sandler, Xiao-Ou Shu, Honglin Song, Jack A Taylor, Soo-Hwang Teo, Kathryn L Terry, Pamela J Thompson, Shelley S Tworoger, Penelope M Webb, Nicolas Wentzensen, Lynne R Wilkens, Stacey Winham, Yin-Ling Woo, Anna H Wu, Hannah Yang, Wei Zheng, Argyrios Ziogas, Catherine M Phelan, Joellen M Schildkraut, Andrew Berchuck, Ellen L Goode, Paul Dp Pharoah, Thomas A Sellers
Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance (P < 5...
July 4, 2016: Human Molecular Genetics
Joseph P Bielawski, Jennifer L Baker, Joseph Mingrone
This unit provides protocols for using the CODEML program from the PAML package to make inferences about episodic natural selection in protein-coding sequences. The protocols cover inference tasks such as maximum likelihood estimation of selection intensity, testing the hypothesis of episodic positive selection, and identifying sites with a history of episodic evolution. We provide protocols for using the rich set of models implemented in CODEML to assess robustness, and for using bootstrapping to assess if the requirements for reliable statistical inference have been met...
2016: Current Protocols in Bioinformatics
Akhtar Rasool Asif, Nabeel Ijaz, Ruheena Javed, Abdur Rahman Ansari, Muhammd Awais, Hasan Riaz
Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphism in IL-32 gene. By using FST based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and Fst...
April 22, 2016: Asian-Australasian Journal of Animal Sciences
Shu-Ying Zhao, Ling-Yun Chen, John K Muchuku, Guang-Wan Hu, Qing-Feng Wang
The giant lobelias in East African mountains are good models for studying molecular mechanisms of adaptation to different altitudes. In this study, we generated RNA-seq data of a middle-altitude species Lobelia aberdarica and a high-altitude species L. telekii, followed by selective pressure estimation of their orthologous genes. Our aim was to explore the important genes potentially involved in adaptation to different altitudes. About 9.3 Gb of clean nucleotides, 167,929-170,534 unigenes with total lengths of 159,762,099-171,138,936 bp for each of the two species were generated...
2016: Frontiers in Plant Science
Jinxiang Liu, Jiajun Jiang, Zhongkai Wang, Yan He, Quanqi Zhang
Background. Following the two rounds of whole-genome duplication that occurred during deuterostome evolution, a third genome duplication occurred in the lineage of teleost fish and is considered to be responsible for much of the biological diversification within the lineage. GATA2, a member of GATA family of transcription factors, is an important regulator of gene expression in hematopoietic cell in mammals, yet the role of this gene or its putative paralogs in ray-finned fishes remains relatively unknown. Methods...
2016: PeerJ
Bernd Steinwender, Amali H Thrimawithana, Ross Crowhurst, Richard D Newcomb
Moths use their sense of smell to find food sources, mating partners and oviposition sites. For this they possess a family of odorant receptors (ORs). Some ORs are used by both sexes whereas others have sex-specific roles. For example, male moths possess ORs specifically tuned to sex pheromones produced by conspecific females. Here we identify sets of ORs from the antennae of New Zealand endemic leafroller moths Planotortrix octo (48 ORs) and P. excessana (47 ORs) using an RNA-Seq approach. Two orthologous ORs show male-biased expression in the adult antennae of both species (OR7 and OR30) and one other OR in each species was female-biased in its expression (PoctOR25, PexcOR14) by qPCR...
2016: PloS One
Qianghua Xu, Chi Zhang, Dongsheng Zhang, Huapeng Jiang, Sihua Peng, Yang Liu, Kai Zhao, Congcong Wang, Liangbiao Chen
BACKGROUND: Erythropoietin (EPO) is a glycoprotein hormone that plays a principal regulatory role in erythropoiesis and initiates cell homeostatic responses to environmental challenges. The Qinghai-Tibet Plateau is a natural laboratory for hypoxia adaptation. Gymnocypris dobula is a highly specialized plateau schizothoracine fish that is restricted to > 4500 m high-altitude freshwater rivers and ponds in the Qinghai-Tibet Plateau. The role of EPO in the adaptation of schizothoracine fish to hypoxia is unknown...
2016: BMC Evolutionary Biology
Caroline Daigle, Daniel P Matton
BACKGROUND: Members of the plant MAP Kinases superfamily have been mostly studied in Arabidopsis thaliana and little is known in most other species. In Solanum chacoense, a wild species close to the common potato, it had been reported that members of a specific group in the MEKK subfamily, namely ScFRK1 and ScFRK2, are involved in male and female reproductive development. Apart from these two kinases, almost nothing is known about the roles of this peculiar family. METHODS: MEKKs were identified using BLAST and hidden Markov model (HMM) to build profiles using the 21 MEKKs from A...
2015: BMC Genomics
Xiaorong Peng, Haibo Wu, Xiuming Peng, Changzhong Jin, Nanping Wu
INTRODUCTION: The HIV epidemic in men who have sex with men (MSM) continues to grow in most countries. However, the phylodynamic and virological differences among HIV-1 strains circulating in MSM and other populations are not well characterized. METHODS: Nearly full-length genomes (NFLGs) of the HIV-1 CRF01_AE were obtained from the Los Alamos HIV database. Phylogenetic analyses were conducted using the NFLG, gag, pol and env genes, using the maximum likelihood method...
2015: PloS One
Jennifer Permuth-Wey, William J Fulp, Brett M Reid, Zhihua Chen, Christina Georgeades, Jin Q Cheng, Anthony Magliocco, Dung-Tsa Chen, Johnathan M Lancaster
Cancer stem cells (CSC) contribute to epithelial ovarian cancer (EOC) progression and therapeutic response. We hypothesized that germline single nucleotide polymorphisms (SNPs) in CSC-related genes may predict an initial therapeutic response for women newly diagnosed with EOC. A nested case-control design was used to study 361 women with advanced-stage serous EOC treated with surgery followed by first-line platinum-based combination therapy at Moffitt Cancer Center or as part of The Cancer Genome Atlas Study...
February 1, 2016: International Journal of Cancer. Journal International du Cancer
Andrew Ndhlovu, Pierre M Durand, Scott Hazelhurst
The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry...
2015: Database: the Journal of Biological Databases and Curation
Claudia Gaviria-Agudelo, Chukwuemika Aroh, Naureen Tareen, Edward K Wakeland, MinSoo Kim, Lawson A Copley
INTRODUCTION: The association between severity of illness of children with osteomyelitis caused by Methicillin-resistant Staphylococcus aureus (MRSA) and genomic variation of the causative organism has not been previously investigated. The purpose of this study is to assess genomic heterogeneity among MRSA isolates from children with osteomyelitis who have diverse severity of illness. MATERIALS AND METHODS: Children with osteomyelitis were prospectively studied between 2010 and 2011...
2015: PloS One
Ying Wang, Liandong Yang, Bo Wu, Zhaobin Song, Shunping He
Triplophysa dalaica, endemic species of Qinghai-Tibetan Plateau, is informative for understanding the genetic basis of adaptation to hypoxic conditions of high altitude habitats. Here, a comprehensive gene repertoire for this plateau fish was generated using the Illumina deep paired-end high-throughput sequencing technology. De novo assembly yielded 145, 256 unigenes with an average length of 1632 bp. Blast searches against GenBank non-redundant database annotated 74,594 (51.4%) unigenes encoding for 30,047 gene descriptions in T...
July 10, 2015: Gene
Jingzhen Wang, Xueying Yu, Bo Hu, Jinsong Zheng, Wuhan Xiao, Yujiang Hao, Wenhua Liu, Ding Wang
Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf...
2015: Scientific Reports
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"