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https://www.readbyqxmd.com/read/27917706/the-changes-of-positive-selection-within-env-gene-of-hiv-1-b-crf07_bc-and-crf08_bc-from-china-over-time
#1
Tingting Li, Binlian Sun, Yanyan Jiang, Haiyan Zeng, Yanpeng Li, Yan Wang, Rongge Yang
: It is not clear about the possible evolutionary changes of the three predominant strains of HIV-1 in China over the course of the epidemic. Envelope (env) gene of HIV-1 is a good target for this evolutionary pressure for its enriched epitopes. METHODS: We collected 159 full or part of env sequences sampled between 1997 and 2010 from database of China, we calculated the genetic distance, detected the positively selected sites by PAML suite and then compared the number using Fisher's exact test between the early period 1997 to 2003and the late period2004 to 2010...
December 5, 2016: Current HIV Research
https://www.readbyqxmd.com/read/27911851/inherited-variants-affecting-rna-editing-may-contribute-to-ovarian-cancer-susceptibility-results-from-a-large-scale-collaboration
#2
Jennifer B Permuth, Brett Reid, Madalene Earp, Y Ann Chen, Alvaro N A Monteiro, Zhihua Chen, Aocs Study Group, Georgia Chenevix-Trench, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Adriaan Vanderstichele, Els Van Niewenhuyse, Ignace Vergote, Mary Anne Rossing, Jennifer Anne Doherty, Jenny Chang-Claude, Kirsten Moysich, Kunle Odunsi, Marc T Goodman, Yurii B Shvetsov, Lynne R Wilkens, Pamela J Thompson, Thilo Dörk, Natalia Bogdanova, Ralf Butzow, Heli Nevanlinna, Liisa Pelttari, Arto Leminen, Francesmary Modugno, Robert P Edwards, Roberta B Ness, Joseph Kelley, Florian Heitz, Beth Karlan, Jenny Lester, Susanne K Kjaer, Allan Jensen, Graham Giles, Michelle Hildebrandt, Dong Liang, Karen H Lu, Xifeng Wu, Douglas A Levine, Maria Bisogna, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Shelley S Tworoger, Elizabeth M Poole, Elisa V Bandera, Brooke Fridley, Julie Cunningham, Stacey J Winham, Sara H Olson, Irene Orlow, Line Bjorge, Lambertus A Kiemeney, Leon Massuger, Tanja Pejovic, Melissa Moffitt, Nhu Le, Linda S Cook, Angela Brooks-Wilson, Linda E Kelemen, Jacek Gronwald, Jan Lubinski, Nicolas Wentzensen, Louise A Brinton, Jolanta Lissowska, Hanna Yang, Estrid Hogdall, Claus Hogdall, Lene Lundvall, Paul D P Pharoah, Honglin Song, Ian Campbell, Diana Eccles, Iain McNeish, Alice Whittemore, Valerie McGuire, Weiva Sieh, Joseph Rothstein, Catherine M Phelan, Harvey Risch, Steven Narod, John McLaughlin, Hoda Anton-Culver, Argyrios Ziogas, Usha Menon, Simon Gayther, Susan J Ramus, Aleksandra Gentry-Maharaj, Celeste Leigh Pearce, Anna H Wu, Jolanta Kupryjanczyk, Agnieszka Dansonka-Mieszkowska, Joellen M Schildkraut, Jin Q Cheng, Ellen L Goode, Thomas A Sellers
RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleotide polymorphisms (SNPs) in ADAR genes modify EOC susceptibility, potentially by altering ovarian tissue gene expression. Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 controls, we evaluated the associations of 5,303 SNPs in ADAD1, ADAR, ADAR2, ADAR3, and SND1...
July 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27896727/measuring-natural-selection
#3
Anders Gonçalves da Silva
In this chapter, I review the basic algorithm underlying the CODEML model implemented in the software package PAML. This is intended as a companion to the software's manual, and a primer to the extensive literature available on CODEML. At the end of this chapter, I hope that you will be able to understand enough of how CODEML operates to plan your own analyses.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27836483/outcome-of-adolescents-and-young-adults-compared-with-pediatric-patients-with-acute-myeloid-and-promyelocytic-leukemia
#4
Syed Sameer Nasir, Smith Giri, Sara Nunnery, Mike G Martin
BACKGROUND: Studies on the outcome of adolescents and young adults (AYAs) with acute myeloid leukemia (AML) and acute promyelocytic leukemia (APL) are limited. METHODS: We compared the outcome of AYA (19-30 years) patients with AML and PML and pediatric (0-18 years) patients with AML (pAMLs) and APL (pAPLs) utilizing the Surveillance Epidemiology and End Results-18 registry. Early mortality rate (EMR), defined as mortality within 1 month of diagnosis, was used as a surrogate for treatment-related mortality...
September 17, 2016: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/27717385/l1-and-l2-gene-polymorphisms-in-hpv-58-and-hpv-33-implications-for-vaccine-design-and-diagnosis
#5
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
https://www.readbyqxmd.com/read/27703851/evolution-history-of-duplicated-smad3-genes-in-teleost-insights-from-japanese-flounder-paralichthys-olivaceus
#6
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
https://www.readbyqxmd.com/read/27635052/complex-patterns-of-association-between-pleiotropy-and-transcription-factor-evolution
#7
Kevin N Chesmore, Jacquelaine Bartlett, Chao Cheng, Scott M Williams
Pleiotropy has been claimed to constrain gene evolution but specific mechanisms 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 (TFs). We therefore analyzed the evolutionary rates of full TF proteins, along with their DNA binding domains and protein-protein interacting domains (PID) in light of the degree of pleiotropy, measured by the number of TF-TF interactions, or the number of DNA-binding targets...
October 23, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27624472/rapid-evolutionary-rates-and-unique-genomic-signatures-discovered-in-the-first-reference-genome-for-the-southern-ocean-salp-salpa-thompsoni-urochordata-thaliacea
#8
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
https://www.readbyqxmd.com/read/27598391/genetic-variation-of-goat-interferon-regulatory-factor-3-gene-and-its-implication-in-goat-evolution
#9
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
https://www.readbyqxmd.com/read/27597435/lmap-lightweight-multigene-analyses-in-paml
#10
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
https://www.readbyqxmd.com/read/27378695/exome-genotyping-arrays-to-identify-rare-and-low-frequency-variants-associated-with-epithelial-ovarian-cancer-risk
#11
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
https://www.readbyqxmd.com/read/27322407/inference-of-episodic-changes-in-natural-selection-acting-on-protein-coding-sequences-via-codeml
#12
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
https://www.readbyqxmd.com/read/27165029/genetic-signature-of-strong-recent-positive-selection-at-il-32-gene-in-goat
#13
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
https://www.readbyqxmd.com/read/27148313/genetic-adaptation-of-giant-lobelias-lobelia-aberdarica-and-lobelia-telekii-to-different-altitudes-in-east-african-mountains
#14
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
https://www.readbyqxmd.com/read/27019782/origin-and-evolution-of-gata2a-and-gata2b-in-teleosts-insights-from-tongue-sole-cynoglossus-semilaevis
#15
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
https://www.readbyqxmd.com/read/27003722/odorant-receptors-of-the-new-zealand-endemic-leafroller-moth-species-planotortrix-octo-and-p-excessana
#16
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
https://www.readbyqxmd.com/read/26768152/analysis-of-the-erythropoietin-of-a-tibetan-plateau-schizothoracine-fish-gymnocypris-dobula-reveals-enhanced-cytoprotection-function-in-hypoxic-environments
#17
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
https://www.readbyqxmd.com/read/26645086/genome-wide-analysis-of-mapkkks-shows-expansion-and-evolution-of-a-new-mekk-class-involved-in-solanaceous-species-sexual-reproduction
#18
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
https://www.readbyqxmd.com/read/26623642/heterogeneous-evolution-of-hiv-1-crf01_ae-in-men-who-have-sex-with-men-msm-and-other-populations-in-china
#19
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
https://www.readbyqxmd.com/read/26264211/stat3-polymorphisms-may-predict-an-unfavorable-response-to-first-line-platinum-based-therapy-for-women-with-advanced-serous-epithelial-ovarian-cancer
#20
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
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