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https://www.readbyqxmd.com/read/28767699/molecular-evolutionary-patterns-of-nad-sirtuin-aging-signaling-pathway-across-taxa
#1
Uma Gaur, Jianbo Tu, Diyan Li, Yue Gao, Ting Lian, Boyuan Sun, Deying Yang, Xiaolan Fan, Mingyao Yang
A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD+/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that MRPS5 and PPARGC1A were under significant constraints because of their functional significance...
2017: PloS One
https://www.readbyqxmd.com/read/28735726/molecular-adaptive-convergence-in-the-%C3%AE-globin-in-subterranean-octodontid-rodents
#2
Ivanna H Tomasco, Nicolás Boullosa, Federico G Hoffmann, Enrique P Lessa
Tuco-tucos (Ctenomys) and related coruros (Spalacopus) are South American subterranean rodents. An energetically demanding lifestyle within the hypoxic/hypercapnic underground atmosphere may change the selective regime on genes involved in O2 transport in blood. In addition, some species of tuco-tucos may be found at high altitude, thus facing additional reductions in changes O2 availabily. We examined sequence variation in the alpha globin subunit gene of hemoglobine in these lineages, within a robust phylogenetic context...
July 20, 2017: Gene
https://www.readbyqxmd.com/read/28648850/complete-genome-analysis-of-dengue-virus-type-3-isolated-from-the-2013-dengue-outbreak-in-yunnan-china
#3
Xiaodan Wang, Dehong Ma, Xinwei Huang, Lihua Li, Duo Li, Yujiao Zhao, Lijuan Qiu, Yue Pan, Junying Chen, Juemin Xi, Xiyun Shan, Qiangming Sun
In the past few decades, dengue has spread rapidly and is an emerging disease in China. An unexpected dengue outbreak occurred in Xishuangbanna, Yunnan, China, resulting in 1331 patients in 2013. In order to obtain the complete genome information and perform mutation and evolutionary analysis of causative agent related to this largest outbreak of dengue fever. The viruses were isolated by cell culture and evaluated by genome sequence analysis. Phylogenetic trees were then constructed by Neighbor-Joining methods (MEGA6...
June 23, 2017: Virus Research
https://www.readbyqxmd.com/read/28502652/comparative-and-evolutionary-analysis-of-an-adapter-molecule-myd88-in-invertebrate-metazoans
#4
Yipeng Ren, Junli Xue, Huanhuan Yang, Baoping Pan, Wenjun Bu
The myeloid differentiation factor 88 (MyD88) is an essential adapter in Toll-like receptor (TLR) signalling pathways, with TLR the first pattern-recognition receptor (PRR) that was discovered in Drosophila. In the present study, a MyD88 gene was identified and characterized from a commercially important shellfish, Scapharca subcrenata, including a DEATH domain and TIR domain conserved within other molluscs. Furthermore, comparative genomic evidence revealed that MyD88 was of different lengths and contained quantitative exon and intron regions, which might be involved in specific mechanisms...
May 11, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28149689/polymorphism-in-the-major-histocompatibility-complex-mhc-class-ii-b-genes-of-the-rufous-backed-bunting-emberiza-jankowskii
#5
Dan Li, Keping Sun, Yunjiao Zhao, Aiqing Lin, Shi Li, Yunlei Jiang, Jiang Feng
Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size...
2017: PeerJ
https://www.readbyqxmd.com/read/28141822/e6-and-e7-gene-polymorphisms-in-human-papillomavirus-types-58-and-33-identified-in-southwest-china
#6
Zuyi Chen, Yaling Jing, Qiang Wen, Xianping Ding, Tao Wang, Xuemei Mu, Yuwei Chenzhang, Man Cao
Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV). The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216) and HPV-58 (E6, E7: n = 405) E6 and E7 genes were sequenced and compared to others submitted to GenBank...
2017: PloS One
https://www.readbyqxmd.com/read/28031539/recurrent-genetic-defects-on-chromosome-5q-in-myeloid-neoplasms
#7
Naoko Hosono, Hideki Makishima, Reda Mahfouz, Bartlomiej Przychodzen, Kenichi Yoshida, Andres Jerez, Thomas LaFramboise, Chantana Polprasert, Michael J Clemente, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Masashi Sanada, Edward Cui, Amit K Verma, Michael A McDevitt, Alan F List, Yogen Saunthararajah, Mikkael A Sekeres, Jacqueline Boultwood, Seishi Ogawa, Jaroslaw P Maciejewski
BACKGROUND: Deletion of chromosome 5q (del(5q)) is the most common karyotypic abnormality in myeloid neoplasms. MATERIALS AND METHODS: To define the pathogenic molecular features associated with del(5q), next-generation sequencing was applied to 133 patients with myeloid neoplasms (MDS; N = 69, MDS/MPN; N = 5, sAML; N = 29, pAML; N = 30) with del(5q) as a sole abnormally or a part of complex karyotype and results were compared to molecular features of patients diploid for chr5...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/27983727/the-complexity-of-interpreting-genomic-data-in-patients-with-acute-myeloid-leukemia
#8
A Nazha, A Zarzour, K Al-Issa, T Radivoyevitch, H E Carraway, C M Hirsch, B Przychodzen, B J Patel, M Clemente, S R Sanikommu, M Kalaycio, J P Maciejewski, M A Sekeres
Acute myeloid leukemia (AML) is a heterogeneous neoplasm characterized by the accumulation of complex genetic alterations responsible for the initiation and progression of the disease. Translating genomic information into clinical practice remained challenging with conflicting results regarding the impact of certain mutations on disease phenotype and overall survival (OS) especially when clinical variables are controlled for when interpreting the result. We sequenced the coding region for 62 genes in 468 patients with secondary AML (sAML) and primary AML (pAML)...
December 16, 2016: Blood Cancer Journal
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
#9
Tingting Li, Binlian Sun, Yanyan Jiang, Haiyan Zeng, Yanpeng Li, Yan Wang, Rongge Yang
BACKGROUND: 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 2003 and the late period 2004 to 2010...
2017: 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
#10
Jennifer B Permuth, Brett Reid, Madalene Earp, Y Ann Chen, Alvaro N A Monteiro, Zhihua Chen, 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...
November 8, 2016: Oncotarget
https://www.readbyqxmd.com/read/27896727/measuring-natural-selection
#11
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
#12
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
#13
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
#14
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
#15
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
#16
Nathaniel K Jue, Paola G Batta-Lona, Sarah Trusiak, Craig Obergfell, Ann Bucklin, Michael J O'Neill, Rachel 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 >50% of the estimated 602 Mb (±173 Mb) genome size for S...
October 30, 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
#17
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
#18
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
#19
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 D P 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...
August 15, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/27322407/inference-of-episodic-changes-in-natural-selection-acting-on-protein-coding-sequences-via-codeml
#20
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
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