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https://www.readbyqxmd.com/read/29617175/maximum-likelihood-approach-suggests-positive-selection-in-platelet-integrin-%C3%AE-iib%C3%AE-3-in-mammalian-species
#1
Luís Bernardo Pina-Cabral, Miguel Carneiro, Begoña Criado, Pedro José Esteves
Platelet integrin αIIbβ3 is crucial for platelet aggregation. Although structural and functional characteristics of this protein have been extensively studied, the evolutionary pattern studies of this protein complex in mammals are scarce. Here, we addressed this question using maximum likelihood approaches to identify codons that are evolving under positive selection. Likelihood of positive selection was estimated using CODEML implemented in PAML software applied to integrin αIIbβ3 derived from nucleotide sequences of 10 different mammalian species...
April 4, 2018: Platelets
https://www.readbyqxmd.com/read/29510674/evolutionary-analysis-of-mitochondrially-encoded-proteins-of-toad-headed-lizards-phrynocephalus-along-an-altitudinal-gradient
#2
Yuanting Jin, Yubin Wo, Haojie Tong, Sen Song, Lixun Zhang, Richard P Brown
BACKGROUND: Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time)...
March 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29467795/genome-wide-study-of-yabby-genes-in-upland-cotton-and-their-expression-patterns-under-different-stresses
#3
Zhaoen Yang, Qian Gong, Lingling Wang, Yuying Jin, Jianping Xi, Zhi Li, Wenqiang Qin, Zuoren Yang, Lili Lu, Quanjia Chen, Fuguang Li
Members of the YABBY gene family, a small plant-specific family of genes, have been proposed to function in specifying abaxial cell fate. Although to date little has been learned about cotton YABBY genes, completion of the cotton genome enables a comprehensive genome-wide analysis of YABBY genes in cotton. Here, a total of 12, 12, and 23 YABBY genes were identified in Gossypium arboreum (2n = 26, A2 ), G. raimondii (2n = 26, D5 ), and G. hirsutum (2n = 4x = 52, [AD]t ), respectively. Sequence analysis showed that the N-terminal zinc-finger and C-terminal YABBY domains in YABBY proteins are highly conserved among cotton, Arabidopsis , and rice...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29338495/clinical-challenges-in-de-novo-pediatric-acute-myeloid-leukemia
#4
Kim Klein, Valérie de Haas, Gertjan J L Kaspers
Although the prognosis of pediatric acute myeloid leukemia (pAML) has improved, with current survival rates up to 75%, relapse rates remain high. Areas covered: The low number of patients, the heterogeneous genomic landscape of AML, novel diagnostic techniques, divergent available treatment protocols, and dose-limiting toxicity of conventional agents all contribute to the complexity of AML treatment. This review gives an overview of the current clinical challenges with respect to diagnostics, treatment, and supportive care in pAML...
March 2018: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/29273445/selective-pressure-on-the-protein-coding-genes-of-the-pufferfish-is-correlated-with-phenotypic-traits
#5
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
February 2018: Marine Genomics
https://www.readbyqxmd.com/read/29141193/evolution-of-the-clock-and-bmal1-genes-in-a-subterranean-rodent-species-lasiopodomys-mandarinus
#6
Hong Sun, Yifeng Zhang, Yuhua Shi, Yangwei Li, Wei Li, Zhenlong Wang
Lasiopodomys mandarinus, a subterranean rodent, spends its entire life underground. To test whether the CLOCK and BMAL1 genes of L. mandarinus have undergone adaptive evolution to underground darkness, we cloned and analyzed their complete cDNA sequences, using Lasiopodomys brandtii as a control. The phylogenetic trees of the CLOCK and BMAL1 genes were similar to the trees of the conserved Cyt b gene,further, L. mandarinus clustered with L. brandtii and Microtus ochrogaster in the phylogenetic tree. The Q-rich region of the CLOCK gene in L...
November 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29026839/missing-the-benefit-of-metformin-in-acute-myeloid-leukemia-a-problem-of-contrast
#7
Alice C Ceacareanu, George K Nimako, Zachary A P Wintrob
OBJECTIVE: To evaluate whether metformin's cancer-related benefits reported in patients with solid tumors (ST) are also present in acute myeloid leukemia (AML) patients. METHODS: Baseline demographic and clinical history for all diabetes mellitus patients newly diagnosed with AML or cancer of the breast, ovary, prostate, gastrointestinal tract, lung, or kidney at Roswell Park Cancer Institute in Buffalo, NY (January 2003-December 2010, n = 924) was collected. Overall survival (OS) and disease-free survival (DFS) were assessed by Kaplan-Meier (KM) analysis and Cox proportional hazards regression (hazard ratio [HR])...
July 2017: Journal of Research in Pharmacy Practice
https://www.readbyqxmd.com/read/28870858/molecular-characterization-and-expression-analysis-of-the-large-yellow-croaker-larimichthys-crocea-chemokine-receptors-cxcr2-cxcr3-and-cxcr4-after-bacterial-and-poly-i-c-challenge
#8
Xiaoxu Liu, Lisen Kang, Wei Liu, Bao Lou, Changwen Wu, Lihua Jiang
The large yellow croaker (Larimichthys crocea) has a well-developed innate immune system. We studied a component of this system, chemokine receptor CXCR family. In this study, we report the full-length open reading frames, as well as the identification and characterization of the chemokine receptor genes CXCR2 (LycCXCR2), CXCR3 (LycCXCR3), and CXCR4 (LycCXCR4) of large yellow croaker. We report that LycCXCR3 and LycCXCR4 are evolving neutrally according to PAML analyses. Quantitative real-time PCR analysis revealed that CXCR transcripts were expressed in all examined tissues...
September 8, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28859145/positively-selected-amino-acid-replacements-within-the-rubisco-enzyme-of-oak-trees-are-associated-with-ecological-adaptations
#9
Carmen Hermida-Carrera, Mario A Fares, Ángel Fernández, Eustaquio Gil-Pelegrín, Maxim V Kapralov, Arnau Mir, Arántzazu Molins, José Javier Peguero-Pina, Jairo Rocha, Domingo Sancho-Knapik, Jeroni Galmés
Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28767699/molecular-evolutionary-patterns-of-nad-sirtuin-aging-signaling-pathway-across-taxa
#10
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-gene-in-subterranean-octodontid-rodents
#11
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...
September 10, 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
#12
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
#13
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...
November 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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