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https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#1
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27909914/association-of-snp-variants-of-mhc-class-ii-drb-gene-with-thermo-physiological-traits-in-tropical-goats
#2
Abdulmojeed Yakubu, Adebowale E Salako, Marcos De Donato, Sunday O Peters, Michael I Takeet, Mathew Wheto, Moses Okpeku, Ikhide G Imumorin
Host defense in vertebrates depend on many secreted regulatory proteins such as major histocompatibility complex (MHC) class II which provide important regulatory and effector functions of T cells. Gene polymorphism in the second exon of Capra-DRB gene in three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS), and Sahel (SH)] was analyzed by restriction fragment length polymorphisms (RFLP). Four restriction enzymes, BsaHI, AluI, HaeIII, and SacII, were utilized. The association between the polymorphic sites and some heat tolerance traits were also investigated in a total of 70 WAD, 90 RS, and 50 SH goats...
December 1, 2016: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#3
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27893787/selection-signatures-in-four-lignin-genes-from-switchgrass-populations-divergently-selected-for-in-vitro-dry-matter-digestibility
#4
Shiyu Chen, Shawn M Kaeppler, Kenneth P Vogel, Michael D Casler
Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection...
2016: PloS One
https://www.readbyqxmd.com/read/27886141/comprehensive-transcriptome-analysis-provides-evidence-of-local-thermal-adaptation-in-three-loaches-genus-misgurnus
#5
Shaokui Yi, Sai Wang, Jia Zhong, Weimin Wang
The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified...
November 24, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27879145/variations-in-endothelin-receptor-b-subtype-2-ednrb2-coding-sequences-and-mrna-expression-levels-in-four-muscovy-duck-plumage-colour-phenotypes
#6
N Wu, H Qin, M Wang, Y Bian, B Dong, G Sun, W Zhao, G Chang, Q Xu, G Chen
1. Endothelin receptor B subtype 2 (EDNRB2) is a paralog of EDNRB, which encodes a 7-transmembrane G-protein coupled receptor. Previous studies reported that EDNRB was essential for melanoblast migration in mammals and ducks. 2. Muscovy ducks have different plumage colour phenotypes. Variations in EDNRB2 coding sequences and mRNA expression levels were investigated in 4 different Muscovy duck plumage colour phenotypes, including black, black mutant, silver and white head. 3. The EDNRB2 gene from Muscovy duck was cloned; it had a length of 6435 bp and encoded 437 amino acids...
November 23, 2016: British Poultry Science
https://www.readbyqxmd.com/read/27871225/genomic-epidemiology-of-lineage-4-mycobacterium-tuberculosis-subpopulations-in-new-york-city-and-new-jersey-1999-2009
#7
Tyler S Brown, Apurva Narechania, John R Walker, Paul J Planet, Pablo J Bifani, Sergios-Orestis Kolokotronis, Barry N Kreiswirth, Barun Mathema
BACKGROUND: Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27842877/identification-of-a-novel-mutation-at-the-primary-dimer-interface-of-gyra-conferring-fluoroquinolone-resistance-in-clostridium-difficile
#8
Micheál Mac Aogáin, Shauna Kilkenny, Claire Walsh, Sinéad Lindsay, Geraldine Moloney, Trefor Morris, Sophie Jones, Thomas R Rogers
The aim of this study was to determine whether alternative resistance mechanisms, other than mutation in the quinolone resistance-determining region (QRDR) of DNA gyrase, could confer fluoroquinolone resistance in Clostridium difficile. An in vitro-generated C. difficile mutant exhibiting increased fluoroquinolone resistance was isolated through antibiotic selection on ciprofloxacin. The QRDR of this mutant was investigated by chain-termination sequencing and was found to be devoid of mutation. To determine the nature of the non-QRDR resistance mechanism in this strain, the genomes of the mutant and wild-type strains were sequenced...
December 2015: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27836448/multilocus-amplicon-sequencing-of-pseudomonas-aeruginosa-cystic-fibrosis-airways-isolates-collected-prior-to-and-after-early-antipseudomonal-chemotherapy
#9
Sebastian Fischer, Leonie Greipel, Jens Klockgether, Marie Dorda, Lutz Wiehlmann, Nina Cramer, Burkhard Tümmler
BACKGROUND: Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa. METHODS: During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa - positive after the first round of antipseudomonal chemotherapy...
November 8, 2016: Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society
https://www.readbyqxmd.com/read/27833609/a-case-of-il-7r-deficiency-caused-by-a-novel-synonymous-mutation-and-implications-for-mutation-screening-in-scid-diagnosis
#10
Fernando Gallego-Bustos, Valer Gotea, José T Ramos-Amador, Rebeca Rodríguez-Pena, Juana Gil-Herrera, Ana Sastre, Aitor Delmiro, Ghadi Rai, Laura Elnitski, Luis I González-Granado, Luis M Allende
Reported synonymous substitutions are generally non-pathogenic, and rare pathogenic synonymous variants may be disregarded unless there is a high index of suspicion. In a case of IL7 receptor deficiency severe combined immunodeficiency (SCID), the relevance of a non-reported synonymous variant was only suspected through the use of additional in silico computational tools, which focused on the impact of mutations on gene splicing. The pathogenic nature of the variant was confirmed using experimental validation of the effect on mRNA splicing and IL7 pathway function...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27830284/sequence-diversification-in-recessive-alleles-of-two-host-factor-genes-suggests-adaptive-selection-for-bymovirus-resistance-in-cultivated-barley-from-east-asia
#11
Ping Yang, Antje Habekuß, Bernhard J Hofinger, Kostya Kanyuka, Benjamin Kilian, Andreas Graner, Frank Ordon, Nils Stein
Two distinct patterns of sequence diversity for the recessive alleles of two host factors HvPDIL5 - 1 and HvEIF4E indicated the adaptive selection for bymovirus resistance in cultivated barley from East Asia. Plant pathogens are constantly challenging plant fitness and driving resistance gene evolution in host species. Little is known about the evolution of sequence diversity in host recessive resistance genes that interact with plant viruses. Here, by combining previously published and newly generated targeted re-sequencing information, we systematically analyzed natural variation in a broad collection of wild (Hordeum spontaneum; Hs) and domesticated barleys (Hordeum vulgare; Hv) using the full-length coding sequence of the two host factor genes, HvPDIL5-1 and HvEIF4E, conferring recessive resistance to the agriculturally important Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV)...
November 9, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27829056/genome-wide-identification-characterization-and-stress-responsive-expression-profiling-of-genes-encoding-lea-late-embryogenesis-abundant-proteins-in-moso-bamboo-phyllostachys-edulis
#12
Zhuo Huang, Xiao-Juan Zhong, Jiao He, Si-Han Jin, Han-Du Guo, Xiao-Fang Yu, Yu-Jue Zhou, Xi Li, Ming-Dong Ma, Qi-Bing Chen, Hai Long
Late embryogenesis abundant (LEA) proteins have been identified in a wide range of organisms and are believed to play a role in the adaptation of plants to stress conditions. In this study, we performed genome-wide identification of LEA proteins and their coding genes in Moso bamboo (Phyllostachys edulis) of Poaceae. A total of 23 genes encoding LEA proteins (PeLEAs) were found in P. edulis that could be classified to six groups based on Pfam protein family and homologous analysis. Further in silico analyses of the structures, gene amount, and biochemical characteristics were conducted and compared with those of O...
2016: PloS One
https://www.readbyqxmd.com/read/27825516/adaptation-of-escherichia-coli-traversing-from-the-faecal-environment-to-the-urinary-tract
#13
Karen L Nielsen, Marc Stegger, Paul A Godfrey, Michael Feldgarden, Paal S Andersen, Niels Frimodt-Møller
The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient's own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria in order to traverse the perineum and successfully infect the urinary tract. Here, matching pairs of faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments...
December 2016: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/27818095/genetic-markers-associated-with-dihydroartemisinin-piperaquine-failure-in-plasmodium-falciparum-malaria-in-cambodia-a-genotype-phenotype-association-study
#14
Roberto Amato, Pharath Lim, Olivo Miotto, Chanaki Amaratunga, Dalin Dek, Richard D Pearson, Jacob Almagro-Garcia, Aaron T Neal, Sokunthea Sreng, Seila Suon, Eleanor Drury, Dushyanth Jyothi, Jim Stalker, Dominic P Kwiatkowski, Rick M Fairhurst
BACKGROUND: As the prevalence of artemisinin-resistant Plasmodium falciparum malaria increases in the Greater Mekong subregion, emerging resistance to partner drugs in artemisinin combination therapies seriously threatens global efforts to treat and eliminate this disease. Molecular markers that predict failure of artemisinin combination therapy are urgently needed to monitor the spread of partner drug resistance, and to recommend alternative treatments in southeast Asia and beyond. METHODS: We did a genome-wide association study of 297 P falciparum isolates from Cambodia to investigate the relationship of 11 630 exonic single-nucleotide polymorphisms (SNPs) and 43 copy number variations (CNVs) with in-vitro piperaquine 50% inhibitory concentrations (IC50s), and tested whether these genetic variants are markers of treatment failure with dihydroartemisinin-piperaquine...
November 3, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27816910/progressive-and-biased-divergent-evolution-underpins-the-origin-and-diversification-of-peridinin-dinoflagellate-plastids
#15
Richard G Dorrell, Christen M Klinger, Robert J Newby, Erin R Butterfield, Elisabeth Richardson, Joel B Dacks, Christopher J Howe, R Ellen R Nisbet, Chris Bowler
Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organisation of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons...
November 4, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27813549/biological-serological-and-molecular-typing-of-potato-virus-y-pvy-isolates-from-tunisia
#16
M Tayahi, C Gharsallah, N Khamassy, H Fakhfakh, F Djilani-Khouadja
In Tunisia, potato virus Y (PVY) currently presents a significant threat to potato production, reducing tuber yield and quality. Three hundred and eighty-five potato samples (six different cultivars) collected in autumn 2007 from nine regions in Tunisia were tested for PVY infection by DAS-ELISA. The virus was detected in all regions surveyed, with an average incidence of 80.26%. Subsequently, a panel of 82 Tunisian PVY isolates (PVY-TN) was subjected to systematic biological, serological and molecular typing using immunocapture reverse-transcription polymerase chain reaction and a series of PVY(OC)- and PVY(N)-specific monoclonal antibodies...
October 17, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27812419/genome-wide-identification-and-characterization-of-tify-family-genes-in-moso-bamboo-phyllostachys-edulis-and-expression-profiling-analysis-under-dehydration-and-cold-stresses
#17
Zhuo Huang, Si-Han Jin, Han-Du Guo, Xiao-Juan Zhong, Jiao He, Xi Li, Ming-Yan Jiang, Xiao-Fang Yu, Hai Long, Ming-Dong Ma, Qi-Bing Chen
The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. One PeTIFY belongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively...
2016: PeerJ
https://www.readbyqxmd.com/read/27812361/transcriptome-analysis-of-green-peach-aphid-myzus-persicae-insight-into-developmental-regulation-and-inter-species-divergence
#18
Rui Ji, Yujun Wang, Yanbin Cheng, Meiping Zhang, Hong-Bin Zhang, Li Zhu, Jichao Fang, Keyan Zhu-Salzman
Green peach aphid (Myzus persicae) and pea aphid (Acyrthosiphon pisum) are two phylogenetically closely related agricultural pests. While pea aphid is restricted to Fabaceae, green peach aphid feeds on hundreds of plant species from more than 40 families. Transcriptome comparison could shed light on the genetic factors underlying the difference in host range between the two species. Furthermore, a large scale study contrasting gene expression between immature nymphs and fully developed adult aphids would fill a previous knowledge gap...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27812022/the-mutation-p-e113k-in-the-schiff-base-counterion-of-rhodopsin-is-associated-with-two-distinct-retinal-phenotypes-within-the-same-family
#19
Charlotte Reiff, Marta Owczarek-Lipska, Georg Spital, Carsten Röger, Hebke Hinz, Christoph Jüschke, Holger Thiele, Janine Altmüller, Peter Nürnberg, Romain Da Costa, John Neidhardt
The diagnoses of retinitis pigmentosa (RP) and stationary night blindness (CSNB) are two distinct clinical entities belonging to a group of clinically and genetically heterogeneous retinal diseases. The current study focused on the identification of causative mutations in the RP-affected index patient and in several members of the same family that reported a phenotype resembling CSNB. Ophthalmological examinations of the index patient confirmed a typical form of RP. In contrast, clinical characterizations and ERGs of another affected family member showed the Riggs-type CSNB lacking signs of RP...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27808114/cassava-brown-streak-virus-has-a-rapidly-evolving-genome-implications-for-virus-speciation-variability-diagnosis-and-host-resistance
#20
Titus Alicai, Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Geoffrey Okao-Okuja, Resty Nanvubya, Lilliane Kiiza, Laura Kubatko, Monica A Kehoe, Laura M Boykin
Cassava is a major staple food for about 800 million people in the tropics and sub-tropical regions of the world. Production of cassava is significantly hampered by cassava brown streak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The disease is suppressing cassava yields in eastern Africa at an alarming rate. Previous studies have documented that CBSV is more devastating than UCBSV because it more readily infects both susceptible and tolerant cassava cultivars, resulting in greater yield losses...
November 3, 2016: Scientific Reports
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