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https://www.readbyqxmd.com/read/28431355/genome-wide-identification-and-analysis-of-the-populus-trichocarpa-tify-gene-family
#1
Yue Wang, Feng Pan, Danmei Chen, Wenyuan Chu, Huanlong Liu, Yan Xiang
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome...
April 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28431284/mitovirus-uga-trp-codon-usage-parallels-that-of-host-mitochondria
#2
Max L Nibert
Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28431232/genome-wide-mapping-of-drosha-cleavage-sites-on-primary-micrornas-and-noncanonical-substrates
#3
Baekgyu Kim, Kyowon Jeong, V Narry Kim
MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed "formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq)," which allows identification of DROSHA cleavage sites at single-nucleotide resolution...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28428799/a-novel-cytoplasmic-male-sterility-in-brassica-napus-inap-cms-with-carpelloid-stamens-via-protoplast-fusion-with-chinese-woad
#4
Lei Kang, Pengfei Li, Aifan Wang, Xianhong Ge, Zaiyun Li
A novel cytoplasmic male sterility (CMS) in Brassica napus (inap CMS) was selected from the somatic hybrid with Isatis indigotica (Chinese woad) by recurrent backcrossing. The male sterility was caused by the conversion of tetradynamous stamens into carpelloid structures with stigmatoid tissues at their tips and ovule-like tissues in the margins, and the two shorter stamens into filaments without anthers. The feminized development of the stamens resulted in the complete lack of pollen grains, which was stable in different years and environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428791/genome-wide-association-study-for-pre-harvest-sprouting-resistance-in-a-large-germplasm-collection-of-chinese-wheat-landraces
#5
Yong Zhou, Hao Tang, Meng-Ping Cheng, Kwame O Dankwa, Zhong-Xu Chen, Zhan-Yi Li, Shang Gao, Ya-Xi Liu, Qian-Tao Jiang, Xiu-Jin Lan, Zhi-En Pu, Yu-Ming Wei, You-Liang Zheng, Lee T Hickey, Ji-Rui Wang
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428554/network-assisted-analysis-of-gwas-data-identifies-a-functionally-relevant-gene-module-for-childhood-onset-asthma
#6
Y Liu, M Brossard, C Sarnowski, A Vaysse, M Moffatt, P Margaritte-Jeannin, F Llinares-López, M H Dizier, M Lathrop, W Cookson, E Bouzigon, F Demenais
The number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28428243/genome-wide-transcription-and-functional-analyses-reveal-heterogeneous-molecular-mechanisms-driving-pyrethroids-resistance-in-the-major-malaria-vector-anopheles-funestus-across-africa
#7
Jacob M Riveron, Sulaiman S Ibrahim, Charles Mulamba, Rousseau Djouaka, Helen Irving, Murielle J Wondji, Intan H Ishak, Charles S Wondji
Pyrethroid resistance in malaria vector, An. Funestus is increasingly reported across Africa, threatening the sustainability of pyrethroid-based control interventions including long lasting insecticidal Nets (LLINs). Managing this problem requires understanding of the molecular basis of the resistance from different regions of the continent, to establish whether it is being driven by a single or independent selective events. Here, using a genome-wide transcription profiling of pyrethroid resistant populations from Southern (Malawi), East (Uganda) and West Africa (Benin), we investigated the molecular basis of resistance, revealing strong differences between the different African regions...
April 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28427344/genome-wide-identification-of-genes-probably-relevant-to-the-adaptation-of-schizothoracins-teleostei-cypriniformes-to-the-uplift-of-the-qinghai-tibet-plateau
#8
Wei Chi, Xufa Ma, Jiangong Niu, Ming Zou
BACKGROUND: Molecular adaptation to the severe environments present during the uplift of the Qinghai-Tibet Plateau has attracted the attention of researchers. The divergence of the three specialization groups of schizothoracins (Primitive, Specialized and Highly Specialized) may correspond to the three phases of plateau uplift. Based on the transcripts of representative species of the three specialized groups and an outgroup, genes in schizothoracins that may have played important roles during the adaptation to new environments were investigated...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#9
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28427323/detection-of-qtl-for-traits-related-to-adaptation-to-sub-optimal-climatic-conditions-in-chickens
#10
Ching-Yi Lien, Michèle Tixier-Boichard, Shih-Wen Wu, Woei-Fuh Wang, Chen Siang Ng, Chih-Feng Chen
BACKGROUND: Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS: An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption)...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28426286/on-the-evolution-of-lactase-persistence-in-humans
#11
Laure Ségurel, Céline Bon
Lactase persistence-the ability of adults to digest the lactose in milk-varies widely in frequency across human populations. This trait represents an adaptation to the domestication of dairying animals and the subsequent consumption of their milk. Five variants are currently known to underlie this phenotype, which is monogenic in Eurasia but mostly polygenic in Africa. Despite being a textbook example of regulatory convergent evolution and gene-culture coevolution, the story of lactase persistence is far from clear: Why are lactase persistence frequencies low in Central Asian herders but high in some African hunter-gatherers?Whywas lactase persistence strongly selected for even though milk processing can reduce the amount of lactose? Are there other factors, outside of an advantage of caloric intake, that contributed to the selective pressure for lactase persistence? It is time to revisit what we know and still do not know about lactase persistence in humans...
April 19, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#12
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28424564/new-developments-in-the-management-of-narcolepsy
#13
REVIEW
Vivien C Abad, Christian Guilleminault
Narcolepsy is a life-long, underrecognized sleep disorder that affects 0.02%-0.18% of the US and Western European populations. Genetic predisposition is suspected because of narcolepsy's strong association with HLA DQB1*06-02, and genome-wide association studies have identified polymorphisms in T-cell receptor loci. Narcolepsy pathophysiology is linked to loss of signaling by hypocretin-producing neurons; an autoimmune etiology possibly triggered by some environmental agent may precipitate hypocretin neuronal loss...
2017: Nature and Science of Sleep
https://www.readbyqxmd.com/read/28424424/leukocyte-telomere-length-related-genetic-variants-in-acyp2-contribute-to-the-risk-of-esophageal-carcinoma-in-chinese-han-population
#14
Quan Fang, Lihong Hui, Zhaorui Min, Lifeng Liu, Yuan Shao
BACKGROUND: Short leukocyte telomere length has been associated with significantly increased risk of esophageal carcinoma. A previous genome-wide association study demonstrated that ACYP2 was associated with leukocyte telomere length. However, the role of ACYP2 genetic variants on esophageal carcinoma susceptibility is still unknown. Therefore, we investigated whether ACYP2 polymorphisms have impact on the risk of esophageal carcinoma in Chinese. MATERIALS AND METHODS: We conducted a case-control study among 386 cases and 495 healthy controls from northwest China...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424354/less-effective-selection-leads-to-larger-genomes
#15
Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen, Michèle Weiss-Gayet, Andaine Seguin-Orlando, Luca Ermini, Clio Der Sarkissian, N Pierre Charrier, David Eme, Florian Mermillod-Blondin, Laurent Duret, Cristina Vieira, Ludovic Orlando, Christophe Douady
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28424085/the-within-host-population-dynamics-of-mycobacterium-tuberculosis-vary-with-treatment-efficacy
#16
Andrej Trauner, Qingyun Liu, Laura E Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E Barry, Qian Gao
BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics...
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28423615/exoc3l2-rs597668-variant-contributes-to-alzheimer-s-disease-susceptibility-in-asian-population
#17
Qing-Jian Wu, Shu-Yin Sun, Cheng-Jun Yan, Zi-Cui Cheng, Ming-Feng Yang, Zi-Fei Li, Hou-Wen Cheng, Ti-Kun Fang
Recent genome-wide association studies have established the association between EXOC3L2 rs597668 variant and Alzheimer's disease (AD) in European population. However, recent studies reported inconsistent results in Asian population. Here, we performed a systematic review and meta-analysis to evaluate the impact of rs597668 on AD risk in Asian population using a total of 8686 samples including 2855 cases and 5831 controls. Meanwhile, we selected 17,008 AD cases and 37,154 controls in European population to evaluate the potential heterogeneity between East Asian and European populations...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423309/the-natural-product-cavinafungin-selectively-interferes-with-zika-and-dengue-virus-replication-by-inhibition-of-the-host-signal-peptidase
#18
David Estoppey, Chia Min Lee, Marco Janoschke, Boon Heng Lee, Kah Fei Wan, Hongping Dong, Philippe Mathys, Ireos Filipuzzi, Tim Schuhmann, Ralph Riedl, Thomas Aust, Olaf Galuba, Gregory McAllister, Carsten Russ, Martin Spiess, Tewis Bouwmeester, Ghislain M C Bonamy, Dominic Hoepfner
Flavivirus infections by Zika and dengue virus impose a significant global healthcare threat with no US Food and Drug Administration (FDA)-approved vaccination or specific antiviral treatment available. Here, we present the discovery of an anti-flaviviral natural product named cavinafungin. Cavinafungin is a potent and selectively active compound against Zika and all four dengue virus serotypes. Unbiased, genome-wide genomic profiling in human cells using a novel CRISPR/Cas9 protocol identified the endoplasmic-reticulum-localized signal peptidase as the efficacy target of cavinafungin...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422514/vitamin-c-prevents-offspring-dna-methylation-changes-associated-with-maternal-smoking-in-pregnancy
#19
Lyndsey E Shorey-Kendrick, Cindy T McEvoy, Betsy Ferguson, Julja Burchard, Byung S Park, Lina Gao, Brittany H Vuylsteke, Kristin F Milner, Cynthia D Morris, Eliot R Spindel
BACKGROUND: Infants whose mothers smoked during pregnancy demonstrate lifelong decreases in pulmonary function. DNA methylation changes associated with maternal smoking during pregnancy have been described in placenta and cord blood at delivery, in fetal lung, and in buccal epithelium and blood during childhood. We recently demonstrated in a randomized clinical trial (NCT00632476) that vitamin C supplementation to pregnant smokers can lessen the impact of maternal smoking on offspring pulmonary function and decrease the incidence of wheeze at one year of age...
April 19, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28422318/computational-analysis-of-breast-cancer-gwas-loci-identifies-the-putative-deleterious-effect-of-stxbp4-and-znf404-gene-variants
#20
Tariq Ahmad Masoodi, Babajan Banaganapalli, Venkatesh Vaidyanathan, Venkateswar Rao Talluri, Noor Ahmad Shaik
The genome-wide association studies (GWAS) have enabled us in identifying different breast cancer susceptibility loci. However, majority of these are non-coding variants with no annotated biological function. We investigated such 78 noncoding genome wide associated SNPs of breast cancer and further expanded the list to 2162 variants with strong linkage-disequilibrium (LD, r2 ≥0.8). Using multiple publically available algorithms such as CADD, GWAVA and FATHAMM, we classified all these variants in to deleterious, damaging or benign categories...
April 19, 2017: Journal of Cellular Biochemistry
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