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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/28431280/interleukin-1-receptor-associated-kinase-1-is-a-potential-therapeutic-target-of-anti-inflammatory-therapy-for-systemic-lupus-erythematosus
#3
Mingfang Li, Datang Yu, Bing Ni, Fei Hao
Systemic lupus erythematosus (SLE) is a chronic autoimmune inflammatory disease and currently has no effective therapy. The genome-wide analyses indicate that interleukin-1 receptor associated kinase 1 (IRAK1) is associated with the susceptibility of SLE in humans. In the present study, we identified that IRAK1 was overexpressed and hyper-activated in splenic mononuclear cells from B6.MRL-Fas(lpr)/Nju (B6.lpr) mice and peripheral blood mononuclear cells (PBMCs) from SLE patients. Intraperitoneal treatment with a small molecular inhibitor of IRAK1 (IRAK1/4 inhibitor or IRAK-Inh) significantly mitigated inflammatory responses and renal injury in B6...
April 18, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28431232/genome-wide-mapping-of-drosha-cleavage-sites-on-primary-micrornas-and-noncanonical-substrates
#4
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/28431168/identifying-new-susceptibility-genes-on-dopaminergic-and-serotonergic-pathways-for-the-framing-effect-in-decision-making
#5
Xiaoxue Gao, Jinting Liu, Pingyuan Gong, Junhui Wang, Wan Fang, Hongming Yan, Lusha Zhu, Xiaolin Zhou
The framing effect refers the tendency to be risk-averse when options are presented positively but be risk-seeking when the same options are presented negatively during decision-making. This effect has been found to be modulated by the serotonin transporter gene (SLC6A4) and the catechol-o-methyltransferase gene (COMT) polymorphisms, which are on the dopaminergic and serotonergic pathways and which are associated with affective processing. The current study aimed to identify new genetic variations of genes on dopaminergic and serotonergic pathways that may contribute to individual differences in the susceptibility to framing...
April 19, 2017: Social Cognitive and Affective Neuroscience
https://www.readbyqxmd.com/read/28431028/hybrid-de-novo-genome-assembly-of-the-chinese-herbal-fleabane-erigeron-breviscapus
#6
Jing Yang, Guanghui Zhang, Jing Zhang, Hui Liu, Wei Chen, Xiao Wang, Yahe Li, Yang Dong, Shengchao Yang
Background: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28431021/patterns-of-genome-wide-diversity-and-population-structure-in-the-drosophila-athabasca-species-complex
#7
Karen M Wong Miller, Ryan R Bracewell, Michael B Eisen, Doris Bachtrog
The Drosophila athabasca species complex contains three recently diverged, prezygotically isolated semispecies (Western-Northern, Eastern-A, and Eastern-B) that are distributed across North America and share zones of sympatry. Inferences based on a handful of loci suggest that this complex might be an ideal system for studying the genetics of incipient speciation and the evolution of prezygotic isolating mechanisms, but patterns of differentiation have not been characterized systematically. Here, we assembled a draft genome for D...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430989/gene-fractionation-and-function-in-the-ancient-subgenomes-of-maize
#8
Simon Renny-Byfield, Eli Rodgers-Melnick, Jeffrey Ross-Ibarra
The maize genome experienced an ancient whole genome duplication approximately 10 million years ago and the duplicate subgenomes have since experienced reciprocal gene loss (fractionation) such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here we take advantage of published genome-wide SNP and phenotype association data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared to their lowly expressed counterparts...
April 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28430865/unmet-needs-in-the-first-line-treatment-of-follicular-lymphoma
#9
C Casulo, L Nastoupil, N H Fowler, J W Friedberg, C R Flowers
For the majority of patients with newly diagnosed follicular lymphoma (FL), current treatments, while not curative, allow for long remission durations. However, several important needs remain unaddressed. Studies have consistently shown that approximately 20% of patients with FL experience disease progression within 2 years of first-line treatment, and consequently have a 50% risk of death in 5 years. Better characterization of this group of patients at diagnosis may provide insight into those in need of alternate or intensive therapies, facilitate a precision approach to inform clinical trials, and allow for improved patient counseling...
April 18, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28430825/discovery-and-fine-mapping-of-adiposity-loci-using-high-density-imputation-of-genome-wide-association-studies-in-individuals-of-african-ancestry-african-ancestry-anthropometry-genetics-consortium
#10
Maggie C Y Ng, Mariaelisa Graff, Yingchang Lu, Anne E Justice, Poorva Mudgal, Ching-Ti Liu, Kristin Young, Lisa R Yanek, Mary F Feitosa, Mary K Wojczynski, Kristin Rand, Jennifer A Brody, Brian E Cade, Latchezar Dimitrov, Qing Duan, Xiuqing Guo, Leslie A Lange, Michael A Nalls, Hayrettin Okut, Salman M Tajuddin, Bamidele O Tayo, Sailaja Vedantam, Jonathan P Bradfield, Guanjie Chen, Wei-Min Chen, Alessandra Chesi, Marguerite R Irvin, Badri Padhukasahasram, Jennifer A Smith, Wei Zheng, Matthew A Allison, Christine B Ambrosone, Elisa V Bandera, Traci M Bartz, Sonja I Berndt, Leslie Bernstein, William J Blot, Erwin P Bottinger, John Carpten, Stephen J Chanock, Yii-Der Ida Chen, David V Conti, Richard S Cooper, Myriam Fornage, Barry I Freedman, Melissa Garcia, Phyllis J Goodman, Yu-Han H Hsu, Jennifer Hu, Chad D Huff, Sue A Ingles, Esther M John, Rick Kittles, Eric Klein, Jin Li, Barbara McKnight, Uma Nayak, Barbara Nemesure, Adesola Ogunniyi, Andrew Olshan, Michael F Press, Rebecca Rohde, Benjamin A Rybicki, Babatunde Salako, Maureen Sanderson, Yaming Shao, David S Siscovick, Janet L Stanford, Victoria L Stevens, Alex Stram, Sara S Strom, Dhananjay Vaidya, John S Witte, Jie Yao, Xiaofeng Zhu, Regina G Ziegler, Alan B Zonderman, Adebowale Adeyemo, Stefan Ambs, Mary Cushman, Jessica D Faul, Hakon Hakonarson, Albert M Levin, Katherine L Nathanson, Erin B Ware, David R Weir, Wei Zhao, Degui Zhi, Donna K Arnett, Struan F A Grant, Sharon L R Kardia, Olufunmilayo I Oloapde, D C Rao, Charles N Rotimi, Michele M Sale, L Keoki Williams, Babette S Zemel, Diane M Becker, Ingrid B Borecki, Michele K Evans, Tamara B Harris, Joel N Hirschhorn, Yun Li, Sanjay R Patel, Bruce M Psaty, Jerome I Rotter, James G Wilson, Donald W Bowden, L Adrienne Cupples, Christopher A Haiman, Ruth J F Loos, Kari E North
Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes...
April 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28430790/whole-genome-sequencing-suggests-mechanisms-for-22q11-2-deletion-associated-parkinson-s-disease
#11
Nancy J Butcher, Daniele Merico, Mehdi Zarrei, Lucas Ogura, Christian R Marshall, Eva W C Chow, Anthony E Lang, Stephen W Scherer, Anne S Bassett
OBJECTIVES: To investigate disease risk mechanisms of early-onset Parkinson's disease (PD) associated with the recurrent 22q11.2 deletion, a genetic risk factor for early-onset PD. METHODS: In a proof-of-principle study, we used whole-genome sequencing (WGS) to investigate sequence variants in nine adults with 22q11.2DS, three with neuropathologically confirmed early-onset PD and six without PD. Adopting an approach used recently to study schizophrenia in 22q11...
2017: PloS One
https://www.readbyqxmd.com/read/28430581/association-between-en1-rs4144782-and-susceptibility-of-knee-osteoarthritis-a-case-control-study
#12
Li Haohuan, Zhang Xiaolong, Cao Yiping, Hu Song, Peng Fei, Zhou Jianlin, Li Jianping
Osteoarthritis (OA) is a complex disease that affects the whole joint, resulting from the combined influence of biomechanical factors and genetic factors. The heritable component for primary OA accounts for about 60% of variation in population liability to the disease. So far, genome-wide association studies (GWAS) and candidate gene studies have established many OA-related loci. However, these findings account for only a rather small fraction of the genetic component. To further reveal the genetic architecture of OA, we conducted this case-control study to explore the association of locus EN1 rs4144782 and knee OA susceptibility in a Chinese population...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430105/switching-of-metabolic-programs-in-response-to-light-availability-is-an-essential-function-of-the-cyanobacterial-circadian-output-pathway
#13
Anna M Puszynska, Erin K O'Shea
The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect, and demonstrate that the rpaA(-) strain cannot maintain appropriate energy status at night, does not accumulate carbon reserves during the day, and is defective in transcription of genes crucial for utilization of carbohydrate stores at night...
April 21, 2017: ELife
https://www.readbyqxmd.com/read/28430102/variable-virulence-phenotype-of-xenorhabdus-bovienii-%C3%AE-proteobacteria-enterobacteriaceae-in-the-absence-of-their-vector-hosts
#14
John G McMullen, Rebecca McQuade, Jean-Claude Ogier, Sylvie Pagès, Sophie Gaudriault, S Patricia Stock
Xenorhabdus bovienii bacteria have a dual lifestyle: they are mutualistic symbionts to many species of Steinernema nematodes and are pathogens to a wide array of insects. Previous studies have shown that virulence of X.bovienii-Steinernema spp. pairs decreases when the nematodes associate with non-cognate bacterial strains. However, the virulence of the X. bovienii strains alone has not been fully investigated. In this study, we characterized the virulence of nine X. bovienii strains in Galleria mellonella and Spodoptera littoralis and performed a comparative genomic analysis to correlate observed phenotypes with strain genotypes...
April 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28430084/the-spo0a-sini-sinr-regulatory-circuit-plays-an-essential-role-in-biofilm-formation-nematicidal-activities-and-plant-protection-in-bacillus-cereus-ar156
#15
Sunde Xu, Nan Yang, Shiyu Zheng, Fang Yan, Chunhao Jiang, Yiyang Yu, Jianhua Guo, Yunrong Chai, Yun Chen
The rhizosphere bacterium Bacillus cereus AR156 is capable of forming biofilms, killing nematodes, and protecting plants. However, the underlying molecular mechanisms of these processes are not well understood. In this study, we found that the isogenic mutants ΔBcspo0A and ΔBcsinI have significantly reduced colonization and nematicidal activity in vitro and biological control efficacy on the tomato plant under greenhouse conditions. We further investigated the role of the spo0A-sinI-sinR regulatory circuit in biofilm formation, killing against nematodes, and biological control in AR156...
April 21, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28429804/identifying-tagging-snps-for-african-specific-genetic-variation-from-the-african-diaspora-genome
#16
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timothy D O'Connor, Gonçalo R Abecasis, Genevieve L Wojcik, Christopher R Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E Kenny, Carlos Bustamante, Terri H Beaty, Rasika A Mathias, Kathleen C Barnes, Zhaohui S Qin
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429797/sirtuins-in-the-phylum-basidiomycota-a-role-in-virulence-in-cryptococcus-neoformans
#17
Samantha D M Arras, Jessica L Chitty, Maha S I Wizrah, Paige E Erpf, Benjamin L Schulz, Milos Tanurdzic, James A Fraser
Virulence of Cryptococcus neoformans is regulated by a range of transcription factors, and is also influenced by the acquisition of adaptive mutations during infection. Beyond the temporal regulation of virulence factor production by transcription factors and these permanent microevolutionary changes, heritable epigenetic modifications such as histone deacetylation may also play a role during infection. Here we describe the first comprehensive analysis of the sirtuin class of NAD+ dependent histone deacetylases in the phylum Basidiomycota, identifying five sirtuins encoded in the C...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429735/phylogenetic-analysis-of-metastatic-progression-in-breast-cancer-using-somatic-mutations-and-copy-number-aberrations
#18
David Brown, Dominiek Smeets, Borbála Székely, Denis Larsimont, A Marcell Szász, Pierre-Yves Adnet, Françoise Rothé, Ghizlane Rouas, Zsófia I Nagy, Zsófia Faragó, Anna-Mária Tőkés, Magdolna Dank, Gyöngyvér Szentmártoni, Nóra Udvarhelyi, Gabriele Zoppoli, Lajos Pusztai, Martine Piccart, Janina Kulka, Diether Lambrechts, Christos Sotiriou, Christine Desmedt
Several studies using genome-wide molecular techniques have reported various degrees of genetic heterogeneity between primary tumours and their distant metastases. However, it has been difficult to discern patterns of dissemination owing to the limited number of patients and available metastases. Here, we use phylogenetic techniques on data generated using whole-exome sequencing and copy number profiling of primary and multiple-matched metastatic tumours from ten autopsied patients to infer the evolutionary history of breast cancer progression...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429252/analysis-of-global-gene-expression-profiles-during-the-flowering-initiation-process-of-lilium%C3%A2-%C3%A3-%C3%A2-formolongi
#19
Yu-Fan Li, Ming-Fang Zhang, Meng Zhang, Gui-Xia Jia
The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70...
April 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28429243/slco1b1-polymorphisms-and-plasma-estrone-conjugates-in-postmenopausal-women-with-er-%C3%A2-breast-cancer-genome-wide-association-studies-of-the-estrone-pathway
#20
Tanda M Dudenkov, James N Ingle, Aman U Buzdar, Mark E Robson, Michiaki Kubo, Irada Ibrahim-Zada, Anthony Batzler, Gregory D Jenkins, Tracy L Pietrzak, Erin E Carlson, Poulami Barman, Matthew P Goetz, Donald W Northfelt, Alvaro Moreno-Aspita, Clark V Williard, Krishna R Kalari, Yusuke Nakamura, Liewei Wang, Richard M Weinshilboum
BACKGROUND: Estrone (E1), the major circulating estrogen in postmenopausal women, promotes estrogen-receptor positive (ER+) breast tumor growth and proliferation. Two major reactions contribute to E1 plasma concentrations, aromatase (CYP19A1) catalyzed E1 synthesis from androstenedione and steroid sulfatase (STS) catalyzed hydrolysis of estrone conjugates (E1Cs). E1Cs have been associated with breast cancer risk and may contribute to tumor progression since STS is expressed in breast cancer where its activity exceeds that of aromatase...
April 20, 2017: Breast Cancer Research and Treatment
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