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https://www.readbyqxmd.com/read/28637190/evolution-of-the-sperm-methylome-of-primates-is-associated-with-retrotransposon-insertions-and-genome-instability
#1
Kei Fukuda, Yukihiro Inoguchi, Kenji Ichiyanagi, Tomoko Ichiyanagi, Yasuhiro Go, Masashi Nagano, Yojiro Yanagawa, Noboru Takaesu, Yasuyuki Ohkawa, Hiroo Imai, Hiroyuki Sasaki
Changes in gene expression resulting from epigenetic and/or genetic changes play an important role in the evolutionary divergence of phenotypes. To explore how epigenetic and genetic changes are linked during primate evolution, we have compared the genome-wide DNA methylation profiles (methylomes) of humans and chimpanzees, which have a 1.2% DNA sequence divergence, of sperm, the frontal cortices, B cells, and neutrophils. We revealed that species-specific differentially methylated regions (S-DMRs), ranging from several hundred bp to several kb, were frequently associated with sequence changes in transcription factor binding sites and insertions of Alu and SVA retrotransposons...
June 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28636540/implementation-and-utilization-of-the-molecular-tumor-board-to-guide-precision-medicine
#2
REVIEW
Shuko Harada, Rebecca Arend, Qian Dai, Jessica A Levesque, Thomas S Winokur, Rongjun Guo, Martin J Heslin, Lisle Nabell, L Burt Nabors, Nita A Limdi, Kevin A Roth, Edward E Partridge, Gene P Siegal, Eddy S Yang
BACKGROUND: With rapid advances in genomic medicine, the complexity of delivering precision medicine to oncology patients across a university health system demanded the creation of a Molecular Tumor Board (MTB) for patient selection and assessment of treatment options. The objective of this report is to analyze our progress to date and discuss the importance of the MTB in the implementation of personalized medicine. MATERIALS AND METHODS: Patients were reviewed in the MTB for appropriateness for comprehensive next generation sequencing (NGS) cancer gene set testing based on set criteria that were in place...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636437/tobacco-rattle-virus-trv-mediated-silencing-of-nicotiana-benthamiana-argonautes-nbagos-reveals-new-antiviral-candidates-and-dominant-effects-of-trv-nbago1
#3
Denis Odokonyero, Maria R Mendoza, Peter Moffett, Herman B Scholthof
The objective of this study was to determine the contribution of different ARGONAUTE proteins in Nicotiana benthamiana (NbAGOs) to the defense against silencing sensitive GFP-expressing viral constructs based on Tomato bushy stunt virus (TBSV) (Tombusvirus), Sunn-hemp mosaic virus (Tobamovirus), and Foxtail mosaic virus (Potexvirus). Upon Tobacco rattle virus (TRV)-mediated down-regulation of NbAGO1, 4, 5, or 6, no effects were noted on susceptibility to any virus construct, whereas knockdown of NbAGO2 specifically prevented silencing of P19-defective TBSV (TGdP19)...
June 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/28636181/identification-of-biomarkers-for-early-diagnosis-of-acute-myocardial-infarction
#4
Wen-Han Ge, Yong Lin, Sen Li, Xuefeng Zong, Zhong-Chun Ge
Acute myocardial infarction (AMI) is a common disease with serious consequences in mortality and cost. Here we aim to screen the differentially expressed genes (DEGs) as biomarkers for early diagnosis of AMI. The microarray data of AMI was downloaded from Gene Expression Omnibus (GEO), including two independent types of research GSE66360 and GSE62646. The DEGs between control and processed samples were screened out by using limma package. Meanwhile, we performed functional analysis of GO terms and/or KEGG pathways to observe the enriched pathways of the DEGs...
June 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28635965/identification-genealogical-structure-and-population-genetics-of-s-alleles-in-malus-sieversii-the-wild-ancestor-of-domesticated-apple
#5
X Ma, Z Cai, W Liu, S Ge, L Tang
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28635628/identification-and-validation-of-reference-genes-for-seashore-paspalum-response-to-abiotic-stresses
#6
Yu Liu, Jun Liu, Lei Xu, Hui Lai, Yu Chen, Zhimin Yang, Bingru Huang
Seashore paspalum (Paspalum vaginatum) is among the most salt- and cadmium-tolerant warm-season perennial grass species widely used as turf or forage. The objective of this study was to select stable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) analysis of seashore paspalum in response to four abiotic stresses. The stability of 12 potential reference genes was evaluated by four programs (geNorm, NormFinder, BestKeeper, and RefFinder). U2AF combined with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) showed stable expression in Cd-treated leaves and cold-treated roots...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635135/the-gene-expression-landscape-of-pine-seedling-tissues
#7
Rafael A Cañas, Zhen Li, M Belén Pascual, Vanessa Castro-Rodríguez, Concepción Ávila, Lieven Sterck, Yves Van de Peer, Francisco M Cánovas
Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells...
June 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28634817/identification-of-the-acclimation-genes-in-transcriptomic-responses-to-heat-stress-of-white-pekin-duck
#8
Jun-Mo Kim, Kyu-Sang Lim, Mijeong Byun, Kyung-Tai Lee, Young-Rok Yang, Mina Park, Dajeong Lim, Han-Ha Chai, Han-Tae Bang, Jong Hwangbo, Yang-Ho Choi, Yong-Min Cho, Jong-Eun Park
White Pekin duck is an important meat resource in the livestock industries. However, the temperature increase due to global warming has become a serious environmental factor in duck production, because of hyperthermia. Therefore, identifying the gene regulations and understanding the molecular mechanism for adaptation to the warmer environment will provide insightful information on the acclimation system of ducks. This study examined transcriptomic responses to heat stress treatments (3 and 6 h at 35 °C) and control (C, 25 °C) using RNA-sequencing analysis of genes from the breast muscle tissue...
June 20, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28634147/csahi-study-2-validation-of-multi-electrode-array-systems-mea60-2100-for-prediction-of-drug-induced-proarrhythmia-using-human-ips-cell-derived-cardiomyocytes-assessment-of-reference-compounds-and-comparison-with-non-clinical-studies-and-clinical-information
#9
Yumiko Nozaki, Yayoi Honda, Hitoshi Watanabe, Shota Saiki, Kiyotaka Koyabu, Tetsuji Itoh, Chiho Nagasawa, Chiaki Nakamori, Chiaki Nakayama, Hiroshi Iwasaki, Shinobu Suzuki, Kohji Tanaka, Etsushi Takahashi, Kaori Miyamoto, Kaoru Morimura, Atsuhiro Yamanishi, Hiroko Endo, Junko Shinozaki, Hisashi Nogawa, Tadahiro Shinozawa, Fumiyo Saito, Takeshi Kunimatsu
With the aim of reconsidering ICH S7B and E14 guidelines, a new in vitro assay system has been subjected to worldwide validation to establish a better prediction platform for potential drug-induced QT prolongation and the consequent TdP in clinical practice. In Japan, CSAHi HEART team has been working on hiPS-CMs in the MEA (hiPS-CMs/MEA) under a standardized protocol and found no inter-facility or lot-to-lot variability for proarrhythmic risk assessment of 7 reference compounds. In this study, we evaluated the responses of hiPS-CMs/MEA to another 31 reference compounds associated with cardiac toxicities, and gene expression to further clarify the electrophysiological characteristics over the course of culture period...
June 17, 2017: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/28633981/development-of-a-propidium-monoazide-polymerase-chain-reaction-assay-for-detection-of-viable-lactobacillus-brevis-in-beer
#10
Yanlin Ma, Yang Deng, Zhenbo Xu, Junyan Liu, Jianjun Dong, Hua Yin, Junhong Yu, Zongming Chang, Dongfeng Wang
The spoilage of beer by bacteria is of great concern to the brewer as this can lead to turbidity and abnormal flavors. The polymerase chain reaction (PCR) method for detection of beer-spoilage bacteria is highly specific and provides results much faster than traditional microbiology techniques. However, one of the drawbacks is the inability to differentiate between live and dead cells. In this paper, the combination of propidium monoazide (PMA) pretreatment and conventional PCR had been described. The established PMA-PCR identified beer spoilage Lactobacillus brevis based not on their identity, but on the presence of horA gene which we show to be highly correlated with the ability of beer spoilage LAB to grow in beer...
June 3, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/28633900/analytical-and-clinical-performance-of-a-chikungunya-qrt-pcr-for-central-and-south-america
#11
Thomas Edwards, Leticia Del Carmen Castillo Signor, Christopher Williams, Clément Larcher, Mauricio Espinel, Jane Theaker, Evelin Donis, Luis E Cuevas, Emily R Adams
Chikungunya was introduced into the Americas in 2015 causing a pandemic across the continent. Testing during the acute phase of infection relies on qRT-PCR, but available assays have a number of limitations. A qRT-PCR assay specific to the chikungunya E1 gene was designed using sequence data from contemporary strains. A probit analysis established the 95% limit of detection as 19.6 copies per reaction. We compared the assay with a US Centers for Disease Control (CDC) chikungunya qRT-PCR as the reference standard...
June 8, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28631610/a-large-gene-family-in-fission-yeast-encodes-spore-killers-that-subvert-mendel-s-law
#12
Wen Hu, Zhao-Di Jiang, Fang Suo, Jin-Xin Zheng, Wan-Zhong He, Li-Lin Du
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them...
June 20, 2017: ELife
https://www.readbyqxmd.com/read/28631330/foxo-transcription-factors-at-the-interface-of-metabolism-and-cancer
#13
REVIEW
Wolfgang Link, Pablo J Fernandez-Marcos
Diabetes refers to a group of metabolic diseases characterized by impaired insulin signalling and high blood glucose. A growing body of epidemiological evidence links diabetes to several types of cancer but the underlying molecular mechanisms are poorly understood. The signalling cascade connecting insulin and FOXO proteins provides a compelling example for a conserved pathway at the interface between insulin signalling and cancer. FOXOs are transcription factors that orchestrate programs of gene expression known to control a variety of processes in response to cellular stress...
June 19, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28630104/evidence-for-adaptive-introgression-of-disease-resistance-genes-among-closely-related-arabidopsis-species
#14
Jesper Bechsgaard, Tove Hedegaard Jorgensen, Mikkel Heide Schierup
The generation and maintenance of functional variation in the pathogen defense system of plants is central to the constant evolutionary battle between hosts and parasites. If a species is susceptible to a given pathogen, hybridisation and subsequent introgression of a resistance allele from a related species can potentially be an important source of new immunity and is therefore expected to be selected for in a process referred to as adaptive introgression. Here we survey sequence variation in ten resistance (R) genes and compare with 37 reference genes in natural populations of the two closely related and interfertile species Arabidopsis lyrata and A...
June 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28629947/temporal-microbiota-changes-of-high-protein-diet-intake-in-a-rat-model
#15
Chunlong Mu, Yuxiang Yang, Zhen Luo, Weiyun Zhu
Alterations of specific microbes serve as important indicators that link gut health with specific diet intake. Although a six-week high-protein diet (45% protein) upregulates the pro-inflammatory response and oxidative stress in colon of rats, the dynamic alteration of gut microbiota remains unclear. To dissect temporal changes of microbiota, dynamic analyses of fecal microbiota were conducted using a rat model. Adult rats were fed a normal-protein diet or an HPD for 6 weeks, and feces collected at different weeks were used for microbiota and metabolite analysis...
June 16, 2017: Anaerobe
https://www.readbyqxmd.com/read/28629725/relationship-between-histopathological-status-of-the-helicobacter-pylori-infected-patients-and-proteases-of-h-pylori-in-isolates-carrying-diverse-virulence-genotypes
#16
Somayyeh Gharibi, Tahereh Falsafi, Masoud Alebouyeh, Nastaran Farzi, Farzam Vaziri, Mohamad Reza Zali
Helicobacter pylori is the main cause of several gastroduodenal diseases in Humans. Among various virulence factors of H. pylori, proteases may also be involved in its pathogenicity. In this study, relationship between proteolytic activity of H. pylori strains and histopathological changes of the stomach was investigated in the patients infected with strains carrying diverse virulence factors. H. pylori strains were isolated from the biopsies of 116 patients who referred to hospital for their gastroduodenal disorders, in Tehran, Iran...
June 16, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28629614/molecular-detection-methods-of-resistance-to-antituberculosis-drugs-in-mycobacterium-tuberculosis
#17
F Brossier, W Sougakoff
OBJECTIVE: Molecular methods predict drug resistance several weeks before phenotypic methods and enable rapid implementation of appropriate therapeutic treatment. We aimed to detail the most representative molecular tools used in routine practice for the rapid detection of resistance to antituberculosis drugs among Mycobacterium tuberculosis strains. MATERIALS AND METHODS: The molecular diagnosis of resistance to antituberculosis drugs in clinical samples or from in vitro cultures is based on the detection of the most common mutations in the genes involved in the development of resistance in M...
June 16, 2017: Médecine et Maladies Infectieuses
https://www.readbyqxmd.com/read/28629498/rodentibacter-gen-nov-including-rodentibacter-pneumotropicus-comb-nov-rodentibacter-heylii-sp-nov-rodentibacter-myodis-sp-nov-rodentibacter-ratti-sp-nov-rodentibacter-heidelbergensis-sp-nov-rodentibacter-trehalosifermentans-sp-nov-rodentibacter-rarus-sp-nov
#18
Sadhana Adhikary, Werner Nicklas, Magne Bisgaard, Ron Boot, Peter Kuhnert, Torsten Waberschek, Bent Aalbæk, Bozena Korczak, Henrik Christensen
Rodentibacter gen. nov. is proposed based on isolation and phenotypic characterization of strains, predominantly from rodents. The strains showed 86 % or higher rpoB gene sequence similarity and indicated a genus-level relationship within Pasteurellaceae. The strains compared at 16S rRNA gene sequence level showed 93.8 % or higher similarity, and their genus-level relationship within Pasteurellaceae was confirmed by phenotypic analysis. The type species Rodentibacter pneumotropicus comb. nov. is reclassified from [Pasteurella] pneumotropica with type strain NCTC 8141T (=CCUG 12398T)...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28628844/serum-micrornas-in-buffalo-cows-potential-biomarkers-of-pregnancy
#19
Gabriella Guelfi, Valentina Stefanetti, Silvio De Luca, Andrea Giontella, Vittoria Lucia Barile, Olimpia Barbato
MiRNAs (microRNA) constitute a large family of single-stranded, non-coding small RNAs. Although the functions and target genes of most miRNAs are still unknown, it has been well established that they are involved in embryogenesis, organogenesis and neonatal birth. In recent decades, interest in buffalo breeding has largely increased worldwide thus focusing the attention on this species as a dairy purpose animal. Problems related to long calving interval, late puberty and seasonal anestrus hamper reproductive efficiency in this species...
June 4, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28627812/genetics-of-alcohol-consumption-in-drosophila-melanogaster
#20
Sophia Fochler, Tatiana V Morozova, Morgan R Davis, Alexander W Gearhart, Wen Huang, Trudy F C Mackay, Robert R H Anholt
Individual variation in alcohol consumption in human populations is determined by genetic, environmental, social and cultural factors. In contrast to humans, genetic contributions to complex behavioral phenotypes can be readily dissected in Drosophila, where both the genetic background and environment can be controlled and behaviors quantified through simple high-throughput assays. Here, we measured voluntary consumption of ethanol in ~3,000 individuals of each sex from an advanced intercross population derived from 37 lines of the Drosophila melanogaster Genetic Reference Panel...
June 19, 2017: Genes, Brain, and Behavior
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