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https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#1
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28820884/let-s-rise-up-to-unite-taxonomy-and-technology
#2
Holly M Bik
What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts...
August 2017: PLoS Biology
https://www.readbyqxmd.com/read/28820495/human-papillomavirus-and-the-dna-damage-response-exploiting-host-repair-pathways-for-viral-replication
#3
REVIEW
Chelsey C Spriggs, Laimonis A Laimins
High-risk human papillomaviruses (HPVs) are the causative agents of cervical and other genital cancers. In addition, HPV infections are associated with the development of many oropharyngeal cancers. HPVs activate and repress a number of host cellular pathways to promote their viral life cycles, including those of the DNA damage response. High-risk HPVs activate the ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR) DNA damage repair pathways, which are essential for viral replication (particularly differentiation-dependent genome amplification)...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820213/chip-scale-alignment-of-long-dna-nanofibers-on-a-patterned-self-assembled-monolayer
#4
J Xia, M Su
Controlled alignment of long DNA nanofibers is challenging. This communication reports a method to align human genomic DNA with nearly unlimited length using lithographically produced micro-patterns of self-assembled monolayers (SAMs) with positively charged terminal groups. The micro-patterns act as local DNA reservoirs to supply DNAs for nanofiber formation, and can also stretch and align DNA nanofibers to form an ordered array by controlling the dewetting profile. By reducing the size and inter-patch distance of a micro-patch, a nearly uniform array of long DNA nanofibers can be patterned over a large area...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28820138/processes-underlying-rabies-virus-incursions-across-us-canada-border-as-revealed-by-whole-genome-phylogeography
#5
Hannah Trewby, Susan A Nadin-Davis, Leslie A Real, Roman Biek
Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen's spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks...
September 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28819832/protective-role-of-humic-acids-against-picloram-induced-genomic-instability-and-dna-methylation-in-phaseolus-vulgaris
#6
Mahmut Sinan Taspinar, Murat Aydin, Burcu Sigmaz, Nalan Yildirim, Guleray Agar
Picloram (4-amino-3,5,6-trichloropicolinic acid) is a liquid auxinic herbicide used to control broad-leaved weeds. Picloram is representing a possible hazard to ecosystems and human health. Therefore, in this study, DNA methylation changes and DNA damage levels in Phaseolus vulgaris exposed to picloram, as well as whether humic acid (HA) has preventive effects on these changes were investigated. Random amplified polymorphic DNA (RAPD) techniques were used for identification of DNA damage and coupled restriction enzyme digestion-random amplification (CRED-RA) techniques were used to detect the changed pattern of DNA methylation...
August 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28819830/identification-and-characterization-of-tyrosine-kinases-in-anole-lizard-indicate-the-conserved-tyrosine-kinase-repertoire-in-vertebrates
#7
Ake Liu, Funan He, Xun Gu
The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified...
August 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28819692/molecular-characterization-of-atypical-antigenic-variants-of-canine-rabies-virus-reveals-its-reintroduction-by-wildlife-vectors-in-southeastern-mexico
#8
Fabiola Garcés-Ayala, Nidia Aréchiga-Ceballos, Joanna M Ortiz-Alcántara, Elizabeth González-Durán, Sandra I Pérez-Agüeros, Alfonso Méndez-Tenorio, Belem Torres-Longoria, Irma López-Martínez, Lucía Hernández-Rivas, José Alberto Díaz-Quiñonez, José Ernesto Ramírez-González
Rabies is an infectious viral disease that is practically always fatal following the onset of clinical signs. In Mexico, the last case of human rabies transmitted by dogs was reported in 2006 and canine rabies has declined significantly due to vaccination campaigns implemented in the country. Here we report on the molecular characterization of six rabies virus strains found in Yucatan and Chiapas, remarkably, four of them showed an atypical reaction pattern when antigenic characterization with a reduced panel of eight monoclonal antibodies was performed...
August 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28819228/convergent-and-divergent-genetic-changes-in-the-genome-of-chinese-and-european-pigs
#9
Jing Wang, Huiying Zou, Lei Chen, Xi Long, Jing Lan, Wenjie Liu, Li Ma, Chao Wang, Xinyu Xu, Liming Ren, Zhenglong Gu, Ning Li, Xiaoxiang Hu, Yaofeng Zhao, Yiqiang Zhao
Since 10,000 BC, continuous human selection has led to intense genetic and phenotypic changes in pig (Sus scrofa) domestication. Through whole genome analysis of 257 individuals, we demonstrated artificial unidirectional and bidirectional selection as the primary force to shape the convergent and divergent changes between Chinese domestic pigs (CHD) and European domestic pigs (EUD). We identified 31 genes in unidirectional selection regions that might be related to fundamental domestication requirements in pigs...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819179/identification-of-polo-like-kinases-as-potential-novel-drug-targets-for-influenza-a-virus
#10
Marie O Pohl, Jessica von Recum-Knepper, Ariel Rodriguez-Frandsen, Caroline Lanz, Emilio Yángüez, Stephen Soonthornvacharin, Thorsten Wolff, Sumit K Chanda, Silke Stertz
In recent years genome-wide RNAi screens have revealed hundreds of cellular factors required for influenza virus infections in human cells. The long-term goal is to establish some of them as drug targets for the development of the next generation of antivirals against influenza. We found that several members of the polo-like kinases (PLK), a family of serine/threonine kinases with well-known roles in cell cycle regulation, were identified as hits in four different RNAi screens and we therefore studied their potential as drug target for influenza...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#11
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819029/loss-of-the-tumor-suppressor-stag2-promotes-telomere-recombination-and-extends-the-replicative-lifespan-of-normal-human-cells
#12
Zharko Daniloski, Susan Smith
Sister chromatids are held together by cohesin, a tripartite ring with a peripheral SA1/2 subunit, where SA1 is required for telomere cohesion and SA2 for centromere cohesion. The STAG2 gene encoding SA2 is often inactivated in human cancer, but not in in a manner associated with aneuploidy. Thus, how these tumors maintain chromosomal cohesion and how STAG2 loss contributes to tumorigenesis remain open questions. Here we show that, despite a loss in centromere cohesion, sister chromatids in STAG2 mutant tumor cells maintain cohesion in mitosis at chromosome arms and telomeres...
August 17, 2017: Cancer Research
https://www.readbyqxmd.com/read/28819001/epigenomics-and-human-adaptation-to-high-altitude
#13
Colleen Glyde Julian
Over the past decade, major technological and analytical advancements have propelled efforts towards identifying the molecular mechanisms that govern human adaptation to high altitude. Despite remarkable progress with respect to the identification of adaptive genomic signals that are strongly associated with the 'hypoxia-tolerant' physiological characteristics of high-altitude populations, many questions regarding the fundamental biological processes underlying human adaptation remain unanswered. Vital to address these enduring questions will be to determine the role of epigenetic processes, or non-sequence based features of the genome, that are not only critical for the regulation of transcriptional responses to hypoxia but heritable across generations...
August 17, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28818916/a-pathology-atlas-of-the-human-cancer-transcriptome
#14
Mathias Uhlen, Cheng Zhang, Sunjae Lee, Evelina Sjöstedt, Linn Fagerberg, Gholamreza Bidkhori, Rui Benfeitas, Muhammad Arif, Zhengtao Liu, Fredrik Edfors, Kemal Sanli, Kalle von Feilitzen, Per Oksvold, Emma Lundberg, Sophia Hober, Peter Nilsson, Johanna Mattsson, Jochen M Schwenk, Hans Brunnström, Bengt Glimelius, Tobias Sjöblom, Per-Henrik Edqvist, Dijana Djureinovic, Patrick Micke, Cecilia Lindskog, Adil Mardinoglu, Fredrik Ponten
Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation...
August 18, 2017: Science
https://www.readbyqxmd.com/read/28818896/genome-sequences-of-three-novel-isolates-of-human-parainfluenza-virus-2-associated-with-acute-respiratory-infection
#15
J L Kennedy, J C Kincaid, K C Schwalm, A N Stoner, T J Abramo, T M Thompson, O Hardin, C Putt, D L Dinwiddie
Using target capture of viral nucleic acid and next-generation sequencing, we generated the genome sequences of three novel human parainfluenza virus 2 isolates. Isolates ACRI_0185 (GenBank accession number MF077311), ACRI_0230 (MF077312), and ACRI_0248 (MF077313) were collected in October 2016, February 2017, and March 2017, respectively, from pediatric patients with acute respiratory infection in Arkansas.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818891/complete-genome-sequence-of-pseudoalteromonas-piscicida-strain-de2-b-a-bacterium-with-broad-inhibitory-activity-toward-human-and-fish-pathogens
#16
Gary P Richards, David S Needleman, Michael A Watson
Pseudoalteromonas piscicida strain DE2-B is a halophilic bacterium which has broad inhibitory activity toward vibrios and other human and fish pathogens. We report the first closed genome sequence for this species, which consists of two chromosomes (4,128,210 and 1,188,838 bp). Annotation revealed multiple genes encoding proteases with potential antibacterial properties.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818889/genome-sequences-of-five-multidrug-resistant-escherichia-coli-sequence-type-117-isolates-recovered-from-dairy-calves
#17
Seon-Woo Kim, Jeffrey S Karns, Jo Ann S Van Kessel, Bradd J Haley
Escherichia coli sequence type 117 (ST117) strains have been recovered from poultry with colibacillosis, as well as from urinary tract infections and fatal septic infections in humans. To further investigate ST117 isolates recovered from nonpoultry food animals, we sequenced the genomes of five ST117 isolates from dairy calves in Pennsylvania.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818887/draft-genome-sequences-of-escherichia-coli-o104-strains-of-bovine-and-human-origin
#18
Pragathi B Shridhar, Isha R Patel, Jayanthi Gangiredla, Mark K Mammel, Lance Noll, Xiaorong Shi, Jianfa Bai, Christopher A Elkins, Nancy Strockbine, T G Nagaraja
Cattle harbor and shed in their feces several Escherichia coli O104 serotypes. All O104 strains examined were intimin negative and belonged to the B1 phylogroup, and some were Shiga toxigenic. We report here the genome sequences of bovine O104:H7 (n = 5), O104:H23 (n = 2), O104:H8 (n = 1), and O104:H12 (n = 1) isolates and human clinical isolates of O104:H7 (n = 5).
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818566/a-synthetic-human-cytomegalovirus-pp65-ie1-fusion-antigen-efficiently-induces-and-expands-virus-specific-t-cells
#19
Ellen K Link, Christine Brandmüller, Yasemin Suezer, Stefanie Ameres, Asisa Volz, Andreas Moosmann, Gerd Sutter, Michael H Lehmann
Infection with human cytomegalovirus (HCMV) can cause severe complications in newborns and immunocompromised patients, and a prophylactic or therapeutic vaccine against HCMV is not available. Here, we generated a HCMV vaccine candidate fulfilling the regulatory requirements for GMP-compliant production and clinical testing. A novel synthetic fusion gene consisting of the coding sequences of HCMV pp65 and IE1 having a deleted nuclear localization sequence and STAT2 binding domain was introduced into the genome of the attenuated vaccinia virus strain MVA...
August 14, 2017: Vaccine
https://www.readbyqxmd.com/read/28818477/human-imprinting-disorders-principles-practice-problems-and-progress
#20
REVIEW
Deborah J G Mackay
Epigenetic regulation orchestrates gene expression with exquisite precision, over a huge dynamic range and across developmental space and time, permitting genomically-homogeneous humans to develop and adapt to their surroundings. Every generation, these epigenetic marks are re-set twice: in the germline, to enable differentiation of sperm and eggs, and at fertilisation, to create the totipotent zygote that then begins growth and differentiation into a new human. A small group of genes evades the second, zygotic wave of epigenetic reprogramming, and these genes retain an epigenetic 'imprint' of the parent from whom they were inherited...
August 14, 2017: European Journal of Medical Genetics
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