Read by QxMD icon Read

Genomic selection

Musaffe Tuna, Christopher I Amos
Approximately 18% of all human cancers have a viral etiology, and human papillomavirus (HPV) has been identified as one of the most prevalent viruses that plays causative role in nearly all cervical cancers and, in addition, in subset of head and neck, anal, penile and vulvar cancers. The recent introduction of next generation sequencing (NGS) and other 'omics' approaches have resulted in comprehensive knowledge on the pathogenesis of HPV-driven tumors. Specifically, these approaches have provided detailed information on genomic HPV integration sites, disrupted genes and pathways, and common and distinct genetic and epigenetic alterations in different human HPV-associated cancers...
October 23, 2016: Oncotarget
Katarzyna Modzelewska, Elena F Boer, Timothy L Mosbruger, Daniel Picard, Daniela Anderson, Rodney R Miles, Mitchell Kroll, William Oslund, Theodore J Pysher, Joshua D Schiffman, Randy Jensen, Cicely A Jette, Annie Huang, Rodney A Stewart
Malignant brain tumors are the leading cause of cancer-related deaths in children. Primitive neuroectodermal tumors of the CNS (CNS-PNETs) are particularly aggressive embryonal tumors of unknown cellular origin. Recent genomic studies have classified CNS-PNETs into molecularly distinct subgroups that promise to improve diagnosis and treatment; however, the lack of cell- or animal-based models for these subgroups prevents testing of rationally designed therapies. Here, we show that a subset of CNS-PNETs co-express oligoneural precursor cell (OPC) markers OLIG2 and SOX10 with coincident activation of the RAS/MAPK (mitogen-activated protein kinase) pathway...
October 25, 2016: Cell Reports
Chwan Hong Foo, Christina L Rootes, Karla Cowley, Glenn A Marsh, Cathryn M Gould, Celine Deffrasnes, Christopher J Cowled, Reuben Klein, Sarah J Riddell, Deborah Middleton, Kaylene J Simpson, Lin-Fa Wang, Andrew G D Bean, Cameron R Stewart
Hendra and Nipah viruses (family Paramyxoviridae, genus Henipavirus) are bat-borne viruses that cause fatal disease in humans and a range of other mammalian species. Gaining a deeper understanding of host pathways exploited by henipaviruses for infection may identify targets for new anti-viral therapies. Here we have performed genome-wide high-throughput agonist and antagonist screens at biosafety level 4 to identify host-encoded microRNAs (miRNAs) impacting henipavirus infection in human cells. Members of the miR-181 and miR-17~93 families strongly promoted Hendra virus infection...
October 2016: PLoS Pathogens
Nanna Hellum Nielsen, Ahmed Jahoor, Jens Due Jensen, Jihad Orabi, Fabio Cericola, Vahid Edriss, Just Jensen
Genomic selection was recently introduced in plant breeding. The objective of this study was to develop genomic prediction for important seed quality parameters in spring barley. The aim was to predict breeding values without expensive phenotyping of large sets of lines. A total number of 309 advanced spring barley lines tested at two locations each with three replicates were phenotyped and each line was genotyped by Illumina iSelect 9Kbarley chip. The population originated from two different breeding sets, which were phenotyped in two different years...
2016: PloS One
Yosuke Hirotsu, Yuichiro Kojima, Kenichiro Okimoto, Kenji Amemiya, Hitoshi Mochizuki, Masao Omata
BACKGROUND: Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for each cancer type. However, it is unclear to what extent significantly mutated genes need to be examined for detecting genetic alterations in gastric cancer patients. Here, we constructed two custom-made sequencing panels of different scales, the Selective hotspot Panel and the Comprehensive Panel, to analyze genetic alterations in 21 resected specimens endoscopically obtained from 20 gastric cancer patients, and we assessed how many mutations were detectable using these different panels...
October 26, 2016: BMC Genomics
Lydiane Gaborieau, Gregory G Brown
BACKGROUND: The plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection...
October 26, 2016: BMC Genomics
Nan Song, Hu Li, Fan Song, Wanzhi Cai
The Polyneoptera represents one of the earliest insect radiations, comprising the majority of hemimetabolous orders, in which many species have great economic importance. Here, we sequenced eleven mitochondrial genomes of the polyneopteran insects by using high throughput pooled sequencing technology, and presented a phylogenetic reconstruction for this group based on expanded mitochondrial genome data. Our analyses included 189 taxa, of which 139 species represent all the major polyneopteran lineages. Multiple results support the monophyly of Polyneoptera, the monophyly of Dictyoptera, and the monophyly of Orthoptera...
October 26, 2016: Scientific Reports
Jonathan B Puritz, John R Gold, David S Portnoy
Conservation and management of exploited species depends on accurate knowledge of how genetic variation is partitioned across a fishery, especially as it relates to recruitment. Using double-digest restriction-site associated DNA sequencing, we surveyed variation in 7,382 single nucleotide polymorphisms (SNPs) in red snapper (Lutjanus campechanus) young-of-the-year (YOY) sampled at six localities and in adults sampled at two localities in the northern Gulf of Mexico. Significant genetic heterogeneity was detected between the two adult samples, separated by ~600 km, and at spatial scales less than five kilometers among samples of  YOY...
October 26, 2016: Scientific Reports
Iben Daugaard, Diana Dominguez, Tina E Kjeldsen, Lasse S Kristensen, Henrik Hager, Tomasz K Wojdacz, Lise Lotte Hansen
Lung cancer is the number one cause of cancer-related deaths worldwide. DNA methylation is an epigenetic mechanism that regulates gene expression, and disease-specific methylation changes can be targeted as biomarkers. We have compared the genome-wide methylation pattern in tumor and tumor-adjacent normal lung tissue from four lung adenocarcinoma (LAC) patients using DNA methylation microarrays and identified 74 differentially methylated regions (DMRs). Eighteen DMRs were selected for validation in a cohort comprising primary tumors from 52 LAC patients and tumor-adjacent normal lung tissue from 32 patients by methylation-sensitive high resolution melting (MS-HRM) analysis...
October 26, 2016: Scientific Reports
Ali Ebrahim, Elizabeth Brunk, Justin Tan, Edward J O'Brien, Donghyuk Kim, Richard Szubin, Joshua A Lerman, Anna Lechner, Anand Sastry, Aarash Bordbar, Adam M Feist, Bernhard O Palsson
Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi-level analysis of genomic, transcriptomic, ribosomal profiling, proteomic and fluxomic data. First, we show that pairwise integration of primary omics data reveals regularities that tie cellular processes together in Escherichia coli: the number of protein molecules made per mRNA transcript and the number of ribosomes required per translated protein molecule...
October 26, 2016: Nature Communications
Ahmad Chaddad, Christian Desrosiers, Lama Hassan, Camel Tanougast
OBJECTIVE: Predicting the survival outcome of glioblastoma multiforme (GBM) patients is of key importance to clinicians for selecting the optimal course of treatment. The goal of this study is to evaluate the usefulness of geometric shape features, extracted from MRI images, as a potential non-invasive way to characterize GBM tumors and predict the overall survival times of GBM patients. METHODS: The data of 40 GBM patients were obtained from the Cancer Genome Atlas and Cancer Imaging Archive...
October 26, 2016: British Journal of Radiology
Alexander O Vargas, Quirin Krabichler, Carlos Guerrero-Bosagna
Paul Kammerer was the most outstanding neo-Lamarckian experimentalist of the early 20th century. He reported spectacular results in the midwife toad, including crosses of environmentally modified toads with normal toads, where acquired traits were inherited in Mendelian fashion. Accusations of fraud generated a great scandal, ending with Kammerer's suicide. Controversy reignited in the 1970s, when journalist Arthur Koestler argued against these accusations. Since then, others have argued that Kammerer's results, even if real, were not groundbreaking and could be explained by somatic plasticity, inadvertent selection, or conventional genetics...
October 26, 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
Victoria M Pearson, S Brian Caudle, Darin R Rokyta
Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq...
2016: PeerJ
Thomas Vercruysse, Jolien De Bie, Jasper Neggers, Maarten Jacquemyn, Els Vanstreels, Jonathan Leo Schmid-Burgk, Veit Hornung, Erkan Baloglu, Yosef Landesman, William Senapedis, Sharon Shacham, Antonis Dagklis, Jan Cools, Dirk Daelemans
PURPOSE: Human exportin-1 (XPO1) is the key nuclear-cytoplasmic transport protein that exports many cargo proteins out of the nucleus. Inducing nuclear accumulation of these proteins by inhibition of XPO1 causes cancer cell death. First clinical validation of pharmacological inhibition of XPO1 was obtained with the Selective Inhibitor of Nuclear Export (SINE) compound selinexor (KPT-330) demonstrating activity in Phase-II/IIb clinical trials when dosed 1 - 3 times weekly. The second-generation SINE compound KPT-8602 shows improved tolerability and can be dosed daily...
October 25, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Luciano Rogério Braatz de Andrade, Roberto Fritsche Neto, Ítalo Stefanine Correia Granato, Gustavo César Sant'Ana, Pedro Patric Pinho Morais, Aluízio Borém
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection...
2016: PloS One
Gous Miah, Mohd Y Rafii, Mohd R Ismail, Adam B Puteh, Harun A Rahim, Mohammad A Latif
BACKGROUND: The rice cultivar MR219 is famous for its better yield and long and fine grain quality; however, it is susceptible to blast disease. The main objective of this study was to introgress blast resistance genes into MR219 through marker-assisted selection (MAS). The rice cultivar MR219 was used as the recurrent parent, and Pongsu Seribu 1 was used as the donor. RESULTS: Marker-assisted foreground selection was performed using RM6836 and RM8225 to identify plants possessing blast resistance genes...
October 24, 2016: Journal of the Science of Food and Agriculture
Danielle Ahn, Hernán Peñaloza, Zheng Wang, Matthew Wickersham, Dane Parker, Purvi Patel, Antonius Koller, Emily I Chen, Susan M Bueno, Anne-Catrin Uhlemann, Alice Prince
Adaptive changes in the genome of a locally predominant clinical isolate of the multidrug-resistant Klebsiella pneumoniae ST258 (KP35) were identified and help to explain the selection of this strain as a successful pulmonary pathogen. The acquisition of 4 new ortholog groups, including an arginine transporter, enabled KP35 to outcompete related ST258 strains lacking these genes. KP35 infection elicited a monocytic response, dominated by Ly6C(hi) monocytic myeloid-derived suppressor cells that lacked phagocytic capabilities, expressed IL-10, arginase, and antiinflammatory surface markers...
October 20, 2016: JCI Insight
Julie B Hébert, Sonja J Scheffer, David J Hawthorne
Evolutionary radiations have been well documented in plants and insects, and natural selection may often underly these radiations. If radiations are adaptive, the diversity of species could be due to ecological speciation in these lineages. Agromyzid flies exhibit patterns of repeated host-associated radiations. We investigated whether host-associated population divergence and evidence of divergent selection exist in the leaf miner Phytomyza glabricola on its sympatric host plants, the holly species, Ilex coriacea and I...
September 2016: Ecology and Evolution
Michael J Wade, Devin M Drown
We use population genetic models to investigate the cooperative and conflicting synergistic fitness effects between genes from the nucleus and the mitochondrion. By varying fitness parameters, we examine the scope for conflict relative to cooperation among genomes and the utility of the "gene's eye view" analytical approach, which is based on the marginal average fitness of specific alleles. Because sexual conflict can maintain polymorphism of mitochondrial haplotypes, we can explore two types of evolutionary conflict (genomic and sexual) with one epistatic model...
September 2016: Ecology and Evolution
Pengjun Xu, Roberto Feuda, Bin Lu, Haijun Xiao, Robert I Graham, Kongming Wu
BACKGROUND: Retrotransposed genes are different to other types of genes as they originate from a processed mRNA and are then inserted back into the genome. For a long time, the contribution of this mechanism to the origin of new genes, and hence to the evolutionary process, has been questioned as retrogenes usually lose their regulatory sequences upon insertion and generally decay into pseudogenes. In recent years, there is growing evidence, notably in mammals, that retrotransposition is an important process driving the origin of new genes, but the evidence in insects remains largely restricted to a few model species...
2016: Mobile DNA
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"