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Genomic selection

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https://www.readbyqxmd.com/read/28550065/exceptional-durable-response-to-everolimus-in-a-patient-with-biphenotypic-breast-cancer-harboring-an-stk11-variant
#1
Christine A Parachoniak, Andrew Rankin, Bernadette Gaffney, Ryan Hartmaier, Dan Spritz, Rachel L Erlich, Vincent A Miller, Deborah Morosini, Phil Stephens, Jeffrey S Ross, John Keech, Juliann Chmielecki
Metastatic triple negative breast cancer comprises 12-17% of breast cancers and carries a poor prognosis relative to other breast cancer subtypes. Treatment options in this disease are largely limited to systemic chemotherapy. A majority of clinical studies assessing efficacy of targeted therapeutics (e.g. the mTOR inhibitor everolimus) in advanced breast cancer patients have not utilized predictive genomic biomarker-based selection and have reported only modest improvement in clinical outcome relative to standard of care...
May 26, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28550058/whole-genome-and-core-genome-multilocus-sequence-typing-and-single-nucleotide-polymorphism-analyses-of-listeria-monocytogenes-associated-with-an-outbreak-linked-to-cheese-united-states-2013
#2
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28550056/biofilm-formation-potential-of-heat-resistant-escherichia-coli-dairy-isolates-and-complete-genome-of-mdr-heat-resistant-strain-fam21845
#3
Roger Marti, Michael Schmid, Sandra Kulli, Kerstin Schneeberger, Javorka Naskova, Susanne Knøchel, Christian H Ahrens, Jörg Hummerjohann
We tested the biofilm formation potential of 30 heat resistant and six heat sensitive E. coli dairy isolates. The production of curli and cellulose, static biofilm formation on polystyrene (PS) and stainless steel, formation of biofilm under dynamic conditions (Bioflux), and initial adhesion rates (IAR) were evaluated. Biofilm formation varied greatly between strains, media and assay. Our results highlight the importance of the experimental setup to determine biofilm formation under conditions of interest, as correlation between different assays was often not given...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28550046/genome-instability-a-conserved-mechanism-of-ageing
#4
REVIEW
Jan Vijg, Xiao Dong, Brandon Milholland, Lei Zhang
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals...
May 26, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/28550025/mineralocorticoid-receptor-null-mice-informing-cell-type-specific-roles
#5
Timothy James Cole, Morag Young
The mineralocorticoid receptor (MR) mediates the actions of two important adrenal corticosteroid hormones, aldosterone and cortisol. The cell signalling roles of the MR in vivo have expanded enormously since the cloning of human MR gene 30 years ago and the first MR gene knockout in mice nearly 20 years ago. Complete ablation of the MR revealed important roles postnatally for regulation of kidney epithelial functions, with MR-null mice dying 1-2 weeks postnatally from renal salt wasting and hyperkalaemia, with elevated plasma renin and aldosterone...
May 26, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28549993/evolution-of-thyroid-hormone-signaling-in-animals-non-genomic-and-genomic-modes-of-action
#6
REVIEW
Elias Taylor, Andreas Heyland
Much research has focused on vertebrate thyroid hormone (TH) synthesis and their function in development and metabolism. While important differences in TH synthesis and signaling exist, comparative studies between vertebrates fail to explain the evolutionary origins of this important regulatory axis. For that, one needs to make sense out of the diverse TH effects which have been described in invertebrate phyla but for which a mechanistic understanding is largely missing. Almost every major group of non-vertebrate animals possesses the capability to synthesize and metabolize thyroid hormones and there is evidence for a nuclear thyroid hormone receptor mediated mechanism in the bilateria, especially in molluscs, echinoderms, cephalochordates and ascidians...
May 23, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28549454/genomic-adaptation-to-agricultural-environments-cabbage-white-butterflies-pieris-rapae-as-a-case-study
#7
Kristin L Sikkink, Megan E Kobiela, Emilie C Snell-Rood
BACKGROUND: Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades...
May 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28549175/selfing-in-haploid-plants-and-efficacy-of-selection-codon-usage-bias-in-the-model-moss-physcomitrella-patens
#8
Péter Szövényi, Kristian K Ullrich, Stefan A Rensing, Daniel Lang, Nico van Gessel, Hans K Stenøien, Elena Conti, Ralf Reski
Long term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support...
May 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28548943/intra-tumour-molecular-heterogeneity-of-clear-cell-renal-cell-carcinoma-reveals-the-diversity-of-the-response-to-targeted-therapies-using-patient-derived-xenograft-models
#9
Baoan Hong, Yong Yang, Sheng Guo, Shayiremu Duoerkun, Xiaohu Deng, Dawei Chen, Shijun Yu, Wubin Qian, Qixiang Li, Qing Li, Kan Gong, Ning Zhang
Inter- and intra-tumour molecular heterogeneity is increasingly recognized in clear cell renal cell carcinoma (ccRCC). It may partially explain the diversity of responses to targeted therapies and the various clinical outcomes. In this study, a 56-year-old male ccRCC patient with multiple metastases received radical nephrectomy and resection of the metastatic tumour in chest wall. The surgical specimens were implanted into nude mice to establish patient-derived xenograft (PDX) models with KI2367 model derived from the primary tumour and KI2368 model from the metastastic tumour...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#10
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28548087/the-distinct-metabolic-phenotype-of-lung-squamous-cell-carcinoma-defines-selective-vulnerability-to-glycolytic-inhibition
#11
Justin Goodwin, Michael L Neugent, Shin Yup Lee, Joshua H Choe, Hyunsung Choi, Dana M R Jenkins, Robin J Ruthenborg, Maddox W Robinson, Ji Yun Jeong, Masaki Wake, Hajime Abe, Norihiko Takeda, Hiroko Endo, Masahiro Inoue, Zhenyu Xuan, Hyuntae Yoo, Min Chen, Jung-Mo Ahn, John D Minna, Kristi L Helke, Pankaj K Singh, David B Shackelford, Jung-Whan Kim
Adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) are the two predominant subtypes of non-small cell lung cancer (NSCLC) and are distinct in their histological, molecular and clinical presentation. However, metabolic signatures specific to individual NSCLC subtypes remain unknown. Here, we perform an integrative analysis of human NSCLC tumour samples, patient-derived xenografts, murine model of NSCLC, NSCLC cell lines and The Cancer Genome Atlas (TCGA) and reveal a markedly elevated expression of the GLUT1 glucose transporter in lung SqCC, which augments glucose uptake and glycolytic flux...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547520/small-scale-intraspecific-patterns-of-adaptive-immunogenetic-polymorphisms-and-neutral-variation-in-lake-superior-lake-trout
#12
Shauna M Baillie, Riley R Hemstock, Andrew M Muir, Charles C Krueger, Paul Bentzen
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake...
May 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28547384/a-new-putative-deltapartitivirus-recovered-from-dianthus%C3%A2-amurensis
#13
Hongliu An, Guanlin Tan, Guihong Xiong, Meirong Li, Shouguo Fang, Saif Ul Islam, Songbai Zhang, Fan Li
Two double stranded RNAs (dsRNA), likely representing the genome of a novel deltapartitivirus, provisionally named carnation cryptic virus 3 (CCV3), were recovered from Dianthus amurensis. The two dsRNAs were 1,573 (dsRNA1) and 1,561 (dsRNA2) bp in size, each containing a single open reading frame (ORF) encoding a 475- and 411-aa protein, respectively. The 475-aa protein contains a conserved RNA dependent RNA polymerase (RdRp) domain which shows significant homology to RdRps of established or putative partitiviruses, particularly those belonging to the genus Deltapartitivirus...
May 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28546965/ribonuclease-from-bacillus-acts-as-an-antiviral-agent-against-negative-and-positive-sense-single-stranded-human-respiratory-rna-viruses
#14
Raihan Shah Mahmud, Christin Müller, Yulia Romanova, Ahmed Mostafa, Vera Ulyanova, Stephan Pleschka, Olga Ilinskaya
Bacillus pumilus ribonuclease (binase) was shown to be a promising antiviral agent in animal models and cell cultures. However, the mode of its antiviral action remains unknown. To assess the binase effect on intracellular viral RNA we have selected single stranded negative- and positive-sense RNA viruses, influenza virus, and rhinovirus, respectively, which annually cause respiratory illnesses and are characterized by high contagious nature, mutation rate, and antigen variability. We have shown that binase exerts an antiviral effect on both viruses at the same concentration, which does not alter the spectrum of A549 cellular proteins and expression of housekeeping genes...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28546495/complete-genome-sequence-of-streptomyces-sp-sge12-which-produces-antibacterial-and-fungicidal-activities
#15
Jianguo Xu, Min Xu, Kai Liu, Qinyin Peng, Meifeng Tao
Streptomyces sp. Sge12 was isolated from forest soil and exhibited remarkable antimicrobial activities against selected fungi and Gram-positive bacteria. Here, we report the complete genome sequence of this strain, which contains 37 putative secondary metabolite gene clusters.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546383/drosophila-simulans-a-species-with-improved-resolution-in-evolve-and-resequence-studies
#16
Neda Barghi, Raymond Tobler, Viola Nolte, Christian Schlötterer
The combination of experimental evolution with high-throughput sequencing of pooled individuals - i.e. Evolve and Resequence; E&R - is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ~60 generations in a novel hot environment for D...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28545854/transcriptome-wide-identification-of-host-genes-targeted-by-tomato-spotted-wilt-virus-derived-small-interfering-rnas
#17
Shunmugiah V Ramesh, Sarah Williams, Madhu Kappagantu, Neena Mitter, Hanu R Pappu
RNA silencing mechanism functions as a major defense against invading viruses. The caveat in the RNA silencing mechanism is that the effector small interfering RNAs (siRNAs) act on any RNA transcripts with sequence complementarity irrespective of target's origin. A subset of highly expressed viral small interfering RNAs (vsiRNAs) derived from the tomato spotted wilt virus (TSWV; Tospovirus: Bunyaviridae) genome was analyzed for their propensity to downregulate the tomato transcriptome. A total of 11898 putative target sites on tomato transcripts were found to exhibit a propensity for down regulation by TSWV-derived vsiRNAs...
May 22, 2017: Virus Research
https://www.readbyqxmd.com/read/28545455/the-effect-of-weight-loss-on-hdl-subfractions-and-lcat-activity-in-two-genotypes-of-apoa-ii-265t-c-polymorphism
#18
Masoumeh Moradi, Maryam Mahmoudi, Ahmad Saedisomeolia, Roxana Zahirihashemi, Fariba Koohdani
BACKGROUND: People may have different responses to the same environmental changes. It has been reported that genome variations may be responsible for these differences. Also, HDL subfractions may be influenced by different genetic variations. The aim of the present study was to determine gene-diet interactions and to evaluate the influence of weight loss on HDL subfractions between two genotypes of -265 T>C APOA-II polymorphism. METHODS: In the present study, 56 overweight and obese patients with type 2 diabetes mellitus were selected from 697 genotype-specified subjects...
May 25, 2017: Nutrition Journal
https://www.readbyqxmd.com/read/28545453/genome-wide-methylation-analysis-reveals-differentially-methylated-loci-that-are-associated-with-an-age-dependent-increase-in-bovine-fibroblast-response-to-lps
#19
Filiz T Korkmaz, David E Kerr
BACKGROUND: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS)...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545405/genetic-complexity-of-miscanthus-cell-wall-composition-and-biomass-quality-for-biofuels
#20
Tim van der Weijde, Claire L Alvim Kamei, Edouard I Severing, Andres F Torres, Leonardo D Gomez, Oene Dolstra, Chris A Maliepaard, Simon J McQueen-Mason, Richard G F Visser, Luisa M Trindade
BACKGROUND: Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program...
May 25, 2017: BMC Genomics
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