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https://www.readbyqxmd.com/read/28550622/genomic-instability-related-to-zinc-deficiency-and-excess-in-an-in-vitro-model-is-the-upper-estimate-of-the-physiological-requirements-recommended-for-children-safe
#1
Gisel Padula, María Virginia Ponzinibbio, Rocío Celeste Gambaro, Analía Isabel Seoane
Micronutrients are important for the prevention of degenerative diseases due to their role in maintaining genomic stability. Therefore, there is international concern about the need to redefine the optimal mineral and vitamin requirements to prevent DNA damage. We analyzed the cytostatic, cytotoxic, and genotoxic effect of in vitro zinc supplementation to determine the effects of zinc deficiency and excess and whether the upper estimate of the physiological requirement recommended for children is safe. To achieve zinc deficiency, DMEM/Ham's F12 medium (HF12) was chelated (HF12Q)...
May 26, 2017: In Vitro Cellular & Developmental Biology. Animal
https://www.readbyqxmd.com/read/28550524/cop9-signalosome-subunit-pfcsne-regulates-secondary-metabolism-and-conidial-formation-in-pestalotiopsis-fici
#2
Yanjing Zheng, Xiuna Wang, Xiaoling Zhang, Wei Li, Gang Liu, Shihua Wang, Xiufeng Yan, Huixi Zou, Wen-Bing Yin
The COP9 signalosome (CSN) is a highly conserved multiprotein complex in all eukaryotes and involved in regulation of organism development. In filamentous fungi, several lines of evidence indicate that fungal development and secondary metabolism (SM) are mediated by the fifth subunit of CSN, called CsnE. Here we uncover a connection with CsnE and conidial formation as well as SM regulation in the plant endophytic fungus Pestalotiopsis fici. A homology search of the P. fici genome with CsnE, involved in sexual development and SM in Aspergillus nidulans, identified PfCsnE...
May 25, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28550453/exchange-of-genetic-sequences-between-viruses-and-hosts
#3
Robin A Weiss
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes...
May 28, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28550432/molecular-characterization-of-a-novel-luteovirus-from-peach-identified-by-high-throughput-sequencing
#4
L-P Wu, H-W Liu, M Bateman, Z Liu, R Li
Contigs with sequence homologies to cherry-associated luteovirus were identified by high-throughput sequencing analysis in two peach accessions. Complete genomic sequences of the two isolates of this virus were determined to be 5,819 and 5,814 nucleotides long, respectively. The genome of the new virus is typical of luteoviruses, containing eight open reading frames in a very similar arrangement. Its genomic sequence is 58-74% identical to those of other members of the genus Luteovirus. These sequences thus belong to a new virus, which we have named "peach-associated luteovirus"...
May 26, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28550412/differential-expression-of-poplar-sucrose-nonfermenting1-related-protein-kinase-2-genes-in-response-to-abiotic-stress-and-abscisic-acid
#5
Xiang Yu, Arika Takebayashi, Taku Demura, Misato Ohtani
Knowledge on the responses of woody plants to abiotic stress can inform strategies to breed improved tree varieties and to manage tree species for environmental conservation and the production of lignocellulosic biomass. In this study, we examined the expression patterns of poplar (Populus trichocarpa) genes encoding members of the sucrose nonfermenting1-related protein kinase 2 (SnRK2) family, which are core components of the abiotic stress response. The P. trichocarpa genome contains twelve SnRK2 genes (PtSnRK2...
May 26, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28550408/bacillus-pumilus-strain-yspmk11-as-plant-growth-promoter-and-bicontrol-agent-against-sclerotinia-sclerotiorum
#6
Manoj Kaushal, Ajay Kumar, Rajesh Kaushal
A study was executed in a direction to attenuate Sclerotinia stalk rot (SSR) disease through biocontrol agent and also to enhance crop productivity. Culture filtrate of bacterial strain YSPMK11 inhibited growth of Sclerotinia sclerotiorum in vitro which also exhibited higher plant growth promoting attributes. Interaction studies revealed maximum (81.50%) growth inhibition at 35 °C and pH 7.0 after 72 h incubation period with 15% culture filtrate. Based upon 16S rRNA gene sequence strain, YSPMK11 was identified as Bacillus pumilus...
June 2017: 3 Biotech
https://www.readbyqxmd.com/read/28550381/treatment-of-dyslipidemia-using-crispr-cas9-genome-editing
#7
REVIEW
Alexandra C Chadwick, Kiran Musunuru
PURPOSE OF REVIEW: Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) has recently emerged as a top genome editing technology and has afforded investigators the ability to more easily study a number of diseases. This review discusses CRISPR/Cas9's advantages and limitations and highlights a few recent reports on genome editing applications for alleviating dyslipidemia through disruption of proprotein convertase subtilisin/kexin type 9 (PCSK9)...
July 2017: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/28550345/bacillus-zanthoxyli-sp-nov-a-novel-nematicidal-bacterium-isolated-from-chinese-red-pepper-zanthoxylum-bungeanum-maxim-leaves-in-china
#8
Ma Li, Cao Yong Hong, Wang Xiao Yan, Zheng Shuai Chao, Yang Cheng Gang, Duo Jin Ling, Zhou Xing Kui, Xi Jia Qin, Zhu Ming Liang, Mo Ming He
A novel strain, 1433(T), was isolated from leaves of Chinese red pepper (Huajiao, Zanthoxylum bungeanum Maxim) collected from Gansu province in northwestern China, and was characterised by a polyphasic approach. Cells of strain 1433(T) were observed to be Gram-stain positive, aerobic, asporogenous, rod shaped, motile and to have peritrichous flagella. The strain was observed to grow at a range of temperatures and pH, 4-45 °C (optimum 28-32 °C) and 6.0-10.0 (optimum pH 6.0-7.0), respectively. Growth was found to occur in the presence of 0-7% (w/v) NaCl [optimum 0-3% (w/v)]...
May 26, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28550313/quantification-of-hepatocellular-carcinoma-heterogeneity-with-multiparametric-magnetic-resonance-imaging
#9
Stefanie J Hectors, Mathilde Wagner, Octavia Bane, Cecilia Besa, Sara Lewis, Romain Remark, Nelson Chen, M Isabel Fiel, Hongfa Zhu, Sacha Gnjatic, Miriam Merad, Yujin Hoshida, Bachir Taouli
Tumour heterogeneity poses a significant challenge for treatment stratification. The goals of this study were to quantify heterogeneity in hepatocellular carcinoma (HCC) using multiparametric magnetic resonance imaging (mpMRI), and to report preliminary data correlating quantitative MRI parameters with advanced histopathology and gene expression in a patient subset. Thirty-two HCC patients with 39 HCC lesions underwent mpMRI including diffusion-weighted imaging (DWI), blood-oxygenation-level-dependent (BOLD), tissue-oxygenation-level-dependent (TOLD) and dynamic contrast-enhanced (DCE)-MRI...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28550310/a-to-i-editing-in-human-mirnas-is-enriched-in-seed-sequence-influenced-by-sequence-contexts-and-significantly-hypoedited-in-glioblastoma-multiforme
#10
Deepanjan Paul, Ashis Narayan Sinha, Arjun Ray, Megha Lal, Subhashree Nayak, Anchal Sharma, Bharati Mehani, Debasish Mukherjee, Saurabh V Laddha, Ashish Suri, Chitra Sarkar, Arijit Mukhopadhyay
Editing in microRNAs, particularly in seed can significantly alter the choice of their target genes. We show that out of 13 different human tissues, different regions of brain showed higher adenosine to inosine (A-to-I) editing in mature miRNAs. These events were enriched in seed sequence (73.33%), which was not observed for cytosine to uracil (17.86%) editing. More than half of the edited miRNAs showed increased stability, 72.7% of which had ΔΔG values less than -6.0 Kcal/mole and for all of them the edited adenosines mis-paired with cytosines on the pre-miRNA structure...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28550296/reducing-mitochondrial-reads-in-atac-seq-using-crispr-cas9
#11
Lindsey Montefiori, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory Crawford, Marcelo Nobrega, Noboru Jo Sakabe
ATAC-seq is a high-throughput sequencing technique that identifies open chromatin. Depending on the cell type, ATAC-seq samples may contain ~20-80% of mitochondrial sequencing reads. As the regions of open chromatin of interest are usually located in the nuclear genome, mitochondrial reads are typically discarded from the analysis. We tested two approaches to decrease wasted sequencing in ATAC-seq libraries generated from lymphoblastoid cell lines: targeted cleavage of mitochondrial DNA fragments using CRISPR technology and removal of detergent from the cell lysis buffer...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28550290/differential-methylation-is-associated-with-non-syndromic-cleft-lip-and-palate-and-contributes-to-penetrance-effects
#12
Lucas Alvizi, Xiayi Ke, Luciano Abreu Brito, Rimante Seselgyte, Gudrun E Moore, Philip Stanier, Maria Rita Passos-Bueno
Non-syndromic cleft lip and/or palate (NSCLP) is a common congenital malformation with a multifactorial model of inheritance. Although several at-risk alleles have been identified, they do not completely explain the high heritability. We postulate that epigenetic factors as DNA methylation might contribute to this missing heritability. Using a Methylome-wide association study in a Brazilian cohort (67 NSCLP, 59 controls), we found 578 methylation variable positions (MVPs) that were significantly associated with NSCLP...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28550245/amyloid-burden-in-obstructive-sleep%C3%A2-apnea
#13
Chang-Ho Yun, Ho-Young Lee, Seung Ku Lee, Hyun Kim, Hyung Suk Seo, Seong Ae Bang, Sang Eun Kim, Douglas N Greve, Rhoda Au, Chol Shin, Robert J Thomas
To test the hypothesis that excessive amyloid deposition is a biological link between obstructive sleep apnea (OSA) and Alzheimer's disease, we determined whether OSA increases cerebral amyloid burden, relative to controls, using Pittsburgh Compound B (PiB) PET imaging. The subjects were adult participants (age 50-65 years) from the Korean Genome and Epidemiology Study. Polysomnography, brain MRI including 3D images, and a detailed neuro-cognitive function test battery were done in 2011-2012. Nineteen OSA subjects (Apnea-Hypopnea Index [AHI] ≥15/h, 21...
May 26, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28550207/atx3-atx4-and-atx5-encode-putative-h3k4-methyltransferases-and-are-critical-for-plant-development
#14
Liqun Chen, Jinhong Luo, Zhenhai Cui, Ming Xue, Li Wang, Xiaoyu Zhang, Wojtek P Pawlowski, Yan He
Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. Here we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5...
May 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28550183/somatic-mutation-spectrum-in-monoclonal-gammopathy-of-undetermined-significance-indicates-a-less-complex-genomic-landscape-compared-to-multiple-myeloma
#15
Aneta Mikulasova, Christopher P Wardell, Alexander Murison, Eileen M Boyle, Graham H Jackson, Jan Smetana, Zuzana Kufova, Ludek Pour, Viera Sandecka, Martina Almasi, Pavla Vsianska, Evzen Gregora, Petr Kuglik, Roman Hajek, Faith E Davies, Gareth J Morgan, Brian A Walker
Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about the molecular mechanism of malignant transformation. We have performed whole exome sequencing together with CGH+SNP array analysis in 33 flow-cytometry separated abnormal plasma cell samples from MGUS patients to describe somatic gene mutations and chromosome changes at the genome-wide level...
May 26, 2017: Haematologica
https://www.readbyqxmd.com/read/28550093/causal-effect-of-plasminogen-activator-inhibitor-type-1-on-coronary-heart-disease
#16
REVIEW
Ci Song, Stephen Burgess, John D Eicher, Christopher J O'Donnell, Andrew D Johnson
BACKGROUND: Plasminogen activator inhibitor type 1 (PAI-1) plays an essential role in the fibrinolysis system and thrombosis. Population studies have reported that blood PAI-1 levels are associated with increased risk of coronary heart disease (CHD). However, it is unclear whether the association reflects a causal influence of PAI-1 on CHD risk. METHODS AND RESULTS: To evaluate the association between PAI-1 and CHD, we applied a 3-step strategy. First, we investigated the observational association between PAI-1 and CHD incidence using a systematic review based on a literature search for PAI-1 and CHD studies...
May 26, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28550087/transcriptional-networks-in-rodent-models-support-a-role-for-gut-brain-communication-in-neurogenic-hypertension-a-review-of-the-evidence
#17
Jasenka Zubcevic, Ashley Baker, Christopher J Martyniuk
Hypertension (HTN) is the most prevalent condition observed in primary health care. Hypertension shows complex etiology, and neuroinflammation, overactive sympathetic drive, and the microbiome are associated with the disease. To obtain mechanistic perspective into neurogenic HTN, we first constructed a framework for transcriptional regulators of the disease using the Comparative Toxicogenomics Database. This approach yielded a core group of 178 transcripts that are prevalent in HTN, including leptin and neuropeptide Y...
May 26, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28550083/normal-and-cancerous-tissues-release-extrachromosomal-circular-dna-eccdna-into-the-circulation
#18
Pankaj Kumar, Laura Dillon, Yoshiyuki Shibata, Amir A Jazaeri, David R Jones, Anindya Dutta
Cell-free circulating linear DNA is being explored for non-invasive diagnosis and management of tumors and fetuses, the so-called liquid biopsy. Previously, we observed the presence of small extrachromosomal circular DNA (eccDNA), called microDNA, in the nuclei of mammalian tissues and cell lines. Now, we demonstrate that cell-free microDNA derived from uniquely mapping regions of the genome is detectable in plasma and serum from both mice and humans and that they are significantly longer (30-60% >250 bases) than cell-free circulating linear DNA (~150 bases)...
May 26, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28550066/rapid-whole-genome-sequencing-identifies-a-novel-homozygous-npc1-variant-associated-with-niemann-pick-type-c1-disease-in-a-7-week-old-male-with-cholestasis
#19
Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, Rcigm Investigators, Stephen F Kingsmore
Niemann-Pick Type C disease (NPC; OMIM #257220) is an inborn error of intracellular cholesterol trafficking. It is an autosomal recessive disorder caused predominantly by mutations in NPC1. While characterized as a progressive neurological disorder, it can also cause cholestasis and liver dysfunction due to intrahepatocyte lipid accumulation. We report a 7 week old who was admitted with neonatal cholestasis, who was diagnosed with a novel homozygous stop-gain variant in NPC1 by rapid whole genome sequencing (WGS)...
May 26, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28550065/exceptional-durable-response-to-everolimus-in-a-patient-with-biphenotypic-breast-cancer-harboring-an-stk11-variant
#20
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
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