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https://www.readbyqxmd.com/read/28441662/buffalo-leukemia-inhibitory-factor-induces-differentiation-and-dome-like-secondary-structures-in-cos-1-cells
#1
Gurjeet Kaur, Syed Azmal Ali, Shikha Pachauri, Dhruba Malakar, Jai K Kaushik, Ashok K Mohanty, Sudarshan Kumar
This study aimed to understand the molecular characteristics of buffalo leukemia inhibitory factor (BuLIF) and the generation of a stably transfected COS-1_BuLIF cell line for its functional characterization. Cumulus cells, isolated from oocytes, were separated, and total cDNA was prepared. The BuLIF gene was ligated into the cloning vector pJET1.2/blunt and expression vector pAcGFP-N1 which was transfected into COS-1 cells and confirmed by qRT-PCR and Western blot. BuLIF was immunoprecipitated and evaluated through a MTT assay...
April 26, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28441530/aubergine-controls-germline-stem-cell-self-renewal-and-progeny-differentiation-via-distinct-mechanisms
#2
Xing Ma, Xiujuan Zhu, Yingying Han, Benjamin Story, Trieu Do, Xiaoqing Song, Su Wang, Ying Zhang, Marco Blanchette, Madelaine Gogol, Kate Hall, Allison Peak, Perera Anoja, Ting Xie
Piwi family protein Aubergine (Aub) maintains genome integrity in late germ cells of the Drosophila ovary through Piwi-associated RNA-mediated repression of transposon activities. Although it is highly expressed in germline stem cells (GSCs) and early progeny, it remains unclear whether it plays any roles in early GSC lineage development. Here we report that Aub promotes GSC self-renewal and GSC progeny differentiation. RNA-iCLIP results show that Aub binds the mRNAs encoding self-renewal and differentiation factors in cultured GSCs...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28441463/rapidsnps-a-new-computational-pipeline-for-rapidly-identifying-key-genetic-variants-reveals-previously-unidentified-snps-that-are-significantly-associated-with-individual-platelet-responses
#3
Bajuna Rashid Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits...
2017: PloS One
https://www.readbyqxmd.com/read/28441395/molecular-phylogeny-of-oncaeidae-copepoda-using-nuclear-ribosomal-internal-transcribed-spacer-its-rdna
#4
Iole Di Capua, Fulvio Maffucci, Raimondo Pannone, Maria Grazia Mazzocchi, Elio Biffali, Alberto Amato
Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI)...
2017: PloS One
https://www.readbyqxmd.com/read/28441029/variable-susceptibility-to-cigarette-smoke-induced-emphysema-in-34-inbred-strains-of-mice-implicates-abi3bp-in-emphysema-susceptibility
#5
Josiah E Radder, Alyssa D Gregory, Adriana S Leme, Michael H Cho, Yanxia Chu, Neil J Kelly, Per Bakke, Amund Gulsvik, Augusto A Litonjua, David Sparrow, Terri H Beaty, James D Crapo, Edwin K Silverman, Yingze Zhang, Annerose Berndt, Steven D Shapiro
RATIONALE: Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge of the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. OBJECTIVE: To measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD...
April 25, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28440800/the-trichodesmium-consortium-conserved-heterotrophic-co-occurrence-and-genomic-signatures-of-potential-interactions
#6
Michael D Lee, Nathan G Walworth, Erin L McParland, Fei-Xue Fu, Tracy J Mincer, Naomi M Levine, David A Hutchins, Eric A Webb
The nitrogen (N)-fixing cyanobacterium Trichodesmium is globally distributed in warm, oligotrophic oceans, where it contributes a substantial proportion of new N and fuels primary production. These photoautotrophs form macroscopic colonies that serve as relatively nutrient-rich substrates that are colonized by many other organisms. The nature of these associations may modulate ocean N and carbon (C) cycling, and can offer insights into marine co-evolutionary mechanisms. Here we integrate multiple omics-based and experimental approaches to investigate Trichodesmium-associated bacterial consortia in both laboratory cultures and natural environmental samples...
April 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28440475/a-nine-mirna-signature-as-a-potential-diagnostic-marker-for-breast-carcinoma-an-integrated-study-of-1-110-cases
#7
Dan-Dan Xiong, Jun Lv, Kang-Lai Wei, Zhen-Bo Feng, Ji-Tian Chen, Ke-Cheng Liu, Gang Chen, Dian-Zhong Luo
Growing evidence indicates that microRNAs (miRNAs) play critical roles in the initiation and progression of breast carcinoma (BC) and are promising diagnostic biomarkers. In the present study, we aimed to identify a multi-marker miRNA pool with high diagnostic performance for BC. We collected miRNA expression profiles of BC samples and normal breast tissues from The Cancer Genome Atlas (TCGA) and screened differentially expressed miRNAs by conducting two‑sample t-tests and by calculating log2 fold-change (log2FC) ratios...
April 25, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28440335/mycobacterium-tuberculosis-pe_pgrs41-enhances-the-intracellular-survival-of-m-smegmatis-within-macrophages-via-blocking-innate-immunity-and-inhibition-of-host-defense
#8
Wanyan Deng, Quanxin Long, Jie Zeng, Ping Li, Wenmin Yang, Xinchun Chen, Jianping Xie
The success of Mycobacterium tuberculosis (M. tuberculosis) as a pathogen is largely contributes to its ability to manipulate the host immune responses. The genome of M. tuberculosis encodes multiple immune-modulatory proteins, including several members of the multi-genic PE_PPE family. Despite of intense research, the roles of PE_PGRS proteins in mycobacterial pathogenesis remain elusive. The function of M. tuberculosis PE_PGRS41, characterized by an extended and unique C-terminal domain, was studied. Expression of PE_PGRS41 in Mycobacterium smegmatis, a non-pathogenic species intrinsically deficient of PE_PGRS, severely impaired the resistance of the recombinant to multiple stresses via altering the cell wall integrity...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439991/melatonin-a-pleiotropic-molecule-that-modulates-dna-damage-response-and-repair-pathways
#9
REVIEW
Maryam Majidinia, Alireza Sadeghpour, Saeed Mehrzadi, Russel J Reiter, Nasrin Khatami, Bahman Yousefi
DNA repair is responsible for maintaining the integrity of the genome. Perturbations in the DNA repair pathways have been identified in several human cancers. Thus, compounds targeting DNA damage response (DDR) hold great promise in cancer therapy. A great deal of effort, in pursuit of new anticancer drugs, has been devoted to understanding the basic mechanisms and functions of the cellular DNA repair machinery. Melatonin, a widely-produced indoleamine in all organisms is associated with a reduced risk of cancer and has multiple regulatory roles on the different aspects of the DDR and DNA repair...
April 25, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28439871/application-of-chemical-genomics-to-plant-bacteria-communication-a-high-throughput-system-to-identify-novel-molecules-modulating-the-induction-of-bacterial-virulence-genes-by-plant-signals
#10
Elodie Vandelle, Maria Rita Puttilli, Andrea Chini, Giulia Devescovi, Vittorio Venturi, Annalisa Polverari
The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439853/crispr-cas-mediated-in-planta-gene-targeting
#11
Simon Schiml, Friedrich Fauser, Holger Puchta
The recent emergence of the CRISPR/Cas system has boosted the possibilities for precise genome engineering approaches throughout all kingdoms of life. The most common application for plants is targeted mutagenesis, whereby a Cas9-mediated DNA double-strand break (DSB) is repaired by mutagenic nonhomologous end joining (NHEJ). However, the site-specific alteration of a genomic sequence or integration of a transgene relies on the precise repair by homologous recombination (HR) using a suitable donor sequence: this poses a particular challenge in plants, as NHEJ is the preferred repair mechanism for DSBs in somatic tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439535/a-murine-preclinical-syngeneic-transplantation-model-for-breast-cancer-precision-medicine
#12
Lorenzo Federico, Zechen Chong, Dong Zhang, Daniel J McGrail, Wei Zhao, Kang Jin Jeong, Christopher P Vellano, Zhenlin Ju, Mihai Gagea, Shuying Liu, Shreya Mitra, Jennifer B Dennison, Philip L Lorenzi, Robert Cardnell, Lixia Diao, Jing Wang, Yiling Lu, Lauren A Byers, Charles M Perou, Shiaw-Yih Lin, Gordon B Mills
We previously demonstrated that altered activity of lysophosphatidic acid in murine mammary glands promotes tumorigenesis. We have now established and characterized a heterogeneous collection of mouse-derived syngeneic transplants (MDSTs) as preclinical platforms for the assessment of personalized pharmacological therapies. Detailed molecular and phenotypic analyses revealed that MDSTs are the most heterogeneous group of genetically engineered mouse models (GEMMs) of breast cancer yet observed. Response of MDSTs to trametinib, a mitogen-activated protein kinase (MAPK) kinase inhibitor, correlated with RAS/MAPK signaling activity, as expected from studies in xenografts and clinical trials providing validation of the utility of the model...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28439277/expression-of-pennisetum-glaucum-eukaryotic-translational-initiation-factor-4a-pgeif4a-confers-improved-drought-salinity-and-oxidative-stress-tolerance-in-groundnut
#13
Tata Santosh Rama Bhadra Rao, Juturu Vijaya Naresh, Palakolanu Sudhakar Reddy, Malireddy K Reddy, Garladinne Mallikarjuna
Eukaryotic translational initiation factor 4A belong to family of helicases, involved in multifunctional activities during stress and non-stress conditions. The eIF4A gene was isolated and cloned from semi-arid cereal crop of Pennisetum glaucum. In present study, the PgeIF4A gene was expressed under the regulation of stress inducible Arabidopsis rd29A promoter in groundnut (cv JL-24) with bar as a selectable marker. The de-embryonated cotyledons were infected with Agrobacterium tumefaciens (LBA4404) carrying rd29A:PgeIF4A construct and generated high frequency of multiple shoots in phosphinothricin medium...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439124/characterisation-of-a-cell-free-synthesised-g-protein-coupled-receptor
#14
Patrick J Shilling, Fabian Bumbak, Daniel J Scott, Ross A D Bathgate, Paul R Gooley
G-protein coupled receptors are the largest family of integral membrane proteins found within the human genome. They function as receptors and modulators to a wide range of ligands and responses which are crucial for human health. GPCR study, specifically the investigation of structure and interaction to cognate ligands, is of high priority. Limitations for structural study can be traced in part, to obtaining suitable quantities of recombinant protein. We sought to address the limitations of traditional recombinant technologies by utilising an Escherichia coli based cell-free protein synthesis (CFPS) approach for production of a thermostable neurotensin receptor 1 (en2NTS1)...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439089/transcriptome-analysis-on-the-exoskeleton-formation-in-early-developmetal-stages-and-reconstruction-scenario-in-growth-moulting-in-litopenaeus-vannamei
#15
Yi Gao, Jiankai Wei, Jianbo Yuan, Xiaojun Zhang, Fuhua Li, Jianhai Xiang
Exoskeleton construction is an important issue in shrimp. To better understand the molecular mechanism of exoskeleton formation, development and reconstruction, the transcriptome of the entire developmental process in Litopenaeus vannamei, including nine early developmental stages and eight adult-moulting stages, was sequenced and analysed using Illumina RNA-seq technology. A total of 117,539 unigenes were obtained, with 41.2% unigenes predicting the full-length coding sequence. Gene Ontology, Clusters of Orthologous Group (COG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and functional annotation of all unigenes gave a better understanding of the exoskeleton developmental process in L...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28438939/emergence-and-evolution-of-multidrug-resistant-klebsiella-pneumoniae-with-both-blakpc-and-blactx-m-integrated-in-chromosome
#16
Weihua Huang, Guiqing Wang, Robert Sebra, Jian Zhuge, Changhong Yin, Maria E Aguero-Rosenfeld, Audrey N Schuetz, Nevenka Dimitrova, John T Fallon
The extended-spectrum β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14 and NY9, carrying both blaCTX-M and blaKPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, blaCTX-M and blaKPC were carried on two different plasmids...
April 24, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28438806/emerging-affinity-based-proteomic-technologies-for-large-scale-plasma-profiling-in-cardiovascular-disease
#17
REVIEW
J Gustav Smith, Robert E Gerszten
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28438193/pathos-a-decision-support-system-for-reporting-high-throughput-sequencing-of-cancers-in-clinical-diagnostic-laboratories
#18
Kenneth D Doig, Andrew Fellowes, Anthony H Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A Doyle, Ella R Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T Papenfuss, Stephen B Fox
BACKGROUND: The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout...
April 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28437752/dna-repair-and-damage-pathways-in-breast-cancer-development-and-therapy
#19
REVIEW
Maryam Majidinia, Bahman Yousefi
DNA damage/repair constitutes several key pathways working in concert to eliminate DNA lesions and maintain genome stability and integrity. Defective components in DNA damage and repair machinery are an underlying cause for the development and progression of different types of cancers, and breast cancer is no exception. In this paper, we will briefly explain the importance of DNA damage and repair, introduce the current classification schemes for breast cancer, and review the known defects in the repair machinery that have been associated with the risk of breast cancer...
April 21, 2017: DNA Repair
https://www.readbyqxmd.com/read/28437135/d3gb-an-interactive-genome-browser-for-r-python-and-wordpress
#20
David Barrios, Carlos Prieto
Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web...
February 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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