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https://www.readbyqxmd.com/read/29161534/omics-and-bioinformatics-time-for-new-data-analysis-approaches
#1
Chenyu Li, Wei Jiang, Yan Xu
No abstract text is available yet for this article.
November 21, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29161519/bioinformatics-advances-to-accelerate-omics-innovations-and-applications-in-the-postgenomic-era
#2
Jayshree Advani, Yashwanth Subbannayya, Harsha Gowda, Aditi Chatterjee
No abstract text is available yet for this article.
November 21, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29161470/resequencing-of-a-mutant-bearing-an-iron-starvation-recovery-phenotype-defines-slr1658-as-a-new-player-in-the-regulatory-network-of-a-model-cyanobacterium
#3
Hagit Zer, Ketty Margulis, Jens Georg, Yoram Shotland, Gergana Kostova, Laure Sultan, Wolfgang R Hess, Nir Keren
Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161332/osteoglycin-inhibition-by-microrna-mir-155-impairs-myogenesis
#4
Paula Paccielli Freire, Sarah Santiloni Cury, Grasieli de Oliveira, Geysson Javier Fernandez, Leonardo Nazario Moraes, Bruno Oliveira da Silva Duran, Juarez Henrique Ferreira, César Seigi Fuziwara, Edna Teruko Kimura, Maeli Dal-Pai-Silva, Robson Francisco Carvalho
Skeletal myogenesis is a regulated process in which mononucleated cells, the myoblasts, undergo proliferation and differentiation. Upon differentiation, the cells align with each other, and subsequently fuse to form terminally differentiated multinucleated myotubes. Previous reports have identified the protein osteoglycin (Ogn) as an important component of the skeletal muscle secretome, which is expressed differentially during muscle development. However, the posttranscriptional regulation of Ogn by microRNAs during myogenesis is unknown...
2017: PloS One
https://www.readbyqxmd.com/read/29160413/long-non-coding-rna-chchd4p4-promotes-epithelial-mesenchymal-transition-and-inhibits-cell-proliferation-in-calcium-oxalate-induced-kidney-damage
#5
C Zhang, J Yuan, H Hu, W Chen, M Liu, J Zhang, S Sun, Z Guo
Kidney stone disease is a major cause of chronic renal insufficiency. The role of long non-coding RNAs (lncRNAs) in calcium oxalate-induced kidney damage is unclear. Therefore, we aimed to explore the roles of lncRNAs in glyoxylate-exposed and healthy mouse kidneys using microarray technology and bioinformatics analyses. A total 376 mouse lncRNAs were differentially expressed between the two groups. Using BLAST, 15 lncRNA homologs, including AU015836 and CHCHD4P4, were identified in mice and humans. The AU015836 expression in mice exposed to glyoxylate and the CHCHD4P4 expression in human proximal tubular epithelial (HK-2) cells exposed to calcium oxalate monohydrate were analyzed, and both lncRNAs were found to be upregulated in response to calcium oxalate...
November 13, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29160327/imbalance-in-amino-acid-and-purine-metabolisms-at-the-hypothalamus-in-inflammation-associated-depression-by-gc-ms
#6
Yu Wu, Yonghong Li, Yanjuan Jia, Chaojun Wei, Hui Xu, Rui Guo, Yuanting Li, Jing Jia, Xiaoming Qi, Xiaoling Gao
Hypothalamic dysfunction is a key factor in depression; increasing evidence highlights neuroinflammation abnormalities as well as imbalances in neurotransmitters and the purinergic system in the pathophysiology of depression. However, little is known about the metabolomic changes in the hypothalamus of depressed patients with neuroinflammation. Herein, taking advantage of the well-established lipopolysaccharide (LPS)-induced depression mouse model, we measured metabolic changes in the hypothalamus using gas chromatography-mass spectrometry (GC-MS)...
November 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29159897/identification-and-characterization-of-two-variants-of-the-hfq-srna-chaperone-in-the-fish-pathogen-piscirickettsia-salmonis
#7
S H Marshall, P Flores-Herrera, F A Henríquez, F A Gómez
Small RNA and chaperone proteins form synergistic duos that play pivotal roles in controlling gene expression in bacteria. This is the case for Hfq, a highly pleiotropic pretranslational modulator of general protein expression, which responds to harsh environmental conditions and influences fitness and virulence in a wide range of pathogenic Enterobacteria. Given this relevancy, we evaluated the presence and potential role of Hfq in the fish pathogen Piscirickettsia salmonis, a Gram-negative bacterium that threatens the sustainability of Chilean salmon production...
November 21, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/29159179/mir-31-functions-as-an-oncomir-which-promotes-epithelial-mesenchymal-transition-via-regulating-bap1-in-cervical-cancer
#8
Nan Wang, Yong Li, Jianhong Zhou
MicroRNA-31 (miR-31) functions as tumor suppressors or oncogenes that are involved in tumor behavior. However, the function of miR-31 in cervical carcinogenesis remains unclear. The aim of this study was to validate the potential role of miR-31 and BRCA1-associated protein-1 (BAP1) on regulating epithelial-mesenchymal transition (EMT) in cervical cancer. In the present study, qRT-PCR assay revealed that the expression of miR-31 was upregulated in human cervical cancer cells and clinical tissues. Results of wound healing and cell migration assay revealed that knockdown of miR-31 inhibited cell metastasis and migration...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29158994/detection-of-bacterial-contaminants-and-hybrid-sequences-in-the-genome-of-the-kelp-saccharina-japonica-using-taxoblast
#9
Simon M Dittami, Erwan Corre
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/29158876/challenges-in-the-setup-of-large-scale-next-generation-sequencing-analysis-workflows
#10
REVIEW
Pranav Kulkarni, Peter Frommolt
While Next-Generation Sequencing (NGS) can now be considered an established analysis technology for research applications across the life sciences, the analysis workflows still require substantial bioinformatics expertise. Typical challenges include the appropriate selection of analytical software tools, the speedup of the overall procedure using HPC parallelization and acceleration technology, the development of automation strategies, data storage solutions and finally the development of methods for full exploitation of the analysis results across multiple experimental conditions...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/29158838/crispr-genome-engineering-for-human-pluripotent-stem-cell-research
#11
REVIEW
Somali Chaterji, Eun Hyun Ahn, Deok-Ho Kim
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity...
2017: Theranostics
https://www.readbyqxmd.com/read/29158724/comparative-proteomic-analysis-between-nitrogen-supplemented-and-starved-conditions-in-magnaporthe-oryzae
#12
Yeonyee Oh, Suzanne L Robertson, Jennifer Parker, David C Muddiman, Ralph A Dean
Background: Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. Methods: M. oryzae strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source...
2017: Proteome Science
https://www.readbyqxmd.com/read/29158538/pinapl-py-a-comprehensive-web-application-for-the-analysis-of-crispr-cas9-screens
#13
Philipp N Spahn, Tyler Bath, Ryan J Weiss, Jihoon Kim, Jeffrey D Esko, Nathan E Lewis, Olivier Harismendy
Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158290/a-comparative-proteome-profile-of-female-mouse-gonads-suggests-a-tight-link-between-the-electron-transport-chain-and-meiosis-initiation
#14
Cong Shen, Mingrui Li, Pan Zhang, Yueshuai Guo, Hao Zhang, Bo Zheng, Hui Teng, Tao Zhou, Xuejiang Guo, Ran Huo
Generation of haploid gametes by meiosis is a unique property of germ cells and is critical for sexual reproduction. Leaving mitosis and entering meiosis is a key step in germ cell development. Several inducers or intrinsic genes are known to be important for meiotic initiation, but the regulation of meiotic initiation, especially at the protein level, is still not well understood. We constructed a comparative proteome profile of female mouse fetal gonads at specific time points (11.5, 12.5, and 13.5 days post coitum), spanning a critical window for initiation of meiosis in female germ cells...
November 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29158166/the-association-between-caspase-5-gene-polymorphisms-and-rheumatoid-arthritis-in-a-chinese-population
#15
Huan Rui, Ting Yan, Zhiyong Hu, Ruiping Liu, Liqun Wang
Genetic factors are widely recognized to have a substantial effect on the susceptibility to rheumatoid arthritis (RA). We examined the contribution of caspase-5 (CASP5) gene polymorphisms to RA risk in a Chinese population. We conducted a case-control study involving 500 RA patients and 500 controls and performed co-expression analysis to identify genes associated with CASP5. We attempted to analyze the functions of these genes by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. We carried out genotyping using a custom-by-design 48-Plex SNP (single nucleotide polymorphism) Scan™ Kit...
November 17, 2017: Gene
https://www.readbyqxmd.com/read/29157945/food-allergy-a-review-and-update-on-epidemiology-pathogenesis-diagnosis-prevention-and-management
#16
Scott H Sicherer, Hugh A Sampson
This review provides general information to serve as a primer for those embarking on understanding food allergy and also details advances and updates in epidemiology, pathogenesis, diagnosis and treatment that have occurred over the four years since our last comprehensive review. Although firm prevalence data are lacking, there is a strong impression that food allergy has increased, and rates as high as ∼10% have been documented. Genetic, epigenetic and environmental risk factors are being increasingly elucidated, opening the potential for improved prevention and treatment strategies targeted to those at risk...
November 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29157673/circulating-micrornas-as-biomarkers-for-pediatric-astrocytomas
#17
Javier Enrique López-Aguilar, Miguel A Velázquez-Flores, Luis A Simón-Martínez, Richard Ávila-Miranda, Marco A Rodríguez-Florido, Ruth Ruiz-Esparza Garrido
BACKGROUND AND AIMS: Since MicroRNAs (miRNAs) are potent regulators of gene expression, their expression and function alterations are associated with different types of cancer, including pediatric astrocytoma. Since the secretion of miRNAs by tumors into corporal fluids has made it possible to identify biomarkers in cancer, their deter mination in pediatric astrocytoma is vital. In order to gain insight into the mechanisms controlled by miRNAs in these neoplasms, we tested the expression of miRNAs 130a, 145, 335, 1303, and let-7g-3p by qPCR in tumors and blood serum from pediatric patients with astrocytoma...
May 2017: Archives of Medical Research
https://www.readbyqxmd.com/read/29157295/single-cell-multiplexed-cytokine-profiling-of-cd19-car-t-cells-reveals-a-diverse-landscape-of-polyfunctional-antigen-specific-response
#18
Qiong Xue, Emily Bettini, Patrick Paczkowski, Colin Ng, Alaina Kaiser, Timothy McConnell, Olja Kodrasi, Máire F Quigley, James Heath, Rong Fan, Sean Mackay, Mark E Dudley, Sadik H Kassim, Jing Zhou
BACKGROUND: It remains challenging to characterize the functional attributes of chimeric antigen receptor (CAR)-engineered T cell product targeting CD19 related to potency and immunotoxicity ex vivo, despite promising in vivo efficacy in patients with B cell malignancies. METHODS: We employed a single-cell, 16-plex cytokine microfluidics device and new analysis techniques to evaluate the functional profile of CD19 CAR-T cells upon antigen-specific stimulation. CAR-T cells were manufactured from human PBMCs transfected with the lentivirus encoding the CD19-BB-z transgene and expanded with anti-CD3/anti-CD28 coated beads...
November 21, 2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/29157267/transcriptomic-analysis-reveals-the-key-immune-related-signalling-pathways-of-sebastiscus-marmoratus-in-response-to-infection-with-the-parasitic-ciliate-cryptocaryon-irritans
#19
Fei Yin, Dong Qian
BACKGROUND: False kelpfish (Sebastiscus marmoratus) is one of the target species in artificial breeding in China, and is susceptible to infection by Cryptocaryon irritans, which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of S. marmoratus against C. irritans infection. METHODS: We carried out an extensive analysis of the transcriptome of S. marmoratus immune-related tissues...
November 21, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29157262/immunoproteomic-analysis-of-the-excretory-secretory-products-of-trichinella-pseudospiralis-adult-worms-and-newborn-larvae
#20
Yang Wang, Xue Bai, Haichao Zhu, Xuelin Wang, Haining Shi, Bin Tang, Pascal Boireau, Xuepeng Cai, Xuenong Luo, Mingyuan Liu, Xiaolei Liu
BACKGROUND: The nematode Trichinella pseudospiralis is an intracellular parasite of mammalian skeletal muscle cells and exists in a non-encapsulated form. Previous studies demonstrated that T. pseudospiralis could induce a lower host inflammatory response. Excretory-secretory (ES) proteins as the most important products of host-parasite interaction may play the main functional role in alleviating host inflammation. However, the ES products of T. pseudospiralis early stage are still unknown...
November 21, 2017: Parasites & Vectors
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