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https://www.readbyqxmd.com/read/28423944/emerging-roles-of-long-non-coding-rnas-in-plant-response-to-biotic-and-abiotic-stresses
#1
Naghmeh Nejat, Nitin Mantri
Spectacular progress in high-throughput transcriptome sequencing and expression profiling using next-generation sequencing technologies have recently revolutionized molecular biology and allowed massive advances in identifying the genomic regions and molecular mechanisms underlying transcriptional regulation of growth, development, and stress response. Through recent research, non-coding RNAs, in particular long non-coding RNAs, have emerged as key regulators of transcription in eukaryotes. Long non-coding RNAs are vastly heterogeneous groups of RNAs that execute a broad range of essential roles in various biological processes at the epigenetic, transcriptional, and post-transcriptional levels...
April 20, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28420614/applications-of-genome-editing-tools-in-precision-medicine-research
#2
Li Shuang, Yang Yuanyuan, Qiu Yan, Chen Yanhao, Xu Luwei, Ding Qiurong
The emergence of genome editing tools, such as the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, has enabled researchers to achieve somatic and germline genomic manipulations in cell lines and model organisms. Within a couple of years, genome editing is now being rapidly developed for multiple applications and widely used in biomedical researches, including creation of disease models with desired genetic mutations, screening in a high-throughput manner for drug resistance genes, and making appropriate editions to genes in vivo for disease treatment...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28410032/predicting-responses-to-contemporary-environmental-change-using-evolutionary-response-architectures
#3
Rachael A Bay, Noah Rose, Rowan Barrett, Louis Bernatchez, Cameron K Ghalambor, Jesse R Lasky, Rachel B Brem, Stephen R Palumbi, Peter Ralph
Rapid environmental change currently presents a major threat to global biodiversity and ecosystem functions, and understanding impacts on individual populations is critical to creating reliable predictions and mitigation plans. One emerging tool for this goal is high-throughput sequencing technology, which can now be used to scan the genome for signs of environmental selection in any species and any system. This explosion of data provides a powerful new window into the molecular mechanisms of adaptation, and although there has been some success in using genomic data to predict responses to selection in fields such as agriculture, thus far genomic data are rarely integrated into predictive frameworks of future adaptation in natural populations...
May 2017: American Naturalist
https://www.readbyqxmd.com/read/28402686/the-creation-and-implementation-of-an-outpatient-pulmonary-embolism-treatment-protocol
#4
Christopher Kabrhel, Rachel Rosovsky, Christopher Baugh, Blair Alden Parry, Erin Deadmon, Charlotte Kreger, Nicholas Giordano
The ability to rapidly and accurately risk-stratify patients with venous thromboembolism (VTE), and the availability of direct acting oral anticoagulants have reduced the need for intravenous anticoagulation for patients with deep vein thrombosis (DVT) and pulmonary embolism (PE). Emergency physicians are generally reluctant to discharge patients with VTE without defined and reliable follow up in place, and VTE patients treated with anticoagulants can be at risk for complications related to recurrent VTE and bleeding...
April 21, 2017: Hospital Practice (Minneapolis)
https://www.readbyqxmd.com/read/28402221/an-update-on-the-use-of-c-elegans-for-preclinical-drug-discovery-screening-and-identifying-anti-infective-drugs
#5
Wooseong Kim, Gabriel Lambert Hendricks, Kiho Lee, Eleftherios Mylonakis
The emergence of antibiotic-resistant and -tolerant bacteria is a major threat to human health. Although efforts for drug discovery are ongoing, conventional bacteria-centered screening strategies have thus far failed to yield new classes of effective antibiotics. Therefore, new paradigms for discovering novel antibiotics are of critical importance. Caenorhabditis elegans, a model organism used for in vivo, offers a promising solution for identification of anti-infective compounds. Areas covered:This review examines the advantages of C...
April 12, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28401169/epigenetic-regulations-in-diabetic-nephropathy
#6
REVIEW
Zeyuan Lu, Na Liu, Feng Wang
Diabetic nephropathy (DN) is a chronic complication of diabetes and the most common cause of end-stage kidney disease. It has been reported that multiple factors are involved in the pathogenesis of DN, while the molecular mechanisms that lead to DN are still not fully understood. Numerous risk factors for the development of diabetic nephropathy have been proposed, including ethnicity and inherited genetic differences. Recently, with the development of high-throughput technologies, there is emerging evidence that suggests the important role of epigenetic mechanisms in the pathogenesis of DN...
2017: Journal of Diabetes Research
https://www.readbyqxmd.com/read/28400754/mineral-ecology-surface-specific-colonization-and-geochemical-drivers-of-biofilm-accumulation-composition-and-phylogeny
#7
Aaron A Jones, Philip C Bennett
This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70-90% of the variance in phylogenetic diversity regardless of environmental pressures...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28400082/immune-dysregulation-in-immunodeficiency-disorders-the-role-of-t-cell-receptor-sequencing
#8
REVIEW
Gabriel K Wong, James M Heather, Sara Barmettler, Mark Cobbold
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency...
April 8, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28396820/a-plasmid-library-of-full-length-zebrafish-rab-proteins-for-in-vivo-cell-biology
#9
REVIEW
Thomas E Hall, Nick Martel, Harriet P Lo, Zherui Xiong, Robert G Parton
The zebrafish is an emerging model for highly sophisticated medium-throughput experiments such as genetic and chemical screens. However, studies of entire protein families within this context are often hampered by poor genetic resources such as clone libraries. Here we describe a complete collection of 76 full-length open reading frame clones for the zebrafish rab protein family. While the mouse genome contains 60 rab genes and the human genome 63, we find that 18 zebrafish rab genes have 2, and in the case of rab38, 3 paralogues...
2017: Cellular Logistics
https://www.readbyqxmd.com/read/28396124/lactobacilli-and-pediococci-as-versatile-cell-factories-evaluation-of-strain-properties-and-genetic-tools
#10
REVIEW
Elleke F Bosma, Jochen Forster, Alex Toftgaard Nielsen
This review discusses opportunities and bottlenecks for cell factory development of Lactic Acid Bacteria (LAB), with an emphasis on lactobacilli and pediococci, their metabolism and genetic tools. In order to enable economically feasible bio-based production of chemicals and fuels in a biorefinery, the choice of product, substrate and production organism is important. Currently, the most frequently used production hosts include Escherichia coli and Saccharomyces cerevisiae, but promising examples are available of alternative hosts such as LAB...
April 7, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28393677/in-silico-high-throughput-virtual-screening-and-molecular-dynamics-simulation-study-to-identify-inhibitor-for-adeabc-efflux-pump-of-acinetobacter-baumannii
#11
Privita Verma, Monalisa Tiwari, Vishvanath Tiwari
Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT etc...
April 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28392481/protein-array-based-approaches-for-biomarker-discovery-in-cancer
#12
REVIEW
Yi Huang, Heng Zhu
Biomarkers are deemed to be potential tools in early diagnosis, therapeutic monitoring, and prognosis evaluation for cancer, with simplicity as well as economic advantages compared with computed tomography and biopsy. However, most of current cancer biomarkers present insufficient sensitivity as well as specificity. Therefore, there is urgent requirement for the discovery of biomarkers for cancer. As one of the most exciting emerging technologies, protein array provides a versatile and robust platform in cancer proteomics research because it shows tremendous advantages of miniaturized features, high throughput, and sensitive detections in last decades...
April 6, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392047/monitoring-drug-serum-protein-interactions-for-early-adme-prediction-through-surface-plasmon-resonance-technology
#13
Edoardo Fabini, U Helena Danielson
Many molecules fail to reach the market due to poor pharmacokinetic (PK) properties, rendering the potential drug virtually unavailable for the primary target despite efficient administration to the body. PK properties of endogenous and exogenous compounds in mammals are dependent, among other factors, on their ability to interact with serum proteins. The extent of binding can greatly influence their ADME (adsorption, distribution, metabolism and execration) profile. Reliable and cost-effective bioavailability studies, early in the drug discovery process, can lead to an improvement of the success rate for compounds entering clinical trials...
March 28, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28389595/cancer-immunogenomics-computational-neoantigen-identification-and-vaccine-design
#14
Jasreet Hundal, Christopher A Miller, Malachi Griffith, Obi L Griffith, Jason Walker, Susanna Kiwala, Aaron Graubert, Joshua McMichael, Adam Coffman, Elaine R Mardis
The application of modern high-throughput genomics to the study of cancer genomes has exploded in the past few years, yielding unanticipated insights into the myriad and complex combinations of genomic alterations that lead to the development of cancers. Coincident with these genomic approaches have been computational analyses that are capable of multiplex evaluations of genomic data toward specific therapeutic end points. One such approach is called "immunogenomics" and is now being developed to interpret protein-altering changes in cancer cells in the context of predicted preferential binding of these altered peptides by the patient's immune molecules, specifically human leukocyte antigen (HLA) class I and II proteins...
April 7, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28388542/emerging-proteomics-biomarkers-and-prostate-cancer-burden-in-africa
#15
REVIEW
Henry A Adeola, Jonathan M Blackburn, Timothy R Rebbeck, Luiz F Zerbini
Various biomarkers have emerged via high throughput omics-based approaches for use in diagnosis, treatment, and monitoring of prostate cancer. Many of these have yet to be demonstrated as having value in routine clinical practice. Moreover, there is a dearth of information on validation of these emerging prostate biomarkers within African cohorts, despite the huge burden and aggressiveness of prostate cancer in men of African descent. This review focusses of the global landmark achievements in prostate cancer proteomics biomarker discovery and the potential for clinical implementation of these biomarkers in Africa...
March 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28388465/synthetic-rna-based-switches-for-mammalian-gene-expression-control
#16
REVIEW
Simon Ausländer, Martin Fussenegger
Synthetic ribonucleic acid (RNA)-based gene switches control RNA functions in a ligand-responsive manner. Key building blocks are aptamers that specifically bind to small molecules or protein ligands. Engineering approaches often combine rational design and high-throughput screening to identify optimal connection sites or sequences. In this report, we discuss basic principles and emerging design strategies for the engineering of RNA-based gene switches in mammalian cells. Their small size compared with those of transcriptional gene switches, together with advancements in design strategies and performance, may bring RNA-based switches to the forefront of biomedical and biotechnological applications...
April 4, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28385420/less-is-more-efficacy-of-rapid-3d-t2-space-in-ed-patients-with-acute-atypical-low-back-pain
#17
Nicholas A Koontz, Richard H Wiggins, Megan K Mills, Michael S McLaughlin, Elaine C Pigman, Yoshimi Anzai, Lubdha M Shah
RATIONALE AND OBJECTIVES: Emergency department (ED) patients with acute low back pain (LBP) may present with ambiguous clinical findings that pose diagnostic challenges to exclude cauda equina syndrome (CES). As a proof of concept, we aimed to determine the efficacy of a rapid lumbar spine (LS) magnetic resonance imaging (MRI) screening protocol consisting of a single 3D-T2 SPACE FS (3D-T2 Sampling Perfection with Application optimized Contrasts using different flip angle Evolution fat saturated) sequence relative to conventional LS MRI to exclude emergently treatable pathologies in this complex patient population...
April 3, 2017: Academic Radiology
https://www.readbyqxmd.com/read/28384412/second-era-of-omics-in-caries-research-moving-past-the-phase-of-disillusionment
#18
M M Nascimento, E Zaura, A Mira, N Takahashi, J M Ten Cate
Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries...
April 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28383500/a-qos-optimization-approach-in-cognitive-body-area-networks-for-healthcare-applications
#19
Tauseef Ahmed, Yannick Le Moullec
Wireless body area networks are increasingly featuring cognitive capabilities. This work deals with the emerging concept of cognitive body area networks. In particular, the paper addresses two important issues, namely spectrum sharing and interferences. We propose methods for channel and power allocation. The former builds upon a reinforcement learning mechanism, whereas the latter is based on convex optimization. Furthermore, we also propose a mathematical channel model for off-body communication links in line with the IEEE 802...
April 6, 2017: Sensors
https://www.readbyqxmd.com/read/28383245/exploring-the-chemistry-of-genetic-information-storage-and-propagation-through-polymerase-engineering
#20
Gillian Houlihan, Sebastian Arangundy-Franklin, Philipp Holliger
Nucleic acids are a distinct form of sequence-defined biopolymer. What sets them apart from other biopolymers such as polypeptides or polysaccharides is their unique capacity to encode, store, and propagate genetic information (molecular heredity). In nature, just two closely related nucleic acids, DNA and RNA, function as repositories and carriers of genetic information. They therefore are the molecular embodiment of biological information. This naturally leads to questions regarding the degree of variation from this seemingly ideal "Goldilocks" chemistry that would still be compatible with the fundamental property of molecular heredity...
April 6, 2017: Accounts of Chemical Research
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