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https://www.readbyqxmd.com/read/28811264/protein-coding-genes-as-hosts-for-noncoding-rna-expression
#1
REVIEW
Vincent Boivin, Gabrielle Deschamps-Francoeur, Michelle S Scott
With the emergence of high-throughput sequence characterization methods and the subsequent improvements in gene annotations, it is becoming increasingly clear that a large proportion of eukaryotic protein-coding genes (as many as 50% in human) serve as host genes for non-coding RNA genes. Amongst the most extensively characterized embedded non-coding RNA genes, small nucleolar RNAs and microRNAs represent abundant families. Encoded individually or clustered, in sense or antisense orientation with respect to their host and independently expressed or dependent on host expression, the genomic characteristics of embedded genes determine their biogenesis and the extent of their relationship with their host gene...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28810832/genome-wide-analysis-of-basic-helix-loop-helix-bhlh-transcription-factors-in-brachypodium-distachyon
#2
Xin Niu, Yuxiang Guan, Shoukun Chen, Haifeng Li
BACKGROUND: As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS: A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28809826/high-throughput-screening-for-protein-based-inheritance-in-s-cerevisiae
#3
James S Byers, Daniel F Jarosz
The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived inheritance encoded in protein conformation (rather than sequence) has long been viewed as paradigm-shifting but rare. The best characterized examples of such epigenetic elements are prions, which possess a self-assembling behavior that can drive the heritable manifestation of new phenotypes. Many archetypal prions display a striking N/Q-rich sequence bias and assemble into an amyloid fold...
August 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28808998/microfluidics-mass-spectrometry-of-protein-carbohydrate-interactions-applications-to-the-development-of-therapeutics-and-biomarker-discovery
#4
Alina D Zamfir
The functional interactions of carbohydrates and their protein receptors are the basis of biological events critical to the evolution of pathological states. Hence, for the past years, such interactions have become the focus of research for the development of therapeutics and discovery of novel glycan biomarkers based on their binding affinity. Due to the high sensitivity, throughput, reproducibility, and capability to ionize minor species in heterogeneous mixtures, microfluidics-mass spectrometry (MS) has recently emerged as a method of choice in protein-glycan interactomics...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28804569/dynamic-registration-for-gigapixel-serial-whole-slide-images
#5
Blair J Rossetti, Fusheng Wang, Pengyue Zhang, George Teodoro, Daniel J Brat, Jun Kong
High-throughput serial histology imaging provides a new avenue for the routine study of micro-anatomical structures in a 3D space. However, the emergence of serial whole slide imaging poses a new registration challenge, as the gigapixel image size precludes the direct application of conventional registration techniques. In this paper, we develop a three-stage registration with multi-resolution mapping and propagation method to dynamically produce registered subvolumes from serial whole slide images. We validate our algorithm with gigapixel images of serial brain tumor sections and synthetic image volumes...
April 2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
https://www.readbyqxmd.com/read/28802868/development-and-implementation-of-an-ultrasound-guided-peripheral-intravenous-catheter-program-for-emergency-nurses
#6
Courtney Edwards, Jodi Jones
PROBLEM: Emergency medical care often necessitates placement of peripheral intravenous (PIV) catheters. When traditional methods for obtaining PIV access are not successful, ultrasound guidance is a rescue technique for peripheral vascular placement that improves the quality of patient care. METHODS: The aim of this training program was to develop a process where emergency nurses would be competent to perform ultrasound guided PIV to improve the quality of patient care delivered while reducing throughput time...
August 9, 2017: Journal of Emergency Nursing: JEN: Official Publication of the Emergency Department Nurses Association
https://www.readbyqxmd.com/read/28802624/a-portable-real-time-in-situ-gamma-ray-analysis-system
#7
Cong Wei, Kelly Garnick, Thomas Scott, Elon Malkin, Jennifer Szymanski, Steve Laskos, Jeffrey Raimondi, James Cocks, Kara Morris, Wilhelm Mueller, James Zickefoose
A portable CeBr3 based gamma-ray detection system was designed and built for rapid turnaround, high throughput, real-time, and in situ sample analysis. The new technique allows automated data transmission from the field unit to a central laboratory controller to ensure laboratory quality of the data collected by field users without gamma-ray spectroscopy expertise. The method validation data indicates that the system's data quality objectives are adequate for radiological or nuclear emergency response or targeted surveillance programs where gamma-ray analysis is needed...
August 2, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28799506/antibody-epitope-analysis-to-investigate-folded-structure-allosteric-conformation-and-evolutionary-lineage-of-proteins
#8
Sienna Wong, J-P Jin
Study of folded structure of proteins provides insights into their biological functions, conformational dynamics and molecular evolution. Current methods of elucidating folded structure of proteins are laborious, low-throughput, and constrained by various limitations. Arising from these methods is the need for a sensitive, quantitative, rapid and high-throughput method not only analyzing the folded structure of proteins, but also to monitor dynamic changes under physiological or experimental conditions. In this focused review, we outline the foundation and limitations of current protein structure-determination methods prior to discussing the advantages of an emerging antibody epitope analysis for applications in structural, conformational and evolutionary studies of proteins...
August 11, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28798873/a-novel-viral-lineage-distantly-related-to-herpesviruses-discovered-within-fish-genome-sequence-data
#9
Amr Aswad, Aris Katzourakis
Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28795660/systems-and-synthetic-biology-perspective-of-the-versatile-plant-pathogenic-and-polysaccharide-producing-bacterium-xanthomonas-campestris
#10
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features...
August 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28795201/downstream-processing-technologies-capturing-and-final-purification-opportunities-for-innovation-change-and-improvement-a-review-of-downstream-processing-developments-in-protein-purification
#11
Nripen Singh, Sibylle Herzer
Increased pressure on upstream processes to maximize productivity has been crowned with great success, although at the cost of shifting the bottleneck to purification. As drivers were economical, focus is on now on debottlenecking downstream processes as the main drivers of high manufacturing cost. Devising a holistically efficient and economical process remains a key challenge. Traditional and emerging protein purification strategies with particular emphasis on methodologies implemented for the production of recombinant proteins of biopharmaceutical importance are reviewed...
August 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28794488/nanogrid-single-nucleus-rna-sequencing-reveals-phenotypic-diversity-in-breast-cancer
#12
Ruli Gao, Charissa Kim, Emi Sei, Theodoros Foukakis, Nicola Crosetto, Leong-Keat Chan, Maithreyan Srinivasan, Hong Zhang, Funda Meric-Bernstam, Nicholas Navin
Single cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop a high-throughput 3' single-nucleus RNA sequencing approach that combines nanogrid technology, automated imaging, and cell selection to sequence up to ~1800 single nuclei in parallel. We compare the transcriptomes of 485 single nuclei to 424 single cells in a breast cancer cell line, which shows a high concordance (93...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28790328/desiccation-tolerance-in-bryophytes-the-dehydration-and-rehydration-transcriptomes-in-the-desiccation-tolerant-bryophyte-bryum-argenteum
#13
Bei Gao, Xiaoshuang Li, Daoyuan Zhang, Yuqing Liang, Honglan Yang, Moxian Chen, Yuanming Zhang, Jianhua Zhang, Andrew J Wood
The desiccation tolerant bryophyte Bryum argenteum is an important component of desert biological soil crusts (BSCs) and is emerging as a model system for studying vegetative desiccation tolerance. Here we present and analyze the hydration-dehydration-rehydration transcriptomes in B. argenteum to establish a desiccation-tolerance transcriptomic atlas. B. argenteum gametophores representing five different hydration stages (hydrated (H0), dehydrated for 2 h (D2), 24 h (D24), then rehydrated for 2 h (R2) and 48 h (R48)), were sampled for transcriptome analyses...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790144/impact-of-physician-navigators-on-productivity-indicators-in-the-ed
#14
Alexander K Leung, Gaurav Puri, Bingshu E Chen, Zhenxian Gong, Eddie Chan, Edward Feng, Marko Duic
OBJECTIVES: We created Physician Navigators in our ED to help improve emergency physician (EP) productivity. We aimed to quantify the effect of Physician Navigators on measures of EP productivity: patient seen per hour (Pt/hr), and turn-around time (TAT) to discharge. Secondary objectives included examining their impact on measures of ED throughput for non-resuscitative patients: ED length of stay (LOS), door-to-physician time and left-without-being-seen rates (LWBS). METHODS: In this retrospective study, 6845 clinical shifts worked by 20 EPs at a community ED in Newmarket, Canada from 1 January 2012 to 31 March 2015 were evaluated...
August 8, 2017: Emergency Medicine Journal: EMJ
https://www.readbyqxmd.com/read/28789584/monoclonal-antibodies-technologies-for-early-discovery-and-engineering
#15
Patrick J Kennedy, Carla Oliveira, Pedro L Granja, Bruno Sarmento
Antibodies are essential in modern life sciences biotechnology. Their architecture and diversity allow for high specificity and affinity to a wide array of biochemicals. Combining monoclonal antibody (mAb) technology with recombinant DNA and protein expression links antibody genotype with phenotype. Yet, the ability to select and screen for high affinity binders from recombinantly-displayed, combinatorial libraries unleashes the true power of mAbs and a flood of clinical applications. The identification of novel antibodies can be accomplished by a myriad of in vitro display technologies from the proven (e...
August 8, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28780386/salivary-microbiome-in-non-oral-disease-a-summary-of-evidence-and-commentary
#16
REVIEW
Aneesha Acharya, Yuki Chan, Supriya Kheur, Li Jian Jin, Rory M Watt, Nikos Mattheos
OBJECTIVE: The advent of high-throughput sequencing and 'omic' technologies is facilitating an 'open-ended' understanding of the human microbial community and its interplay with health. This commentary aims to present key perspectives and summarize current evidence from metagenomic studies of salivary microbiota in relation to general health and systemic diseases. DESIGN: A narrative review of studies that described salivary microbiome composition in relation to various general health conditions was conducted and the main results were summarized...
July 29, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28771006/continuous-hydrothermal-synthesis-of-inorganic-nanoparticles-applications-and-future-directions
#17
Jawwad A Darr, Jingyi Zhang, Neel M Makwana, Xiaole Weng
Nanomaterials are at the leading edge of the emerging field of nanotechnology. Their unique and tunable size-dependent properties (in the range 1-100 nm) make these materials indispensable in many modern technological applications. In this Review, we summarize the state-of-art in the manufacture and applications of inorganic nanoparticles made using continuous hydrothermal flow synthesis (CHFS) processes. First, we introduce ideal requirements of any flow process for nanoceramics production, outline different approaches to CHFS, and introduce the pertinent properties of supercritical water and issues around mixing in flow, to generate nanoparticles...
August 3, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28769905/high-throughput-chemical-screening-identifies-compounds-that-inhibit-different-stages-of-the-phytophthora-agathidicida-and-phytophthora-cinnamomi-life-cycles
#18
Scott A Lawrence, Charlotte B Armstrong, Wayne M Patrick, Monica L Gerth
Oomycetes in the genus Phytophthora are among the most damaging plant pathogens worldwide. Two important species are Phytophthora cinnamomi, which causes root rot in thousands of native and agricultural plants, and Phytophthora agathidicida, which causes kauri dieback disease in New Zealand. As is the case for other Phytophthora species, management options for these two pathogens are limited. Here, we have screened over 100 compounds for their anti-oomycete activity, as a potential first step toward identifying new control strategies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28768924/a-novel-high-throughput-virtual-screening-protocol-to-discover-new-indoleamine-2-3-dioxygenase-1-ido1-inhibitors
#19
Haojie Xu, Yunlong Song, Qing Yang
Indoleamine 2,3-dioxygenase 1 (IDO1) plays an important role in the immune escape of tumors and has emerged as a promising target for cancer immunotherapy. Despite its potential in immuno-oncology, very few chemotypes have been reported to date. Here, we disigned a novel high throughput virtual screening (HTVS) cascade protocol, combining both pharmacophore modeling and molecular docking and it was employed to query commercially available compounds to identify novel inhibitors. Among the 23 compounds selected for the in vitro IDO1 inhibitory activity assay, five compounds exhibit greater than 20% inhibition at a test concentration of 10 µM, with two compounds having an IC50 value of 23...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28767065/do-multiwell-plate-high-throughput-assays-measure-loss-of-cell-viability-following-exposure-to-genotoxic-agents
#20
Razmik Mirzayans, Bonnie Andrais, David Murray
Cell-based assays in multiwell plates are widely used for radiosensitivity and chemosensitivity assessment with different mammalian cell types. Despite their relative ease of performance, such assays lack specificity as they do not distinguish between the cytostatic (reversible/sustained growth arrest) and cytotoxic (loss of viability) effects of genotoxic agents. We recently reported studies with solid tumor-derived cell lines demonstrating that radiosensitivity as measured by multiwell plate colorimetric (e...
August 2, 2017: International Journal of Molecular Sciences
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