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https://www.readbyqxmd.com/read/28095400/computational-analysis-of-residue-interaction-networks-and-coevolutionary-relationships-in-the-hsp70-chaperones-a-community-hopping-model-of-allosteric-regulation-and-communication
#1
Gabrielle Stetz, Gennady M Verkhivker
Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28093458/single-cell-gene-expression-analysis-reveals-diversity-among-human-spermatogonia
#2
N Neuhaus, J Yoon, N Terwort, S Kliesch, J Seggewiss, A Huge, R Voss, S Schlatt, R V Grindberg, H R Schöler
STUDY QUESTION: Is the molecular profile of human spermatogonia homogeneous or heterogeneous when analysed at the single-cell level? SUMMARY ANSWER: Heterogeneous expression profiles may be a key characteristic of human spermatogonia, supporting the existence of a heterogeneous stem cell population. WHAT IS KNOWN ALREADY: Despite the fact that many studies have sought to identify specific markers for human spermatogonia, the molecular fingerprint of these cells remains hitherto unknown...
January 15, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28092515/towards-a-run-to-run-adaptive-artificial-pancreas-in-silico-results
#3
Chiara Toffanin, Roberto Visentin, Mirko Messori, Federico Di Palma, Lalo Magni, Claudio Cobelli
: Contemporary and future outpatient long-term artificial pancreas (AP) studies need to cope with the well-known large intra- and inter-day glucose variability occurring in type 1 diabetic (T1D) subjects. Here we propose an adaptive Model Predictive Control (MPC) strategy to account for it and test it in silico. METHODS: A Run-to-Run (R2R) approach adapts the subcutaneous basal insulin delivery during the night and the carbohydrate-to-insulin ratio (CR) during the day, based on some performance indices calculated from subcutaneous continuous glucose sensor data...
January 11, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28090219/integrated-microfluidic-aptasensor-for-mass-spectrometric-detection-of-vasopressin-in-human-plasma-ultrafiltrate
#4
J Yang, J Zhu, R Pei, J A Oliver, D W Landry, M N Stojanovic, Q Lin
We present a microfluidic aptamer-based biosensor for detection of low-molecular-weight biomarkers in patient samples. Using a microfluidic device that integrates aptamer-based specific analyte extraction, isocratic elution, and detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, we demonstrate rapid, sensitive and label-free detection of arginine vasopressin (AVP) in human plasma ultrafiltrate. AVP molecules in complex matrices are specifically captured by an aptamer that is immobilized on microbeads via affinity binding in a microchamber...
July 14, 2016: Analytical Methods: Advancing Methods and Applications
https://www.readbyqxmd.com/read/28089917/micrornas-and-dicer1-are-regulated-by-1-25-dihydroxyvitamin-d-in-prostate-stroma
#5
Shweta Dambal, Angeline A Giangreco, Andres M Acosta, Andrew Fairchild, Zachary Richards, Ryan Deaton, Dennis Wagner, Reinhold Vieth, Peter H Gann, Andre Kajdacsy-Balla, Theodorus Van der Kwast, Larisa Nonn
Vitamin D deficiency increases the risk of lethal prostate adenocarcinomas (PCa) and the majority of older men are deficient. Although PCa arises from the epithelium, the surrounding stroma has hormonal regulatory control over the epithelium and contributes to carcinogenesis. Herein, we describe regulation of microRNAs (miRs) by the active hormone dihydroxyvitamin D (1,25(OH)2D) in human prostate stroma. 1,25(OH)2D binds the vitamin D receptor (VDR) transcription factor to regulate gene expression, including miRs, which have emerged as potent regulators of protein expression...
January 12, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28089213/a-genome-wide-profiling-of-brain-dna-hydroxymethylation-in-alzheimer-s-disease
#6
Jinying Zhao, Yun Zhu, Jingyun Yang, Lin Li, Hao Wu, Philip L De Jager, Peng Jin, David A Bennett
INTRODUCTION: DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS: Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology...
January 6, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28087055/graft-modification-of-cotton-with-phosphate-group-and-its-application-to-the-enrichment-of-phosphopeptides
#7
Xiao-Mei He, Xi Chen, Bi-Feng Yuan, Yu-Qi Feng
Grafting copolymerization, especially "grafting from" approach, has attracted a great attention for the preparation of cellulose-based materials with various functionalities. In this study, a novel phosphate group-containing cotton fiber-based material, CF-NH2-AZO-p(VPA-x), was successfully synthesized by a "grafting from" radical polymerization approach using vinyl phosphonic acid (VPA) as monomer. The phosphate group content of CF-NH2-AZO-p(VPA-x) could be easily regulated by adjusting the concentration of VPA monomer...
January 9, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28075563/particulate-formation-from-a-copper-oxide-based-oxygen-carrier-in-chemical-looping-combustion-for-co2-capture
#8
Feng He, William Patrick Linak, Shuang Deng, Fanxing Li
Attrition behavior and particle loss of a copper oxide-based oxygen carrier from a methane chemical looping combustion (CLC) process was investigated in a fluidized bed reactor. The aerodynamic diameters of most elutriated particulates, after passing through a horizontal settling duct, range between 2 and 5 μm. A notable number of submicron particulates are also identified. Oxygen carrier attrition was observed to lead to increased CuO loss resulting from the chemical looping reactions, i.e., Cu is enriched in small particles generated primarily from fragmentation in the size range of 10-75 μm...
January 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28070340/civil-society-engagement-in-multi-stakeholder-dialogue-a-qualitative-study-exploring-the-opinions-and-perceptions-of-meta-members
#9
Gemma L Buckland-Merrett, Catherine Kilkenny, Tim Reed
BACKGROUND: The Medicines Transparency Alliance (MeTA) is an initiative that brings together all stakeholders in the medicines market to create a multi-stakeholder dialogue and improve access, availability and affordability of medicines. Key to this multi-stakeholder dialogue is the participation of Civil Society Organisations. A recent MeTA annual review, identified uneven engagement of civil society organisations in the multi-stakeholder process. This study was designed to explore the engagement of Civil Society Organisations in the MeTA multi-stakeholder process and the factors influencing their participation...
2017: Journal of Pharmaceutical Policy and Practice
https://www.readbyqxmd.com/read/28068756/hydrophilic-mesoporous-silica-materials-for-highly-specific-enrichment-of-n-linked-glycopeptide
#10
Nianrong Sun, Jiawen Wang, Jizong Yao, Chun-Hui Deng
Hydrophilic interaction liquid chromatography (HILIC) is a significant enrichment strategy in glycoproteomics profiling. In this report, hydrophilic magnetic mesoporous silica materials (Fe3O4@mSiO2-IDA) were designed and synthesized as an outstanding enrichment platform for glycopeptide analysis. By taking advantage of their merits, such as large surface area, excellent hydrophilicity and unbiased affinity toward all types of glycopeptides, the Fe3O4@mSiO2-IDA nanomaterials were successfully applied to capture glycopeptides from complex samples...
January 4, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28068078/enriching-nanoparticles-via-acoustofluidics
#11
Zhangming Mao, Peng Li, Mengxi Wu, Hunter Bachman, Nicolas Mesyngier, Xiasheng Guo, Sheng Liu, Francesco Costanzo, Tony Jun Huang
Focusing and enriching submicrometer and nanometer scale objects is of great importance for many applications in biology, chemistry, engineering, and medicine. Here, we present an acoustofluidic chip that can generate single vortex acoustic streaming inside a glass capillary through using low-power acoustic waves (only 5 V is required). The single vortex acoustic streaming that is generated, in conjunction with the acoustic radiation force, is able to enrich submicrometer- and nanometer-sized particles in a small volume...
January 9, 2017: ACS Nano
https://www.readbyqxmd.com/read/28067918/structural-insights-into-the-secretin-translocation-channel-in-the-type-ii-secretion-system
#12
Zhaofeng Yan, Meng Yin, Dandan Xu, Yongqun Zhu, Xueming Li
The secretin GspD of the type II secretion system (T2SS) forms a channel across the outer membrane in Gram-negative bacteria to transport substrates from the periplasm to the extracellular milieu. The lack of an atomic-resolution structure of the GspD channel hinders the investigation of substrate translocation mechanism of T2SS. Here we report cryo-EM structures of two GspD channels (∼1 MDa), from Escherichia coli K12 and Vibrio cholerae, at ∼3 Å resolution. The structures reveal a pentadecameric channel architecture, wherein three rings of GspD N domains form the periplasmic channel...
January 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28058811/proteomic-characterization-of-microdissected-breast-tissue-environment-provides-a-protein-level-overview-of-malignant-transformation
#13
René B H Braakman, Christoph Stingl, Madeleine M A Tilanus-Linthorst, Carolien H M Deurzen, Mieke A M Timmermans, Marcel Smid, John A Foekens, Theo M Luider, John W M Martens, Arzu Umar
Both healthy and cancerous breast tissue is heterogeneous, which is a bottle-neck for proteomics-based biomarker analysis, as it obscures the cellular origin of a measured protein. We therefore aimed at obtaining a protein-level interpretation of malignant transformation through global proteome analysis of a variety of laser capture microdissected cells originating from benign and malignant breast tissues. We compared proteomic differences between these tissues, both from cells of epithelial origin and the stromal environment, and performed string analysis...
January 5, 2017: Proteomics
https://www.readbyqxmd.com/read/28057745/reciprocal-insulation-analysis-of-hi-c-data-shows-that-tads-represent-a-functionally-but-not-structurally-privileged-scale-in-the-hierarchical-folding-of-chromosomes
#14
Yinxiu Zhan, Luca Mariani, Iros Barozzi, Edda G Schulz, Nils Bluthgen, Michael Stadler, Guido Tiana, Luca Giorgetti
Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions...
January 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28057026/advances-in-rare-cell-isolation-an-optimization-and-evaluation-study
#15
Stefan Schreier, Piamsiri Sawaisorn, Rachanee Udomsangpetch, Wannapong Triampo
BACKGROUND: Rare nucleated CD45 negative cells in peripheral blood may be malignant such as circulating tumor cells. Untouched isolation thereof by depletion of normal is favored yet still technological challenging. We optimized and evaluated a novel magnetic bead-based negative selection approach for enhanced enrichment of rare peripheral blood nucleated CD45 negative cells and investigated the problem of rare cell contamination during phlebotomy. METHODS: Firstly, the performance of the magnetic cell separation system was assessed using leukocytes and cultivated fibroblast cells in regard to depletion efficiency and the loss of cells of interest...
January 5, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#16
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28044981/differential-methylation-between-ethnic-sub-groups-reflects-the-effect-of-genetic-ancestry-and-environmental-exposures
#17
Joshua M Galanter, Christopher R Gignoux, Sam S Oh, Dara Torgerson, Maria Pino-Yanes, Neeta Thakur, Celeste Eng, Donglei Hu, Scott Huntsman, Harold J Farber, Pedro C Avila, Emerita Brigino-Buenaventura, Michael A LeNoir, Kelly Meade, Denise Serebrisky, William Rodríguez-Cintrón, Rajesh Kumar, Jose R Rodríguez-Santana, Max A Seibold, Luisa N Borrell, Esteban G Burchard, Noah Zaitlen
Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75...
3, 2017: ELife
https://www.readbyqxmd.com/read/28018390/emerging-technologies-for-the-production-of-renewable-liquid-transport-fuels-from-biomass-sources-enriched-in-plant-cell-walls
#18
REVIEW
Hwei-Ting Tan, Kendall R Corbin, Geoffrey B Fincher
Plant cell walls are composed predominantly of cellulose, a range of non-cellulosic polysaccharides and lignin. The walls account for a large proportion not only of crop residues such as wheat straw and sugarcane bagasse, but also of residues of the timber industry and specialist grasses and other plants being grown specifically for biofuel production. The polysaccharide components of plant cell walls have long been recognized as an extraordinarily large source of fermentable sugars that might be used for the production of bioethanol and other renewable liquid transport fuels...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28012241/a-rapid-differential-display-analysis-of-nasal-swab-fingerprints-to-distinguish-allergic-from-non-allergic-rhinitis-subjects-by-mesoporous-silica-particles-and-maldi-tof-mass-spectrometry
#19
Nicola Lombardo, Mariaimmacolata Preianò, Giuseppina Maggisano, Maria Stella Murfuni, Luigi Messina, Girolamo Pelaia, Rocco Savino, Rosa Terracciano
Discriminating different rhinitis cases can sometimes be difficult as the diagnostic criteria used to identify the various subgroups are not always unambiguous. The nasal fluid (NF) highly reflects the pathophysiology of these inflammatory diseases. However, its collection, as nasal lavage fluid (NLF), may cause discomfort. Due to the non-invasiveness and rapidity of collection, nasal swab might represents an alternative to overcome these problems and also an ideal source of biomarkers. In this study we demonstrate that the combined use of mesoporous silica (MPS) with MALDI-TOF MS allows the rapid detection of differential nasal peptide profiles from nasal swabs of healthy (H), allergic rhinitis (AR) and non-allergic rhinitis (NAR) subjects...
December 23, 2016: Proteomics
https://www.readbyqxmd.com/read/28012110/enrichment-of-serum-biomarkers-by-magnetic-metal-organic-framework-composites
#20
Ji-Ping Wei, Heng Wang, Tao Luo, Zhi-Jiang Zhou, Yan-Feng Huang, Bin Qiao
Highly efficient extraction of peptides from serum is critical for finding serum biomarkers using mass spectrometry, which still remains a great challenge. Currently, a bottom-up proteomics approach has been applied to discover serum biomarkers. However, the approach was labor intensive, time and cost consuming, and cannot meet the requirements for clinical application. In this work, Fe3O4/C@MIL-100 composites were synthesized to efficiently capture peptides from microwave-assisted formic acid digests of BSA and human serum prior to MALDI-TOF MS analysis...
December 23, 2016: Analytical and Bioanalytical Chemistry
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