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https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#1
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28534297/single-frequency-impedance-analysis-on-reduced-graphene-oxide-screen-printed-electrode-for-biomolecular-detection
#2
Rajesh, Shobhita Singal, Ravinder K Kotnala
A biofunctionalized reduced graphene oxide (rGO)-modified screen-printed carbon electrode (SPCE) was constructed as an immunosensor for C-reactive protein (CRP) detection, a biomarker released in early stage acute myocardial infarction. A different approach of single frequency analysis (SFA) study was utilized for the biomolecular sensing, by monitoring the response in phase angle changes obtained at an optimized frequency resulting from antigen-antibody interactions. A set of measurements were carried out to optimize a frequency where a maximum change in phase angle was observed, and in this case, we found it at around 10 Hz...
May 22, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28532394/circularlogo-a-lightweight-web-application-to-visualize-intra-motif-dependencies
#3
Zhenqing Ye, Tao Ma, Michael T Kalmbach, Surendra Dasari, Jean-Pierre A Kocher, Liguo Wang
BACKGROUND: The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. RESULT: We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies...
May 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28530743/multicellular-tumor-invasion-and-plasticity-in-biomimetic-materials
#4
Susan E Leggett, Amanda S Khoo, Ian Y Wong
Cancer cell invasion through the extracellular matrix is associated with metastatic spread and therapeutic resistance. In carcinomas, the detachment and dissemination of individual cells has been associated with an epithelial-mesenchymal transition, but tumors can also invade using collective, multicellular phenotypes. This malignant tumor progression is also associated with alignment and stiffening of the surrounding extracellular matrix. Historically, tumor invasion has been investigated using 2D monolayer culture, small animal models or patient histology...
May 22, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28530340/-can-post-traumatic-stress-disorder-be-prevented-with-glucocorticoids
#5
REVIEW
Hagit Cohen, Zeev Kaplan, Joseph Zohar
Glucocorticoids (GCs) play a major role in orchestrating the complex physiological and behavioral reactions essential for the maintenance of homeostasis. These compounds enable the organism to prepare for, respond to and cope with the acute demands of physical and emotional stressors. The appropriate GC release, commensurate with stressor severity, enables the body to properly contain stress responses so as to promote recovery by rapidly restoring homeostasis. Indeed, inadequate GC release following stress not only delays recovery by disrupting biological homeostasis in the short run but can also interfere with the processing or interpretation of stressful information that results in long-term disruptions in memory integration...
December 2016: Harefuah
https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#6
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28529409/an-experimental-check-of-backscattering-interferometry
#7
Michael M Baksh, M G Finn
Backscattering interferometry (BSI) was used to determine the association constants for four well-known biomolecular interactions: protein A + IgG, trypsin + antitrypsin, trypsin + p-aminobenzamidine, and antithrombin + heparin. Each gave well-defined binding curves and Kd values in close agreement with published findings obtained using other techniques. These results stand in direct contrast to the claims in a 2015 publication in this journal (Discussion of "Back Scattering Interferometry revisited-a theoretical and experimental investigation" Jørgensen, T...
May 2017: Sensors and Actuators. B, Chemical
https://www.readbyqxmd.com/read/28523911/cup-shaped-nanoantenna-arrays-for-zeptoliter-volume-biochemistry-and-plasmonic-sensing-in-the-visible-wavelengths-range
#8
Rokas Drevinskas, Tomas Rakickas, Algirdas Selskis, Lorenzo Rosa, Ramunas Valiokas
Although three-dimensional shaping of metallic nanostructures is an important strategy for control and manipulation of localized surface plasmon resonance (LSPR), its implementation in high-throughput, on-chip fabrication of plasmonic devices remains to be challenging. Here we demonstrate nanocontact-based large area fabrication of a novel, LSPR-active Au architecture consisting of periodic arrays of reduced symmetry nanoantennas having sub-50 nm, out-of-plane features. Namely, by combining nanosphere and molecular self-assembly processes we have patterned evaporated polycrystalline Au films for chemical etching of nanocups with controlled aspect ratios (an outer diameter d=100 nm, void volumes of 18 or 39 zeptoliters)...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28521682/repurposing-of-copper-ii-chelating-drugs-for-the-treatment-of-neurodegenerative-diseases
#9
Valeria Lanza, Danilo Milardi, Giuseppe Di Natale, Giuseppe Pappalardo
BACKGROUND: There is mounting urgency to find new drugs for the treatment of neurodegenerative disorders. A large number of reviews has exhaustively described either the molecular or clinical aspects of neurodegenerative diseases as Alzheimer's (AD) and Parkinson's (PD). Conversely, reports outlining how known drugs in use for other diseases can be also effective as therapeutic agents in neurodegenerative diseases are less reported. This review focuses on the current uses of some copper(II) interacting molecules as potential drug candidates in neurodegeneration...
May 17, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28521258/synchrotron-based-x-ray-microscopy-for-sub-100nm-resolution-cell-imaging
#10
REVIEW
Ying Zhu, Jichao Zhang, Aiguo Li, Yuanqing Zhang, Chunhai Fan
Microscopic imaging provides a straightforward approach to deepen our understanding of cellular events. While the resolution of optical microscopes is generally limited to 200-300nm due to the diffraction limit, there has been ever growing interest in studying cells at the sub-100nm regime. By exploiting the short wavelength, long penetration depth and elemental specificity of X-rays, synchrotron-based X-ray microscopy (XRM) has demonstrated its power in exploring the structure and function of cells at the nanometer resolution...
May 15, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28520893/using-bayesian-modeling-in-frequentist-adaptive-enrichment-designs
#11
Noah Simon, Richard Simon
Our increased understanding of the mechanistic heterogeneity of diseases has pushed the development of targeted therapeutics. We do not expect all patients with a given disease to benefit from a targeted drug; only those in the target population. That is, those with sufficient dysregulation in the biomolecular pathway targeted by treatment. However, due to complexity of the pathway, and/or technical issues with our characterizing assay, it is often hard to characterize the target population until well into large-scale clinical trials...
May 17, 2017: Biostatistics
https://www.readbyqxmd.com/read/28520402/catch-and-release-engineered-allosterically-regulated-%C3%AE-roll-peptides-enable-on-off-biomolecular-recognition
#12
Beyza Bulutoglu, Kevin Dooley, Géza R Szilvay, Mark Blenner, Scott Banta
Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide...
May 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28516911/electrostatic-melting-in-a-single-molecule-field-effect-transistor-with-applications-in-genomic-identification
#13
Sefi Vernick, Scott M Trocchia, Steven B Warren, Erik F Young, Delphine Bouilly, Ruben L Gonzalez, Colin Nuckolls, Kenneth L Shepard
The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28511021/the-selectivity-challenge-in-organic-solvent-nanofiltration-membrane-and-process-solutions
#14
Patrizia Marchetti, Ludmila Peeva, Andrew Livingston
Recent development of organic solvent nanofiltration (OSN) materials has been overwhelmingly directed toward tight membranes with ultrahigh permeance. However, emerging research into OSN applications is suggesting that improved separation selectivity is at least as important as further increases in membrane permeance. Membrane solutions are being proposed to improve selectivity, mostly by exploiting solute/solvent/membrane interactions and by fabricating tailored membranes. Because achieving a perfect separation with a single membrane stage is difficult, process engineering solutions, such as membrane cascades, are also being advocated...
May 16, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28510311/rapid-microfluidic-dilution-for-single-molecule-spectroscopy-of-low-affinity-biomolecular-complexes
#15
Niels Zijlstra, Fabian Dingfelder, Bengt Wunderlich, Franziska Zosel, Stephan Benke, Daniel Nettels, Benjamin Schuler
To enable the investigation of low-affinity biomolecular complexes with confocal single-molecule spectroscopy, we have developed a microfluidic device that allows a concentrated sample to be diluted by up to five orders of magnitude within milliseconds, at the physical limit dictated by diffusion. We demonstrate the capabilities of the device by studying the dissociation kinetics and structural properties of low-affinity protein complexes using single-molecule two-color and three-color Förster resonance energy transfer (FRET)...
May 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28508788/kalis-an-ehealth-system-for-biomedical-risk-analysis-of-drugs
#16
Alban Shoshi, Ulrich Müller, Arben Shoshi, Venus Ogultarhan, Ralf Hofestädt
BACKGROUND: In Germany, adverse drug reactions and events cause hospitalizations, which lead to numerous thousands of deaths and several million Euros in additional health costs annually. OBJECTIVES: Approximately one in two deaths could be avoided by an appropriate system for risk analysis of drugs. METHODS: The integration and storage of several data sources from life sciences are an ongoing need to address various questions with respect to drug therapy...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28508366/isolation-and-proteomic-analysis-of-microvesicles-and-exosomes-from-ht22-cells-and-primary-neurons
#17
Richard Witas, Dale Chaput, Hirah Khan, Stanley M Stevens, David Kang
Exosomes and microvesicles are extracellular vesicles (EVs) released by most cell types. The role of EVs as a method of intercellular communication has led to these vesicles becoming a major area of interest in a variety of scientific fields including neuroscience. Emerging evidence is now demonstrating that the biomolecular composition of EVs, especially exosomes, can play a role in the progression of disease including various neurodegenerative diseases and cancer. In addition to the miRNA profiles of EVs, these vesicles also show interesting changes in protein expression profiles under different physiological and pathological conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508363/glycoproteins-enrichment-and-lc-ms-ms-glycoproteomics-in-central-nervous-system-applications
#18
Rui Zhu, Ehwang Song, Ahmed Hussein, Firas H Kobeissy, Yehia Mechref
Proteins and glycoproteins play important biological roles in central nervous systems (CNS). Qualitative and quantitative evaluation of proteins and glycoproteins expression in CNS is critical to reveal the inherent biomolecular mechanism of CNS diseases. This chapter describes proteomic and glycoproteomic approaches based on liquid chromatography/tandem mass spectrometry (LC-MS or LC-MS/MS) for the qualitative and quantitative assessment of proteins and glycoproteins expressed in CNS. Proteins and glycoproteins, extracted by a mass spectrometry friendly surfactant from CNS samples, were subjected to enzymatic (tryptic) digestion and three down-stream analyses: (1) a nano LC system coupled with a high-resolution MS instrument to achieve qualitative proteomic profile, (2) a nano LC system combined with a triple quadrupole MS to quantify identified proteins, and (3) glycoprotein enrichment prior to LC-MS/MS analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508346/testosterone-insulin-like-effects-an-in-vitro-study-on-the-short-term-metabolic-effects-of-testosterone-in-human-skeletal-muscle-cells
#19
C Antinozzi, F Marampon, C Corinaldesi, E Vicini, P Sgrò, G B Vannelli, A Lenzi, C Crescioli, L Di Luigi
PURPOSE: Testosterone by promoting different metabolic pathways contributes to short-term homeostasis of skeletal muscle, the largest insulin-sensitive tissue and the primary site for insulin-stimulated glucose utilization. Despite evidences indicate a close relationship between testosterone and glucose metabolism, the molecular mechanisms responsible for a possible testosterone-mediated insulin-like effects on skeletal muscle are still unknown. METHODS: Here we used undifferentiated proliferating or differentiated human fetal skeletal muscle cells (Hfsmc) to investigate the short-term effects of testosterone on the insulin-mediated biomolecular metabolic machinery...
May 15, 2017: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/28507297/a-one-pot-three-component-double-click-method-for-synthesis-of-67-cu-labeled-biomolecular-radiotherapeutics
#20
Katsumasa Fujiki, Shinya Yano, Takeshi Ito, Yuki Kumagai, Yoshinori Murakami, Osamu Kamigaito, Hiromitsu Haba, Katsunori Tanaka
A one-pot three-component double-click process for preparing tumor-targeting agents for cancer radiotherapy is described here. By utilizing DOTA (or NOTA) containing tetrazines and the TCO-substituted aldehyde, the two click reactions, the tetrazine ligation (an inverse electron-demand Diels-Alder cycloaddition) and the RIKEN click (a rapid 6π-azaelectrocyclization), could simultaneously proceed under mild conditions to afford covalent attachment of the metal chelator DOTA or NOTA to biomolecules such as to albumin and anti-IGSF4 antibody without altering their activities...
May 15, 2017: Scientific Reports
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