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https://www.readbyqxmd.com/read/28338015/simultaneously-measuring-multiple-protein-interactions-and-their-correlations-in-a-cell-by-protein-interactome-footprinting
#1
Si-Wei Luo, Zhi Liang, Jia-Rui Wu
Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#2
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334916/mocap-large-scale-inference-of-transcription-factor-binding-sites-from-chromatin-accessibility
#3
Xi Chen, Bowen Yu, Nicholas Carriero, Claudio Silva, Richard Bonneau
Differential binding of transcription factors (TFs) at cis-regulatory loci drives the differentiation and function of diverse cellular lineages. Understanding the regulatory interactions that underlie cell fate decisions requires characterizing TF binding sites (TFBS) across multiple cell types and conditions. Techniques, e.g. ChIP-Seq can reveal genome-wide patterns of TF binding, but typically requires laborious and costly experiments for each TF-cell-type (TFCT) condition of interest. Chromosomal accessibility assays can connect accessible chromatin in one cell type to many TFs through sequence motif mapping...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334628/superwetting-and-aptamer-functionalized-shrink-induced-high-surface-area-electrochemical-sensors
#4
A Hauke, L S Selva Kumar, M Y Kim, J Pegan, M Khine, H Li, K W Plaxco, J Heikenfeld
Electrochemical sensing is moving to the forefront of point-of-care and wearable molecular sensing technologies due to the ability to miniaturize the required equipment, a critical advantage over optical methods in this field. Electrochemical sensors that employ roughness to increase their microscopic surface area offer a strategy to combatting the loss in signal associated with the loss of macroscopic surface area upon miniaturization. A simple, low-cost method of creating such roughness has emerged with the development of shrink-induced high surface area electrodes...
March 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#5
Dominik Kopczynski, Harald Barsnes, Pål R Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends
Summary: The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331791/one-dimensional-earth-abundant-nanomaterials-for-water-splitting-electrocatalysts
#6
REVIEW
Jun Li, Gengfeng Zheng
Hydrogen fuel acquisition based on electrochemical or photoelectrochemical water splitting represents one of the most promising means for the fast increase of global energy need, capable of offering a clean and sustainable energy resource with zero carbon footprints in the environment. The key to the success of this goal is the realization of robust earth-abundant materials and cost-effective reaction processes that can catalyze both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER), with high efficiency and stability...
March 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28331587/a-simple-fast-and-repeatable-survey-method-for-underwater-visual-3d-benthic-mapping-and-monitoring
#7
Oscar Pizarro, Ariell Friedman, Mitch Bryson, Stefan B Williams, Joshua Madin
Visual 3D reconstruction techniques provide rich ecological and habitat structural information from underwater imagery. However, an unaided swimmer or diver struggles to navigate precisely over larger extents with consistent image overlap needed for visual reconstruction. While underwater robots have demonstrated systematic coverage of areas much larger than the footprint of a single image, access to suitable robotic systems is limited and requires specialized operators. Furthermore, robots are poor at navigating hydrodynamic habitats such as shallow coral reefs...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28326631/group-treatment-for-substance-abuse-a-stages-of-change-therapy-manual-2nd-edn-mary-velasquez-cathy-crouch-nanette-stokes-stephens-carlo-c-diclemente-new-york-usa-the-guildford-press-2016-isbn-978-1-4625-2340-5-308%C3%A2-pp-paperback-price-75-00-available-to-purchase
#8
https://www.readbyqxmd.com/read/28326444/quantitative-radiographic-assessment-of-the-anatomic-attachment-sites-of-the-anterior-and-posterior-complexes-of-the-proximal-tibiofibular-joint
#9
Daniel Cole Marchetti, Jorge Chahla, Gilbert Moatshe, Erik L Slette, Robert F LaPrade
PURPOSE: Quantitative guidelines for radiographic identification of the anterior and posterior ligaments of the proximal tibiofibular joint have not been well defined. The purpose of this study was to provide reproducible, quantitative descriptions of radiographic landmarks identifying the anterior and posterior ligament complexes of the proximal tibiofibular joint. It was hypothesized that consistent quantitative data regarding the radiographic location of the anterior and posterior proximal tibiofibular joint ligament complexes could be identified...
March 21, 2017: Knee Surgery, Sports Traumatology, Arthroscopy: Official Journal of the ESSKA
https://www.readbyqxmd.com/read/28325897/energy-use-and-carbon-footprints-differ-dramatically-for-diverse-wastewater-derived-carbonaceous-substrates-an-integrated-exploration-of-biokinetics-and-life-cycle-assessment
#10
Yanbo Li, Xu Wang, David Butler, Junxin Liu, Jiuhui Qu
Energy neutrality and reduction of carbon emissions are significant challenges to the enhanced sustainability of wastewater treatment plants (WWTPs). Harvesting energy from wastewater carbonaceous substrates can offset energy demands and enable net power generation; yet, there is limited research about how carbonaceous substrates influence energy and carbon implications of WWTPs with integrated energy recovery at systems-level. Consequently, this research uses biokinetics modelling and life cycle assessment philology to explore this notion, by tracing and assessing the quantitative flows of energy embodied or captured, and by exploring the carbon footprint throughout an energy-intensive activated sludge process with integrated energy recovery facilities...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325300/one-step-biallelic-and-scarless-correction-of-a-%C3%AE-thalassemia-mutation-in-patient-specific-ipscs-without-drug-selection
#11
Yali Liu, Yi Yang, Xiangjin Kang, Bin Lin, Qian Yu, Bing Song, Ge Gao, Yaoyong Chen, Xiaofang Sun, Xiaoping Li, Lei Bu, Yong Fan
Monogenic disorders (MGDs), which are caused by single gene mutations, have a serious effect on human health. Among these, β-thalassemia (β-thal) represents one of the most common hereditary hematological diseases caused by mutations in the human hemoglobin β (HBB) gene. The technologies of induced pluripotent stem cells (iPSCs) and genetic correction provide insights into the treatments for MGDs, including β-thal. However, traditional approaches for correcting mutations have a low efficiency and leave a residual footprint, which leads to some safety concerns in clinical applications...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28322529/-interventi-di-popolazione-per-contrastare-l-epidemia-di-prodotti-insalubri
#12
Giuseppe Gorini
"The multinational corporations producing tobacco, alcohol, soft drinks, and processed foods have a role of vectors in the increase of chronic diseases, so that one can speak of manufacturing epidemics. The main aim of this paper is to conduct a literature review on different approaches in population-based interventions to stem the rise in consumption of unhealthy products. Different approaches were found: • command-and-control regulations: the route is definitely more advanced for tobacco with the implementation of an international treaty, which requires 180 ratifying states to implement a series of tobacco control policies...
January 2017: Epidemiologia e Prevenzione
https://www.readbyqxmd.com/read/28322436/modelling-hydraulic-transport-and-anaerobic-uptake-by-paos-and-gaos-during-wastewater-feeding-in-ebpr-granular-sludge-reactors
#13
David G Weissbrodt, Christof Holliger, Eberhard Morgenroth
New-generation bioprocesses using granular sludge aim for a high-rate removal of nutrients from wastewater with low footprint. Achieving enhanced biological phosphorus removal (EBPR) relies on the design of sludge beds and wastewater feeding conditions to optimally load the biomass and to select for polyphosphate- (PAOs) over glycogen-accumulating organisms (GAOs) and other heterotrophs. A hydraulic-metabolic mathematical model was developed to elucidate the impact of hydraulic transport patterns and environmental conditions on the PAO/GAO competition during up-flow feeding through an EBPR granular sludge bed...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28321908/reduced-field-of-view-single-shot-spiral-perfusion-imaging
#14
Yang Yang, Li Zhao, Xiao Chen, Peter W Shaw, Jorge A Gonzalez, Frederick H Epstein, Craig H Meyer, Christopher M Kramer, Michael Salerno
PURPOSE: To develop a single-shot spiral perfusion pulse sequence with outer-volume suppression (OVS) to achieve whole-heart coverage with a short temporal footprint of 10 ms per slice location. METHODS: A highly accelerated single-shot variable density spiral pulse sequence with an integrated OVS module for reduced field of view (rFOV) perfusion imaging with 2 mm spatial resolution was developed and evaluated in simulations, phantom experiments and in clinical patients with (n = 8) or without (n = 8) OVS...
March 20, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28321475/the-forgotten-joint-quantifying-the-anatomy-of-the-proximal-tibiofibular-joint
#15
Jack Anavian, Daniel Cole Marchetti, Gilbert Moatshe, Erik L Slette, Jorge Chahla, Alex W Brady, David M Civitarese, Robert F LaPrade
PURPOSE: Limited objective data exist detailing the quantitative anatomy of the individual bundles of the proximal tibiofibular joint and their relation to surgically pertinent osseous landmarks. The purpose of this study was to qualitatively and quantitatively describe the ligamentous anatomy of the proximal tibiofibular joint and its relation to relevant bony landmarks. METHODS: Ten non-paired, fresh-frozen cadaveric knee specimens were dissected to identify the proximal tibiofibular joint ligament bundles...
March 20, 2017: Knee Surgery, Sports Traumatology, Arthroscopy: Official Journal of the ESSKA
https://www.readbyqxmd.com/read/28321426/quantitative-anatomic-analysis-of-the-native-ligamentum-teres
#16
Jacob D Mikula, Erik L Slette, Jorge Chahla, Alex W Brady, Renato Locks, Christiano A C Trindade, Matthew T Rasmussen, Robert F LaPrade, Marc J Philippon
BACKGROUND: While recent studies have addressed the biomechanical function of the ligamentum teres and provided descriptions of ligamentum teres reconstruction techniques, its detailed quantitative anatomy remains relatively undocumented. Moreover, there is a lack of consensus in the literature regarding the number and morphology of the acetabular attachments of the ligamentum teres. PURPOSE: To provide a clinically relevant quantitative anatomic description of the native human ligamentum teres...
February 2017: Orthopaedic Journal of Sports Medicine
https://www.readbyqxmd.com/read/28321365/testing-the-habituation-assumption-underlying-models-of-parasitoid-foraging-behavior
#17
Paul K Abram, Antonino Cusumano, Katrina Abram, Stefano Colazza, Ezio Peri
BACKGROUND: Habituation, a form of non-associative learning, has several well-defined characteristics that apply to a wide range of physiological and behavioral responses in many organisms. In classic patch time allocation models, habituation is considered to be a major mechanistic component of parasitoid behavioral strategies. However, parasitoid behavioral responses to host cues have not previously been tested for the known, specific characteristics of habituation. METHODS: In the laboratory, we tested whether the foraging behavior of the egg parasitoid Trissolcus basalis shows specific characteristics of habituation in response to consecutive encounters with patches of host (Nezara viridula) chemical contact cues (footprints), in particular: (i) a training interval-dependent decline in response intensity, and (ii) a training interval-dependent recovery of the response...
2017: PeerJ
https://www.readbyqxmd.com/read/28319431/evaluation-of-the-risk-factors-for-a-rotator-cuff-retear-after-repair-surgery
#18
Yeong Seok Lee, Jeung Yeol Jeong, Chan-Deok Park, Seung Gyoon Kang, Jae Chul Yoo
BACKGROUND: A retear is a significant clinical problem after rotator cuff repair. However, no study has evaluated the retear rate with regard to the extent of footprint coverage. PURPOSE: To evaluate the preoperative and intraoperative factors for a retear after rotator cuff repair, and to confirm the relationship with the extent of footprint coverage. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: Data were retrospectively collected from 693 patients who underwent arthroscopic rotator cuff repair between January 2006 and December 2014...
March 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28319132/measuring-subglacial-bedform-orientation-length-and-longitudinal-asymmetry-method-assessment
#19
Marco G Jorge, Tracy A Brennand
Geospatial analysis software provides a range of tools that can be used to measure landform morphometry. Often, a metric can be computed with different techniques that may give different results. This study is an assessment of 5 different methods for measuring longitudinal, or streamlined, subglacial bedform morphometry: orientation, length and longitudinal asymmetry, all of which require defining a longitudinal axis. The methods use the standard deviational ellipse (not previously applied in this context), the longest straight line fitting inside the bedform footprint (2 approaches), the minimum-size footprint-bounding rectangle, and Euler's approximation...
2017: PloS One
https://www.readbyqxmd.com/read/28318117/transcriptional-regulation-of-cpsq-mfpabc-and-mfpabc-by-calr%C3%A2-in-vibrio-parahaemolyticus
#20
He Gao, Lingyu Zhang, George Osei-Adjei, Wenhui Yang, Dongsheng Zhou, Xinxiang Huang, Huiying Yang, Zhe Yin, Yiquan Zhang
The cpsQ-mfpABC locus is transcribed as two operons, i.e., cpsQ-mfpABC and mfpABC, in Vibrio parahaemolyticus, and both of them are all required for biofilm formation. CalR belongs to the LysR-type transcriptional regulator family, and was originally identified as a repressor of the swarming motility and T3SS1 genes expression in V. parahaemolyticus. In the present work, a combination of qRT-PCR, primer extension, LacZ fusion expression, electrophoretic mobility shift assay, and DNase I footprinting assays were employed to elucidate the regulatory mechanisms of cpsQ-mfpABC and mfpABC by CalR...
March 20, 2017: MicrobiologyOpen
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