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Protein footprinting

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https://www.readbyqxmd.com/read/28439033/genome-wide-identification-of-resd-nsrr-and-fur-binding-in-bacillus-subtilis-during-anaerobic-fermentative-growth-by-in-vivo-footprinting
#1
Onuma Chumsakul, Divya P Anantsri, Tai Quirke, Taku Oshima, Kensuke Nakamura, Shu Ishikawa, Michiko M Nakano
Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28437684/fibrillar-disruption-by-ac-electric-field-induced-oscillation-a-case-study-with-human-serum-albumin
#2
Shubhatam Sen, Monojit Chakraborty, Snigdha Goley, Swagata Dasgupta, Sunando DasGupta
The effect of oscillation induced by a frequency-dependent alternating current (AC) electric field to dissociate preformed amyloid fibrils has been investigated. An electrowetting-on-dielectric type setup has been used to apply the AC field of varying frequencies on preformed fibrils of human serum albumin (HSA). The disintegration potency has been monitored by a combination of spectroscopic and microscopic techniques. The experimental results suggest that the frequency of the applied AC field plays a crucial role in the disruption of preformed HSA fibrils...
April 13, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28432532/a-portable-battery-powered-microfluidic-impedance-cytometer-with-smartphone-readout-towards-personal-health-monitoring
#3
Niloy Talukder, Abbas Furniturewalla, Tuan Le, Matthew Chan, Shreyas Hirday, Xinnan Cao, Pengfei Xie, Zhongtian Lin, Azam Gholizadeh, Steve Orbine, Mehdi Javanmard
We present a portable system for personalized blood cell counting consisting of a microfluidic impedance cytometer and portable analog readout electronics, feeding into an analog-to-digital converter (ADC), and being transmitted via Bluetooth to a user-accessible mobile application. We fabricated a microfluidic impedance cytometer with a novel portable analog readout. The novel design of the analog readout, which consists of a lock-in-amplifier followed by a high-pass filter stage for subtraction of drift and DC offset, and a post-subtraction high gain stage, enables detection of particles and cells as small as 1 μm in diameter, despite using a low-end 8-bit ADC...
June 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28416612/a-biochemical-and-biophysical-model-of-g-quadruplex-dna-recognition-by-positive-coactivator-of-transcription-4
#4
Wezley C Griffin, Jun Gao, Alicia K Byrd, Shubeena Chib, Kevin D Raney
DNA sequences that are guanine-rich have received considerable attention due to their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4) which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA) binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA...
April 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28408495/expanding-the-genetic-code-of-mammalian-cells
#5
REVIEW
James S Italia, Yunan Zheng, Rachel E Kelemen, Sarah B Erickson, Partha S Addy, Abhishek Chatterjee
In the last two decades, unnatural amino acid (UAA) mutagenesis has emerged as a powerful new method to probe and engineer protein structure and function. This technology enables precise incorporation of a rapidly expanding repertoire of UAAs into predefined sites of a target protein expressed in living cells. Owing to the small footprint of these genetically encoded UAAs and the large variety of enabling functionalities they offer, this technology has tremendous potential for deciphering the delicate and complex biology of the mammalian cells...
April 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28393682/new-feed-ingredients-the-insect-opportunity
#6
L W D van Raamsdonk, H J van der Fels-Klerx, J de Jong
In the framework of sustainability and a circular economy, new ingredients for feed are desired and, to this end, initiatives for implementing such novel ingredients have been started. The initiatives include a range of different sources, of which insects are of particular interest. Within the European Union, generally, a new feed ingredient should comply with legal constraints in terms of 'yes, provided that' its safety commits to a range of legal limits for heavy metals, mycotoxins, pesticides, contaminants, pathogens etc...
April 10, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28386335/dl-3-n-butylphthalide-improves-functional-recovery-in-rats-with-spinal-cord-injury-by-inhibiting-endoplasmic-reticulum-stress-induced-apoptosis
#7
Zili He, Yulong Zhou, Yan Huang, Qingqing Wang, Binbin Zheng, Hongyu Zhang, Jiawei Li, Yanlong Liu, Fenzan Wu, Xie Zhang, Songlin Tong, Maofeng Wang, Zhouguang Wang, Huacheng He, Huazi Xu, Jian Xiao
Endoplasmic reticulum (ER) stress-induced apoptosis occurs in the spinal cord following traumatic spinal cord injury (SCI). Dl-3-n-butylphthalide (NBP) exerts an neuroprotective effects against both ischemic brain injury and neurodegenerative diseases; however, the relationship between ER stress-induced apoptosis and the therapeutic effect of NBP in SCI remains unclear. In this study, moderate spinal cord injuries were induced in Sprague-Dawley (SD) rats with a vascular clip. NBP was administered by oral (80 mg/kg/d) gavage 2 h before injury and then once daily for 28 d thereafter...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28365549/greenhouse-gas-balance-of-mountain-dairy-farms-as-affected-by-grassland-carbon-sequestration
#8
Sara Salvador, Mirco Corazzin, Alberto Romanzin, Stefano Bovolenta
Recent studies on milk production have often focused on environmental impacts analysed using the Life Cycle Assessment (LCA) approach. In grassland-based livestock systems, soil carbon sequestration might be a potential sink to mitigate greenhouse gas (GHG) balance. Nevertheless, there is no commonly shared methodology. In this work, the GHG emissions of small-scale mountain dairy farms were assessed using the LCA approach. Two functional units, kg of Fat and Protein Corrected Milk (FPCM) and Utilizable Agricultural Land (UAL), and two different emissions allocations methods, no allocation and physical allocation, which accounts for the co-product beef, were considered...
March 30, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28344080/translation-of-circrnas
#9
Nagarjuna Reddy Pamudurti, Osnat Bartok, Marvin Jens, Reut Ashwal-Fluss, Christin Stottmeister, Larissa Ruhe, Mor Hanan, Emanuel Wyler, Daniel Perez-Hernandez, Evelyn Ramberger, Shlomo Shenzis, Moshe Samson, Gunnar Dittmar, Markus Landthaler, Marina Chekulaeva, Nikolaus Rajewsky, Sebastian Kadener
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry...
April 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28338015/simultaneously-measuring-multiple-protein-interactions-and-their-correlations-in-a-cell-by-protein-interactome-footprinting
#10
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
#11
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/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#12
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/28325897/energy-use-and-carbon-footprints-differ-dramatically-for-diverse-wastewater-derived-carbonaceous-substrates-an-integrated-exploration-of-biokinetics-and-life-cycle-assessment
#13
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/28321365/testing-the-habituation-assumption-underlying-models-of-parasitoid-foraging-behavior
#14
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/28295098/optofluidic-biomolecule-sensors-based-on-a-si-h-microrings-embedded-in-silicon-glass-microchannels
#15
T Lipka, L Moldenhauer, L Wahn, H K Trieu
The large-scale and low-cost fabrication of high sensitivity sensors for the real-time detection of biochemicals and molecular substances opens up new opportunities in the areas of bioanalytic screening and medical diagnostics. Planar integrated photonic resonators that can be fabricated with a low footprint, in spatial and wavelength multiplexed arrangements, and that enable integration with microfluidics on the wafer scale have emerged as a promising sensing platform for these application fields. We realized an optofluidic and label-free biosensor that is based on hydrogenated amorphous silicon microring resonators embedded in silicon/glass microfluidic channels for analyte injection and biomolecule immobilization...
March 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28294433/transcriptional-regulation-of-adhesive-properties-of-bacillus-subtilis-to-extracellular-matrix-proteins-through-the-fibronectin-binding-protein-yloa
#16
Facundo Rodriguez Ayala, Carlos Bauman, Marco Bartolini, Ester Saball, Marcela Salvarrey, Cecilia Leñini, Sebastián Cogliati, Mark Strauch, Roberto Grau
Bacterial adherence to extracellular matrix proteins (ECMp) plays important roles during host-pathogen interaction, however its genetic regulation remains poorly understood. yloA of the model bacterium Bacillus subtilis shows high homology to genes encoding fibronectin-binding proteins of Gram-positive pathogens. Here, we characterized the regulatory network of YloA-dependent adhesive properties of the probiotic B. subtilis natto (Bsn). YloA-proficient, but not YloA-deficient, Bsn specifically bound to ECMp in a concentration-dependent manner and were proficient in biofilm formation...
March 13, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28277927/knockdown-of-bc200-rna-expression-reduces-cell-migration-and-invasion-by-destabilizing-mrna-for-calcium-binding-protein-s100a11
#17
Heegwon Shin, Jungmin Lee, Youngmi Kim, Seonghui Jang, Yunhee Lee, Semi Kim, Younghoon Lee
Although BC200 RNA is best known as a neuron-specific non-coding RNA, it is overexpressed in various cancer cells. BC200 RNA was recently shown to contribute to metastasis in several cancer cell lines, but the underlying mechanism was not understood in detail. To examine this mechanism, we knocked down BC200 RNA in cancer cells, which overexpress the RNA, and examined cell motility, profiling of ribosome footprints, and the correlation between cell motility changes and genes exhibiting altered ribosome profiles...
March 1, 2017: RNA Biology
https://www.readbyqxmd.com/read/28275051/protein-footprinting-comes-of-age-mass-spectrometry-for-biophysical-structure-assessment
#18
Liwen Wang, Mark R Chance
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF)...
March 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28268296/the-effect-of-multiple-thin-film-coatings-of-protein-loaded-sol-gel-on-total-multi-electrode-array-thickness
#19
Matthew D McDermott, Kevin J Otto
Tetramethyl orthosilicate shows promise as a thin-film delivery vehicle for multi-electrode arrays for drug release and electrical performance; however, its effect upon device footprint has yet to be assessed. Using a previously established silicon wafer chip model, the thickness of one, two, and four protein doped coatings of sol-gel were analyzed via profilometry. Coating thickness was found to be 0.4μm, 1.1μm and 2.2μm on each side of the device. This addition to a native MEA is minimal when compared to other drug delivery paradigms currently associated with neural implants...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268179/vibrio-parahaemolyticus-calr-down-regulates-the-thermostable-direct-hemolysin-tdh-gene-transcription-and-thereby-inhibits-hemolytic-activity
#20
Yiquan Zhang, Ying Zhang, He Gao, Lingyu Zhang, Zhe Yin, Xinxiang Huang, Dongsheng Zhou, Huiying Yang, Wenhui Yang, Li Wang
TDH, encoded by tdh gene, is a major virulent determinant of V. parahaemolyticus that controls various biological activities, such as hemolytic activity, cytotoxicity, and enterotoxicity. The hemolytic activity on Wagatsuma agar ascribed to TDH is called Kanagawa phenomenon (KP). All KP positive strains contain tdh1 and tdh2 genes, but tdh2 is predominantly responsible for KP. CalR is a regulatory protein that was originally identified as a repressor of swarming motility and T3SS1 gene expression in V. parahaemolyticus...
May 20, 2017: Gene
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