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Protein footprinting

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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/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28255747/mapping-the-binding-interface-of-vegf-and-a-monoclonal-antibody-fab-1-fragment-with-fast-photochemical-oxidation-of-proteins-fpop-and-mass-spectrometry
#12
Ying Zhang, Aaron T Wecksler, Patricia Molina, Galahad Deperalta, Michael L Gross
We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states...
March 2, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28249561/reactome-pathway-analysis-a-high-performance-in-memory-approach
#13
Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner, Pablo Marin-Garcia, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob
BACKGROUND: Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. RESULTS: Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method...
March 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28246168/role-of-glycine-221-in-catalytic-activity-of-hyaluronan-binding-protein-2
#14
Fabian Stavenuiter, Eduard H T M Ebberink, Koen Mertens, Alexander B Meijer
Hyaluronan-Binding Protein 2 (HABP2) is a Ca(2+)-dependent serine protease with putative roles in blood coagulation and fibrinolysis. A G221E substitution, known as the Marburg-I polymorphism, reportedly affects HABP2 function and has been associated with increased risk for cardiovascular disease. However, the importance of Gly-221 for HABP2 activity is unclear. Here, we used G221E, G221A, and G221S mutants to assess the role of Gly-221 in HABP2 catalysis. The G221E variant failed to activate single-chain urokinase-type plasminogen activator (scuPA), and the G221A and G221S variants displayed moderately reduced scuPA-activation...
February 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28245801/differentiation-of-ncrnas-from-small-mrnas-in-escherichia-coli-o157-h7-edl933-ehec-by-combined-rnaseq-and-riboseq-ryhb-encodes-the-regulatory-rna-ryhb-and-a-peptide-ryhp
#15
Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A Keim, Siegfried Scherer
BACKGROUND: While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. RESULTS: Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28243589/nuclear-compartmentalization-contributes-to-stage-specific-gene-expression-control-in-trypanosoma-cruzi
#16
Lucía Pastro, Pablo Smircich, Andrés Di Paolo, Lorena Becco, María A Duhagon, José Sotelo-Silveira, Beatriz Garat
In the protozoan parasite Trypanosoma cruzi, as in other trypanosomatids, transcription of protein coding genes occurs in a constitutive fashion, producing large polycistronic transcription units. These units are composed of non-functionally related genes which are pervasively processed to yield each mRNA. Therefore, post-transcriptional processes are crucial to regulate gene expression. Considering that nuclear compartmentalization could contribute to gene expression regulation, we comparatively studied the nuclear, cytoplasmic and whole cell transcriptomes of the non-infective epimastigote stage of T...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28231112/a-comparison-of-carbon-footprint-and-production-cost-of-different-pasta-products-based-on-whole-egg-and-pea-flour
#17
Antonia Nette, Patricia Wolf, Oliver Schlüter, Andreas Meyer-Aurich
Feed and food production are inter alia reasons for high greenhouse gas emissions. Greenhouse gas emissions could be reduced by the replacement of animal components with plant components in processed food products, such as pasta. The main components currently used for pasta are semolina, and water, as well as additional egg. The hypothesis of this paper is that the substitution of whole egg with plant-based ingredients, for example from peas, in such a product might lead to reduced greenhouse gas emissions (GHG) and thus a reduced carbon footprint at economically reasonable costs...
March 4, 2016: Foods (Basel, Switzerland)
https://www.readbyqxmd.com/read/28226455/the-effect-of-multiple-thin-film-coatings-of-protein-loaded-sol-gel-on-total-multi-electrode-array-thickness
#18
Matthew D McDermott, Kevin J Otto, Matthew D McDermott, Kevin J Otto, 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/28195200/dynamical-footprint-of-cross-reactivity-in-a-human-autoimmune-t-cell-receptor
#19
Amit Kumar, Francesco Delogu
The present work focuses on the dynamical aspects of cross-reactivity between myelin based protein (MBP) self-peptide and two microbial peptides (UL15, PMM) for Hy.1B11 T-cell receptor (TCR). This same TCR was isolated from a patient suffering from multiple sclerosis (MS). The study aims at highlighting the chemical interactions underlying recognition mechanisms between TCR and the peptides presented by Major Histocompatibility Complex (MHC) proteins, which form a crucial component in adaptive immune response against foreign antigens...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193728/mobile-introns-shape-the-genetic-diversity-of-their-host-genes
#20
Jelena Repar, Tobias Warnecke
Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron...
February 13, 2017: Genetics
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