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Protein footprinting

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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
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28143479/droplet-based-microfluidic-high-throughput-screening-of-heterologous-enzymes-secreted-by-the-yeast-yarrowia-lipolytica
#5
Thomas Beneyton, Stéphane Thomas, Andrew D Griffiths, Jean-Marc Nicaud, Antoine Drevelle, Tristan Rossignol
BACKGROUND: Droplet-based microfluidics is becoming an increasingly attractive alternative to microtiter plate techniques for enzymatic high-throughput screening (HTS), especially for exploring large diversities with lower time and cost footprint. In this case, the assayed enzyme has to be accessible to the substrate within the water-in-oil droplet by being ideally extracellular or displayed at the cell surface. However, most of the enzymes screened to date are expressed within the cytoplasm of Escherichia coli cells, which means that a lysis step must take place inside the droplets for enzyme activity to be assayed...
January 31, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28137575/a-cautionary-tale-on-the-inclusion-of-variable-posttranslational-modifications-in-database-dependent-searches-of-mass-spectrometry-data
#6
J Svozil, K Baerenfaller
Mass spectrometry-based proteomics allows in principle the identification of unknown target proteins of posttranslational modifications and the sites of attachment. Including a variety of posttranslational modifications in database-dependent searches of high-throughput mass spectrometry data holds the promise to gain spectrum assignments to modified peptides, thereby increasing the number of assigned spectra, and to identify potentially interesting modification events. However, these potential benefits come for the price of an increased search space, which can lead to reduced scores, increased score thresholds, and erroneous peptide spectrum matches...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28134924/a-novel-pre-fusion-conformation-specific-neutralizing-epitope-on-the-respiratory-syncytial-virus-fusion-protein
#7
Jarrod J Mousa, Nurgun Kose, Pranathi Matta, Pavlo Gilchuk, James E Crowe
Respiratory syncytial virus (RSV) remains a major human pathogen, infecting the majority of infants before age two and causing re-infection throughout life. Despite decades of RSV research, there is no licensed RSV vaccine. Most candidate vaccines studied to date have incorporated the RSV fusion (F) surface glycoprotein, because the sequence of F is highly conserved among strains of RSV. To better define the human B cell response to RSV F, we isolated from a single donor 13 new neutralizing human monoclonal antibodies (mAbs) that recognize the RSV F protein in the pre-fusion conformation...
January 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28132389/an-improved-method-for-identifying-specific-dna-protein-binding-sites-in-vitro
#8
Liangyan Wang, Huizhi Lu, Yunguang Wang, Su Yang, Hong Xu, Kaiying Cheng, Ye Zhao, Bing Tian, Yuejin Hua
Binding of proteins to specific DNA sequences is essential for a variety of cellular processes such as DNA replication, transcription and responses to external stimuli. Chromatin immunoprecipitation is widely used for determining intracellular DNA fragments bound by a specific protein. However, the subsequent specific or accurate DNA-protein-binding sequence is usually determined by DNA footprinting. Here, we report an alternative method for identifying specific sites of DNA-protein-binding (designated SSDP) in vitro...
January 28, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28130304/ccpa-and-cody-coordinate-acetate-metabolism-in-streptococcus-mutans
#9
Jeong Nam Kim, Robert A Burne
: In the dental caries pathogen Streptococcus mutans, phosphotransacetylase (Pta) and acetate kinase (Ack) convert pyruvate into acetate with the concomitant generation of ATP. The genes for this pathway are tightly regulated by multiple environmental and intracellular inputs, but the basis for differential expression of the genes for Pta and Ack in S. mutans had not been investigated. Here, we show that inactivation in S. mutans of ccpA or codY reduced the activity of the ackA promoter, whereas a ccpA mutant displayed elevated pta promoter activity...
January 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28129109/motor-coordinative-and-cognitive-dysfunction-caused-by-mutant-tdp-43-could-be-reversed-by-inhibiting-its-mitochondrial-localization
#10
Wenzhang Wang, Hiroyuki Arakawa, Luwen Wang, Ogoegbunam Okolo, Sandra L Siedlak, Yinfei Jiang, Ju Gao, Fei Xie, Robert B Petersen, Xinglong Wang
Dominant missense mutations in TAR DNA-binding protein 43 (TDP-43) cause amyotrophic lateral sclerosis (ALS), and the cytoplasmic accumulation of TDP-43 represents a pathological hallmark in ALS and frontotemporal lobar degeneration (FTD). Behavioral investigation of the transgenic mouse model expressing the disease-causing human TDP-43 M337V mutant (TDP-43(M337V) mice) is encumbered by premature death in homozygous transgenic mice and a reported lack of phenotype assessed by tail elevation and footprint in hemizygous transgenic mice...
January 4, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28124731/digestion-and-metabolism-of-low-and-high-residual-feed-intake-nellore-bulls
#11
Sarah Figueiredo Martins Bonilha, Renata Helena Branco, Maria Eugênia Zerlotti Mercadante, Joslaine Noely Dos Santos Gonçalves Cyrillo, Fábio Morato Monteiro, Enilson Geraldo Ribeiro
Understanding the reasons why animals of similar performances have different feed requirements is important to increase profits for cattle producers and to decrease the environmental footprint of beef cattle production. This study was carried out aiming to identify the associations between residual feed intake (RFI) and animal performance, nutrient digestibility, and blood metabolites related to energy balance of young Nellore bulls during the finishing period. Animals previously classified as low (n = 13) and high RFI (n = 12), with average initial body weight of 398 kg and age of 503 days were used...
January 26, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28119822/gene-therapy-for-a-mouse-model-of-glucose-transporter-1-deficiency-syndrome
#12
Sachie Nakamura, Hitoshi Osaka, Shin-Ichi Muramatsu, Naomi Takino, Mika Ito, Shiho Aoki, Eriko F Jimbo, Kuniko Shimazaki, Tatsushi Onaka, Sumio Ohtsuki, Tetsuya Terasaki, Takanori Yamagata
OBJECTIVE: We generated an adeno-associated virus (AAV) vector in which the human SLC2A1 gene was expressed under the synapsin I promoter (AAV-hSLC2A1) and examined if AAV-hSLC2A1 administration can lead to functional improvement in GLUT1-deficient mice. METHODS: AAV-hSLC2A1 was injected into heterozygous knock-out murine Glut1 (GLUT1(+/-)) mice intraperitoneally (systemic; 1.85 × 10(11) vg/mouse) or intra-cerebroventricularly (local; 1.85 × 10(10) vg/mouse)...
March 2017: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/28102671/structural-analysis-of-the-glycosylated-intact-hiv-1-gp120-b12-antibody-complex-using-hydroxyl-radical-protein-footprinting
#13
Xiaoyan Li, Oliver C Grant, Keigo Ito, Aaron Wallace, Shixia Wang, Peng Zhao, Lance Wells, Shan Lu, Robert J Woods, Joshua S Sharp
Glycoprotein gp120 is a surface antigen and virulence factor of human immunodeficiency virus 1. Broadly neutralizing antibodies (bNAbs) that react to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system because of its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28098154/structural-basis-of-ligand-interaction-with-atypical-chemokine-receptor-3
#14
Martin Gustavsson, Liwen Wang, Noortje van Gils, Bryan S Stephens, Penglie Zhang, Thomas J Schall, Sichun Yang, Ruben Abagyan, Mark R Chance, Irina Kufareva, Tracy M Handel
Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28090586/holliday-junction-trap-shows-how-cells-use-recombination-and-a-junction-guardian-role-of-recq-helicase
#15
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A Halliday, Hsin-Yu Lin, David Magnan, John P Pribis, Devon M Fitzgerald, Holly M Hamilton, Megan Richters, Ralf B Nehring, Xi Shen, Lei Li, David Bates, P J Hastings, Christophe Herman, Makkuni Jayaram, Susan M Rosenberg
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28089819/lentivirus-mediated-silencing-of-the-ctgf-gene-suppresses-the-formation-of-glial-scar-tissue-in-a-rat-model-of-spinal-cord-injury
#16
Yuan Wang, Qin-Jie Kong, Jing-Chuan Sun, Yong Yang, Hai-Bo Wang, Qiang Zhang, Jian-Gang Shi
BACKGROUND CONTEXT: - One of the many reactive changes following an Spinal cord injury (SCI) is the formation of a glial scar, a reactive cellular process whereby glial cells accumulate and surround central nervous system (CNS) injury sites to seal in the wound. Thus the inhibition of glial scar is of great importance for SCI recovery. PURPOSE: - This study aimed to explore the effect of lentivirus-mediated silencing of the CTGF gene on the formation of glial scar tissue in a rat model of spinal cord injury (SCI)...
January 9, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28069952/toxic-prn-poly-dipeptides-encoded-by-the-c9orf72-repeat-expansion-block-nuclear-import-and-export
#17
Kevin Y Shi, Eiichiro Mori, Zehra F Nizami, Yi Lin, Masato Kato, Siheng Xiang, Leeju C Wu, Ming Ding, Yonghao Yu, Joseph G Gall, Steven L McKnight
The toxic proline:arginine (PRn) poly-dipeptide encoded by the (GGGGCC)n repeat expansion in the C9orf72 form of heritable amyotrophic lateral sclerosis (ALS) binds to the central channel of the nuclear pore and inhibits the movement of macromolecules into and out of the nucleus. The PRn poly-dipeptide binds to polymeric forms of the phenylalanine:glycine (FG) repeat domain, which is shared by several proteins of the nuclear pore complex, including those in the central channel. A method of chemical footprinting was used to characterize labile, cross-β polymers formed from the FG domain of the Nup54 protein...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28060339/the-chip-exo-method-identifying-protein-dna-interactions-with-near-base-pair-precision
#18
Andrea A Perreault, Bryan J Venters
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28057466/expression-of-the-alae-gene-is-positively-regulated-by-the-global-regulator-lrp-in-response-to-intracellular-accumulation-of-l-alanine-in-escherichia-coli
#19
Kohei Ihara, Kazuki Sato, Hatsuhiro Hori, Yumiko Makino, Shuji Shigenobu, Tasuke Ando, Emiko Isogai, Hiroshi Yoneyama
The alaE gene in Escherichia coli encodes an l-alanine exporter that catalyzes the active export of l-alanine using proton electrochemical potential. In our previous study, alaE expression was shown to increase in the presence of l-alanyl-l-alanine (Ala-Ala). In this study, the global regulator leucine-responsive regulatory protein (Lrp) was identified as an activator of the alaE gene. A promoter less β-galactosidase gene was fused to an alaE upstream region (240 nucleotides). Cells that were lacZ-deficient and harbored this reporter plasmid showed significant induction of β-galactosidase activity (approximately 17-fold) in the presence of 6 mM l-alanine, l-leucine, and Ala-Ala...
January 3, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28052104/insertional-mutagenesis-by-crispr-cas9-ribonucleoprotein-gene-editing-in-cells-targeted-for-point-mutation-repair-directed-by-short-single-stranded-dna-oligonucleotides
#20
Natalia Rivera-Torres, Kelly Banas, Pawel Bialk, Kevin M Bloh, Eric B Kmiec
CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells...
2017: PloS One
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