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https://www.readbyqxmd.com/read/28655184/characterization-of-a-coupled-dna-replication-and-translesion-synthesis-polymerase-supraholoenzyme-from-archaea
#1
Matthew T Cranford, Aurea M Chu, Joshua K Baguley, Robert J Bauer, Michael A Trakselis
The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits...
June 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28655155/evolution-of-cytochrome-c-oxidase-in-hypoxia-tolerant-sculpins-cottidae-actinopterygii
#2
Gigi Y Lau, Milica Mandic, Jeffrey G Richards
Vertebrate hypoxia tolerance can emerge from modifications to the oxygen (O2) transport cascade, but whether there is adaptive variation to O2 binding at the terminus of this cascade, mitochondrial cytochrome c oxidase (COX), is not known. In order to address the hypothesis that hypoxia tolerance is associated with enhanced O2 binding by mitochondria we undertook a comparative analysis of COX O2 kinetics across species of intertidal sculpins (Cottidae, Actinopterygii) that vary in hypoxia tolerance. Our analysis revealed a significant relationship between hypoxia tolerance (critical O2 tension of O2 consumption rate; Pcrit), mitochondrial O2 binding affinity (O2 tension at which mitochondrial respiration was half maximal; P50), and COX O2-binding affinity (apparent Michaelis-Menten constant for O2 binding to COX; Km,app O2)...
June 24, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28655069/delivery-of-parasite-cdg7_flc_0990-rna-transcript-into-intestinal-epithelial-cells-during-cryptosporidium-parvum-infection-suppresses-host-cell-gene-transcription-through-epigenetic-mechanisms
#3
Yang Wang, Ai-Yu Gong, Shibin Ma, Xiqiang Chen, Juliane K Strauss-Soukup, Xian-Ming Chen
Cryptosporidial infection causes dysregulated transcription of host genes key to intestinal epithelial homeostasis, but the underlying mechanisms remain obscure. Previous studies demonstrate that several C. parvum RNA transcripts are selectively delivered into epithelial cells during host cell invasion and may modulate gene transcription in infected cells. We report here that C. parvum infection suppresses the transcription of LRP5, SLC7A8, and IL33 genes in infected intestinal epithelium. Trans-suppression of these genes in infected host cells is associated with promoter enrichment of suppressive epigenetic markers (i...
June 27, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28654907/knockdown-of-malat1-expression-inhibits-huvec-proliferation-by-upregulation-of-mir-320a-and-downregulation-of-foxm1-expression
#4
Jian-Yong Sun, Zheng-Wei Zhao, Wei-Miao Li, Guang Yang, Peng-Yu Jing, Pei Li, Hai-Zhou Dang, Zhao Chen, Yong-An Zhou, Xiao-Fei Li
Regulation of cancer angiogenesis could be a useful strategy in cancer therapy. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA (lncRNA), and can induce cancer cell proliferation, while lncRNAs, generally are able to act as microRNA (miRNA) sponges. The latter is a type of competitive endogenous RNA (ceRNA) that regulates expression of the targeting miRNAs and protein-coding genes. This study investigated the proliferative role of MALAT1 in human umbilical vein endothelial cells (HUVECs) and the underlying molecular events...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28654884/specific-and-selective-probes-for-staphylococcus-aureus-from-phage-displayed-random-peptide-libraries
#5
Laura M De Plano, Santina Carnazza, Grazia M L Messina, Maria Giovanna Rizzo, Giovanni Marletta, Salvatore P P Guglielmino
Staphylococcus aureus is a major human pathogen causing health care-associated and community-associated infections. Early diagnosis is essential to prevent disease progression and to reduce complications that can be serious. In this study, we selected, from a 9-mer phage peptide library, a phage clone displaying peptide capable of specific binding to S. aureus cell surface, namely St.au9IVS5 (sequence peptide RVRSAPSSS).The ability of the isolated phage clone to interact specifically with S. aureus and the efficacy of its bacteria-binding properties were established by using enzyme linked immune-sorbent assay (ELISA)...
June 17, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28654809/interactions-between-stepwise-eluted-sub-fractions-of-fulvic-acids-and-protons-revealed-by-fluorescence-titration-combined-with-eem-parafac
#6
Fanhao Song, Fengchang Wu, Fei Guo, Hao Wang, Weiying Feng, Min Zhou, Yanghui Deng, Yingchen Bai, Baoshan Xing, John P Giesy
In aquatic environments, pH can control environmental behaviors of fulvic acid (FA) via regulating hydrolysis of functional groups. Sub-fractions of FA, eluted using pyrophosphate buffers with initial pHs of 3.0 (FA3), 5.0 (FA5), 7.0 (FA7), 9.0 (FA9) and 13.0 (FA13), were used to explore interactions between the various, operationally defined, FA fractions and protons, by use of EEM-PARAFAC analysis. Splitting of peaks (FA3 and FA13), merging of peaks (FA7), disappearance of peaks (FA9 and FA13), and red/blue-shifting of peaks were observed during fluorescence titration...
June 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28654778/a-new-platform-for-serological-analysis-based-on-porous-3-dimensional-polyethylene-sinter-bodies
#7
Mohammed Alasel, Michael Keusgen
A new sensitive and selective platform, three-dimensional immunosensor, has been developed for a rapid serological diagnosis; detection of a Borrelia infection was considered as a model assay. The immunosensor is based on a 3-dimensional (3D) porous solid surface (sinter body) with dimensions of 2×2.5mm where a recombinant variable lipoprotein surface-exposed protein (VlsE; Borrelia-antigen) is immobilized by different techniques. The sinter body served as a robust and inexpensive carrier, which facilitated a successful hydrophobic adsorption as well as covalent immobilization of the antigen with sufficient amounts of on the surface...
June 20, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28654769/structural-and-functional-characterization-of-the-triticale-x-triticosecale-wittm-phytocystatin-trcc-8-and-its-dimerization-dependent-inhibitory-activity
#8
Beata Prabucka, Marcin Mielecki, Magdalena Chojnacka, Wiesław Bielawski, Mariusz Czarnocki-Cieciura, Sławomir Orzechowski
Phytocystatins are a group of proteins with significant potential to regulate activities of cysteine proteinases of native and pest/pathogen origins. The two-domain triticale (x Triticosecale Wittm.) phytocystatin TrcC-8 was characterized in this study. This protein belongs to the second group of phytocystatins and contains all the conserved sequences and motifs as well as both N-terminal (CY) and C-terminal (CY-L) domains that are characteristic of phytocystatins with the C-terminal extension. We demonstrated that TrcC-8 forms stable dimers with a significantly reduced inhibitory activity against papain compared to the activity of monomers, indicating the regulatory nature of the oligomerization...
June 24, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28654754/potential-strategies-to-target-protein-protein-interactions-in-the-dna-damage-response-and-repair-pathways
#9
Naoaki Fujii
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, based on functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent...
June 27, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28654752/in-silico-prediction-of-the-toxic-potential-of-lupeol
#10
Manuel Antonio Ruiz-Rodríguez, Angelo Vedani, Ana Lidia Flores-Mireles, Manuel Humberto Chairez-Ramirez, Jose Alberto Gallegos-Infante, Ruben F Gonzalez-Laredo
Lupeol is a natural triterpenoid found in many plant species such as mango. This compound is the principal active component of many traditional herbal medicines. In the past decade, a considerable number of publications dealt with lupeol and its analogues due to the interest in their pharmacological activities against cancer, inflammation, arthritis, diabetes, and heart disease. To identify further potential applications of lupeol and its analogues, it is necessary to investigate their mechanisms of action, particularly, their interaction with off-target proteins that may trigger adverse effects or toxicity...
June 27, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28654751/substrate-recognition-mechanism-of-the-putative-yeast-carnosine-n-methyltransferase
#11
Xiwen Liu, Jialiang Wu, Yujie Sun, Wei Xie
Anserine (β-alanyl-N(Pi) -methyl-L-histidine) is a natural metabolite present in skeletal muscle and the central nervous system of vertebrates, and plays important physiological roles in living organisms. The production of anserine is catalyzed by carnosine N-methyltransferases, which transfer a methyl group to carnosine (β-alanyl-L-histidine). However, the structural basis of the substrate recognition for the enzymes is unknown. We present the crystal structure of the putative carnosine N-methyltransferase from yeast named YNL092W in complex with SAH, solved by the single-wavelength anomalous dispersion (SAD) method...
June 27, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28654729/signor-a-database-of-causal-relationships-between-biological-entities-a-short-guide-to-searching-and-browsing
#12
Prisca Lo Surdo, Alberto Calderone, Gianni Cesareni, Livia Perfetto
SIGNOR (http://signor.uniroma2.it), the SIGnaling Network Open Resource, is a database designed to store experimentally validated causal interactions, i.e., interactions where a source entity has a regulatory effect (up-regulation, down-regulation, etc.) on a second target entity. SIGNOR acts both as a source of signaling information and a support for data analysis, modeling, and prediction. A user-friendly interface features the ability to search entries for any given protein or group of proteins and to display their interactions graphically in a network view...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654728/finding-similar-nucleotide-sequences-using-network-blast-searches
#13
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654715/a-secondary-structure-element-present-in-a-wide-range-of-fucosylated-glycoepitopes
#14
Mario Schubert, Thomas Aeschbacher, Mirko Zierke, Martin Smieško, Mayeul Collot, Jean-Maurice Mallet, Beat Ernst, Frédéric H-T Allain
The increasing understanding of the essential role of carbohydrates in development, and in a wide range of diseases fuels a rapidly growing interest in the basic principles governing carbohydrate-protein interactions. A still heavily debated issue regarding the recognition process is the degree of flexibility or rigidity of oligosaccharides. Combining NMR structure determination based on extensive experimental data with density functional theory (DFT) and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond...
June 27, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28654687/combined-single-cell-quantitation-of-host-and-siv-genes-and-proteins-ex-vivo-reveals-host-pathogen-interactions-in-individual-cells
#15
Diane L Bolton, Kathleen McGinnis, Greg Finak, Pratip Chattopadhyay, Raphael Gottardo, Mario Roederer
CD4 T cells harboring HIV-1/SIV represent a formidable hurdle to eradicating infection, and yet their detailed phenotype remains unknown. Here we integrate two single-cell technologies, flow cytometry and highly multiplexed quantitative RT-PCR, to characterize SIV-infected CD4 T cells directly ex vivo. Within individual cells, we correlate the cellular phenotype, in terms of host protein and RNA expression, with stages of the viral life cycle defined by combinatorial expression of viral RNAs. Spliced RNA+ infected cells display multiple memory and activation phenotypes, indicating virus production by diverse CD4 T cell subsets...
June 27, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28654660/isolation-and-characterization-of-gmmybj3-an-r2r3-myb-transcription-factor-that-affects-isoflavonoids-biosynthesis-in-soybean
#16
Mingzhu Zhao, Tianliang Wang, Ping Wu, Wenyun Guo, Liantai Su, Ying Wang, Yajing Liu, Fan Yan, Qingyu Wang
Isoflavonoids are secondary metabolites that play a variety of roles in plant-microbe interactions and plant defenses against abiotic stresses. Here we report a new MYB transcription factor (TF) gene, GmMYBJ3, that is involved in the isoflavonoids biosynthesis. The GmMYBJ3 gene is 1,002 bp long and encodes a protein of 333 amino acids. Amino acid sequence analysis showed that GmMYBJ3 is a typical R2R3 MYB TF. Yeast expression experiment demonstrated that GmMYBJ3 has its transcription activity in the nucleus and is transiently expressed in onion epidermal cells...
2017: PloS One
https://www.readbyqxmd.com/read/28654641/biological-effects-of-the-hypomagnetic-field-an-analytical-review-of-experiments-and-theories
#17
Vladimir N Binhi, Frank S Prato
During interplanetary flights in the near future, a human organism will be exposed to prolonged periods of a hypomagnetic field that is 10,000 times weaker than that of Earth's. Attenuation of the geomagnetic field occurs in buildings with steel walls and in buildings with steel reinforcement. It cannot be ruled out also that a zero magnetic field might be interesting in biomedical studies and therapy. Further research in the area of hypomagnetic field effects, as shown in this article, is capable of shedding light on a fundamental problem in biophysics-the problem of primary magnetoreception...
2017: PloS One
https://www.readbyqxmd.com/read/28654636/human-cyclophilin-40-unravels-neurotoxic-amyloids
#18
Jeremy D Baker, Lindsey B Shelton, Dali Zheng, Filippo Favretto, Bryce A Nordhues, April Darling, Leia E Sullivan, Zheying Sun, Parth K Solanki, Mackenzie D Martin, Amirthaa Suntharalingam, Jonathan J Sabbagh, Stefan Becker, Eckhard Mandelkow, Vladimir N Uversky, Markus Zweckstetter, Chad A Dickey, John Koren, Laura J Blair
The accumulation of amyloidogenic proteins is a pathological hallmark of neurodegenerative disorders. The aberrant accumulation of the microtubule associating protein tau (MAPT, tau) into toxic oligomers and amyloid deposits is a primary pathology in tauopathies, the most common of which is Alzheimer's disease (AD). Intrinsically disordered proteins, like tau, are enriched with proline residues that regulate both secondary structure and aggregation propensity. The orientation of proline residues is regulated by cis/trans peptidyl-prolyl isomerases (PPIases)...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28654419/affimers-proteins-are-versatile-and-renewable-affinity-reagents
#19
Christian Tiede, Robert Bedford, Sophie J Heseltine, Gina Smith, Imeshi Wijetunga, Rebecca Ross, Danah AlQallaf, Ashley Pe Roberts, Alexander Balls, Alistair Curd, Ruth E Hughes, Heather Martin, Sarah R Needham, Laura C Zanetti-Domingues, Yashar Sadigh, Thomas P Peacock, Anna A Tang, Naomi Gibson, Hannah Kyle, Geoffrey W Platt, Nicola Ingram, Thomas Taylor, Louise P Coletta, Iain Manfield, Margaret Knowles, Sandra Bell, Filomena Esteves, Azhar Maqbool, Raj K Prasad, Mark Drinkhill, Robin S Bon, Vikesh Patel, Sarah A Goodchild, Marisa Martin-Fernandez, Ray J Owens, Joanne E Nettleship, Michael E Webb, Michael Harrison, Jonathan D Lippiat, Sreenivasan Ponnambalam, Michelle Peckham, Alastair Smith, Paul Ko Ferrigno, Matt Johnson, Michael J McPherson, Darren Charles Tomlinson
Molecular recognition reagents are key tools for understanding biological processes and are used universally by scientists to study protein expression, localisation and interactions. Antibodies remain the most widely used of such reagents and many show excellent performance, although some are poorly characterised or have stability or batch variability issues, supporting the use of alternative binding proteins as complementary reagents for many applications. Here we report on the use of Affimer proteins as research reagents...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28654306/gene-expression-profile-of-peripheral-blood-mononuclear-cells-in-response-to-intracerebral-hemorrhage
#20
Ming Sang, Xuanbin Wang, Hanyao Zhang, Xiaodong Sun, Xudong Ding, Puqing Wang, Rong Jiao, Huaxian Cheng, Sijun Yang, Guibin Zhang
RNA-sequencing, a powerful tool, yields a comprehensive view of whole transcriptome. Intracerebral hemorrhage (ICH) is a devastating form of stroke. To date, RNA-sequencing analysis of ICH has not been reported. Peripheral blood mononuclear cells (PBMCs) were used as a source of mRNA for gene expression profile analysis in stroke. In this study, we performed transcriptome analyses for PBMCs from four ICH patients and four healthy volunteers on Illumina platform. We identified 4040 significantly differentially expressed genes (DEGs)...
June 27, 2017: DNA and Cell Biology
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