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https://www.readbyqxmd.com/read/28527409/molecular-characterization-of-pigeon-torque-teno-virus-pttv-in-jiangsu-province
#1
Zhicheng Zhang, Wei Dai, Dingzhen Dai
The torque teno virus (TTV) is a recently discovered DNA virus that has been detected in many different hosts, including humans, livestock and poultry. To date, there is no report of pigeon TTV (PTTV) from anywhere in the world. To investigate the distribution of PTTV in pigeons from the eastern Chinese province of Jiangsu and characterize their genomes, we employed PCR to detect PTTV in 144 samples collected from 6 pigeon plants in Jiangsu province, amplify complete genomes from representative samples and analyze genetic characteristics using bioinformatics...
May 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28527113/mutant-p53-promotes-cell-spreading-and-migration-via-arhgap44
#2
Jinjin Xu, Jian Jiao, Wei Xu, Lei Ji, Dongjie Jiang, Shaofang Xie, Syeda Kubra, Xiaotao Li, Junjiang Fu, Jianru Xiao, Bianhong Zhang
The tumor suppressor p53 protein is either lost or mutated in about half of all human cancers. Loss of p53 function is well known to influence cell spreading, migration and invasion. While expression of mutant p53 is not equivalent to p53 loss, mutant p53 can acquire new functions to drive cell spreading and migration via different mechanisms. In our study, we found that mutant p53 significantly increased cell spreading and migration when comparing with p53-null cells. RNA-Seq analysis suggested that Rho GTPase activating protein 44 (ARHGAP44) is a new target of mutant p53, which suppressed ARHGAP44 transcription...
May 16, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28526933/protection-of-tubular-epithelial-cells-during-renal-injury-via-post-transcriptional-control-of-bmp7
#3
Jiping Sun, Aiping Yin, Fei Zhao, Wenjing Zhang, Jia Lv, Jing Lv
Severe injury of renal tubular epithelial cells may cause acute renal failure, the progression of which results in renal fibrosis, and obstructive nephropathy. Transforming growth factor β 1 and bone morphogenic protein 7 (BMP7) play contradicting roles in and coordinate the process of epithelial-to-mesenchymal transition of renal tubular epithelial cells, but the molecular regulation of BMP7 remains ill-defined. Here, we addressed this question. We found that after induction of unilateral ureteral obstruction (UUO) in mice, the increases in BMP7 mRNA were much more pronounced than BMP7 protein in kidney, suggesting the presence of post-transcriptional control of BMP7...
May 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28526858/expression-and-activity-of-the-bioh-esterase-of-biotin-synthesis-is-independent-of-genome-context
#4
Xinyun Cao, Lei Zhu, Zhe Hu, John E Cronan
BioH is an α/β-hydrolase required for synthesis of the pimelate moiety of biotin in diverse bacteria. The bioH gene is found in different genomic contexts. In some cases (e.g., Escherichia coli) the gene is not located within a biotin synthetic operon and its transcription is not coregulated with the other biotin synthesis genes. In other genomes such as Pseudomonas aeruginosa the bioH gene is within a biotin synthesis operon and its transcription is coregulated with the other biotin operon genes. The esterases of pimelate moiety synthesis show remarkable genomic plasticity in that in some biotin operons bioH is replaced by other α/ß hydrolases of diverse sequence...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526816/delineation-of-b-cell-epitopes-of-salmonella-enterica-serovar-typhi-hemolysin-e-potential-antibody-therapeutic-target
#5
Chai Fung Chin, Jing Yi Lai, Yee Siew Choong, Amy Amilda Anthony, Asma Ismail, Theam Soon Lim
Hemolysin E (HlyE) is an immunogenic novel pore-forming toxin involved in the pathogenesis of typhoid fever. Thus, mapping of B-cell epitopes of Salmonella enterica serovar Typhi (S. Typhi) is critical to identify key immunogenic regions of HlyE. A random 20-mer peptide library was used for biopanning with enriched anti-HlyE polyclonal antibodies from typhoid patient sera. Bioinformatic tools were used to refine, analyze and map the enriched peptide sequences against the protein to identify the epitopes. The analysis identified both linear and conformational epitopes on the HlyE protein...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526810/bioinformatics-and-in-vitro-experimental-analyses-identify-the-selective-therapeutic-potential-of-interferon-gamma-and-apigenin-against-cervical-squamous-cell-carcinoma-and-adenocarcinoma
#6
Pei-Ming Yang, Chia-Jung Chou, Ssu-Hsueh Tseng, Chien-Fu Hung
The clinical management and treatment of cervical cancer, one of the most commonly diagnosed cancers and a leading cause of cancer-related female death, remains a huge challenge for researchers and health professionals. Cervical cancer can be categorized into two major subtypes: common squamous cell carcinoma (SCC) and adenocarcinoma (AC). Although it is a relatively rare histological subtype of cervical cancer, there has been a steady increase in the incidences of AC. Therefore, new strategies to treat cervical cancer are urgently needed...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28526789/a-novel-iron-dependent-enzyme-that-catalyzes-the-initial-step-in-the-biodegradation-of-n-nitroglycine-by-variovorax-sp-strain-js1663
#7
Kristina M Mahan, Hangping Zheng, Tekle T Fida, Ronald J Parry, David E Graham, Jim C Spain
Nitramines are key constituents of most of the explosives in current use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals, thus understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5- triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#8
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526268/structural-and-functional-aspects-of-the-nonribosomal-peptide-synthetase-condensation-domain-superfamily-discovery-dissection-and-diversity
#9
REVIEW
Kristjan Bloudoff, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28526043/management-of-rare-diseases-of-the-head-neck-and-teeth-results-of-a-french-population-based-prospective-8-year-study
#10
Lisa Friedlander, Rémy Choquet, Eva Galliani, Myriam de Chalendar, Claude Messiaen, Amélie Ruel, Marie-Paule Vazquez, Ariane Berdal, Corinne Alberti, Muriel De La Dure Molla
BACKGROUND: In the last ten years, national rare disease networks have been established in France, including national centres of expertise and regional ones, with storage of patient data in a bioinformatics tool. The aim was to contribute to the development and evaluation of health strategies to improve the management of patients with rare diseases. The objective of this study has been to provide the first national-level data concerning rare diseases of the head, neck and teeth and to assess the balance between demand and supply of care in France...
May 19, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28525976/the-adaptation-of-colorectal-cancer-cells-when-forming-metastases-in-the-liver-expression-of-associated-genes-and-pathways-in-a-mouse-model
#11
Derya Bocuk, Alexander Wolff, Petra Krause, Gabriela Salinas, Annalen Bleckmann, Christina Hackl, Tim Beissbarth, Sarah Koenig
BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related death in men and women. Systemic disease with metastatic spread to distant sites such as the liver reduces the survival rate considerably. The aim of this study was to investigate the changes in gene expression that occur on invasion and expansion of CRC cells when forming metastases in the liver. METHODS: The livers of syngeneic C57BL/6NCrl mice were inoculated with 1 million CRC cells (CMT-93) via the portal vein, leading to the stable formation of metastases within 4 weeks...
May 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28525837/differentially-expressed-jak-stat-signaling-pathway-genes-and-target-micrornas-in-the-spleen-of-necrotic-enteritis-afflicted-chicken-lines
#12
Anh Duc Truong, Deivendran Rengaraj, Yeojin Hong, Cong Thanh Hoang, Yeong Ho Hong, Hyun S Lillehoj
The JAK signal transducer and STAT signaling pathway is an important regulator of cell proliferation, differentiation, survival, motility, apoptosis, immune response, and development. In this study, we used RNA-Sequencing, qRT-PCR, and bioinformatics tools to investigate the differential expression of JAK-STAT pathway genes, their interactions, and regulators in the spleen of two genetically disparate chicken lines (Marek's disease-resistant line 6.3 and MD-susceptible line 7.2) induced necrotic enteritis (NE) disease by co-infection with Eimeria maxima and Clostridium perfringens...
May 13, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28525653/predicted-philogeny-secondary-conformational-structure-and-epitope-antigenicity-of-immunological-sequences-in-poultry
#13
L J Lara, A P Peconick, É J Fassani, A M P Júnior, P R B Chalfun, D L Raymundo, T A Barçante, J M de P Barçante
Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28525546/on-patterns-and-re-use-in-bioinformatics-databases
#14
Michael Bell, Phillip Lord
Motivation: HASH(0x5730208) Results: HASH(0x49751d0)
May 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28525531/phyd3-a-phylogenetic-tree-viewer-with-extended-phyloxml-support-for-functional-genomics-data-visualization
#15
Lukasz Kreft, Alexander Botzki, Frederik Coppens, Klaas Vandepoele, Michiel Van Bel
Motivation: Comparative and evolutionary studies utilise phylogenetic trees to analyse and visualise biological data. Recently, several web-based tools for the display, manipulation, and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available...
May 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28524153/transcriptome-analysis-of-mirna-lncrna-mrna-interactions-in-the-malignant-transformation-process-of-gastric-cancer-initiation
#16
Y Mao, R Liu, H Zhou, S Yin, Q Zhao, X Ding, H Wang
Gastric cancer is a common heterogeneous malignancy that is pathologically characterized by the development of chronic atrophic gastritis and dysplasia of the epithelium. The pathogenic mechanisms at the molecular level are completely unclear. In the present study, we first address the expression network and miRNA-lncRNA-mRNA interaction in the malignant transformation process from normal mucosa and atrophic gastritis to a tumor. First, the long non-coding RNA (lncRNA), micro RNA (miRNA) and messenger RNA (mRNA) expression profiles of normal gastric mucosa, atrophic gastritis, gastric cancer and the peri-tumor tissues were analyzed using microarrays...
May 19, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28523576/proteomic-analysis-of-serum-amyloid-a-as-a-potential-marker-in-intestinal-beh%C3%A3-et-s-disease
#17
Hyun Jung Lee, Jae Hyun Kim, Seung Won Kim, Hyun Ah Joo, Hye Won Lee, You Sun Kim, Soo Jung Park, Sung Pil Hong, Tae Il Kim, Won Ho Kim, Young-Ho Kim, Jae Hee Cheon
BACKGROUND/AIMS: Data regarding biomarkers to understand disease pathogenesis and to assess disease activity of intestinal Behçet's disease (BD) are limited. Therefore, we aimed to investigate the differentially expressed proteins in sera from patients with intestinal BD and to search for biomarkers using mass spectrometry-based proteomic analysis. METHODS: Serum samples were pooled for the screening study, and two-dimensional electrophoresis (2-DE) was performed to characterize the proteins present in intestinal BD patients...
May 18, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28523562/bioinformatics-tools-for-genome-wide-epigenetic-research
#18
Vladimir Espinosa Angarica, Antonio Del Sol
Epigenetics play a central role in the regulation of many important cellular processes, and dysregulations at the epigenetic level could be the source of serious pathologies, such as neurological disorders affecting brain development, neurodegeneration, and intellectual disability. Despite significant technological advances for epigenetic profiling, there is still a need for a systematic understanding of how epigenetics shapes cellular circuitry, and disease pathogenesis. The development of accurate computational approaches for analyzing complex epigenetic profiles is essential for disentangling the mechanisms underlying cellular development, and the intricate interaction networks determining and sensing chromatin modifications and DNA methylation to control gene expression...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523221/reading-lines-within-the-cocaine-addicted-brain
#19
Glenn A Doyle, Tara T Doucet-O'Hare, Matthew J Hammond, Richard C Crist, Adam D Ewing, Thomas N Ferraro, Deborah C Mash, Haig H Kazazian, Wade H Berrettini
INTRODUCTION: Long interspersed element (LINE)-1 (L1) is a type of retrotransposon capable of mobilizing into new genomic locations. Often studied in Mendelian diseases or cancer, L1s may also cause somatic mutation in the developing central nervous system. Recent reports showed L1 transcription was activated in brains of cocaine-treated mice, and L1 retrotransposition was increased in cocaine-treated neuronal cell cultures. We hypothesized that the predisposition to cocaine addiction may result from inherited L1s or somatic L1 mobilization in the brain...
May 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28522994/new-potent-membrane-targeting-antibacterial-peptides-from-viral-capsid-proteins
#20
Susana A Dias, João M Freire, Clara Pérez-Peinado, Marco M Domingues, Diana Gaspar, Nuno Vale, Paula Gomes, David Andreu, Sónia T Henriques, Miguel A R B Castanho, Ana S Veiga
The increasing prevalence of multidrug-resistant bacteria urges the development of new antibacterial agents. With a broad spectrum activity, antimicrobial peptides have been considered potential antibacterial drug leads. Using bioinformatic tools we have previously shown that viral structural proteins are a rich source for new bioactive peptide sequences, namely antimicrobial and cell-penetrating peptides. Here, we test the efficacy and mechanism of action of the most promising peptides among those previously identified against both Gram-positive and Gram-negative bacteria...
2017: Frontiers in Microbiology
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