keyword
MENU ▼
Read by QxMD icon Read
search

Bioinformatics & pathogenicity prediction

keyword
https://www.readbyqxmd.com/read/28637420/bioinformatics-insights-on-targets-receptors-of-amiodarone-in-human-and-acanthamoeba-castellanii
#1
Abdul Baig, Zohaib Rana, H R Ahmad
BACKGROUND: Amiodarone is prescribed for certain cardiac arrhythmias in medical practice. The drug targets and inhibits voltage dependent sodium (Na+v), calcium (Ca+2v), potassium (K+v) channels, and enzymes like cytochrome P450 and oxidosqualene cyclase. Past studies have shown that amiodarone exerts anti-amoebic effects against Trypanosoma cruzi and Acanthamoeba castellanii. OBJECTIVES: The presence of aforementioned targets and the type of cell death induced by amiodarone in these pathogenic eukaryotes like Acanthamoeba castellanii remain to be verified...
June 21, 2017: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/28630199/genome-wide-analysis-of-the-antimicrobial-peptides-in-python-bivittatus-and-characterization-of-cathelicidins-with-potent-antimicrobial-activity-and-low-cytotoxicity
#2
Dayeong Kim, Nagasundarapandian Soundrarajan, Juyeon Lee, Hye-Sun Cho, Minkyeung Choi, Se-Yeoun Cha, Byeongyong Ahn, Hyoim Jeon, Minh Thong Le, Hyuk Song, Jin-Hoi Kim, Chankyu Park
In this study, we sought to identify novel antimicrobial peptides (AMPs) in Python bivittatus through bioinformatic analyses of publicly available genome information and experimental validation. In our analysis of the python genome, we identified 29 AMP-related candidate sequences. Of these, we selected five cathelicidin-like sequences and subjected them to further in silico analyses. The results showed that these sequences likely have antimicrobial activity. The sequences were named Pb-CATH1-Pb-CATH5 according to their sequence similarity to previously reported snake cathelicidins...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#3
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28622862/identification-of-lawsonia-intracellularis-putative-hemolysin-protein-a-and-characterization-of-its-immunoreactivity
#4
Jehyung Kim, Gayeon Won, Suyeon Park, John Hwa Lee
Despite the recent global increase in fatal endemic outbreaks of proliferative enteropathy (PE) caused by the obligate intracellular bacterium Lawsonia intracelluralis (LI) in the swine industry, development of effective prevention strategies or immunodiagnostic tests has been delayed due to the difficulty of cultivating this pathogen in vitro. Although several genetic analyses have been performed at the level of gene transcription after the complete genome sequence of LI was made available, the mechanism of LI infection and virulence genes remain unidentified...
June 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28620585/identification-of-a-large-family-of-slam-dependent-surface-lipoproteins-in-gram-negative-bacteria
#5
Yogesh Hooda, Christine C L Lai, Trevor F Moraes
The surfaces of many Gram-negative bacteria are decorated with soluble proteins anchored to the outer membrane via an acylated N-terminus; these proteins are referred to as surface lipoproteins or SLPs. In Neisseria meningitidis, SLPs such as transferrin-binding protein B (TbpB) and factor-H binding protein (fHbp) are essential for host colonization and infection because of their essential roles in iron acquisition and immune evasion, respectively. Recently, we identified a family of outer membrane proteins called Slam (Surface lipoprotein assembly modulator) that are essential for surface display of neisserial SLPs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28609666/the-hippeastrum-hybridum-pepr1-gene-hppepr1-encodes-a-functional-guanylyl-cyclase-and-is-involved-in-early-response-to-fungal-infection
#6
Brygida Świeżawska, Krzysztof Jaworski, Maria Duszyn, Agnieszka Pawełek, Adriana Szmidt-Jaworska
It is generally known that cyclic GMP widespread in prokaryotic and eukaryotic cells, is involved in essential cellular processes and stress signal transduction. However, in contrast to animals the knowledge about plant guanylyl cyclases (GCs) which catalyze the formation of cGMP from GTP is still quite obscure. Recent studies of plant GCs are focused on identification and functional analysis of a new family of membrane proteins called "moonlighting kinases with GC activity" with guanylyl cyclase catalytic center encapsulated within intracellular kinase domain...
June 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28578022/comprehensive-molecular-characterization-of-a-transgenic-pig-expressing-hcd46-gene
#7
Qin Wang, Ningning Shi, Ying Shang, Xiaofei Liu, Wei Fu, Yiqiang Zhao, Dengke Pan, Xiangmei Lin, Wentao Xu
Molecular characterization of transgenic animals is crucial for the phenotype analysis, unintended effects prediction, commercial and economic requirements. In this study, a comprehensive molecular characterization of a transgenic pig, which expressed hCD46 gene, was verified using next-generation sequencing (NGS). One complete and one incomplete sequence of pBSCD46-neo and multiple backbone fragments were inserted into the host genome. The whole insertion sequence was 28,243bp, and 12bp sequence on the genome was deleted during the transgene...
May 31, 2017: Gene
https://www.readbyqxmd.com/read/28574575/genomics-of-antibiotic-resistance-prediction-in-pseudomonas-aeruginosa
#8
REVIEW
Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Jean-Guillaume Emond-Rheault, Nicholas P Tucker, Roger C Levesque
Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation...
June 2, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28549079/computational-modeling-of-immune-system-of-the-fish-for-a-more-effective-vaccination-in-aquaculture
#9
Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano
Motivation: A computational model equipped with the main immunological features of the sea bass ( Dicentrarchus labrax L. ) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae . Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28546994/sdha-related-tumorigenesis-a-new-case-series-and-literature-review-for-variant-interpretation-and-pathogenicity
#10
Ruth T Casey, David B Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A Andrews, Helen L Simpson, Benjamen Challis, Soo-Mi Park, Venkata R Bulusu, Fiona Lalloo, Douglas E V Pires, Hannah West, Graeme R Clark, Philip S Smith, James Whitworth, Thomas G Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D Hurst, Emma R Woodward, Eamonn R Maher
PURPOSE: To evaluate the role of germline SDHA mutation analysis by (1) comprehensive literature review, (2) description of novel germline SDHA mutations and (3) in silico structural prediction analysis of missense substitutions in SDHA. PATIENTS AND METHODS: A systematic literature review and a retrospective review of the molecular and clinical features of patients identified with putative germline variants in UK molecular genetic laboratories was performed. To evaluate the molecular consequences of SDHA missense variants, a novel model of the SDHA/B/C/D complex was generated and the structural effects of missense substitutions identified in the literature, our UK novel cohort and a further 32 "control missense variants" were predicted by the mCSM computational platform...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546024/mirna-8159-is-involved-in-tlr-signaling-pathway-regulation-after-pathogen-infection-by-direct-targeting-tlr13-in-miiuy-croaker
#11
Junxia Cui, Yunhang Gao, Qing Chu, Dekun Bi, Tianjun Xu
Toll-like receptors (TLRs) play a crucial role in the recognition of immune reactions against invading pathogens. The molecular regulation mechanisms of TLR expression in aquatic organisms remain unclear. MicroRNAs (miRNAs) are small non-coding RNAs that are critical adjustors of immune signaling pathway at the post-transcriptional level and play critical roles in intricate networks of host-pathogen interactions and innate immunity. The critical role of TLRs in host defense for discerning certain kinds of pathogen associated molecular patternsand striking a cascade immune response in fish have been demonstrated...
May 22, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28544481/matching-phenotypes-to-whole-genomes-lessons-learned-from-four-iterations-of-the-personal-genome-project-community-challenges
#12
Binghuang Cai, Biao Li, Nikki Kiga, Janita Thusberg, Timothy Bergquist, Yun-Ching Chen, Noushin Niknafs, Hannah Carter, Collin Tokheim, Violeta Beleva-Guthrie, Christopher Douville, Rohit Bhattacharya, Hui Ting Grace Yeo, Jean Fan, Sohini Sengupta, Dewey Kim, Melissa Cline, Tychele Turner, Mark Diekhans, Jan Zaucha, Lipika R Pal, Chen Cao, Chen-Hsin Yu, Yizhou Yin, Marco Carraro, Manuel Giollo, Carlo Ferrari, Emanuela Leonardi, Silvio C E Tosatto, Jason Bobe, Madeleine Ball, Roger Hoskins, Susanna Repo, George Church, Steven E Brenner, John Moult, Julian Gough, Mario Stanke, Rachel Karchin, Sean D Mooney
The advent of next generation sequencing has dramatically decreased the cost for whole genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28524153/transcriptome-analysis-of-mirna-lncrna-mrna-interactions-in-the-malignant-transformation-process-of-gastric-cancer-initiation
#13
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...
June 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28520167/kmt2b-rare-missense-variants-in-generalized-dystonia
#14
Michael Zech, Robert Jech, Petra Havránková, Anna Fečíková, Riccardo Berutti, Dušan Urgošík, David Kemlink, Tim M Strom, Jan Roth, Evžen Růžička, Juliane Winkelmann
BACKGROUND: Recently a novel syndrome of childhood-onset generalized dystonia originating from mutations in lysine-specific methyltransferase 2B (KMT2B) has been reported. METHODS: We sequenced the exomes of 4 generalized dystonia-affected probands recruited from a Prague movement disorders center (Czech Republic). Bioinformatics analyses were conducted to select candidate causal variants in described dystonia-mutated genes. After cosegregation testing, checklists from the American College of Medical Genetics and Genomics were adopted to judge variant pathogenicity...
May 18, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28506932/refined-annotation-of-the-complete-genome-of-the-phytopathogenic-and-xanthan-producing-xanthomonas-campestris-pv-campestris-strain-b100-based-on-rna-sequence-data
#15
Rabeaa S Alkhateeb, Christian Rückert, Oliver Rupp, Boas Pucker, Gerd Hublik, Daniel Wibberg, Karsten Niehaus, Alfred Pühler, Frank-Jörg Vorhölter
Bioinformatics tools and gene expression data were applied to identify new genes and to enhance the accuracy in genomic feature predictions for Xanthomonas campestris pv. campestris (Xcc) B100, a pathogen of cruciferous plants and model strain for the biosynthesis of xanthan, a polysaccharide with a multitude of commercial applications as a thickening agent. Results from 5'-enriched end RNA sequencing (RNA-seq) and total transcriptome RNA-seq experiments were used for this purpose. Functional gene annotations were updated where new evidence had emerged and start codon predictions were enhanced for 153 protein-coding genes (CDS)...
May 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28506204/antibiotic-effects-of-loperamide-homology-of-human-targets-of-loperamide-with-targets-in-acanthamoeba-spp
#16
Abdul Mannan Baig, Zohaib Rana, M Mohsin Mannan, S Sumayya Tariq, H R Ahmad
BACKGROUND: Loperamide is an anti-diarrheal drug prescribed for non-infectious diarrhea. The drug is an opioid receptor agonist, a blocker of voltage-dependent calcium channel (Cav) and a calmodulin (CaM) inhibitor on human cells. Loperamide has been reported to exert anti-amoebic effects against pathogenic strains of Acanthamoeba castellanii. OBJECTIVES: The precise mode of antibiotic action, cellular target homology with human counterparts and the pattern of cell death induced by loperamide in Acanthamoeba castellanii remain to be established...
April 25, 2017: Recent Patents on Anti-infective Drug Discovery
https://www.readbyqxmd.com/read/28496441/discovery-of-novel-leptospirosis-vaccine-candidates-using-reverse-and-structural-vaccinology
#17
André Alex Grassmann, Frederico Schmitt Kremer, Júlia Cougo Dos Santos, Jéssica Dias Souza, Luciano da Silva Pinto, Alan John Alexander McBride
Leptospira spp. are diderm (two membranes) bacteria that infect mammals causing leptospirosis, a public health problem with global implications. Thousands of people die every year due to leptospirosis, especially in developing countries with tropical climates. Prophylaxis is difficult due to multiple factors, including the large number of asymptomatic hosts that transmit the bacteria, poor sanitation, increasing numbers of slum dwellers, and the lack of an effective vaccine. Several leptospiral recombinant antigens were evaluated as a replacement for the inactivated (bacterin) vaccine; however, success has been limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28494495/mutations-in-lrp5-fzd4-tspan12-ndp-znf408-or-kif11-genes-account-for-38-7-of-chinese-patients-with-familial-exudative-vitreoretinopathy
#18
Feng-Qin Rao, Xue-Bi Cai, Fei-Fei Cheng, Wan Cheng, Xiao-Long Fang, Na Li, Xiu-Feng Huang, Li-Hong Li, Zi-Bing Jin
Purpose: Familial exudative vitreoretinopathy (FEVR) is a severe hereditary retinal disorder characterized by defects in retinal vascular development. To date, six genes have been reported to be responsible for this disease, including LRP5, FZD4, TSPAN12, NDP, ZNF408, and KIF11. The purpose of our study was to investigate the genetic defects in Chinese patients with FEVR through mutational analyses of 31 pedigrees. Methods: Clinical data and peripheral blood were collected from 31 pedigrees with FEVR...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28484437/a-novel-raym_rs09735-raym_rs09740-two-component-signaling-system-regulates-gene-expression-and-virulence-in-riemerella-anatipestifer
#19
Ying Wang, Ti Lu, Xuehuan Yin, Zutao Zhou, Shaowen Li, Mei Liu, Sishun Hu, Dingren Bi, Zili Li
The Gram-negative bacterium Riemerella anatipestifer is an important waterfowl pathogen, causing major economic losses to the duck-producing industry. However, little is known of the virulence factors that mediate pathogenesis during R. anatipestifer infection. In this study, RAYM_RS09735 and RAYM_RS09740 were predicted to form a two-component signaling system (TCS) through bioinformatics analysis. This TCS was highly conserved across the Flavobacteriaceae. A mutant YMΔRS09735/RS09740 strain was constructed to investigate the role of the RAYM_RS09735/RAYM_RS09740 TCS in R...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28480143/analysis-of-microsatellites-from-the-transcriptome-of-downy-mildew-pathogens-and-their-application-for-characterization-of-pseudoperonospora-populations
#20
Emma C Wallace, Lina M Quesada-Ocampo
Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P...
2017: PeerJ
keyword
keyword
17762
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"