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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/29342156/specialized-attachment-structure-of-the-fish-pathogenic-oomycete-saprolegnia-parasitica
#1
Svetlana Rezinciuc, Jose Vladimir Sandoval-Sierra, Yolanda Ruiz-León, Pieter van West, Javier Diéguez-Uribeondo
The secondary cysts of the fish pathogen oomycete Saprolegnia parasitica possess bundles of long hooked hairs that are characteristic to this economically important pathogenic species. Few studies have been carried out on elucidating their specific role in the S. parasitica life cycle and the role they may have in the infection process. We show here their function by employing several strategies that focus on descriptive, developmental and predictive approaches. The strength of attachment of the secondary cysts of this pathogen was compared to other closely related species where bundles of long hooked hairs are absent...
2018: PloS One
https://www.readbyqxmd.com/read/29335000/molecular-characterization-of-babesia-microti-thioredoxin-bmtrx2-and-its-expression-patterns-induced-by-antiprotozoal-drugs
#2
Jingwei Huang, Kang Xiong, Houshuang Zhang, Yanzhen Zhao, Jie Cao, Haiyan Gong, Yongzhi Zhou, Jinlin Zhou
BACKGROUND: Human babesiosis is an infectious disease that is epidemic in various regions all over the world. The predominant causative pathogen of this disease is the intra-erythrocytic parasite Babesia microti. The thioredoxin system is one of the major weapons that is used in the resistance to the reactive oxygen species (ROS) and reactive nitrogen species (RNS) produced by host immune system. In other intra-erythrocytic apicomplexans like the malaria parasite Plasmodium falciparum, anti-oxidative proteins are promising targets for the development of anti-parasitic drugs...
January 15, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29314318/two-novel-cps1-mutations-in-a-case-of-carbamoyl-phosphate-synthetase-1-deficiency-causing-hyperammonemia-and-leukodystrophy
#3
Xihui Chen, Lijuan Yuan, Mao Sun, Qingbo Liu, Yuanming Wu
BACKGROUND: Carbamoyl phosphate synthetase 1 deficiency (CPS1D) is a rare autosomal recessive disorder of the urea cycle, mostly characterized by hyperammonemia and the concomitant leukodystrophy. The onset of CPS1D can be at any age, and the clinical manifestations are variable and atypical. Genetic tests are indispensable for accurate diagnosis of CPS1D on the basis of biochemical tests. METHODS: Blood tandem mass spectrometric analysis and urea organic acidemia screening were performed on a Chinese neonatal patient with low activity, recurrent seizures, and hyperammonemia...
January 4, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29306012/preliminary-study-and-bioinformatics-analysis-on-the-potential-role-of-cagq-in-type-iv-secretion-system-of-h-pylori
#4
Yizheng Yao, Yixin Shen, Linqi Zhu, Ying Ni, Hua Wang, Shihe Shao
Helicobacter pylori (H.pylori), is a major causative agent of chronic gastritis, gastric carcinoma and duodenal ulcer. Remarkably, H.pylori carries cytotoxin-associated gene pathogenicity island (CagPAI) which encodes a type IV secretion system (T4SS). T4SS is capable of forming a syringe-like structure to deliver oncoprotein cytotoxin-associated Antigen (CagA) into gastric epithelial cells and resulting in a cascade of events in host cells, such as induction of pro-inflammatory cytokines, alteration of cellular gene expression and cytoskeletal rearrangements...
January 3, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29304759/a-novel-compound-heterozygous-variant-identified-in-gldc-gene-in-a-chinese-family-with-non-ketotic-hyperglycinemia
#5
Yiming Lin, Zhenzhu Zheng, Wenjia Sun, Qingliu Fu
BACKGROUND: Non-ketotic hyperglycinemia (NKH) is a rare, devastating autosomal recessive disorder of glycine metabolism with a very poor prognosis. Currently, few studies have reported genetic profiling of Chinese NKH patients. This study aimed to identify the genetic mutations in a Chinese family with NKH. METHODS: A Chinese family of Han ethnicity, with three siblings with NKH was studied. Sanger sequencing and multiplex ligation-dependent probe amplification combined with SYBR green real-time quantitative PCR was used to identify potential mutations in the GLDC, AMT and GCSH genes...
January 5, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29288449/surface-proteome-biotinylation-combined-with-bioinformatic-tools-as-a-strategy-for-predicting-pathogen-interacting-proteins
#6
Anita Horvatić, Josipa Kuleš, Nicolas Guillemin, Franjo Martinković, Iva Štimac, Vladimir Mrljak, Mangesh Bhide
Constant advancements in methodology and mass spectrometry instrumentation, genome sequencing and bioinformatic tools have enabled the identification of numerous pathogen proteomes. Identifying the pathogen interacting proteins by means of high-throughput techniques is key for understanding pathogen invasion and survival mechanisms and in such a way proposing specific proteins as pharmaceutical targets. Herein we describe the methodology for the enrichment and identification of pathogen surface proteome using cell surface protein biotinylation followed by LC-MS/MS and bioinformatic analyses of such data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29280312/dysbiosis-signatures-of-gut-microbiota-along-the-sequence-from-healthy-young-patients-to-those-with-overweight-and-obesity
#7
Renyuan Gao, Cuiling Zhu, Hao Li, Mingming Yin, Cheng Pan, Linsheng Huang, Cheng Kong, Xingchun Wang, Yi Zhang, Shen Qu, Huanlong Qin
OBJECTIVE: To investigate the gut microbiota in healthy volunteers (HVs), patients with overweight (OW), and patients with obesity (OB), including those with acanthosis nigricans (AN) or without AN (N-AN). METHODS: Microbial 16S rRNA genes were examined by using pyrosequencing technology and analyzed by using bioinformatics methods. RESULTS: Subjects in the OW and OB groups showed severe disturbances in glycemic control, lipid profile, and inflammatory markers (all P < 0...
December 27, 2017: Obesity
https://www.readbyqxmd.com/read/29260600/recent-insights-into-human-bronchial-proteomics-how-are-we-progressing-and-what-is-next
#8
Heng Wee Tan, Yan-Ming Xu, Dan-Dan Wu, Andy T Y Lau
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries...
December 20, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29258426/inferring-defense-related-gene-families-in-arabidopsis-and-wheat
#9
Rong-Cai Yang, Fred Y Peng, Zhiqiu Hu
BACKGROUND: A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana)...
December 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29251640/a-novel-factor-x-mutation-cys81-by-arg-and-a-reported-factor-vii-polymorphism-arg353-replaced-by-gln-co-occured-in-a-patient
#10
Yanhui Jin, Xiaoli Cheng, Jiayong Zheng, Hong Xia, Lihong Yang, Mingshan Wang
: Coagulation factor X and factor VII (FVII) are both very important components in blood coagulation. To study the molecular pathogenic mechanism of the inherited factor X and FVII deficiency, the factor X activity (FX:C) and FVII activity were tested with one-stage clotting methods. The factor X antigen and factor FVII antigen were tested with ELISA. All the exons, intron-exon boundaries and 5',3'-flanking regions of F10 and F7 genes were amplified by PCR with direct sequencing. The ClustalX software was used to analyze the conservative property of the mutation sites...
December 14, 2017: Blood Coagulation & Fibrinolysis: An International Journal in Haemostasis and Thrombosis
https://www.readbyqxmd.com/read/29251611/-bioinformatics-analysis-of-antimicrobial-resistance-genes-and-prophages-colocalized-in-human-gut-metagenomes
#11
E V Starikova, N A Prianichnikov, E Zdobnov, V M Govorun
The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database...
November 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29247798/circular-rna-expression-profile-of-articular-chondrocytes-in-an-il-1%C3%AE-induced-mouse-model-of-osteoarthritis
#12
Zhibin Zhou, Di Du, Aimin Chen, Lei Zhu
Osteoarthritis (OA) is a widely prevalent degenerative joint disease characterized by articular cartilage degradation and joint inflammation. The pathogenesis of OA remains unclear, leading to a lack of effective treatment. Previous studies have reported that circular RNAs (circRNAs) are involved in the development of various diseases. However, the function of circRNAs and their roles in OA is largely unknown. Therefore, we aimed to investigate changes in circRNA expression and predict their functions in OA by using bioinformatics analysis...
December 13, 2017: Gene
https://www.readbyqxmd.com/read/29247206/a-next-generation-newborn-screening-pilot-study-ngs-on-dried-blood-spots-detects-causal-mutations-in-patients-with-inherited-metabolic-diseases
#13
F Boemer, C Fasquelle, S d'Otreppe, C Josse, V Dideberg, K Segers, V Guissard, V Capraro, F G Debray, V Bours
The range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview of NGS capacities on DBS-extracted DNA but did not focus on the identification of specific disorders. We thus aimed to demonstrate that NGS was reliable for detecting pathogenic mutations on genomic material extracted from DBS. Assuming the future implementation of NGS technologies into newborn screening (NBS), we conducted a pilot study on fifteen patients with inherited metabolic disorders...
December 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29238877/cryptogenic-cholestasis-in-young-and-adults-atp8b1-abcb11-abcb4-and-tjp2-gene-variants-analysis-by-high-throughput-sequencing
#14
Giovanni Vitale, Stefano Gitto, Francesco Raimondi, Alessandro Mattiaccio, Vilma Mantovani, Ranka Vukotic, Antonietta D'Errico, Marco Seri, Robert B Russell, Pietro Andreone
BACKGROUND: Mutations in ATP-transporters ATPB81, ABCB11, and ABCB4 are responsible for progressive familial intrahepatic cholestasis (PFIC) 1, 2 and 3, and recently the gene for tight junction protein-2 (TJP2) has been linked to PFIC4. AIM: As these four genes have been poorly studied in young people and adults, we investigated them in this context here. METHODS: In patients with cryptogenic cholestasis, we analyzed the presence of mutations by high-throughput sequencing...
December 13, 2017: Journal of Gastroenterology
https://www.readbyqxmd.com/read/29238330/an-assessment-of-different-genomic-approaches-for-inferring-phylogeny-of-listeria-monocytogenes
#15
Clémentine Henri, Pimlapas Leekitcharoenphon, Heather A Carleton, Nicolas Radomski, Rolf S Kaas, Jean-François Mariet, Arnaud Felten, Frank M Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel-Yves Mistou, René S Hendriksen
Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29237407/identification-and-in-silico-characterization-of-a-novel-p-p208pfsx1-mutation-in-v-atpase-a3-subunit-associated-with-autosomal-recessive-osteopetrosis-in-a-pakistani-family
#16
Muhammad Ajmal, Asif Mir, Sughra Wahid, Chiea Chuen Khor, Jia Nee Foo, Saima Siddiqi, Mehran Kauser, Salman Akbar Malik, Muhammad Nasir
BACKGROUND: Osteopetrosis is a rare inherited bone disorder mainly described as an increased bone density caused by defective osteoclastic bone resorption. To date, genetic variants of eleven genes have been reported so far to be associated with different types of osteopetrosis. However, malignant infantile osteopetrosis, a lethal form of the disease, is mostly (50%) caused by mutation(s) in TCIRG1 gene. In this study, we investigated a consanguineous Pakistani family clinically and genetically to elucidate underlying molecular basis of the infantile osteopetrosis...
December 13, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/29226722/the-use-of-databases-data-mining-and-immunoinformatics-in-vaccinology-where-are-we
#17
Nagendra R Hegde, S Gauthami, H M Sampath Kumar, Jagadeesh Bayry
Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens...
December 11, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/29217154/production-of-a-chimeric-protein-and-its-potential-application-in-sero-diagnosis-of-mycoplasma-hominis-infection
#18
Saman Saadat, Mohammad M Sajadi, Mohammad Yousef Alikhani, Zahra Rikhtegaran Tehrani, Rasoul Yousefi Mashouf
INTRODUCTION: Mycoplasma hominis is an opportunistic pathogen of the human genital tract. Detection of antibodies against this organism in human serum or plasma is theoretically unreliable because of high variation in bacterial surface antigens. In this study, we applied the bioinformatics tools to design a chimeric protein constructed of specific, conserved and predicted immuno-dominant epitopes from two different membrane proteins, P120 and P80. MATERIAL AND METHODS: Linear B-cell epitopes of P120 and P80 were predicted and evaluated by bioinformatics tools and the designed chimeric protein was expressed in Escherichia coli...
December 4, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29216242/the-oxyr-regulated-phnw-gene-encoding-2-aminoethylphosphonate-pyruvate-aminotransferase-helps-protect-pseudomonas-aeruginosa-from-tert-butyl-hydroperoxide
#19
Warunya Panmanee, Nisanart Charoenlap, Sopapan Atichartpongkul, Aekkapol Mahavihakanont, Matthew D Whiteside, Geoff Winsor, Fiona S L Brinkman, Skorn Mongkolsuk, Daniel J Hassett
The LysR member of bacterial transactivators, OxyR, governs transcription of genes involved in the response to H2O2 and organic (alkyl) hydroperoxides (AHP) in the Gram-negative pathogen, Pseudomonas aeruginosa. We have previously shown that organisms lacking OxyR are rapidly killed by <2 or 500 mM H2O2 in planktonic and biofilm bacteria, respectively. In this study, we first employed a bioinformatic approach to elucidate the potential regulatory breadth of OxyR by scanning the entire P. aeruginosa PAO1 genome for canonical OxyR promoter recognition sequences (ATAG-N7-CTAT-N7-ATAG-N7-CTAT)...
2017: PloS One
https://www.readbyqxmd.com/read/29209284/the-sit-and-wait-hypothesis-in-bacterial-pathogens-a-theoretical-study-of-durability-and-virulence
#20
Liang Wang, Zhanzhong Liu, Shiyun Dai, Jiawei Yan, Michael J Wise
The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence...
2017: Frontiers in Microbiology
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