Read by QxMD icon Read

Bioinformatics & pathogenicity prediction

Yu Xia, Xianghua Wen, Bing Zhang, Yunfeng Yang
Understanding diversity and assembly patterns of microbial communities in activated sludge (AS) is pivotal for addressing fundamental ecological questions and wastewater treatment engineering. Recent applications of molecular methods especially next generation sequencing (NGS) have led to the explosion of information about AS community diversity, including the identification of uncultured taxa, and characterization of low-abundance but environmentally important populations such as antibiotic resistant bacteria and pathogens...
March 15, 2018: Biotechnology Advances
Afsar R Naqvi, Alexandra Seal, Jennifer Shango, Maria Brambila Navarette, Gloria Martinez, Gabriela Chapa, Shirin Hasan, Tejabhiram Yadavalli, Dinesh Jaishankar, Deepak Shukla, Salvador Nares
MicroRNAs (miRNAs) are small, non-coding RNAs of ~18-25 nucleotides that have gained extensive attention as critical regulators in complex gene networks including immune cell lineage commitment, differentiation, maturation, and maintenance of immune homeostasis and function. Many viruses encode miRNAs that directly downregulate the expression of factors of the innate immune system, which includes proteins involved in promoting apoptosis and recruitment. In this study, we examined the expression profiles of three previously identified viral miRNAs (v-miRs) from the human herpesvirus (HHV) family, HSV-1 (miR-H1), KSHV (miR-K12-3-3p), and HCMV (miR-US4) in healthy and diseased periodontal tissues and observed increased levels of v-miRs in diseased tissues...
March 14, 2018: Biochimica et Biophysica Acta
Xinyu Feng, Xiaojian Zhou, Shuisen Zhou, Jingwen Wang, Wei Hu
BACKGROUND: microRNAs (miRNAs) are small non-coding RNAs widely identified in many mosquitoes. They are reported to play important roles in development, differentiation and innate immunity. However, miRNAs in Anopheles sinensis, one of the Chinese malaria mosquitoes, remain largely unknown. METHODS: We investigated the global miRNA expression profile of An. sinensis using Illumina Hiseq 2000 sequencing. Meanwhile, we applied a bioinformatic approach to identify potential miRNAs in An...
March 12, 2018: Parasites & Vectors
Siri Lynne Rydning, Ales Dudesek, Florian Rimmele, Claudia Funke, Stefanie Krüger, Saskia Biskup, Magnus D Vigeland, Hanne S Hjorthaug, Yngve Sejersted, Chantal Tallaksen, Kaja K Selmer, Christoph Kamm
BACKGROUND AND PURPOSE: Hereditary spastic paraplegias (HSP) are clinically and genetically heterogenous monogenic disorders. To date, nearly 70 genes are known to be causative. The aim of this project was to identify the genetic cause of autosomal dominantly inherited pure HSP in two large, unrelated non-consanguineous families. METHODS: The two families were characterized clinically and selected members underwent whole exome sequencing. Potentially disease-causing variants were confirmed by Sanger sequencing and their functional consequences on protein function predicted by bioinformatic prediction tools...
March 12, 2018: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
Archana Singh, Deepti Jain, Chetna Tyagi, Sujata Singh, Sumit Kumar, Indrakant K Singh
Plants are endowed with an innate immune system, which enables them to protect themselves from pest and pathogen. The participation of pathogenesis-related (PR) proteins is one of the most crucial events of inducible plant defense response. Herein, we report the characterization of CaHaPR-4, a Helicoverpa-inducible class II PR-4 protein from chickpea. Bioinformatic analysis of CaHaPR-4 protein indicated the presence of a signal peptide, barwin domain but it lacks the chitin-binding site/hevein domain. The recombinant CaHaPR-4 is bestowed with RNase and bivalent ion-dependent DNase activity...
March 7, 2018: International Journal of Biological Macromolecules
Shachi Gahoi, Satendra Singh, Budhayash Gautam
Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infection is associated with the release of excretory/secretory (ES) proteins into host cytoplasm and interference with the host immune system which make them attractive targets for therapeutic use. The identification of ES proteins through bioinformatics approaches is cost- and time-effective and could be used for screening of potential targets for parasitic diseases for further experimental studies. Here, we identified and functionally annotated 93,949 ES proteins, in the genome of 73 nematodes using integration of various bioinformatics tools...
March 6, 2018: Genomics
Jing Yu, Gan Ai, Danyu Shen, Chunyue Chai, Yuling Jia, Wenjing Liu, Daolong Dou
The basic helix-loop-helix (bHLH) family, one of the largest transcription factor groups in plants, regulates many critical developmental processes. However, their functions in plant defense have not been extensively studied in Nicotiana benthamiana, an important model plant species for phytopathology. Here, we identified N. benthamiana bHLH genes (NbbHLHs) using a whole-genome searching approach, and found that the NbbHLHs are highly enriched and some subfamilies are selectively expanded in N. benthamiana...
March 6, 2018: Genomics
T Guan, H J Wu, L J Zhang, D J Xu, L B Zheng, Y F Yao
Objective: To investigate the possibility of the visual system homeobox 1 (VSX1) gene as a candidate susceptibility gene for Chinese patients with sporadic keratoconus, and to identify sequence variants of the VSX1 gene in such patients. Methods: Cross-sectional study. Genomic DNA was extracted from the leukocytes in the peripheral venous blood of 50 patients with sporadic keratoconus and 50 control subjects without this ocular disorder. Five exons and the intron-exon splicing of the VSX1 gene were amplified by polymerase chain reaction (PCR)...
March 11, 2018: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
Yanjiao Li, Li Li, Zhengjiang Qian, Boya Lin, Jidong Chen, Yixuan Luo, Junle Qu, J Usha Raj, Deming Gou
BACKGROUND: Platelet-derived growth factor BB, a potent mitogen of pulmonary artery smooth muscle cells (PASMCs), has been implicated in pulmonary arterial remodeling, which is a key pathogenic feature of pulmonary arterial hypertension. Previous microRNA profiling in platelet-derived growth factor BB-treated PASMCs found a significantly downregulated microRNA, miR-1281, but it has not been associated with any cellular function, and we investigated the possibility. METHODS AND RESULTS: Real-time quantitative reverse transcription-polymerase chain reaction assay proved that downregulation of miR-1281 was a conserved phenomenon in human and rat PASMCs...
March 7, 2018: Journal of the American Heart Association
Kayley H Janssen, Manisha R Diaz, Matthew Golden, Justin W Graham, Wes Sanders, Matthew C Wolfgang, Timothy L Yahr
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen with distinct acute and chronic virulence phenotypes. Whereas acute virulence is typically associated with expression of a type III secretion system (T3SS), chronic virulence is characterized by biofilm formation. Many of the phenotypes associated with acute and chronic virulence are inversely regulated by RsmA and RsmF. RsmA and RsmF are both members of the CsrA family of RNA-binding proteins and regulate protein synthesis at the post-transcriptional level...
February 20, 2018: Journal of Bacteriology
Darcy Ab Jones, Stefania Bertazzoni, Chala J Turo, Robert A Syme, James K Hane
Effector proteins are important virulence factors of fungal plant pathogens and their prediction largely relies on bioinformatic methods. In this review we outline the current methods for the prediction of fungal plant pathogenicity effector proteins. Some fungal effectors have been characterised and are represented by conserved motifs or in sequence repositories, however most fungal effectors do not generally exhibit high conservation of amino acid sequence. Therefore various predictive methods have been developed around: general properties, structure, position in the genomic landscape, and detection of mutations including repeat-induced point mutations and positive selection...
February 17, 2018: Current Opinion in Microbiology
Anna Gogleva, Hajk-Georg Drost, Sebastian Schornack
Motivation: The secretome denotes the collection of secreted proteins exported outside of the cell. The functional roles of secreted proteins include the maintenance and remodelling of the extracellular matrix as well as signalling between host and non-host cells. These features make secretomes rich reservoirs of biomarkers for disease classification and host-pathogen interaction studies. Common biomarkers are extracellular proteins secreted via classical pathways that can be predicted from sequence by annotating the presence or absence of N-terminal signal peptides...
February 16, 2018: Bioinformatics
Francisco Romero Pastrana, Jolanda Neef, Dennis G A M Koedijk, Douwe de Graaf, José Duipmans, Marcel F Jonkman, Susanne Engelmann, Jan Maarten van Dijl, Girbe Buist
Human antibody responses to pathogens, like Staphylococcus aureus, are important indicators for in vivo expression and immunogenicity of particular bacterial components. Accordingly, comparing the antibody responses to S. aureus components may serve to predict their potential applicability as antigens for vaccination. The present study was aimed at assessing immunoglobulin G (IgG) responses elicited by non-covalently cell surface-bound proteins of S. aureus, which thus far received relatively little attention...
February 19, 2018: Scientific Reports
Xihan Li, Ying Huang, Menghuai Sun, Hong Ji, Hui Dou, Jia Hu, Yanfeng Yan, Xu Wang, Leiyao Chen
Enterovirus 71 (EV71) is the primary pathogen of hand-foot-and-mouth disease (HFMD) in children and virus infections are associated with severe neurological dysfunctions and even death. MIR2911 is a honeysuckle-encoded atypical microRNA with extremely stability. Here, we report that MIR2911 directly inhibits EV71 replication by targeting the VP1 gene. Bioinformatics prediction and luciferase reporter assay showed that MIR2911 could target the VP1 gene of EV71. Transfection experiments using synthetic MIR2911 and extracted RNA from HS decoction shown that each of these preparations was capable of inhibiting EV71 VP1 protein expression; however, these preparations did not impact EV71 mutants in which the MIR2911-binding sites were mutated...
February 16, 2018: Antiviral Research
Gayeon Won, John Hwa Lee
The obligate intracellular Lawsonia intracellularis (LI), the etiological agent of proliferative enteropathy (PE), is an economically important disease in the swine industry. Due to extreme difficulty of in vitro culture of the pathogen, molecular characterization of protein components of LI that are targets of the immune system, is difficult; thus, the scientific evidence to drive the development of preventive measures is lacking. In this work, we investigated the antigenic and functional characteristics of a putative flagellar-associated protein, LI0570, using in silico computational approaches for epitope prediction and an in vitro protein-based molecular assay...
February 15, 2018: Veterinary Research
Nejat Mahdieh, Sahar Mikaeeli, Ali Reza Tavasoli, Zahra Rezaei, Majid Maleki, Bahareh Rabbani
OBJECTIVES: Gangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. PATIENTS AND METHODS: Panel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning...
February 8, 2018: Clinical Neurology and Neurosurgery
Cheng Qi, Jiayue Duan, Qingfeng Shi, Mingguang Wang, Changqing Yan
Insulinomas are functional pancreatic neuroendocrine tumors that cause hypoglycemia and severe morbidity. The aim of our study was to identify gene mutations responsible for tumorigenesis of sporadic insulinoma. Whole exome sequencing analysis was performed on tumors and paired peripheral blood from three patients with insulinomas. After initial analysis, somatic mutations were obtained and a deleterious protein product was further predicted by various bioinformatic programs. Whole exome sequencing identified 55 rare somatic mutations among three insulinoma patients, including MEN1 gene nonsense mutations (c...
February 2018: FEBS Open Bio
Bradley M Hover, Seong-Hwan Kim, Micah Katz, Zachary Charlop-Powers, Jeremy G Owen, Melinda A Ternei, Jeffrey Maniko, Andreia B Estrela, Henrik Molina, Steven Park, David S Perlin, Sean F Brady
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide1 . In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates2,3 . As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome...
February 12, 2018: Nature Microbiology
Lusi Zhang, Youling Liang, Yedi Zhou, Huilan Zeng, Songbai Jia, Jingming Shi
Congenital cataract is leading cause of visual impairment and blindness in children worldwide. Approximately one-third of congenital cataract cases are familial, whose genetic etiology can be distinguished by targeted exome sequencing. Here, a three-generation congenital cataract pedigree was recruited, and physical and ophthalmologic examinations were taken. Targeted exome sequencing of 139 cataract-related genes was performed on the proband III:1. Sanger sequencing was used to validate the presence of variation identified via exome sequencing in family members and 200 controls...
2018: Tohoku Journal of Experimental Medicine
Xiaowen Yang, Jiawei Wang, Guoxia Bing, Pengfei Bie, Yanyan De, Yanli Lyu, Qingmin Wu
Bioinformatics and comparative genomics analysis methods were used to predict unknown pathogen genes based on homology with identified or functionally clustered genes. In this study, the genes of common pathogens were analyzed to screen and identify genes associated with intracellular survival through sequence similarity, phylogenetic tree analysis and the λ-Red recombination system test method. The total 38,952 protein-coding genes of common pathogens were divided into 19,775 clusters. As demonstrated through a COG analysis, information storage and processing genes might play an important role intracellular survival...
January 29, 2018: Gene
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"