• This entailed mining available transcriptomic and/or genomic sequence datasets for the presence of homologues of known TIMPs, predicting secondary structures of defined protein sequences, systematic phylogenetic analyses and assessment of differential expression of genes encoding putative TIMPs in the developmental stages of A. suum , N. americanus and Schistosoma haematobium which infect the mammalian hosts. (biomedcentral.com)
  • A detailed understanding of the molecular biology of parasitic helminths, and in particular of the structure and function of key genes and gene products playing essential roles in host-parasite interactions, could provide a basis for the design of novel therapeutics. (biomedcentral.com)
  • These included genes associated with antioxidant activity, low molecular weight heat shock proteins and Late Embryonic Abundant (LEA) proteins. (nih.gov)
  • Real-time PCR confirmed that LEA transcripts, small heat-shock proteins and some antioxidant genes were upregulated in resting eggs, therefore suggesting that desiccation tolerance is a characteristic feature of resting eggs even though they do not necessarily fully desiccate during dormancy. (nih.gov)
  • Method: Using RNA-seq data, we assembled 9,093 protein-coding genes from which ORFs were predicted to generate a reference proteome. (aber.ac.uk)
  • Regulation of gene expression is primarily controlled by changes in the proteins that occupy genes' regulatory elements. (nature.com)
  • The main difference between genomics and proteomics is that genomics is the study of the entire set of genes in the genome of a cell whereas proteomics is the study of the entire set of proteins produced by the cell. (ssrq.ca)
  • Please see new drop off procedures, Biomedical Mass Spectrometry Center Even though all cells in a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. (ssrq.ca)
  • In this study, we report for the first time a comprehensive transcriptomic/secretome description of expressed genes and proteins secreted by the adult stage of Eudiplozoon nipponicum (Goto, 1891) Khotenovsky, 1985, an obligate sanguivorous monogenean which parasitises the gills of the common carp (Cyprinus carpio). (muni.cz)
  • An in-depth understanding of parasite genomes, host-parasite relationships, the molecular biology of parasites and their functional annotation can help identify therapeutic molecular targets in helminths, from the discovery of novel genes for parasite control with minimum host side effects. (edu.au)
  • The genes encoding these proteins are highly conserved within the Trichinellids, are constituents of mL1 ESP and localized in the parasite stichosome. (westminster.ac.uk)
  • To investigate further the potential role of mutated protein kinases in the development of TGCT and to characterize the prevalence and patterns of point mutations in these tumors, we have sequenced the coding exons and splice junctions of the annotated protein kinase family of 518 genes in a series of seven seminomas and six nonseminomas. (ox.ac.uk)
  • Comparative genomic hybridization and LOH analysis using SNP arrays demonstrated that the 13 TGCTs mutationally screened through the 518 protein kinase genes were uniformly aneuploid with consistent chromosomal gains on 12p, 8q, 7, and X and losses on 13q, 18q, 11q, and 4q. (ox.ac.uk)
  • Protein coding genes were predicted from the masked assembly using a combination of Snap , Fgenesh , Augustus , and the MAKER annotation pipeline using evidence from assembled transcripts, ESTs (GenBank EST database), and protein sequences from F. hepatica and related organisms. (wormbase.org)
  • Interestingly, RNA-seq revealed that G. haimaensis hosts responded to B. pettiboneaei parasitism through significant upregulation of protein and lipid anabolism related genes, and that this parasitism may enhance host mussel nutrient anabolism but inhibit the host's ability to absorb nutrients, thus potentially helping the parasite obtain nutrients from the host. (frontiersin.org)
  • When secreted, these proteins may modify the host's immune response in order to promote longevity of the parasite. (wikipedia.org)
  • In parasitic helminths, such as hookworms, TIMPs have been proposed to play key roles in the host-parasite interplay, including invasion of and establishment in the vertebrate animal hosts. (biomedcentral.com)
  • Among several groups of helminth molecules involved in the host-parasite interplay, protease inhibitors have been the subject of intense investigations due to their roles in a range of fundamental molecular processes, including regulation of host proteases and modulation of the host's immune response [ 18 ]. (biomedcentral.com)
  • In this study we explore the possibility that host phenotypic changes are triggered by the production of mimicry proteins from the parasite by using an ecological model system consisting of the infection of the threespine stickleback (Gasterosteus aculeatus) by the cestode Schistocephalus solidus. (aber.ac.uk)
  • Based on a previously published method, we built two complementary analysis pipelines to i) establish a general classification of protein similarity among various species (pipeline A) and ii) identify candidate mimicry proteins showing specific host-parasite similarities (pipeline B), a key feature underlying the possibility of molecular mimicry. (aber.ac.uk)
  • Four of these candidates correspond to secreted or membrane proteins that could be produced by the parasite and eventually be released in or be in contact with the host to modulate physiological pathways involved in various phenotypes (e.g. behaviors). (aber.ac.uk)
  • Peptide antigens are more specific than natural microbial or parasite protein antigens and easy to prepare, so antibody detection reagents assembled with peptide antigens have low false negative rates and background reactions for detecting antibodies, which are easy for clinical application. (creative-proteomics.com)
  • These findings provide additional evidence that calcium-binding EF-hand proteins play roles in host-parasite interaction. (biomedcentral.com)
  • Bioinformatics analysis also demonstrated that the parasite release proteins by an exosome-like mechanism, which could be of biological interest. (bvsalud.org)
  • This suggests that both proteins may be important for establishment of parasite infection of the intestine and are prophylactic vaccine candidates. (westminster.ac.uk)
  • killing nematode larvae by the host immune response could expose a lot of internal components that happen to be expressed in all life stages of the parasite and some intracellular proteins in the L4, L5 and adult stages may be excreted by way of specific pathways, which may perhaps lead to recognition of those structural proteins by the host immune technique [32]. (lrrk2inhibitor.com)
  • Additionally, the database can also be used to develop protein targets for new drugs to treat helminth infections. (wikipedia.org)
  • Background: Helminth infections cause widespread morbidity and are a significant global disease burden. (bvsalud.org)
  • Infection by soil transmitted parasitic helminths, such as Trichuris spp, are ubiquitous in humans and animals but the mechanisms determining persistence of chronic infections are poorly understood. (manchester.ac.uk)
  • The high prevalence of recurrent malaria, tuberculosis, chronic helminth infections, and water-borne pathogens in developing countries may play an important role in the pathogenesis of HIV-1 infection in persons living in such regions [ 1,2 ]. (lww.com)
  • A total of 15 protein sequences with high homology to known eukaryotic TIMPs were predicted from the complement of sequence data available for parasitic helminths and subjected to in-depth bioinformatic analyses. (biomedcentral.com)
  • Results: Ninety-four tapeworm proteins showed high local sequence homology with stickleback proteins. (aber.ac.uk)
  • They have been implicated in the progression of many diseases and are potentially lucrative drug targets.Objective: To identify kinases in T. solium proteome and prioritize them as drug targets.Methodology: A Hidden Markov Model (HMM) was used to curate and classify kinases into families based on sequence homology to model organisms followed by phylogenetic analysis of each family. (bvsalud.org)
  • The Helminth Secretome Database (HSD) is a repository for helminth proteins predicted using expressed sequence tags (ESTs). (wikipedia.org)
  • Previously identified ESTs, which correspond to known helminth proteins, are used to predict the location and function of newly discovered helminth proteins based on genomic sequencing. (wikipedia.org)
  • The aim of this study was to generate Expressed Sequence Tags (ESTs) for molecular characterisation of processes associated with the formation of resting eggs, their survival during dormancy and hatching. (nih.gov)
  • The 47,926 ESTs expand significantly the current sequence resource of B. plicatilis. (nih.gov)
  • This thesis highlights improved bioinformatics approaches to analyse transcriptomic data from Expressed Sequence Tags (ESTs), and their application to parasitic nematodes. (edu.au)
  • Based on the benchmarking results, a robust transcriptome analysis pipeline (TranSeqAnnotator) has been developed, with contig generation from ESTs and short reads, updated pathway analysis, non-classically secreted protein identification and extensive annotation. (edu.au)
  • The pipeline accepts ESTs, quality values, protein sequences and short reads as input and provides as output, assembled contigs and singletons and their annotations including Gene Ontologies, secretory proteins, mapping to protein domains, motifs, metabolic pathways and interaction databases. (edu.au)
  • We developed genomic locus proteomics (GLoPro), in which we combine CRISPR-based genome targeting, proximity labeling, and quantitative proteomics to discover proteins associated with a specific genomic locus in native cellular contexts. (nature.com)
  • Genomics and Proteomics Proteomics is the study of the entire set of proteins produced by a cell type in order to understand its structure and function. (ssrq.ca)
  • Genomics comprises analysis of genomes, sequencing, and mapping, while proteomics contains the function and 3D structures of proteins, and various protein-protein relations. (ssrq.ca)
  • Proteomics is a branch of molecular biology which studies the complete protein set expressed in a cell in order to understand the structure and function of proteins and how proteins affect the cell processes. (ssrq.ca)
  • Space Ranger is an analysis software which automatically overlays spatial gene expression â ¦ GENOMICS, TRANCRIPTOMICS, PROTEOMICS â ¢ Gene prediction â ¢ ORF Finding â ¢ Metagenomics â ¢ Next Generation Sequencing â ¢ Computer Aided Drug Design 32. (ssrq.ca)
  • For relatively short peptides, such as less than 30 amino acids, Creative Proteomics adopts secondary fragmentation to get the raw data of mass spectrometry, and the theoretical sequence can be obtained by database search or de novo sequencing. (creative-proteomics.com)
  • For longer peptides (>30 amino acids), Creative Proteomics will use three proteases to enzymatically cleave and identify the target peptide separately to obtain fragmented peptide fragments, and then complete the determination of 100% of the peptide sequence after peptide splicing, i.e. by ab initio sequencing. (creative-proteomics.com)
  • Creative Proteomics uses Obitrap Fusion Lumos mass spectrometer combined with Nano-LC nanoliter chromatography technology to provide mass spectrometry-based peptide sequence analysis services and peptide de novo de novo sequencing services, ensuring high resolution and high sensitivity. (creative-proteomics.com)
  • The analysis revealed that a number of non-classically secreted proteins were identified by proteomics but not by bioinformatics, to be addressed in the design of a new analysis pipeline. (edu.au)
  • An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen, Fasciola hepatica: proteins associated with invasion and infection of the mammalian host -- 4. (edu.au)
  • We study such communities using modern genomic, metataxonomic and metagenomic techniques based on next-generation DNA sequencing, proteomics, fingerprinting techniques and subsequent pure-culture isolation, as well as modelling microbial communities in collaboration with Dr. Rosalind Allen (School of Physics & Astronomy). (ed.ac.uk)
  • Additionally, injection of proteins secreted by Fasciola hepatica in nonobese diabetic mice prevented the onset of type I diabetes, with 84% of the mice showing normal glucose levels 26 weeks after injection. (wikipedia.org)
  • The liver fluke Fasciola gigantica secretes excretory-secretory proteins during infection to mediate its interaction with the host. (biomedcentral.com)
  • Data on the link between genomic integration of IS1548 and lineage of the strain obtained by bioinformatic analyses of sequenced genomes of Streptococcus agalactiae available at the National Center for Biotechnology Information â ¦ Genomics is the study of the complete genome of an organism. (ssrq.ca)
  • With only a few nematode genomes completely sequenced, analysis is carried out with transcriptomic data, which requires a number of computational methods for their pre-processing, clustering, assembly and annotation to yield biologically relevant information. (edu.au)
  • The first version of this assembly submitted in late 2013 as part of the 50 Helminth Genomes project. (wormbase.org)
  • International Helminth Genomes Consortium. (wormbase.org)
  • We saw no helminth larvae in the CSF. (cdc.gov)
  • This repetitive DNA is transcribed in muscle-stage larvae although it is not protein coding. (elsevierpure.com)
  • Trichinella spiralis muscle stage larvae (mL1) produce excretory-secreted products (ESPs), a complex mixture of protein, which are believed to be important for establishing or maintaining an infection niche within skeletal muscle and the intestine. (westminster.ac.uk)
  • Here we describe two novel proteins, Secreted from Muscle stage Larvae SML-4 and SML-5 which are 15 kDa and 12 kDa respectively. (westminster.ac.uk)
  • The variability within the proteins of L4 larvae from colitis-affected gut was confirmed inside the HPLC analysis. (lrrk2inhibitor.com)
  • Recombinant 14-3-3 protein reduces toxicity for the larvae of NO production from activated macrophages in vitro [36]. (lrrk2inhibitor.com)
  • Actin is highly conserved throughout evolution andis one of the most abundant proteins in eukaryotic cells. (lrrk2inhibitor.com)
  • ELM server: A new resource after investigating short functional sites in modular eukaryotic proteins. (centralparkcarriagesofficial.org)
  • Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. (bvsalud.org)
  • Most of the peptide antigens used are obtained from analytical screening within the natural proteins of the corresponding pathogens, and some are brand new small peptides screened from peptide libraries. (creative-proteomics.com)
  • Since most secreted proteins are impossible to identify by mass spectrometry (MS) due to their low concentration in the sample, a novel strategy to predict their sequence was applied. (bvsalud.org)
  • Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is now a routinely used technique to inform on protein structure, dynamics, and interactions. (manchester.ac.uk)
  • Conclusions: In this study, we integrated two high-throughput sequencing techniques, mass spectrometry analysis, and comprehensive bioinformatics approach in order to arrive at the first comprehensive description of monogenean transcriptome and secretome. (muni.cz)
  • Failure to recognise the FTT-2 isoform of 14-3-3 protein in L4 of mice for the duration of colitis could contribute to nematode survival. (lrrk2inhibitor.com)
  • The amino acid sequence of these peptide mimetics is different from that of their corresponding cytokines, but they have the activity of cytokines and small molecular weight. (creative-proteomics.com)
  • Furthermore, on the amino acid sequence level, all three factors shared considerable homologies with corresponding host factors. (uni-wuerzburg.de)
  • Alternative splicing of proteins in nematodes from mice with colitis could bring about changes in the major amino acid sequence on the protein, occasionally subtle and often rather dramatic, and may perhaps have an effect on recognition by serum IgG1. (lrrk2inhibitor.com)
  • Ov-FAR-1 and ABA-1A1 may instead behave similarly to extracellular lipid-binding proteins. (wikipedia.org)
  • Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)
  • Helminth proteins can result in a deregulated response to infection, and are implicated in reduced reactivity to other antigens. (wikipedia.org)
  • The native and recombinant hookworm FTT-2 protein expressed in HEK293 cells and S. mansoni 14-3-3 protein were recognized by antibodies and induce humoral and cellular immune responses making them possible vaccine antigens [34]. (lrrk2inhibitor.com)
  • With the advent of Next-Generation sequencing technologies, my focus was to incorporate the assembly and annotation of short reads, and to concentrate on identifying molecules, especially excretory/secretory proteins (ESPs) involved in key biological processes or pathways that might serve as targets for new drugs or vaccines. (edu.au)
  • Moreover, the ability of IL-33 to induce Th2 responses has functional relevance in the context of intestinal helminth infection [ 10 ]. (hindawi.com)
  • One study in Nigeria was undertaken to determine helminth infection status and hygienic conditions in primary schools. (medscape.com)
  • Prevalence of helminth infection was higher in the schools where hygiene conditions (ie, tapwater, handwashing soap) were lacking. (medscape.com)
  • This work is aimed to identify and characterize cysticercal secretion proteins of T. solium cysticerci obtained from 5 naturally infected pigs from Guerrero, Mexico, using 2D-PAGE proteomic analysis. (bvsalud.org)
  • Supported by the availability of gene manipulation technologies such as RNA interference and/or transgenesis, this work provides a basis for future functional explorations of helminth TIMPs and, in particular, of their role/s in fundamental biological pathways linked to long-term establishment in the vertebrate hosts, with a view towards the development of novel approaches for the control of neglected helminthiases. (biomedcentral.com)
  • It enabled us to report the essential physiological pathways and protein molecules involved in their interactions with the fish hosts. (muni.cz)
  • ESPs are predicted by a combination of computational approaches to effectively identity proteins secreted by classical and nonclassical pathways. (edu.au)
  • The recombinant protein, IL-33 containing a hexahistidine tag in the C-terminal, was expressed in Escherichia coli . (hindawi.com)
  • The rabbits were immunized with the purified recombinant protein. (hindawi.com)
  • The high titer (1:32000) polyclonal antibodies with high specificity were obtained by immunizing rabbits with the purified recombinant protein. (hindawi.com)
  • The precursor protein (pre-IL-33) was cleaved by caspase-1 into a mature 18-kDa protein (IL-33) in in vitro experiments using a recombinant protein [ 2 ]. (hindawi.com)
  • In this study, the cloning and expression of mouse IL-33 gene in Escherichia coli (E. coli ), purification of recombinant protein, and generation of polyclonal antibody against IL-33 are described. (hindawi.com)
  • In this study, we investigated the immunomodulatory effects of a recombinant tegumental calcium-binding EF-hand protein 4 of F. gigantica (rFg-CaBP4) on goat monocytes. (biomedcentral.com)
  • Schistosome proteins also contain abundant proteases which and cleave IgE antibodies. (wikipedia.org)
  • Fecal bacteria from 200 children between 2 and 5 years old in Antananarivo, Madagascar, and Bangui, Central African Republic (CAR), were sorted into IgA-positive (IgA+) and IgA-negative (IgA−) populations by flow cytometry and subsequently characterized by 16S rRNA gene sequencing to determine IgA-bacterial targeting. (biomedcentral.com)
  • Differentiating Dracunculus medinensis from D. insignis, by the sequence analysis of the 18S rRNA gene. (medscape.com)
  • Kolaskar and Tongaonkar antigenicity predictions of protein sequences were compared across species and high levels of variation in antigenicity were also identified with each species which possessed their own unique antigenic profile. (sruc.ac.uk)
  • Phylogenetic analysis of TSP-23 proteins suggested evidence of convergent evolution in antigenic lineages as no true inter-species phylogenetic relationships were seen. (sruc.ac.uk)
  • Similar sequences are not detected in other species by hybridisation. (elsevierpure.com)
  • The eggs of most helminth species parasitising humans can easily be distinguished at near a trained laboratory technician (see Figure. (centralparkcarriagesofficial.org)
  • Receptor kinases play an important role in the communication of cells with their environment and could be involved in hormonal communication- mechanisms between parasitic helminths and their mammalian hosts. (uni-wuerzburg.de)
  • I first conducted a comprehensive review of the steps involved in transcriptome data analysis for the development of new semi-automated bioinformatic pipelines and their application to parasitic helminths. (edu.au)
  • The fundamental knowledge presented in this book opens up an entirely new way of approaching DNA chip technology, DNA array assembly, gene expression analysis, assessing changes in genomic DNA, structure-based functional genomics, protein networks, and so on. (ssrq.ca)
  • A functional characterization of all sequences was performed using the algorithms SecretomeP, SignalP, and BlastKOALA. (bvsalud.org)
  • A helminth protein, or helminthic antigen, is a protein derived from a parasitic worm that causes an immune reaction. (wikipedia.org)
  • Helminth proteins modulate the immune response of their hosts, but do not suppress it entirely. (wikipedia.org)
  • Alpha-1, a protein released by schistosome eggs, can also be a chemokine binding protein, preventing the recruitment of other immune cells like neutrophils. (wikipedia.org)
  • Helminths are strong immune modulators and can survive for a long time in adverse host environments. (bvsalud.org)
  • Studies of both whole ESPs and individual cloned proteins have shown that some ESPs are potent immunogens capable of eliciting protective immune responses. (westminster.ac.uk)
  • Proteins are vital parts of living organisms, with many functions. (ssrq.ca)
  • Next Generation Sequencing projects can be directed to Ion Torrent or Illumina sequencing platforms based on which technology is most suitable for the study. (ssrq.ca)
  • The assembly uses Illumina HiSeq2000 paired-end sequencing. (wormbase.org)
  • I am a plant cell biologist and protein biochemist at Oxford Brookes University with expertise in the structure and function of the plant endoplasmic reticulum (ER), membrane proteins and auxin biosynthesis using biochemical techniques as well as high-resolution live cell imaging. (brookes.ac.uk)
  • I further investigated membrane proteins and the targeting of tail-anchored proteins at Sheffield Hallam University. (brookes.ac.uk)
  • I am committed to interdisciplinary research, and an example of the successes gained from this approach is the project with Prof A Nabok (Engineering Sheffield Hallam University) using total internal reflection ellipsometry to quantify protein-membrane interactions on native plant membranes and human cell lines. (brookes.ac.uk)
  • Helminth 14-3-3 protein interacts with the TGF Type-1 receptor and enhances TGF- signalling in the reactivation of tissue-arrested Ancylostoma caninum L3 [35]. (lrrk2inhibitor.com)
  • In total, 108 conserved and 186 differential proteins were identified in five cysticercus cultures. (bvsalud.org)
  • Determining the genomic sequence, however, is only the beginning of genomics. (ssrq.ca)
  • A total of 47,926 sequences were assembled into 18,000 putative transcripts and analyzed using both Blast and GO annotation. (nih.gov)
  • Exploration of E. nipponicum transcriptome-related nucleotide sequences and translated and secreted proteins offer a better understanding of molecular biology and biochemistry of these, often neglected, organisms. (muni.cz)
  • This result supports the possibility of eventually using helminth products to treat type I diabetes in humans as well. (wikipedia.org)
  • Conclusion: In this study, we identified mimicry candidate peptides from a behavior-altering cestode showing specific sequence similarity with host proteins. (aber.ac.uk)
  • peptides consisting of more than 50 amino acids are called proteins. (creative-proteomics.com)
  • There are two common methods for sequence determination of peptides: database search and de novo sequencing method. (creative-proteomics.com)
  • In view of the absence of vitellogenin transcripts, matches to lipoprotein lipase proteins suggest that, similar to the situation in dipterans, these proteins may serve as the yolk proteins in rotifers. (nih.gov)
  • Results from the pipeline for the analysis of short read sequences of the fourth larval stage of Teladorsagia circumcincta (507,124 sequences) are compared to the adult stage EST annotations, as a large-scale application of TranSeqAnnotator. (edu.au)
  • Vaccination with these proteins resulted in an impaired establishment of adult stages and consequently a reduction in the burden of mL1 in BALB/c mice. (westminster.ac.uk)
  • Structural analyses revealed that all three Echinococcus factors displayed domain structures which are characteristic of the respective protein families. (uni-wuerzburg.de)
  • Here I pursued my scientific interests in subcellular protein localisation, bioinformatics, and mathematical modelling. (brookes.ac.uk)
  • for her presentation "A mixed amplicon metabarcoding and sequencing approach for surveillance of drug resistance to levamisole and benzimidazole in Haemonchus spp. (parasite.org.au)
  • The isopropyl-ß- D -thiogalactopyranoside-induced rFg-CaBP4 protein reacted with rat sera containing anti-rFg-CaBP4 polyclonal antibodies in a western blot analysis. (biomedcentral.com)
  • Proteins are quintessential cellular components or biomolecules in any living organism. (ssrq.ca)
  • A number of proteins are able to induce production of IL-10, an anti-inflammatory cytokine. (wikipedia.org)
  • IL-4 and IL-2 induce this subset, by IL-4R directed phosphorylation of STAT6 which, with GATA-sequence binding protein 3 (GATA3), causes transcription of IL-4. (thenewstandardgallery.com)