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Tandem mass spectrometry of intact proteins for characterization of biomarkers from Bacillus cereus T spores.

Intact protein biomarkers from Bacillus cereus T spores have been analyzed by high-resolution tandem Fourier transform ion cyclotron resonance mass spectrometry. Two techniques have been applied for excitation of the isolated multiply charged precursor ion species: sustained off-resonance irradiation/collisionally activated dissociation and electron capture dissociation. Fragmentation-derived sequence tags and BLAST sequence similarity proteome database searches allow unequivocal identification of the major biomarker protein with unprecedented specificity. Sequence-specific fragmentation patterns further confirm protein identification. Moreover, methodology combining accurate mass measurements of intact proteins with additional information contained in a proteome database permits tentative assignment of several other protein biomarkers isolated from the B. cereus T spores. We argue that approaches involving tandem MS of protein biomarkers, combined with bioinformatics, can drastically improve the specificity of individual microorganism identification, particularly in complex environments.

Amino Acid Sequence↗

Computational gene discovery and human disease.

Bioinformatics is now an essential tool in many aspects of human molecular genetics research. Methods for the prediction of gene structure are essential components in genomic sequencing projects and provide the key to deriving protein sequence and locating intron/exon junctions. Sequence comparison and database searching are the pre-eminent approaches for predicting the likely biochemical function of new genes, although sequence profiles derived from families of aligned sequences have advantages in the detection of remote sequence relationships. The use of sequence database analysis for large-scale comparative analysis of genome sequence data from model organisms is emerging as the most important recent development in the application of bioinformatics methods for characterizing candidate disease genes.

Animals↗

Genetic and clinical insights into the coexistence of multiple myeloma and diffuse large B cell lymphoma from a case report and systematic review with bioinformatics analysis.

BACKGROUND: Multiple myeloma (MM) and diffuse large B-cell lymphoma (DLBCL) are B-cell malignancies that rarely coexist in a single patient, presenting significant diagnostic and therapeutic challenges. While MM primarily involves clonal plasma cells, DLBCL is an aggressive lymphoid neoplasm. Investigating shared genetic mutations and understanding their clinical relevance in both cancers could provide novel insights into their pathogenesis and underlying molecular mechanisms, thereby informing future translational research. MATERIALS AND METHODS: A case report was conducted on a 52-year-old male who presented with abdominal pain and anemia. Imaging revealed lymphadenopathy, and biopsy confirmed high-grade DLBCL with concurrent bone marrow involvement suggestive of MM. Laboratory tests identified monoclonal IgM gammopathy, and the patient was treated with R-CHOP (Rituximab, Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone) chemotherapy for DLBCL followed by autologous stem cell transplantation (ASCT) for MM relapse. A systematic review of the literature was performed using PubMed, Scopus, and Web of Science databases to identify cases of patients diagnosed with both MM and DLBCL. Data on patient demographics, clinical features, treatment regimens, and outcomes were extracted. Additionally, bioinformatics analysis was conducted using publicly available genomic data from cBioPortal and IntOGen to identify driver gene mutations in MM and DLBCL. Functional and pathway enrichment analysis was performed with KEGG and Gene Ontology (GO) databases. RESULTS: The case report highlighted a complex clinical course where the patient initially responded well to R-CHOP chemotherapy for DLBCL, achieving remission, but later relapsed with MM, treated with ASCT and lenalidomide. The systematic review revealed 14 eligible studies in which MM and DLBCL often occur in older patients, either simultaneously or sequentially, with variable treatment responses, including complete remission, partial remission, or relapse. The bioinformatics analysis identified several shared function and cancer-related pathways between two cancers including interleukin and cytokine-mediated signaling pathways, regulation of cell cycle, neurotrophin signaling pathway, FOXO signaling pathway, Epstein Barr virus infection, and viral carcinogenesis. CONCLUSION: This study provides valuable insights into the dual occurrence of MM and DLBCL, emphasizing the importance of tailored treatment approaches. The driver mutations identified highlight overlapping oncogenic pathways rather than implying a shared clonal origin, and may inform future studies exploring their biological and clinical implications. Further research into these shared molecular mechanisms could lead to more effective treatments for patients with coexisting MM and DLBCL.

Bioinformatics analysis↗

Ab and T cell epitopes of influenza A virus, knowledge and opportunities.

The Immune Epitope Database and Analysis Resources (IEDB) (www.immuneepitope.org) was recently developed to capture epitope related data. IEDB also hosts various bioinformatics tools that can be used to identify novel epitopes as well as to analyze and visualize existing epitope data. Herein, a comprehensive analysis was undertaken (i) to compile and inventory existing knowledge regarding influenza A epitopes and (ii) to determine possible cross-reactivities of identified epitopes among avian H5N1 and human influenza strains. At present, IEDB contains >600 different epitopes derived from 58 different strains and 10 influenza A proteins. By using the IEDB analysis resources, conservancy analyses were performed, and several conserved and possibly cross-reactive epitopes were identified. Significant gaps in the current knowledge were also revealed, including paucity of Ab epitopes in comparison with T cell epitopes, limited number of epitopes reported for avian influenza strains/subtypes, and limited number of epitopes reported from proteins other than hemagglutinin and nucleoprotein. This analysis provides a resource for researchers to access existing influenza epitope data. At the same time, the analysis illustrates gaps in our collective knowledge that should inspire directions for further study of immunity against the influenza A virus.

Animals↗

KDE Bioscience: platform for bioinformatics analysis workflows.

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

Biological Science Disciplines↗

Genetic polymorphism in Plasmodium falciparum MSPDBL1 and MSPDBL2 and their impact on B- and T-cell immunodominant epitopes in Brazilian malaria-endemic areas.

Merozoite Surface Protein Duffy Binding-like 1 and 2 (MSPDBL1 and MSPDBL2) are involved in erythrocyte invasion by Plasmodium falciparum. Antibodies targeting PfMSPDBL1 and PfMSPDBL2 show strong opsonizing and growth-inhibitory activities, supporting their potential as asexual blood-stage vaccine candidates. Given that the extensive genetic diversity of P. falciparum contributes to immune evasion, identifying polymorphisms in regions encoding PfMSPDBL1 and PfMSPDBL2 is essential to assess their relevance as vaccine targets. In this study, we investigated polymorphisms in the pfmspdbl1 and pfmspdbl2 genes and their impact on potentially antigenic regions within the Duffy Binding-like (DBL) and Secreted Polymorphic Antigen Associated with Merozoite (SPAM) domains. Blood samples were collected from 47 P falciparum-infected individuals from three malaria-endemic areas of the Brazilian Amazon. Genomic DNA was extracted, PCR-amplified, and sequenced. Intrapopulation genetic diversity and Tajima's D values were estimated using bioinformatics tools. Linear B- and T-cell epitopes were predicted using BCPreds and IEDB (Immune Epitope Database), respectively. Two and thirty-two polymorphisms were identified in pfmspdbl1 within the SPAM and DBL domains, respectively, whereas pfmspdbl2 presented two polymorphisms across both domains and a 12 bp insertion in the SPAM domain. Tajima's D values were positive across domains, except for the DBL domain of pfmspdbl2 in Mâncio Lima. Fifteen B-cell and fifteen T-cell epitopes were predicted, with polymorphisms in three B-cell epitopes affecting Vaxijen scores. Together, these findings reveal contrasting evolutionary patterns between PfMSPDBL1 and PfMSPDBL2, with potential implications for antigenicity, and highlight PfMSPDBL2 as a potential candidate for further evaluation in multicomponent blood-stage malaria vaccine development.

Genetic diversity↗

A catalog for the transcripts from the venomous structures of the caterpillar Lonomia obliqua: identification of the proteins potentially involved in the coagulation disorder and hemorrhagic syndrome.

Accidents with the caterpillar Lonomia obliqua are often associated with a coagulation disorder and hemorrhagic syndrome in humans. In the present study, we have constructed cDNA libraries from two venomous structures of the caterpillar, namely the tegument and the bristle. High-throughput sequencing and bioinformatics analyses were performed in parallel. Over one thousand cDNAs were obtained and clustered to produce a database of 538 contigs and singletons (clusters) for the tegument library and 368 for the bristle library. We have thus identified dozens of full-length cDNAs coding for proteins with sequence homology to snake venom prothrombin activator, trypsin-like enzymes, blood coagulation factors and prophenoloxidase cascade activators. We also report cDNA coding for cysteine proteases, Group III phospholipase A2, C-type lectins, lipocalins, in addition to protease inhibitors including serpins, Kazal-type inhibitors, cystatins and trypsin inhibitor-like molecules. Antibacterial proteins and housekeeping genes are also described. A significant number of sequences were devoid of database matches, suggesting that their biologic function remains to be defined. We also report the N-terminus of the most abundant proteins present in the bristle, tegument, hemolymph, and "cryosecretion". Thus, we have created a catalog that contains the predicted molecular weight, isoelectric point, accession number, and putative function for each selected molecule from the venomous structures of L. obliqua. The role of these molecules in the coagulation disorder and hemorrhagic syndrome caused by envenomation with this caterpillar is discussed. All sequence information and the , including figures and tables with hyperlinks to FASTA-formatted files for each contig and the best match to the databases, are available at http://www.ncbi.nih.gov/projects/omes.

Amino Acid Sequence↗

Depositing electron microscopy maps.

A meeting was held at the European Bioinformatics Institute (EBI) in Hinxton, United Kingdom to discuss recent progress in the development of EMD, a database for maps determined by electron microscopy that is now integrated with MSD, the macromolecular structure database at EBI. This meeting of representatives of many of the major image processing groups in electron microscopy also discussed possible software developments that would ease the documentation and deposition of such datasets. The meeting concluded with a strong endorsement of map deposition in electron microscopy and its linkage with the family of archival databases in biomedical research.

Computational Biology↗

Prolidase, a potential enzyme target for melanoma: design of proline-containing dipeptide-like prodrugs.

Bioinformatics tools such as Perl, Visual Basic, Cluster, and TreeView were used to analyze public gene expression databases in order to identify potential enzyme targets for prodrug strategies. The analyses indicated that prolidase might be a desirable enzyme target based on its differential expression in melanoma cancer cell lines and its high substrate specificity for dipeptides containing proline at the carboxy terminus. RT-PCR expression of prolidase and hydrolytic activity against N-glycyl-l-proline (GLY-PRO), a standard substrate of prolidase, determined in tumor cell lines, exhibited a high correlation (r(2) = 0.95). These results suggest the possibility of targeting prolidase with prodrugs of anticancer agents for enhanced selectivity. The feasibility of such a scenario was tested by (a) synthesizing prodrugs of melphalan that comprised linkage of the carboxy terminus of the l-phenylalanine moiety of melphalan to the N-terminus of l and d stereoisomers of proline and (b) determining their bioconversion and antiproliferative activities in SK-MEL-5 cells, a melanoma cancer cell line with high expression levels of prolidase. The results of hydrolysis studies of the l- and d-proline prodrugs of melphalan, designated as prophalan-l and prophalan-d, respectively, indicated a approximately 7-fold higher rate of activation of prophalan-l compared to prophalan-d in SK-MEL-5 cell homogenates. Prophalan-l exhibited cytotoxicity (GI(50) = 74.8 microM) comparable to that of melphalan (GI(50) = 57.0 microM) in SK-MEL-5 cells while prophalan-d was ineffective, suggesting that prolidase-specific activation to the parent drug may be essential for cytotoxic action. Thus, melphalan prodrugs such as prophalan-l that are cleavable by prolidase offer the potential for enhanced selectivity by facilitating cytotoxic activity only in cells overexpressing prolidase.

Amino Acid Sequence↗