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PubMed1998

Characterization of the peptide binding motif of a rhesus MHC class I molecule (Mamu-A*01) that binds an immunodominant CTL epitope from simian immunodeficiency virus.

The majority of immunogenic CTL epitopes bind to MHC class I molecules with high affinity. However, peptides longer or shorter than the optimal epitope rarely bind with high affinity. Therefore, identification of optimal CTL epitopes from pathogens may ultimately be critical for inducing strong CTL responses and developing epitope-based vaccines. The SIV-infected rhesus macaque is an excellent animal model for HIV infection of humans. Although a number of CTL epitopes have been mapped in SIV-infected rhesus macaques, the optimal epitopes have not been well defined, and their anchor residues are unknown. We have now defined the optimal SIV gag CTL epitope restricted by the rhesus MHC class I molecule Mamu-A*01 and defined a general peptide binding motif for this molecule that is characterized by a dominant position 3 anchor (proline). We used peptide elution and sequencing, peptide binding assays, and bulk and clonal CTL assays to demonstrate that the optimal Mamu-A*01-restricted SIV gag CTL epitope was CTPYDINQM(181-189). Mamu-A*01 is unique in that it is found at a high frequency in rhesus macaques, and all SIV-infected Mamu-A*01-positive rhesus macaques studied to date develop an immunodominant gag-specific CTL response restricted by this molecule. Identification of the optimal SIV gag CTL epitope will be critical for a variety of studies designed to induce CD8+ CTL responses specific for SIV in the rhesus macaque.

Animals↗
PubMed2025

In silico prediction method for plant Nucleotide-binding leucine-rich repeat- and pathogen effector interactions.

Plant Nucleotide-binding leucine-rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity following pathogen infection. Genome sequencing advancements have led to the identification of a myriad of NLRs in numerous agriculturally important plant species. However, deciphering which NLRs recognize specific pathogen effectors remains challenging. Predicting NLR-effector interactions in silico will provide a more targeted approach for experimental validation, critical for elucidating function, and advancing our understanding of NLR-triggered immunity. In this study, NLR-effector protein complex structures were predicted using AlphaFold2-Multimer for all experimentally validated NLR-effector interactions reported in literature. Binding affinities- and energies were predicted using 97 machine learning models from Area-Affinity. We show that AlphaFold2-Multimer predicted structures have acceptable accuracy and can be used to investigate NLR-effector interactions in silico. Binding affinities for 58 NLR-effector complexes ranged between -8.5 and -10.6 log(K), and binding energies between -11.8 and -14.4 kcal/mol-1, depending on the Area-Affinity model used. For 2427 "forced" NLR-effector complexes, these estimates showed larger variability, enabling identification of novel NLR-effector interactions with 99% accuracy using an Ensemble machine learning model. The narrow range of binding energies- and affinities for "true" interactions suggest a specific change in Gibbs free energy, and thus conformational change, is required for NLR activation. This is the first study to provide a method for predicting NLR-effector interactions, applicable to all pathosystems. Finally, the NLR-Effector Interaction Classification (NEIC) resource can streamline research efforts by identifying NLRs important for plant-pathogen resistance, advancing our understanding of plant immunity.

Plant Proteins↗
PubMed2002

Intracellular vs extracellular recognition of pathogens--common concepts in mammals and flies.

There are common themes in innate immune defense systems across the animal and plant kingdoms. Pathogen recognition is commonly based on the identification of microbial molecular patterns by defined receptors and the subsequent activation of signaling pathways that initiate a defense response to fend off the invading microorganism. The existence of mammalian Toll-like receptors (TLRs) and the recent identification of two mammalian nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins (NOD1 and NOD2) as intracellular sensors of bacterial products bring new insights into the possibility of extracellular versus intracellular pathogen recognition and signal transduction depending on the nature of the infection. The homology between TLRs and the Toll system in Drosophila suggests that conserved defense mechanisms are likely to be shared by diverse organisms.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Multiplex-PCR and PCR-RFLP assays to monitor water quality against pathogenic bacteria.

In this work we developed and optimized two molecular-based approaches to monitor rapidly, sensitively and specifically bacterial pathogens from three different genera, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp., directly in waters. To achieve this aim, firstly a multiplex-PCR assay (M-PCR) was optimized using a primer pair specific for each pathogen. Secondly, as a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed from the results that the developed M-PCR assay has significant impact on the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within a short time (5 h from sampling to obtain final results), therefore it represents a considerable advancement over other known more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

DNA, Bacterial↗
PubMed2007

A S-adenosylmethionine synthetase gene from the pathogenic piscine hemoflagellate, Cryptobia salmositica.

We report on the identification of a Cryptobia genomic DNA gene, predict it to encode a S-adenosylmethionine synthetase signature 1 motif and propose to name it S-adenosylmethionine synthetase (MAT). The open reading frame of MAT is 1,046 bp with 341 deduced amino acids. The MAT gene was identified using universal genome walking and Southern blot analysis revealed it to be a multi-copy gene. The S-adenosylmethionine synthetase of Cryptobia salmositica amino acid sequence is similar to those of other pathogenic kinetoplastids (Leishmania donovani 71%, Leishmania major 70%, Leishmania infantum 71%, Trypanosoma brucei 72%, Trypanosoma cruzi 70% and T. cruzi strain CL Brener 70%). The C. salmositica MAT has a conserved hexapeptide GAGDQG, which is widely found in bacteria, parasitic protozoans and also in humans. These suggest that MAT may have highly conserved functions such as regulation of gene expression and biosynthesis of a multitude of essential metabolites.

Amino Acid Sequence↗
PubMed2005

Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry.

Helicobacter pylori is one of the most common bacterial pathogens and causes a variety of diseases, such as peptic ulcer or gastric cancer. Despite intensive study of this human pathogen in the last decades, knowledge about its membrane proteins and, in particular, those which are putative components of the type IV secretion system encoded by the cag pathogenicity island (PAI) remains limited. Our aim is to establish a dynamic two-dimensional electrophoresis-polyacrylamide gel electrophoresis (2-DE-PAGE) database with multiple subproteomes of H. pylori (http://www.mpiib-berlin.mpg.de/2D-PAGE) which facilitates identification of bacterial proteins important in pathogen-host interactions. Using a proteomic approach, we investigated the protein composition of two H. pylori fractions: soluble proteins and structure-bound proteins (including membrane proteins). Both fractions differed markedly in the overall protein composition as determined by 2-DE. The 50 most abundant protein spots in each fraction were identified by peptide mass fingerprinting. We detected four cag PAI proteins, numerous outer membrane proteins (OMPs), the vacuolating cytotoxin VacA, other potential virulence factors, and few ribosomal proteins in the structure-bound fraction. In contrast, catalase (KatA), gamma-glutamyltranspeptidase (Ggt), and the neutrophil-activating protein NapA were found almost exclusively in the soluble protein fraction. The results presented here are an important complement to genome sequence data, and the established 2-D PAGE maps provide a basis for comparative studies of the H. pylori proteome. Such subproteomes in the public domain will be effective instruments for identifying new virulence factors and antigens of potential diagnostic and/or curative value against infections with this important pathogen.

Amino Acid Sequence↗
PubMed1996

Microbiology of nontuberculosis mycobacteria.

Recognition of differences, particularly in color and other growth characteristics, between Mycobacterium tuberculosis and other related organisms has led to the identification of the nontuberculosis mycobacteria (NTM). The Runyon Classification, based largely on the presence (or absence) of pigment and rate of growth, was a convenient system for classifying these organisms. Subsequent biochemical analysis has facilitated more precise speciation. However, many of these tests are complex and time consuming and beyond the capacity of most laboratories other than reference centers. The need for accurate identification has become clear because of differences in pathogenicity and treatment between various species and even subspecies of NTM. The recent appearance of rapid diagnostic tests and highly specific genetic identification systems have created new opportunities and challenges with respect to the identification of NTM. This article provides a historic context for the microbiologic study of the organisms, describes key features of the most commonly encountered NTM, notes several important new technical innovations in this field, and considers common clinical issues in relation to the microbiology of NTM.

Bacterial Typing Techniques↗
PubMed2004

Vaccines against Francisella tularensis--past, present and future.

Francisella tularensis is a facultative intracellular bacterial pathogen capable of causing a spectrum of human diseases collectively called tularemia. The pathogen is highly infectious and some strains can cause rapidly lethal infection especially when inhaled. The latter were developed as biological weapons in the past and nowadays cause concern as potential bioterrorism agents. A live attenuated strain of the pathogen was developed more that 40 years ago and remains the sole prophylactic measure against the pathogen. Research to develop better live and subunit vaccines is under way. The former will require an understanding of the virulence factors of F. tularensis and a facile means of mutating them and the latter will require identification of the protective antigens of the pathogen. The current vaccine and its potential replacements are the focus of this review.

Bacterial Vaccines↗
PubMed1993

Restoration of pathogenicity of avirulent Xanthomonas oryzae pv. oryzae and X. campestris pathovars by reciprocal complementation with the hrpXo and hrpXc genes and identification of HrpX function by sequence analyses.

The molecular basis of pathogenesis by Xanthomonas oryzae pv. oryzae has been partly elucidated by the identification of a gene, hrpXo, required for bacterial blight on rice. A mutation in hrpXo results in the loss of pathogenicity on rice and the loss of hypersensitivity on nonhosts such as Datura stramonium and radishes. Pathogenicity and its ability to cause the hypersensitive reaction is restored by complementing the mutant with the heterologous hrpXc gene derived from X. campestris pv. campestris. Conversely, hrpXo complements nonpathogenic mutants of X. campestris pv. campestris and X. campetstris pv, armoraciae. Mutants bearing the heterologous hrpX gene are restored in their abilities to cause diseases typical of their chromosomal background and not the hypersensitive reaction on their respective hosts. The hrpXo and hrpXc genes are therefore functionally equivalent, and this functional equivalence extends into X. campestris pv. armoraciae and possibly into other X. campestris pathovars, since this gene is highly conserved among eight other pathovars tested. Sequence analyses of hrpXo revealed an open reading frame of 1,452 bp with a coding capacity for a protein of 52.3 kDa. The protein contains a consensus domain for possible protein myristoylation whose consequence may result in a loss of recognition by host defense and surveillance systems.

Amino Acid Sequence↗
PubMed2000

Empiric therapy of community-acquired pneumonia.

Community-acquired pneumonia (CAP) remains a common and serious clinical problem despite the availability of potent antibiotics and aggressive supportive measures. The management of CAP begins with recognition of the likely pathogens causing the illness in the individual patient; identification of several simple clinical clues allows the organization of the broad variety of possible organisms into a more manageable list of likely pathogens. Once the most likely pathogens are identified, then initial antibiotics may be chosen to cover those possibilities. A number of treatment guidelines have been introduced in the past 10 years, most of which share more similarities than differences. We review 2 of the more established guidelines, those published by the American Thoracic Society (ATS) and the Infectious Diseases Society of America (IDSA). We also review the likely modifications of the ATS guidelines and discuss the impact of bacterial resistance on antibiotic choices.

Anti-Bacterial Agents↗
PubMed1998

Morphologic criteria for the preliminary identification of Fusarium, Paecilomyces, and Acremonium species by histopathology.

Nontraditional human pathogenic fungi, including Fusarium, Paecilomyces, and Acremonium species, have been increasingly documented as agents of infection in immunocompromised patients and, occasionally, in normal hosts. Although definitive identification of these fungi requires culture, they often can be identified provisionally in tissue sections by a combination of histologic features, including hyaline septate hyphae and characteristic reproductive structures known as phialides and phialoconidia. These morphologic characteristics, although familiar to mycologists, are easily overlooked by histopathologists; as a result, Fusarium species and Paecilomyces lilacinus are frequently misidentified in tissue sections as Aspergillus or Candida species. We identified 19 culture-proved cases of infection with species of Fusarium, Paecilomyces, or Acremonium; retrospectively reviewed histologic specimens stained by routine hematoxylin and eosin, Gomori methenamine silver, and/or periodic acid-Schiff stains; and delineated morphologic criteria that will help pathologists make a preliminary identification of these fungi by histopathology. Adventitious sporulation was found in 9 of 9 infections caused by Paecilomyces species, 7 of 10 infections caused by Fusarium species, and in the single case of infection caused by Acremonium strictum. Histologic recognition of these morphologies may help clinicians select appropriate initial antifungal treatment and manage the infection.

Acremonium↗
PubMed2004

Methods for the isolation and identification of Listeria spp. and Listeria monocytogenes: a review.

Listeria monocytogenes is an important food-borne pathogen and is widely tested for in food, environmental and clinical samples. Identification traditionally involved culture methods based on selective enrichment and plating followed by the characterization of Listeria spp. based on colony morphology, sugar fermentation and haemolytic properties. These methods are the gold standard; but they are lengthy and may not be suitable for testing of foods with short shelf lives. As a result more rapid tests were developed based on antibodies (ELISA) or molecular techniques (PCR or DNA hybridization). While these tests possess equal sensitivity, they are rapid and allow testing to be completed within 48 h. More recently, molecular methods were developed that target RNA rather than DNA, such as RT-PCR, real time PCR or nucleic acid based sequence amplification (NASBA). These tests not only provide a measure of cell viability but they can also be used for quantitative analysis. In addition, a variety of tests are available for sub-species characterization, which are particularly useful in epidemiological investigations. Early typing methods differentiated isolates based on phenotypic markers, such as multilocus enzyme electrophoresis, phage typing and serotyping. These phenotypic typing methods are being replaced by molecular tests, which reflect genetic relationships between isolates and are more accurate. These new methods are currently mainly used in research but their considerable potential for routine testing in the future cannot be overlooked.

Animals↗
PubMedDate not supplied

[Identification of orthopoxvirus species using oligonucleotide micro-chips].

A method for describing the Orthopoxviruses that are pathogenic both to man and animals is described in the article. The method is based on hybridization of a fluorescently labelled amplified DNA sample with oligonucleotides, which were immobilized in a microchip. Species-specific regions within the crmB gene encoding a viral analogue of the tumor necrosis factor receptor, i.e. an important gene determining the pathogenicity of the mentioned Orthopoxviruses type, were used as a target for identification. The identification procedure takes around 6 hours and does not demand any costly equipment (a portable fluorescent microscope can be used).

Animals↗
PubMed2002

Histoplasma capsulatum molecular genetics, pathogenesis, and responsiveness to its environment.

Histoplasma capsulatum is a thermally dimorphic ascomycete that is a significant cause of respiratory and systemic disease in mammals including humans, especially immunocompromised individuals such as AIDS patients. As an environmental mold found in the soil, it is a successful member of a competitive polymicrobial ecosystem. Its host-adapted yeast form is a facultative intracellular pathogen of mammalian macrophages. H. capsulatum faces a variety of environmental changes during the course of infection and must survive under harsh conditions or modulate its microenvironment to achieve success as a pathogen. Histoplasmosis may be considered the fungal homolog of the bacterial infection tuberculosis, since both H. capsulatum and Mycobacterium tuberculosis exploit the macrophage as a host cell and can cause acute or persistent pulmonary and disseminated infection and reactivation disease. The identification and functional analysis of biologically or pathogenically important H. capsulatum genes have been greatly facilitated by the development of molecular genetic experimental capabilities in this organism. This review focuses on responsiveness of this fungus to its environment, including differential expression of genes and adaptive phenotypic traits.

Animals↗
PubMed1997

Media and tests to simplify the recognition and identification of members of the Proteeae.

Several important and diverse human pathogens are found in the tribe Proteeae. By identifying and concentrating on key biochemical reactions, it has been possible to devise six simple media that permit the identification of all the important members of the tribe with ease, speed and accuracy. This was confirmed by optional additional confirmatory media and tests.

Amino Acids↗
PubMed2003

Identification and characterization of SmD183-119-reactive T cells that provide T cell help for pathogenic anti-double-stranded DNA antibodies.

OBJECTIVE: The C-terminal peptide of amino acids 83-119 of the SmD1 protein is a target of the autoimmune response in human and murine lupus. This study was undertaken to test the hypothesis that SmD1(83-119)-reactive T cells play a crucial role in the generation of pathogenic anti-double-stranded DNA (anti-dsDNA) antibodies. METHODS: Splenic or lymph node T cells derived from unmanipulated as well as SmD1(83-119)-immunized NZB/NZW mice were analyzed in vitro by enzyme-linked immunospot (ELISpot) assay to determine T cell help for anti-dsDNA generation induced by the SmD1(83-119) peptide. Cytokines expressed by these T cells were measured by ELISpot assay, enzyme-linked immunosorbent assay, and flow cytometry. SmD1(83-119)- and ovalbumin-specific T cell lines were generated and characterized. RESULTS: The SmD1(83-119) peptide, but not the control peptides, significantly increased the in vitro generation of anti-dsDNA antibodies in cultures from unmanipulated NZB/NZW mice. Interferon-gamma (IFNgamma), interleukin-2 (IL-2), IL-4, transforming growth factor beta, and IL-10 production increased in response to the peptide in young mice; only IFNgamma and IL-2 were increased in older, diseased mice. Activation of SmD1(83-119)-reactive T cells by immunization of NZB/NZW mice resulted in elevated anti-dsDNA synthesis and, later, increased antibodies to SmD1(83-119). Most cells in SmD1(83-119)-specific CD4+ T cell lines helping both antibodies had increased intracellular expression of IFNgamma, and most expressed both IFNgamma and IL-4. CONCLUSION: The SmD1(83-119) peptide plays an important role in generating T cell help for autoantibodies, including anti-dsDNA, and activates different subsets of T cells as defined by distinct cytokine expression. This peptide is an interesting target structure for the modulation of autoreactive T cells, and its characterization may contribute to our understanding of the role of autoantigen-reactive T cells in the pathogenesis of SLE.

Animals↗
PubMed2005

Surveyor Nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects.

Molecular analysis of mitochondrial DNA (mtDNA) is a critical step in diagnosis and genetic counseling of respiratory chain defects. No fast method is currently available for the identification of unknown mtDNA point mutations. We have developed a new strategy based on complete mtDNA PCR amplification followed by digestion with a mismatch-specific DNA endonuclease, Surveyor Nuclease. This enzyme, a member of the CEL nuclease family of plant DNA endonucleases, cleaves double-strand DNA at any mismatch site including base substitutions and small insertions/deletions. After digestion, cleavage products are separated and analyzed by agarose gel electrophoresis. The size of the digestion products indicates the location of the mutation, which is then confirmed and characterized by sequencing. Although this method allows the analysis of 2 kb mtDNA amplicons and the detection of multiple mutations within the same fragment, it does not lead to the identification of homoplasmic base substitutions. Homoplasmic pathogenic mutations have been described. Nevertheless, most homoplasmic base substitutions are neutral polymorphisms while deleterious mutations are typically heteroplasmic. Here, we report that this method can be used to detect mtDNA mutations such as m.3243A>G tRNA(Leu) and m.14709T>C tRNA(Glu) even when they are present at levels as low as 3% in DNA samples derived from patients with respiratory chain defects. Then, we tested five patients suffering from a mitochondrial respiratory chain defect and we identified a variant (m.16189T>C) in two of them, which was previously associated with susceptibility to diabetes and cardiomyopathy. In conclusion, this method can be effectively used to rapidly and completely screen the entire human mitochondrial genome for heteroplasmic mutations and in this context represents an important advance for the diagnosis of mitochondrial diseases.

Base Pair Mismatch↗
PubMed1993

Identification and characterization of the proteolytic enzymes in the developmental stages of the eel-pathogenic nematode Anguillicola crassus.

The proteolytic activities of homogenates prepared from the second larva (L2) and the third larva (L3) as well as the adult stage of the eel-pathogenic nematode Anguillicola crassus were examined using hemoglobin, azocoll, elastin-orcein, and keratin azure as substrates. Whole bodies of L2 larvae, the anterior third of the bodies of L3 larvae, and the anterior fifth of the bodies of adults were studied. Extracts of L2 contained a trypsin-like proteinase exhibiting a molecular weight of 38,000 Da on gelatin-substrate gel electrophoresis. The proteinase showed a pH optimum at 8 and activity against azocoll and keratin. An apparent molecular weight of 25,000 Da was determined for the trypsin-like proteinase of the L3. This enzyme possessed collagenolytic, keratinolytic and slight elastinolytic activity at an optimal pH of 8. Samples of adults contained an aspartyl proteinase with a molecular weight of 90,000 Da. When hemoglobin was used as the substrate, the enzyme displayed optimal activity at pH 5. It was concluded that the proteinases of the larval stages are penetration enzymes, whereas that of the adult stage is a digestive enzyme.

Animals↗