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Results for “Pathogen diversity”

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PubMed2000

Comparative genetics of nucleotide binding site-leucine rich repeat resistance gene homologues in the genomes of two dicotyledons: tomato and arabidopsis.

The presence of a single resistance (R) gene allele can determine plant disease resistance. The protein products of such genes may act as receptors that specifically interact with pathogen-derived factors. Most functionally defined R-genes are of the nucleotide binding site-leucine rich repeat (NBS-LRR) supergene family and are present as large multigene families. The specificity of R-gene interactions together with the robustness of plant-pathogen interactions raises the question of their gene number and diversity in the genome. Genomic sequences from tomato showing significant homology to genes conferring race-specific resistance to pathogens were identified by systematically "scanning" the genome using a variety of primer pairs based on ubiquitous NBS motifs. Over 70 sequences were isolated and 10% are putative pseudogenes. Mapping of the amplified sequences on the tomato genetic map revealed their organization as mixed clusters of R-gene homologues that showed in many cases linkage to genetically characterized tomato resistance loci. Interspecific examination within Lycopersicon showed the existence of a null allele. Consideration of the tomato and potato comparative genetic maps unveiled conserved syntenic positions of R-gene homologues. Phylogenetic clustering of R-gene homologues within tomato and other Solanaceae family members was observed but not with R-gene homologues from Arabidopsis thaliana. Our data indicate remarkably rapid evolution of R-gene homologues during diversification of plant families.

Alleles↗

PubMed2006

Etiology of respiratory disease in non-vaccinated, non-medicated calves in rearing herds.

The aim of this study was to examine the occurrence of bacterial, mycoplasmal and viral pathogens in the lower respiratory tract of calves in all-in all-out calf-rearing units. According to clinical status, non-medicated calves with and without respiratory disease signs were selected of the 40 herds investigated to analyse the micro-organisms present in healthy and diseased calves. Tracheobronchial lavage (TBL) and paired serum samples were analysed for bacteria, mycoplasmas, respiratory syncytial virus (RSV), parainfluenza virus 3 (PIV3), bovine corona virus (BCV) and bovine adenovirus (BAV). Pasteurella multocida was the most common bacterial pathogen. It was isolated from 34% of the TBL samples in 28 herds and was associated with clinical respiratory disease (p < 0.05) when other pathogenic bacteria or mycoplasma were present in the sample. Mannheimia spp. and Histophilus somni were rarely found. Mycoplasma bovis was not detected at all. Ureaplasma diversum was associated with clinical respiratory disease (p < 0.05). TBL samples from healthy or suspect calves were more often negative in bacterial culture than samples from diseased calves (p < 0.05). No viral infections were detected in six herds, while 16-21 herds had RSV, BCV, BAV or PIV3. In the herds that had calves seroconverted to BCV, respiratory shedding of BCV was more frequently observed than faecal shedding. This study showed that the microbial combinations behind BRD were diverse between herds. M. bovis, an emerging pathogen in many countries, was not detected.

Animals↗

PubMed1986

Genetic relationships and clonal structure of strains of Escherichia coli causing neonatal septicemia and meningitis.

Genetic diversity and relationships among 63 isolates of Escherichia coli from infants in Finland with septicemia or meningitis were assessed by analyzing electrophoretic variation in 21 enzymes encoded by chromosomal genes. Thirty-nine multilocus genotypes (electrophoretic types) were distinguished, 23 of which formed a closely related, distinctive subset (group 1) of five or six clones represented by 40 (63%) of the isolates. The remaining isolates represented a second subset of 16 electrophoretic types (group 2) that were, on the average, rather more distantly related to one another. Although the number of electrophoretic types causing neonatal systemic disease is smaller than that occurring in healthy intestinal floras, the pathogenic electrophoretic types are only slightly less diverse genetically. Isolates of group 1 were characterized by relatively high incidences of hemolysin production and S, type 1, type 1C, and P fimbriae. However, because phenotypic characters, considered individually or in combination, did not adequately reflect the overall genetic relationships of isolates, it is recommended that the genetic structure of populations be defined on the basis of multilocus chromosomal genotypes.

Escherichia coli↗

PubMed2005

Genetic diversity and recombination of porcine sapoviruses.

Sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Human SaVs are genetically variable and have been classified into four genogroups (GI, -II, -IV, and -V). To date, only two genetically similar porcine SaV strains have been reported that belong to GIII. To investigate the genetic diversity of porcine SaVs and their genetic relatedness to human strains, we sequenced 286 nucleotides (nt) of the RNA-dependent RNA polymerase (RdRp) region of nine porcine SaVs detected from field pig fecal samples collected in U.S. swine farms during the period from 1999 to 2003. One strain (Po/SaV/MI-QW19/2002/US) was most closely related to human GII SaVs. We also sequenced 3 kb of the viral genome, including the partial RdRp (766 to 790 nt), the complete capsid, the ORF2 and the 3'-untranslated region of four strains representative for the positive farms or for the distinct genetic clusters. From the sequence analysis of the complete capsid, we identified a potential new genogroup of porcine SaVs, with Po/SaV/OH-JJ681/00/US as the representative strain. Furthermore, two potential porcine SaV recombinants were identified. To our knowledge this is the first report of a porcine SaV strain more closely related genetically to human SaVs and the occurrence of porcine SaV recombinants. The presence of porcine SaVs more similar to human SaVs is a significant finding because of the potential for zoonotic infections or generation of porcine/human recombinants if intragenogroup human strains exist.

Animal Husbandry↗

PubMed2026

Biocontrol efficacy of Bacillus albus SSR3 for controlling postharvest fungal pathogens and mycotoxin contamination.

Sweetpotato black rot, caused by Ceratocystis fimbriata, is a major postharvest disease that leads to substantial storage losses worldwide. In this study, a salt-tolerant rhizobacterial strain, Bacillus albus SSR3, was isolated from the rhizosphere of sweetpotato grown in saline-alkali soil, with broad-spectrum antagonistic activity against postharvest fungal pathogens. LC-MS/MS analysis revealed diverse bioactive metabolites associated with its antifungal activity. Integrated transcriptomic and metabolomic analyses showed that SSR3 bioactive metabolites extensively reprogrammed fungal metabolism, particularly pathways involved in carbohydrate and amino acid metabolism, antioxidant defense, and energy production. These alterations were accompanied by disruption of cell wall and membrane integrity, excessive reactive oxygen species accumulation, and mitochondrial dysfunction, ultimately inhibiting fungal growth. Here, we also found that SSR3 bioactive metabolites effectively inhibited aflatoxin B1 production by Aspergillus flavus and deoxynivalenol accumulation in Fusarium graminearum. In vivo assays further demonstrated that SSR3 bioactive metabolites significantly reduced sweetpotato black rot severity and effectively limited fungal colonization and mycotoxin contamination in stored agricultural commodities. Collectively, our findings demonstrate that B. albus SSR3 suppresses postharvest fungal pathogens through coordinated metabolic reprogramming, oxidative stress induction, and cellular integrity disruption, highlighting its potential as a sustainable biocontrol agent for postharvest disease management.

Bacillus albus↗

PubMed1983

Diversity within a human isolate of coxsackie B4: relationship to viral-induced diabetes.

The ability of different strains of a single virus type to produce different pathogenic expressions is well documented within the picornavirus group. Coxsackievirus, group B, type 4 (CB4) has been associated with viral-induced diabetes in man, but expression of its potential to induce diabetes in experimental animals is variable. Evidence is presented here for one of the primary sources of this variability that could explain resulting contradictory reports offered in support or rejection of its diabetogenic potential. C57B1/6 and SWR mice were infected with the Edwards isolate of CB4 (CB4-Edw) and three of its plaque-purified virion "strains." These were designated Edwards isolate-1 (E1), E2, and E3. CB4-Edw, E1, E2, and E3 were serologically similar by infectivity neutralization tests, had identical plaque morphology, and replicated to a similar level in the pancreas. The most profound difference was the level of virus antigen accumulation in the islet cells as determined by immunoperoxidase localization. CB4-Edw had moderate antigen accumulation in most islet cells of SWR mice but was restricted to only a few specific cells within the periphery islets of C57B1/6 mice. Unlike CB4-Edw all three new isolates accumulated antigen in most islet cells of both mouse strains. Virus isolate (strain) E2 showed the most intense accumulation in islet cells. These observations suggest that the Edwards isolate of CB4, like other human isolates of CB4 virus, probably exists as a heterogeneous population of virion strains. The pathogenic consequences and expression of any diabetogenic potential is, therefore, dependent on virus strain selection. This diversity must be considered when evaluating the pathogenic nature of CB4 viruses in experimental animals and the possible role of the viruses in diabetes of man.

Animals↗

PubMed1999

Selection of phage antibodies to surface epitopes of Phytophthora infestans.

Antibodies specific for surface-exposed epitopes on germlings of the plant pathogen, Phytophthora infestans, were isolated from a diverse phage library displaying single-chain Fv (scFv) antibody fragments. The library was subpanned against external soluble components released from mycelia, sporangia and germlings and a discrete population of phage antibodies isolated. Binding of monoclonal phage antibodies was demonstrated by enzyme-linked immunosorbent assay (ELISA) and diversity was established by BstNI restriction enzyme digest patterns. Antibodies were subcloned as fusions at the C-terminus of maltose binding protein (MBP) and expressed as soluble proteins in Escherichia coli. These antibody fusion proteins bound to P. infestans germlings and to mycelial homogenates from various Phytophthora species. The binding activities to mycelial homogenates of fungal species not belonging to the order Peronosporales were substantially lower. Several phage-displayed scFvs were used in conjunction with fluorescently labelled antiphage antibody to visualise the distribution of their cognate epitopes on the surface of the germlings. The combination of procedures developed here with Phytophthora demonstrates the potential of phage antibody technology in isolating antibodies to cell surface and external soluble components of pathogens, some of which may play a role in host/pathogen interactions.

Animals↗

PubMed1989

Marital transitions. A child's perspective.

Despite a recent leveling off of the divorce rate, almost half of the children born in the last decade will experience the divorce of their parents, and most of these children will also experience the remarriage of their parents. Most children initially experience their parents' marital rearrangements as stressful; however, children's responses to their parents marital transitions are diverse. Whereas some exhibit remarkable resiliency and in the long term may actually be enhanced by coping with these transitions, others suffer sustained developmental delays or disruptions. Others appear to adapt well in the early stages of family reorganizations but show delayed effects that emerge at a later time, especially in adolescence. The long-term effects are related more to the child's developmental status, sex, and temperament; the qualities of the home and parenting environments; and to the resources and support systems available to the parents and child than they are to divorce or remarriage per se. In recent years, researchers have begun to move away from the view that single-parent and remarried families are atypical or pathogenic families and are focusing on the diversity of children's responses and to the factors that facilitate or disrupt the development and adjustment of children experiencing their parents' marital transitions.

Adaptation, Psychological↗

PubMed1977

Enteropathogens associated with pediatric diarrhea in Mexico City.

Enteropathogens were investigated as possible agents in pediatric diarrhea occurring in Mexico City during the summer of 1975. Pathogens were identified in 47 (76%) of 62 cases. Rotavirus particles were detected in 16 cases. Enterotoxigenic Escherichia coli was detected in 29 cases; 11 were positive for heat-labile enterotoxin and 18 were positive for only the heat-stable form of enterotoxin. Multiple pathogens were found simultaneously in 15 (24%) of the study population. This study indicates that the etiology of pediatric summertime diarrhea in Mexico City is diverse. ETEC and RV were the most frequently encountered pathogens, yet they frequently occurred together and with other pathogens. ST-only strains of toxigenic E. coli were as frequently recovered as LT-E. coli suggesting that both forms of ETEC must be sought in future field studies.

Child, Preschool↗

PubMed1998

Histological patterns of atherosclerotic plaques in unstable angina patients vary according to clinical presentation.

BACKGROUND: Unstable angina is a heterogeneous clinical syndrome. The diverse clinical presentations of unstable angina may reflect different pathogenic mechanisms within the plaque. OBJECTIVE: To investigate the cellular constituents of culprit coronary atheromatous plaques in patients with stable angina pectoris and patients with diverse clinical presentations of unstable angina. METHODS: 48 patients who underwent coronary atherectomy for management of ischaemic heart disease: 23 had stable angina and 25 had unstable angina. Of the latter, 11 patients were classified as Braunwald's IIB and 14 as Braunwald's IIIB unstable angina. The presence of thrombus, cholesterol clefts, and smooth muscle cell proliferation was assessed in atherectomy samples using standard histological techniques. Monoclonal antibodies were used to identify smooth muscle cells and macrophages within atherosclerotic plaque fragments. RESULTS: Fresh thrombus was more frequently found in patients with Braunwald's IIIB unstable angina (64%) than in patients with stable angina (22%) or IIB unstable angina (27%) (p < 0.0006). A pattern of smooth muscle cell proliferation ("accelerated progression pattern") was observed which was also associated with coronary thrombus. This pattern was present in 30% of patients with stable angina, 64% of patients with IIIB unstable angina, and in all patients (100%) with IIB unstable angina. Atherosclerotic plaques with thrombus, cholesterol clefts, and macrophages were more common in patients with unstable angina than in stable angina patients. CONCLUSION: The presence of a specific smooth muscle cell proliferation (accelerated progression) pattern in patients with unstable angina, particularly in those with Braunwald's IIB unstable angina, suggests that episodic plaque disruption and subsequent healing may be an important mechanism underlying angina symptoms in these patients.

Adult↗

PubMed2006

Plasmid diversity in neisseriae.

Horizontal gene transfer constitutes an important force in prokaryotic genome evolution, and it is well-known that plasmids are vehicles for DNA transfer. Chromosomal DNA is frequently exchanged between pathogenic and commensal neisseriae, but relatively little is known about plasmid diversity and prevalence among these nasopharyngeal inhabitants. We investigated the plasmid contents of 18 Neisseria lactamica isolates and 20 nasopharyngeal Neisseria meningitidis isolates. Of 18 N. lactamica strains, 9 harbored one or more plasmids, whereas only one N. meningitidis isolate contained a plasmid. Twelve plasmids were completely sequenced, while five plasmid sequences from the public databases were also included in the analyses. On the basis of nucleic acid sequences, mobilization, and replicase protein alignments, we distinguish six different plasmid groups (I to VI). Three plasmids from N. lactamica appeared to be highly similar on the nucleotide level to the meningococcal plasmids pJS-A (>99%) and pJS-B (>75%). The genetic organizations of two plasmids show a striking resemblance with that of the recently identified meningococcal disease-associated (MDA) phage, while four putative proteins encoded by these plasmids show 25% to 39% protein identity to those encoded by the MDA phage. The putative promoter of the gene encoding the replicase on these plasmids contains a polycytidine tract, suggesting that replication is subjected to phase variation. In conclusion, extensive plasmid diversity is encountered among commensal neisseriae. Members of three plasmid groups are found in both pathogenic and commensal neisseriae, indicating plasmid exchange between these species. Resemblance between plasmids and MDA phage may be indicative of dissemination of phage-related sequences among pathogenic and commensal neisseriae.

Bacterial Proteins↗

PubMed2003

Importance of ascorbate peroxidases OsAPX1 and OsAPX2 in the rice pathogen response pathways and growth and reproduction revealed by their transcriptional profiling.

We have identified and characterized two rice ascorbate peroxidase (OsAPX1 and OsAPX2) genes against diverse signals known to involve in defense/stress responses, using "2-week-old rice seedling in vitro model system". Oryza sativa ascorbate peroxidase 1 and 2 (OsAPX1/2) share 83% similarity to each other at amino acid level and belong to a small gene family in the rice genome. OsAPX1/2 show a weak constitutive expression in leaves. Their transcripts were up-regulated upon wounding (by cut), and diverse signals such as salicylic acid (SA), ethylene (using the ethylene generator, ethephon), abscisic acid (ABA), hydrogen peroxide, copper sulfate, protein phosphatase (PP) inhibitors, cantharidin (CN), endothall (EN) and okadaic acid (OA), and blast pathogen (Magnaporthe grisea) attack, but surprisingly not by jasmonic acid (JA). Interestingly, the OsAPX2 inductions were more potent and rapid than OsAPX1, whose expression increased gradually with time. These inductions were influenced by light signal(s), and showed requirement for certain de novo synthesized protein factor(s). Intriguingly, OsAPX1/2 mRNAs expression manifested a clear rhythmicity under light/dark cycle. Differential regulation of the OsAPX1/2 expressions by diverse environmental cues, including pathogen, and their developmental regulation in both young and reproductive stages strongly suggests their role in stress-signaling pathways and development in rice.

Amino Acid Sequence↗

PubMed1996

Towards a unified evolutionary genetics of microorganisms.

I propose here that evolutionary genetics, apart from improving our basic knowledge of the taxonomy and evolution of microbes (either eukaryotes or prokaryotes), can also greatly contribute to applied research in microbiology. Evolutionary genetics provides convenient guidelines for better interpreting genetic and molecular data dealing with microorganisms. The three main potential applications of evolutionary genetics in microbiology are (a) epidemiological follow-up (with the necessity of evaluating the stability of microbial genotypes over space and time); (b) taxonomy in the broad sense (better definition and sharper delimitation of presently described taxa, research of hidden genetic subdivisions); and (c) evaluation of the impact of the genetic diversity of microbes on their relevant properties (pathogenicity, resistance to drugs, etc). At present, two main kinds of population structure can be distinguished in natural microbial populations: (a) species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species with occasional bouts of short-term clonality fall into this category); (b) species that are strongly subdivided by either cryptic speciation or clonal evolution. Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations. Moreover, a codified selection of markers with appropriate molecular clocks (in other words: adapted levels of resolution) is sorely needed to answer distinct questions that address different scales of time and space: experimental, epidemic, and evolutionary. The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field. I propose a synthetic approach, relying on the statistical improvements and technical standardizations called for above, to settle a unified evolutionary genetics of microorganisms, valid whatever the species studied, whether eukaryotic (parasitic protozoa and fungi) or prokaryotic (bacteria). Apart from benefits for basic evolutionary research, the anticipated payoff from this synthetic approach is to render routine and common-place the use of microbial evolutionary genetics in the fields of epidemiology, medicine, and agronomy.

Animals↗

PubMed2003

Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens.

Recombination is thought to be rare within Salmonella, as evidenced by absence of gene transfer among SARC strains that represent the broad genetic diversity of the eight primary subspecies of this common facultative intracellular pathogen. We adopted a phylogenetic approach to assess recombination within the mutS gene of 70 SARB strains, a genetically homogeneous population of Salmonella enterica subspecies I strains, which have in common the ability to infect warm-blooded animals. We report here that SARB strains show evidence for widespread recombinational exchange in contrast to results obtained with strains exhibiting species-level genetic variation. Besides extensive allele shuffling, SARB strains showed notably larger recombinagenic patch sizes for mutS (at least approximately 1.1 kb) than previously reported for S. enterica SARC strains. Explaining these experimental dichotomies provides important insight for understanding microbial evolution, because they suggest likely ecologic and genetic barriers that limit extensive gene transfer in the feral setting.

Base Sequence↗

PubMed2025

Global diversity of integrating conjugative elements (ICEs) in Helicobacter pylori and their influence on genome architecture.

Integrating conjugative elements (ICEs) are mobile genetic elements conferring a wide range of beneficial functions upon their bacterial hosts. Generally, they can be activated from their integrated states to undergo horizontal gene transfer via conjugation. In the case of the human gastric pathogen Helicobacter pylori, a paradigm for extensive genetic diversity, highly efficient natural transformation and recombination processes may superimpose canonical transfer of its two ICEs termed ICEHptfs3 and ICEHptfs4, and thus shape their composition substantially. Here, as a part of the Helicobacter pylori Genome Project (HpGP) initiative, we have analyzed high-quality genome sequences from 1011 clinical strains with respect to their ICE content and variability. We show that both elements are highly prevalent in all H. pylori populations, but have a strong tendency for gene erosion. ICE sequence variations reflect the population structure and show a clear signature of increased horizontal transfer. A detailed map of ICE integration sites revealed local preferences, but also how recombination processes result in hybrid elements or genome rearrangements. Population-specific differences in ICE cargo genes might reflect distinct requirements in the biological functions provided by these mobile elements.

Journal Article↗

PubMed2002

MaGiK method of T-Cell receptor repertoire analysis.

T-cell receptor diversity enables the cellular immune response to recognize a broad range of viral and other pathogenic agents. An increasingly common method of characterizing T-cell receptor diversity and usage in response to antigenic challenges involves the identification of clonal expansions by PCR amplification of the CDR3 region of distinct TCRVbeta families. Though clonal expansions often appear evident upon visual inspection of the results, a systematic method is needed for the valid enumeration of these expansions. Here, we describe a novel analysis method, termed the MaGiK method, for systematically identifying and enumerating clonal T-cell expansions and for applying the results to investigations of the T-cell receptor repertoire.

Adult↗

PubMed2005

Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses.

The majority of plant-infecting viruses utilize an RNA genome, suggesting that plants have imposed strict constraints on the evolution of DNA viruses. The geminiviruses represent a family of DNA viruses that has circumvented these impediments to emerge as one of the most successful viral pathogens, causing severe economic losses to agricultural production worldwide. The genetic diversity reflected in present-day geminiviruses provides important insights into the evolution and biology of these pathogens. To maximize replication of their DNA genome, these viruses acquired and evolved mechanisms to manipulate the plant cell cycle machinery for DNA replication, and to optimize the number of cells available for infection. In addition, several strategies for cell-to-cell and long-distance movement of the infectious viral DNA were evolved and refined to be compatible with the constraints imposed by the host endogenous macromolecular trafficking machinery. Mechanisms also evolved to circumvent the host antiviral defense systems. Effectively combatting diseases caused by geminiviruses represents a major challenge and opportunity for biotechnology.

Biological Evolution↗

PubMed2006

The role of dsbA in colonization of the wheat rhizosphere by Pseudomonas fluorescens Q8r1-96.

Certain well-conserved genes in fluorescent Pseudomonas spp. are involved in pathogenic interactions between the bacteria and evolutionarily diverse hosts including plants, insects and vertebrate animals. One such gene, dsbA, encodes a periplasmic disulfide-bond-forming enzyme implicated in the biogenesis of exported proteins and cell surface structures. This study focused on the role of dsbA in Pseudomonas fluorescens Q8r1-96, a biological control strain that produces the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) and is known for its exceptional ability to colonize the roots of wheat and pea. The deduced DsbA protein from Q8r1-96 is similar to other predicted thiol : disulfide interchange proteins and contains a conserved DsbA catalytic site, a pattern associated with the thioredoxin family active site, and a signal peptide and cleavage site. A dsbA mutant of Q8r1-96 exhibited decreased motility and fluorescence, and altered colony morphology; however, it produced more 2,4-DAPG and total phloroglucinol-related compounds and was more inhibitory in vitro to the fungal root pathogen Gaeumannomyces graminis var. tritici than was the parental strain. When introduced separately into a natural soil, Q8r1-96 and the dsbA mutant did not differ in their ability to colonize the rhizosphere of wheat in greenhouse experiments lasting 12 weeks. However, when the two strains were co-inoculated, the parental strain consistently out-competed the dsbA mutant. It was concluded that dsbA does not contribute to the exceptional rhizosphere competence of Q8r1-96, although the dsbA mutation reduces competitiveness when the mutant competes with the parental strain in the same niche in the rhizosphere. The results also suggest that exoenzymes and multimeric cell surface structures are unlikely to have a critical role in root colonization by this strain.

Anti-Bacterial Agents↗