Characterization of a Clp Protease Gene Regulator and the Reaeration Response in Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTB) enters a non-replicating state when exposed to low oxygen tension, a condition the bacillus encounters in granulomas during infection. Determining how mycobacteria enter and maintain this state is a major focus of research. However, from a public health standpoint the importance of latent TB is its ability to reactivate. The mechanism by which mycobacteria return to a replicating state upon re-exposure to favorable conditions is not understood. In this study, we utilized reaeration from a defined hypoxia model to characterize the adaptive response of MTB following a return to favorable growth conditions. Global transcriptional analysis identified the ∼100 gene Reaeration Response, induced relative to both log-phase and hypoxic MTB. This response includes chaperones and proteases, as well as the transcription factor Rv2745c, which we characterize as a Clp protease gene regulator (ClgR) orthologue. During reaeration, genes repressed during hypoxia are also upregulated in a wave of transcription that includes genes crucial to transcription, translation and oxidative phosphorylation and culminates in bacterial replication. In sum, this study defines a new transcriptional response of MTB with potential relevance to disease, and implicates ClgR as a regulator involved in resumption of replication following hypoxia

Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements

The role of transposable elements in sculpting the genome is well appreciated but remains poorly understood. Some organisms, such as humans, do not have active transposons; however, transposable elements were presumably active in their ancestral genomes. Of specific interest is whether the DNA surrounding the sites of transposon excision become recombinogenic, thus bringing about homologous recombination. Previous studies in maize and Drosophila have provided conflicting evidence on whether transposon excision is correlated with homologous recombination. Here we take advantage of an atypical Dissociation (Ds) element, a maize transposon that can be mobilized by the Ac transposase gene in Arabidopsis thaliana, to address questions on the mechanism of Ds excision. This atypical Ds element contains an adjacent 598 base pairs (bp) inverted repeat; the element was allowed to excise by the introduction of an unlinked Ac transposase source through mating. Footprints at the excision site suggest a micro-homology mediated non-homologous end joining reminiscent of V(D)J recombination involving the formation of intra-helix 3′ to 5′ trans-esterification as an intermediate, a mechanism consistent with previous observations in maize, Antirrhinum and in certain insects. The proposed mechanism suggests that the broken chromosome at the excision site should not allow recombinational interaction with the homologous chromosome, and that the linked inverted repeat should also be mobilizable. To test the first prediction, we measured recombination of flanking chromosomal arms selected for the excision of Ds. In congruence with the model, Ds excision did not influence crossover recombination. Furthermore, evidence for correlated movement of the adjacent inverted repeat sequence is presented; its origin and movement suggest a novel mechanism for the evolution of repeated elements. Taken together these results suggest that the movement of transposable elements themselves may not directly influence linkage. Possibility remains, however, for novel repeated DNA sequences produced as a consequence of transposon movement to influence crossover in subsequent generations

Telomeric Trans-Silencing in Drosophila melanogaster: Tissue Specificity, Development and Functional Interactions between Non-Homologous Telomeres

BACKGROUND: The study of P element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences, "TAS") has the capacity to repress in trans, in the female germline, a homologous P-lacZ transgene located in euchromatin. TSE can show variegation in ovaries, displays a maternal effect as well as an epigenetic transmission through meiosis and involves heterochromatin and RNA silencing pathways. PRINCIPAL FINDINGS: Here, we analyze phenotypic and genetic properties of TSE. We report that TSE does not occur in the soma at the adult stage, but appears restricted to the female germline. It is detectable during development at the third instar larvae where it presents the same tissue specificity and maternal effect as in adults. Transgenes located in TAS at the telomeres of the main chromosomes can be silencers which in each case show the maternal effect. Silencers located at non-homologous telomeres functionally interact since they stimulate each other via the maternally-transmitted component. All germinally-expressed euchromatic transgenes tested, located on all major chromosomes, were found to be repressed by a telomeric silencer: thus we detected no TSE escaper. The presence of the euchromatic target transgene is not necessary to establish the maternal inheritance of TSE, responsible for its epigenetic behavior. A single telomeric silencer locus can simultaneously repress two P-lacZ targets located on different chromosomal arms. CONCLUSIONS AND SIGNIFICANCE: Therefore TSE appears to be a widespread phenomenon which can involve different telomeres and work across the genome. It can explain the P cytotype establishment by telomeric P elements in natural Drosophila populations

Plant Diversity Surpasses Plant Functional Groups and Plant Productivity as Driver of Soil Biota in the Long Term

One of the most significant consequences of contemporary global change is the rapid decline of biodiversity in many ecosystems. Knowledge of the consequences of biodiversity loss in terrestrial ecosystems is largely restricted to single ecosystem functions. Impacts of key plant functional groups on soil biota are considered to be more important than those of plant diversity; however, current knowledge mainly relies on short-term experiments.We studied changes in the impacts of plant diversity and presence of key functional groups on soil biota by investigating the performance of soil microorganisms and soil fauna two, four and six years after the establishment of model grasslands. The results indicate that temporal changes of plant community effects depend on the trophic affiliation of soil animals: plant diversity effects on decomposers only occurred after six years, changed little in herbivores, but occurred in predators after two years. The results suggest that plant diversity, in terms of species and functional group richness, is the most important plant community property affecting soil biota, exceeding the relevance of plant above- and belowground productivity and the presence of key plant functional groups, i.e. grasses and legumes, with the relevance of the latter decreasing in time.Plant diversity effects on biota are not only due to the presence of key plant functional groups or plant productivity highlighting the importance of diverse and high-quality plant derived resources, and supporting the validity of the singular hypothesis for soil biota. Our results demonstrate that in the long term plant diversity essentially drives the performance of soil biota questioning the paradigm that belowground communities are not affected by plant diversity and reinforcing the importance of biodiversity for ecosystem functioning

Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment

Biodiversity is rapidly declining1, and this may negatively affect ecosystem processes, including economically important ecosystem services. Previous studies have shown that biodiversity has positive effects on organisms and processes4 across trophic levels. However, only a few studies have so far incorporated an explicit food-web perspective. In an eight-year biodiversity experiment, we studied an unprecedented range of above- and below-ground organisms and multitrophic interactions. A multitrophic data set originating from a single long-term experiment allows mechanistic insights that would not be gained from meta-analysis of different experiments. Here we show that plant diversity effects dampen with increasing trophic level and degree of omnivory. This was true both for abundance and species richness of organisms. Furthermore, we present comprehensive above-ground/below-ground biodiversity food webs. Both above ground and below ground, herbivores responded more strongly to changes in plant diversity than did carnivores or omnivores. Density and richness of carnivorous taxa was independent of vegetation structure. Below-ground responses to plant diversity were consistently weaker than above-ground responses. Responses to increasing plant diversity were generally positive, but were negative for biological invasion, pathogen infestation and hyperparasitism. Our results suggest that plant diversity has strong bottom-up effects on multitrophic interaction networks, with particularly strong effects on lower trophic levels. Effects on higher trophic levels are indirectly mediated through bottom-up trophic cascades

Urban Health: Evidence, Challenges, and Directions

Urbanization is one of the most important demographic shifts worldwide during the past century and represents a substantial change from how most of the world’s population has lived for the past several thousand years. The study of urban health considers how characteristics of the urban environment may affect population health. This paper reviews the empirical research assessing urban living’s impact on population health and our rationale for considering the study of urban health as a distinct field of inquiry. The key factors affecting health in cities can be considered within three broad themes: the physical environment, the social environment, and access to health and social services. The methodologic and conceptual challenges facing the study of urban health, arising both from the limitations of the research to date and from the complexities inherent in assessing the relations among complex urban systems, disease causation, and health are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/40323/2/Galea_Urban Health - Evidence, Challenges, and Directions_2005.pd

Transcriptional analysis of the bovine herpesvirus 1 Cooper isolate

Blot hybridization analysis of infected bovine herpesvirus 1 (BHV-1) cellular RNA isolated at various times post infection and after treatment with specific metabolic inhibitors was used to characterize transcription of the BHV-1 Cooper isolate. Synthesis of BHV-1 RNA was detected as early as 3 h post infection and reached a maximum at six to eight hours post infection. The most transcriptionally active area of the genome was between map units 0.110 to 0.195, within the Hin dIII I fragment. From the entire genome a total of 59 transcripts ranging in size from approximately 0.6 to 10 kilobases were characterized as belonging to one of three distinct classes. Using the protein synthesis inhibitor cycloheximide, three immediate-early transcripts were identified as originating from the internal inverted repeat region between map units 0.734 and 0.842, corresponding to the Hin dIII D fragment. Using phosphonoacetic acid to prevent virus DNA synthesis by inhibition of the BHV-1 DNA polymerase, 28 early transcripts were recognized. The remaining 28 transcripts, classified as late RNA, were detected without the use of metabolic inhibitors at 6 to 8 h post infection. Transcription of early and late RNA was not restricted to any specific area of the genome. Eighty percent of the transcripts from both the Hin dIII A fragment, between map units 0.381 to 0.537 within the unique long segment, and the Hin dIII K fragment, between map units 0.840 to 0.907 of the unique short segment, were designated as belonging to the early class.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41672/1/705_2005_Article_BF01316744.pd

Cryptosporidium and Giardia in swimming pools in the Netherlands

Zwembad gerelateerde explosies van cryptosporidiose zijn regelmatig gerapporteerd in Groot-Brittannie en de Verenigde Staten. De bron van de explosie kon soms achterhaald worden doordat Cryptosporidium oocysten in het zwembadwater of in het terugspoelwater van de zwembadfilters konden worden gedetecteerd. Het voorkomen van Cryptosporidium en Giardia in Nederlandse zwembaden is op vijf locaties onderzocht. Het terugspoelwater van zeven zwembadfilters (van peuterbaden, whirlpools, recreatie- en instructiebaden met verhoogde watertemperatuur) is gedurende een jaar bemonsterd en onderzocht op het voorkomen van Cryptosporidium oocysten en Giardia cysten. In totaal werden 153 monsters terugspoelwater geanalyseerd, 18 monsters (11,8 %) waren positief voor Cryptosporidium (4,6 %), Giardia (5,9 %) of beide (1,3 %). De aanwezigheid van Cryptosporidium oocysten en Giardia cysten in terugspoelwater van zwembadfilters geeft de eerdere aanwezigheid van deze parasieten in het zwembadwater aan. Oocysten en cysten werden eveneens gedetecteerd in het zwembadwater van een peuterbad en van een instructiebad. In de meeste gevallen voldeed het zwembadwater aan de kwaliteitsnormen. Vrijwel alle oocysten en cysten uit het terugspoelwater waren dood, maar in het instructiebad werden levensvatbare en potentieel infectieuze oocysten gedetecteerd. Gebaseerd op de aantallen potentieel infectieuze oocysten en uitgaande van een bezoek aan een besmet zwembad per jaar, resulteerde risico analyse in een geschat infectierisico voor Cryptosporidium dat het algemeen geaccepteerde risico van een infectie per 10.000 personen per jaar overschreed. Het opstellen van richtlijnen voor zwembadbeheerders die aangeven hoe zij dienen te handelen indien fecaal materiaal in een bassin wordt aangetroffen en het informeren van het publiek over het belang van hygiene in zwembaden, zijn aanbevolen maatregelen ter beheersing van het infectierisico.Swimming-pool associated outbreaks of cryptosporidiosis have been frequently reported in the UK and USA. Cryptosporidium oocysts could sometimes be detected in the pool water or the filter backwash water in cases where the source of the outbreak was confirmed. The occurrence of Cryptosporidium and Giardia in swimming pools in the Netherlands was studied at five locations. The backwash water from seven pool filters (from toddler pools, hot whirlpools and recreational and learner pools with an elevated water temperature) was analysed for the presence of Cryptosporidium oocysts and Giardia cysts for a period of one year. Of the total 153 samples of filter backwash water analysed, 18 (11.8 %) were found positive for either Cryptosporidium (4.6 %), Giardia (5.9 %) or both (1.3 %). The presence of Cryptosporidium oocysts and Giardia cysts in filter backwash water indicates previous presence of these parasites in the pool water. Oocysts and cysts were detected in the water of one toddler pool and one learner pool. Pool water quality complied with legal bacteriological standards on most sampling days. Although most of the (oo)cysts in the filter backwash water were dead, viable and potentially infectious oocysts were detected in the learner pool. On the basis of numbers of potentially infectious (oo)cysts detected in the learner pool, and assuming one visit to an infected pool per year, risk assessment indicated an estimated risk of infection with Cryptosporidium that exceeded the generally accepted risk of one infection per 10,000 people per year. Guidelines for pool operators on how to manage faecal accidents and public information on the importance of hygiene in swimming pool complexes are recommended tools in controlling the risk of infection.RIV

Cryptosporidium and Giardia in swimming pools in the Netherlands

Swimming-pool associated outbreaks of cryptosporidiosis have been frequently reported in the UK and USA. Cryptosporidium oocysts could sometimes be detected in the pool water or the filter backwash water in cases where the source of the outbreak was confirmed. The occurrence of Cryptosporidium and Giardia in swimming pools in the Netherlands was studied at five locations. The backwash water from seven pool filters (from toddler pools, hot whirlpools and recreational and learner pools with an elevated water temperature) was analysed for the presence of Cryptosporidium oocysts and Giardia cysts for a period of one year. Of the total 153 samples of filter backwash water analysed, 18 (11.8 %) were found positive for either Cryptosporidium (4.6 %), Giardia (5.9 %) or both (1.3 %). The presence of Cryptosporidium oocysts and Giardia cysts in filter backwash water indicates previous presence of these parasites in the pool water. Oocysts and cysts were detected in the water of one toddler pool and one learner pool. Pool water quality complied with legal bacteriological standards on most sampling days. Although most of the (oo)cysts in the filter backwash water were dead, viable and potentially infectious oocysts were detected in the learner pool. On the basis of numbers of potentially infectious (oo)cysts detected in the learner pool, and assuming one visit to an infected pool per year, risk assessment indicated an estimated risk of infection with Cryptosporidium that exceeded the generally accepted risk of one infection per 10,000 people per year. Guidelines for pool operators on how to manage faecal accidents and public information on the importance of hygiene in swimming pool complexes are recommended tools in controlling the risk of infection.Zwembad gerelateerde explosies van cryptosporidiose zijn regelmatig gerapporteerd in Groot-Brittannie en de Verenigde Staten. De bron van de explosie kon soms achterhaald worden doordat Cryptosporidium oocysten in het zwembadwater of in het terugspoelwater van de zwembadfilters konden worden gedetecteerd. Het voorkomen van Cryptosporidium en Giardia in Nederlandse zwembaden is op vijf locaties onderzocht. Het terugspoelwater van zeven zwembadfilters (van peuterbaden, whirlpools, recreatie- en instructiebaden met verhoogde watertemperatuur) is gedurende een jaar bemonsterd en onderzocht op het voorkomen van Cryptosporidium oocysten en Giardia cysten. In totaal werden 153 monsters terugspoelwater geanalyseerd, 18 monsters (11,8 %) waren positief voor Cryptosporidium (4,6 %), Giardia (5,9 %) of beide (1,3 %). De aanwezigheid van Cryptosporidium oocysten en Giardia cysten in terugspoelwater van zwembadfilters geeft de eerdere aanwezigheid van deze parasieten in het zwembadwater aan. Oocysten en cysten werden eveneens gedetecteerd in het zwembadwater van een peuterbad en van een instructiebad. In de meeste gevallen voldeed het zwembadwater aan de kwaliteitsnormen. Vrijwel alle oocysten en cysten uit het terugspoelwater waren dood, maar in het instructiebad werden levensvatbare en potentieel infectieuze oocysten gedetecteerd. Gebaseerd op de aantallen potentieel infectieuze oocysten en uitgaande van een bezoek aan een besmet zwembad per jaar, resulteerde risico analyse in een geschat infectierisico voor Cryptosporidium dat het algemeen geaccepteerde risico van een infectie per 10.000 personen per jaar overschreed. Het opstellen van richtlijnen voor zwembadbeheerders die aangeven hoe zij dienen te handelen indien fecaal materiaal in een bassin wordt aangetroffen en het informeren van het publiek over het belang van hygiene in zwembaden, zijn aanbevolen maatregelen ter beheersing van het infectierisico

[A trial among laboratories participating in a RIVM/NIVEL sentinel study of incidence and cause of gastro-enteritis.]

Abstract niet beschikbaarIn 1992, in collaboration with the Dutch Institute for Investigation of Primary Health Care (NIVEL) and the National Institute of Public Health and Environmental Protection (RIVM), a national sentinel study of incidence and cause of gastro-enteritis was started. Patients with complaints of gastro-enteritis, consulting participating practitioners, were asked to complete a questionnaire and send a faecal sample to the nearest laboratory for examination. 24 laboratories took part in the study. Samples were investigated for the presence of Salmonella, Shigella and Campylobacter. For adequate interpretation of the results, an investigation of quality assurance in the different laboratories was carried out. The RIVM distributed artificially contaminated, simulated faecal samples. The laboratories were asked to examine these samples, according to their usual methods, for the presence of Salmonella, Shigella and Campylobacter. One laboratory didn't investigate the received samples. The other laboratories were able to demonstrate the presence of Salmonella, Shigella and Campylobacter in samples contaminated with these bacteria. None of the laboratories isolated bacteria from the control sample. Escherichia coli, added to a sample as interfering strain, was suppressed or discriminated by the selective or distinguishing characteristics of the methods used.GHI HIGB VHI VV