Spectrum of heart diseases in a new cardiac service in Nigeria: An echocardiographic study of 1441 subjects in Abeokuta

Background

The recent determination of the complete nucleotide sequence of several Mycobacterium tuberculosis (MTB) genomes allows the use of comparative genomics as a tool for dissecting the nature and consequence of genetic variability within this species. The multiple alignment of the genomes of clinical strains (CDC1551, F11, Haarlem and C), along with the genomes of laboratory strains (H37Rv and H37Ra), provides new insights on the mechanisms of adaptation of this bacterium to the human host.

Findings

The genetic variation found in six M. tuberculosis strains does not involve significant genomic rearrangements. Most of the variation results from deletion and transposition events preferentially associated with insertion sequences and genes of the PE/PPE family but not with genes implicated in virulence. Using a Perl-based software islandsanalyser, which creates a representation of the genetic variation in the genome, we identified differences in the patterns of distribution and frequency of the polymorphisms across the genome. The identification of genes displaying strain-specific polymorphisms and the extrapolation of the number of strain-specific polymorphisms to an unlimited number of genomes indicates that the different strains contain a limited number of unique polymorphisms.

Conclusion

The comparison of multiple genomes demonstrates that the M. tuberculosis genome is currently undergoing an active process of gene decay, analogous to the adaptation process of obligate bacterial symbionts. This observation opens new perspectives into the evolution and the understanding of the pathogenesis of this bacterium.     

Landscape genetics of the Tasmanian devil: implications for spread of an infectious cancer

Emerging infectious diseases are increasingly recognized in species’ declines and extinctions. Landscape genetics can be used as a tool to predict disease emergence and spread. The Tasmanian devil is threatened with extinction by a nearly 100% fatal transmissible cancer, which has spread across 95% of the species’ geographic range in 20 years. Here, we present a landscape genetic analysis in the last remaining uninfected parts of the Tasmanian devil’s geographic range to: describe population genetic structure, characterize genetic diversity, and test the influence of landscape variables on Tasmanian devil gene flow to assess the potential for disease spread. In contrast to previous genetic studies on Tasmanian devils showing evidence for two genetic populations island-wide, our genetic based assignment tests and spatial principal components analyses suggest at least two, and possibly three, populations in a study area that is approximately 15% of the size of the overall species’ geographic range. Positive spatial autocorrelation declined at about 40 km, in contrast to 80 km in eastern populations, highlighting the need for range-wide genetic studies. Strong genetic structure was found between devils in the northern part of the study area and those found south of Macquarie Harbor, with weaker structure found between the northeastern and northwestern portion of our study area. Consistent with previous work, we found low overall genetic diversity, likely owing to a combination of founder effects and extreme weather events thousands of years ago that likely caused large-scale population declines. We also found possible signs of recent bottlenecks, perhaps resulting from forest clearing for dairy farming in the central part of the study area. This human disturbance also may have contributed to weak genetic structuring detected between the northeastern and northwestern part of the study area. Individual-based least cost path modeling showed limited influence of landscape variables on gene flow, with weak effects of variation in elevation in the northeast. In the northwest, however, landscape genetic models did not perform better than the null isolation-by-distance model. At the larger spatial scale of the northern part of the study area, elevation and temperatures were negatively correlated with gene flow, consistent with low dispersal suitability of higher elevation habitats that have lower temperatures and dense, wet vegetation. Overall, Tasmanian devils are a highly vagile species for which dispersal and gene flow appear to be influenced little by landscape features, and spread of devil facial tumor disease to the remaining portion of the devil’s geographic range seems imminent. Nonetheless, strong genetic structure found between the northern and southern portions of our study area, combined with low densities and limited possible colonization of DFTD from the east suggest there is some time for implementation of management strategies.     

Decline of a giant salamander assessed with historical records,environmental DNA and multi‐scale habitat data

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Single-Leaf Resolution of the Temporal Population Dynamics of Aureobasidium pullulans on Apple Leaves

The abundance of phylloplane microorganisms typically varies over several orders of magnitude among leaves sampled concurrently. Because the methods traditionally used to sample leaves are destructive, it has remained unclear whether this high variability is due to fixed differences in habitat quality among leaves or to asynchronous temporal variation in the microbial population density on individual leaves. We developed a novel semidestructive assay to repeatedly sample the same apple leaves from orchard trees over time by removing progressively more proximal ~1-cm-wide transverse segments. Aureobasidium pullulans densities were determined by standard leaf homogenization and plating procedures and were expressed as CFU per square centimeter of segment. The A. pullulans population densities among leaves were lognormally distributed. The variability in A. pullulans population densities among subsections of a given leaf was one-third to one-ninth the variability among whole leaves harvested concurrently. Sequential harvesting of leaf segments did not result in detectable changes in A. pullulans density on residual leaf surfaces. These findings implied that we could infer whole-leaf A. pullulans densities over time by using partial leaves. When this successive sampling regimen was applied over the course of multiple 7- to 8-day experiments, the among-leaf effects were virtually always the predominant source of variance in A. pullulans density estimates. Changes in A. pullulans density tended to be synchronous among leaves, such that the rank order of leaves arrayed with respect to A. pullulans density was largely maintained through time. Occasional periods of asynchrony were observed, but idiosyncratic changes in A. pullulans density did not contribute appreciably to variation in the distribution of populations among leaves. This suggests that persistent differences in habitat (leaf) quality are primarily responsible for the variation in A. pullulans density among leaves in nature.     

Viral determinants of the variable sensitivity of herpes simplex virus strains to gD-mediated interference.

Cells that express glycoprotein D (gD) of herpes simplex virus type 1 (HSV-1) resist infection by HSV-1 and HSV-2 because of interference with viral penetration. The results presented here show that both HSV-1 and HSV-2 gD can mediate interference and that various HSV-1 and HSV-2 strains differ in sensitivity to this interference. The relative degree of sensitivity was not necessarily dependent on whether the cell expressed the heterologous or homologous form of gD but rather on the properties of the virus. Marker transfer experiments revealed that the allele of gD expressed by the virus was a major determinant of sensitivity to interference. Amino acid substitutions in the most distal part of the gD ectodomain had a major effect, but substitutions solely in the cytoplasmic domain also influenced sensitivity to interference. In addition, evidence was obtained that another viral gene(s) in addition to the one encoding gD can influence sensitivity to interference. The results indicate that HSV-1 and HSV-2 gD share determinants required to mediate interference with infection by HSV of either serotype and that the pathway of HSV entry that is blocked by expression of cell-associated gD can be cleared or bypassed through subtle alterations in virion-associated proteins, particularly gD.     

Denaturing Gradient Gel Electrophoresis Can Rapidly Display the Bacterial Diversity Contained in 16S rDNA Clone Libraries

Two different strategies for molecular analysis of bacterial diversity, 16S rDNA cloning and denaturing gradient gel electrophoresis (DGGE), were combined into a single protocol that took advantage of the best attributes of each: the ability of cloning to package DNA sequence information and the ability of DGGE to display a community profile. In this combined protocol, polymerase chain reaction products from environmental DNA were cloned, and then DGGE was used to screen the clone libraries. Both individual clones and pools of randomly selected clones were analyzed by DGGE, and these migration patterns were compared to the conventional DGGE profile produced directly from environmental DNA. For two simple bacterial communities (biofilm from a humics-fed laboratory reactor and planktonic bacteria filtered from an urban freshwater pond), pools of 35–50 clones produced DGGE profiles that contained most of the bands visible in the conventional DGGE profiles, indicating that the clone pools were adequate for identifying the dominant genotypes. However, DGGE profiles of two different pools of 50 clones from a lawn soil clone library were distinctly different from each other and from the conventional DGGE profile, indicating that this small number of clones poorly represented the bacterial diversity in soil. Individual clones with the same apparent DGGE mobility as prominent bands in the humics reactor community profiles were sequenced from the clone plasmid DNA rather than from bands excised from the gel. Because a longer fragment was cloned (∼1500 bp) than was actually analyzed in DGGE (∼350 bp), far more sequence information was available using this approach that could have been recovered from an excised gel band. This clone/DGGE protocol permitted rapid analysis of the microbial diversity in the two moderately complex systems, but was limited in its ability to represent the diversity in the soil microbial community. Nonetheless, clone/DGGE is a promising strategy for fractionating diverse microbial communities into manageable subsets consisting of small pools of clones.     

Conservation genetics of eastern hellbenders <Emphasis Type="Italic">Cryptobranchus alleganiensis alleganiensis</Emphasis> in the Tennessee Valley

The eastern hellbender has declined across much of its range and is a candidate for listing under the Endangered Species Act. Some of the most viable remaining populations exist in the Southern Appalachian Region in the Tennessee Valley watershed; however these populations are highly isolated and fragmented, and occupy several physiographic provinces, suggesting they may exhibit significant levels of genetic differentiation. We investigated genetic and phylogeographic relationships among eastern hellbender populations across the Tennessee Valley, using nuclear microsatellite markers and mitochondrial sequence data. Our population genetic analyses of microsatellite data revealed a strong pattern of isolation by stream distance, and 4 genetically distinct populations. These four populations were mainly associated with major watersheds, although middle Tennessee samples were difficult to assign to any particular population. Our phylogeographic analysis of mtDNA resulted in a strongly supported monophyletic ingroup containing nine largely allopatric clades, which also largely corresponded to major watersheds. Our findings suggest that hellbenders from different watersheds in the Tennessee Valley should be recognized as genetically distinct populations, and care should be taken to balance the needs of rescuing declining populations with translocation or headstart programs, while also preserving genetic diversity across the region.     

Effect of the Peroxisome Proliferator Ciprofibrate on Lipid Peroxidation and 8-Hydroxydeoxyguanosine Formation in Transgenic Mice with Elevated Hepatic Catalase Activity

Peroxisome proliferators are a group of non-genotoxic hepatic carcinogens which have been proposed to act by increasing oxidative damage in the liver. To test this hypothesis, we have produced a transgenic mouse line that has elevated catalase activity specifically in the liver. In this study, we have examined if catalase overexpression influences the induction of lipid peroxidation or oxidative DNA damage, two mechanisms which have been hypothesized to be important in the carcinogenesis by peroxisome proliferators. Transgenic mice or non-transgenic litter mates were fed either 0.01% ciprofibrate or a control diet for 21 days. The activities of fatty acyl CoA oxidase and lauric acid hydroxylase were not significantly affected by catalase overexpression, although the ratio of fatty acyl CoA oxidase to catalase was significantly decreased in transgenic animals. Hepatic lipid peroxidation was estimated by quantifying the concentrations of malondialdehyde and conjugated dienes. Ciprofibrate treatment did not affect either endpoint, but catalase overexpression increased the concentrations of malondialdehyde (in untreated mice only) and conjugated dienes (in both untreated and ciprofibrate-fed mice). Oxidative DNA damage was estimated by quantifying 8-hydroxydeoxyguanosine (8-OHdG) by high-performance liquid chromatography/electrochemical detection. Ciprofibrate treatment significantly increased hepatic 8-OHdG concentrations, in agreement with several previous studies, but catalase overexpression did not significantly affect them, although 8-OHdG concentrations were decreased 50% in untreated mice. These results imply that the metabolism of hydrogen peroxide by catalase is not an important factor in the development of hepatic lipid peroxidation. The decrease in hepatic 8-OHdG in untreated transgenic mice and the increase seen after ciprofibrate administration imply that hydrogen peroxide is important in the formation of 8-OHdG. While the lack of decreased 8-OHdG levels in ciprofibrate-treated transgenic mice does not support this conclusion, it is possible that catalase levels were not sufficiently high to affect this endpoint. Transgenic mice with higher hepatic catalase activities may be required to resolve this issue.