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Search Results: 1 - 10 of 332832 matches for " Michael J Dark "
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Evaluation of the effect of formalin fixation on skin specimens in dogs and cats
Jaimie L. Miller,Michael J. Dark
PeerJ , 2015, DOI: 10.7717/peerj.307
Abstract: Skin and subcutaneous tissues are the origin of most common neoplasms affecting dogs, accounting for approximately one third of all tumors encountered in the species. Surgical excision is frequently the best chance for a cure; determining factors influencing the success of excision are vital for surgical management of cases. This work examined the shrinkage of skin of various lengths from three sites in formalin for both dogs and cats. Tissues were measured on the animal (initial measurement), at the time of excision (post-removal), and after formalin fixation (post-fixation). While shrinkage after tissue removal was found in samples from the thorax, abdomen, and rear leg in dogs and from the rear leg in cats, no significant shrinkage due to formalin fixation was detected in any sample except for the thoracic samples from the dog. Therefore, when determining where to make incisions to effect a surgical cure, initial measurements should take into account tissue shrinkage effects.
Determining the Repertoire of Immunodominant Proteins via Whole-Genome Amplification of Intracellular Pathogens
Michael J. Dark, Anna M. Lundgren, Anthony F. Barbet
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036456
Abstract: Culturing many obligate intracellular bacteria is difficult or impossible. However, these organisms have numerous adaptations allowing for infection persistence and immune system evasion, making them some of the most interesting to study. Recent advancements in genome sequencing, pyrosequencing and Phi29 amplification, have allowed for examination of whole-genome sequences of intracellular bacteria without culture. We have applied both techniques to the model obligate intracellular pathogen Anaplasma marginale and the human pathogen Anaplasma phagocytophilum, in order to examine the ability of phi29 amplification to determine the sequence of genes allowing for immune system evasion and long-term persistence in the host. When compared to traditional pyrosequencing, phi29-mediated genome amplification had similar genome coverage, with no additional gaps in coverage. Additionally, all msp2 functional pseudogenes from two strains of A. marginale were detected and extracted from the phi29-amplified genomes, highlighting its utility in determining the full complement of genes involved in immune evasion.
Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting
Michael J. Dark,William F. Craft,Julia A. Conway
PeerJ , 2015, DOI: 10.7287/peerj.preprints.296v1
Abstract: Histopathology is the most useful tool for diagnosis of a number of diseases, especially cancer. To be effective, histopathology requires that tissues be fixed prior to processing. Formalin is currently the most common histologic fixative, offering many advantages: it is cheap, readily available, and pathologists are routinely trained to examine tissues fixed in formalin. However, formalin fixation substantially degrades tissue DNA, hindering subsequent use in diagnostics and research. We therefore evaluated three alternative fixatives, TissueTek Xpress Molecular Fixative, modified methacarn, and PAXgene, all of which have been proposed as formalin alternatives, to determine their suitability for routine use in a veterinary diagnostic laboratory. This was accomplished by examining the histomorphology of sections produced from fixed tissues as well as the ability to amplify fragments from extracted DNA. Tissues were sampled from two dogs and four cats, fixed for 24-48 hours, and processed routinely. While all fixatives produced acceptable histomorphology, formalin had significantly better morphologic characteristics than the other three fixatives. Alternative fixatives generally had better DNA amplification than formalin, although results varied somewhat depending on the tissue examined. While no fixative is yet ready to replace formalin, the alternative fixatives examined may be useful as adjuncts to formalin in diagnostic practices.
Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting
William F. Craft,Julia A. Conway,Michael J. Dark
PeerJ , 2015, DOI: 10.7717/peerj.377
Abstract: Histopathology is the most useful tool for diagnosis of a number of diseases, especially cancer. To be effective, histopathology requires that tissues be fixed prior to processing. Formalin is currently the most common histologic fixative, offering many advantages: it is cheap, readily available, and pathologists are routinely trained to examine tissues fixed in formalin. However, formalin fixation substantially degrades tissue DNA, hindering subsequent use in diagnostics and research. We therefore evaluated three alternative fixatives, TissueTek Xpress Molecular Fixative, modified methacarn, and PAXgene, all of which have been proposed as formalin alternatives, to determine their suitability for routine use in a veterinary diagnostic laboratory. This was accomplished by examining the histomorphology of sections produced from fixed tissues as well as the ability to amplify fragments from extracted DNA. Tissues were sampled from two dogs and four cats, fixed for 24–48 h, and processed routinely. While all fixatives produced acceptable histomorphology, formalin had significantly better morphologic characteristics than the other three fixatives. Alternative fixatives generally had better DNA amplification than formalin, although results varied somewhat depending on the tissue examined. While no fixative is yet ready to replace formalin, the alternative fixatives examined may be useful as adjuncts to formalin in diagnostic practices.
Comparative genomics and transcriptomics of trait-gene association
Pierlé Sebastián,Dark Michael J,Dahmen Dani,Palmer Guy H
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-669
Abstract: Background The Order Rickettsiales includes important tick-borne pathogens, from Rickettsia rickettsii, which causes Rocky Mountain spotted fever, to Anaplasma marginale, the most prevalent vector-borne pathogen of cattle. Although most pathogens in this Order are transmitted by arthropod vectors, little is known about the microbial determinants of transmission. A. marginale provides unique tools for studying the determinants of transmission, with multiple strain sequences available that display distinct and reproducible transmission phenotypes. The closed core A. marginale genome suggests that any phenotypic differences are due to single nucleotide polymorphisms (SNPs). We combined DNA/RNA comparative genomic approaches using strains with different tick transmission phenotypes and identified genes that segregate with transmissibility. Results Comparison of seven strains with different transmission phenotypes generated a list of SNPs affecting 18 genes and nine promoters. Transcriptional analysis found two candidate genes downstream from promoter SNPs that were differentially transcribed. To corroborate the comparative genomics approach we used three RNA-seq platforms to analyze the transcriptomes from two A. marginale strains with different transmission phenotypes. RNA-seq analysis confirmed the comparative genomics data and found 10 additional genes whose transcription between strains with distinct transmission efficiencies was significantly different. Six regions of the genome that contained no annotation were found to be transcriptionally active, and two of these newly identified transcripts were differentially transcribed. Conclusions This approach identified 30 genes and two novel transcripts potentially involved in tick transmission. We describe the transcriptome of an obligate intracellular bacterium in depth, while employing massive parallel sequencing to dissect an important trait in bacterial pathogenesis.
Conservation in the face of diversity: multistrain analysis of an intracellular bacterium
Michael J Dark, David R Herndon, Lowell S Kappmeyer, Mikel P Gonzales, Elizabeth Nordeen, Guy H Palmer, Donald P Knowles, Kelly A Brayton
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-16
Abstract: These comparisons revealed that A. marginale has a closed-core genome with few highly plastic regions, which include the msp2 and msp3 genes, as well as the aaap locus. Comparison of the Florida and St. Maries genome sequences found that SNPs comprise 0.8% of the longer Florida genome, with 33.5% of the total SNPs between all five strains present in at least two strains and 3.0% of SNPs present in all strains except Florida. Comparison of genomes from three strains of Mycobacterium tuberculosis, Bacillus anthracis, and Nessieria meningiditis, as well as four Chlamydophila pneumoniae strains found that 98.8%–100% of SNPs are unique to each strain, suggesting A. marginale, with 76.0%, has an intermediate level of strain-specific SNPs. Comparison of genomes from other organisms revealed variation in diversity that did not segregate with the environmental niche the bacterium occupies, ranging from 0.00% to 8.00% of the larger pairwise-compared genome.Analysis of multiple A. marginale strains suggests intracellular bacteria have more variable SNP retention rates than previously reported, and may have closed-core genomes in response to the host organism environment and/or reductive evolution.While the recent boom in genome sequencing projects has provided a wealth of information about bacterial metabolism and evolution, we know little about interstrain variation. A firm understanding of the rates and sites of variation is useful in determining genotypic differences associated with phenotypic traits and in formulating control strategies for a number of pathogens. Further, knowledge about the pan-genome of organisms will aid in determining the core genomic requirements, as well as shed more light on events that occur in the various environmental niches bacteria occupy.Most studies of bacterial diversity to date have either utilized specific genomic loci [1,2] or have examined metagenomics of specific environmental niches [3,4]. While these types of studies help elucidate th
Crossing the Pale: Representations of White Western Women in Indian Film and Media
Jann Dark
Transforming Cultures , 2008,
Abstract: Forthcoming
Limits on WIMP cross-sections from the NAIAD experiment at the Boulby Underground Laboratory
The UK Dark Matter Collaboration
Physics , 2005, DOI: 10.1016/j.physletb.2000.09.001
Abstract: The NAIAD experiment (NaI Advanced Detector) for WIMP dark matter searches at the Boulby Underground Laboratory (North Yorkshire, UK) ran from 2000 until 2003. A total of 44.9 kg x years of data collected with 2 encapsulated and 4 unencapsulated NaI(Tl) crystals with high light yield were included in the analysis. We present final results of this analysis carried out using pulse shape discrimination. No signal associated with nuclear recoils from WIMP interactions was observed in any run with any crystal. This allowed us to set upper limits on the WIMP-nucleon spin-independent and WIMP-proton spin-dependent cross-sections. The NAIAD experiment has so far imposed the most stringent constraints on the spin-dependent WIMP-proton cross-section.
Large Synoptic Survey Telescope: Dark Energy Science Collaboration
LSST Dark Energy Science Collaboration
Physics , 2012,
Abstract: This white paper describes the LSST Dark Energy Science Collaboration (DESC), whose goal is the study of dark energy and related topics in fundamental physics with data from the Large Synoptic Survey Telescope (LSST). It provides an overview of dark energy science and describes the current and anticipated state of the field. It makes the case for the DESC by laying out a robust analytical framework for dark energy science that has been defined by its members and the comprehensive three-year work plan they have developed for implementing that framework. The analysis working groups cover five key probes of dark energy: weak lensing, large scale structure, galaxy clusters, Type Ia supernovae, and strong lensing. The computing working groups span cosmological simulations, galaxy catalogs, photon simulations and a systematic software and computational framework for LSST dark energy data analysis. The technical working groups make the connection between dark energy science and the LSST system. The working groups have close linkages, especially through the use of the photon simulations to study the impact of instrument design and survey strategy on analysis methodology and cosmological parameter estimation. The white paper describes several high priority tasks identified by each of the 16 working groups. Over the next three years these tasks will help prepare for LSST analysis, make synergistic connections with ongoing cosmological surveys and provide the dark energy community with state of the art analysis tools. Members of the community are invited to join the LSST DESC, according to the membership policies described in the white paper. Applications to sign up for associate membership may be made by submitting the Web form at http://www.slac.stanford.edu/exp/lsst/desc/signup.html with a short statement of the work they wish to pursue that is relevant to the LSST DESC.
Population, Development and Deforestation in Songea District, Tanzania  [PDF]
Michael J. Haule
Natural Resources (NR) , 2014, DOI: 10.4236/nr.2014.51004
Abstract:

Deforestation is a phenomenon that forms part of environmental degradation. The fact that deforestation is both a source and contributor to global warming, as it reduces the carbon sinks, cannot be contested [1]. A case study research was carried out in Songea Tanzania aimed at establishing whether there was differential participation of people of different demographic characteristics in those activities that lead into tree cover decline. The study revealed that people of different age group and, sex categories played different roles in activities that lead to deforestation such as felling trees for firewood and felling trees for establishing and/or for expanding farms. It was observed that age group and sex categories influenced one’s involvement or participation in deforestation thus contributing differently by both activity and degree of forest cover reduction. This literally means that people of different demographic characteristics of age and sex contributed differently to the ailing deforestation process. From this end, it is logical and implicit arguing that the identification of actors in deforestation-related activities confirms the disaggregated manner by which population acts on the environment. Development of blanket conservation packages that are not focused on age group and sex categories of members the population in question remains too general and in-effective. To be precise, the planning and implementation of effective conservation initiatives has to take into account demographic characteristics of the population in question. The observed reality is that the population engages with the environment not as a unit but in its disaggregated manner, i.e. based on its demographic sub-categories [2]. The theory behind a successful conservation initiative is based on unveiling the mechanism by which population acts when resulting to deforestation.

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