Molecular characterization of Salmonella Enteritidis : comparison of an optimized multi-locus variable-number of tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis

Salmonella Enteritidis (SE) is a genetically homogenous serovar, which makes optimal subtype discrimination crucial for epidemiological research. This study describes the development and evaluation of an optimized multiple-locus variable number tandem-repeat assay (MLVA) for characterization of SE. The typeability and discriminatory power of this MLVA was determined on a selected collection of 60 SE isolates and compared with pulsed-field gel electrophoresis (PFGE) using restriction enzymes XbaI, NotI, or SfiI. In addition, the estimated Wallace coefficient (W) was calculated to assess the congruence of the typing methods. Selection of epidemiologically unrelated isolates and more related isolates (originating from layer farms) was also based on the given phage type (PT). When targeting six loci, MLVA generated 16 profiles, while PFGE produced 10, 9, and 16 pulsotypes using XbaI, NotI, and SfiI, respectively, for the entire strain collection. For the epidemiologically unrelated isolates, MLVA had the highest discriminatory power and showed good discrimination between isolates from different layer farms and among isolates from the same layer farm. MLVA performed together with PT showed higher discriminatory power compared to PFGE using one restriction enzyme together with PT. Results showed that combining PT with the optimized MLVA presented here provides a rapid typing tool with good discriminatory power for characterizing SE isolates of various origins and isolates originating from the same layer farm

Spatial and temporal variation in otolith chemistry for tautog (Tautoga onitis) in Narragansett Bay and Rhode Island coastal ponds

The elemental composition of otoliths may provide valuable information for establishing connectivity between fish nursery grounds and adult fish populations. Concentrations of Rb, Mg, Ca, Mn, Sr, Na, K, Sr, Pb, and Ba were determined by using solution-based inductively coupled plasma mass spectrometry in otoliths of young-of-the year tautog (Tautoga onitis) captured in nursery areas along the Rhode Island coast during two consecutive years. Stable oxygen (δ18O) and carbon (δ13C) isotopic ratios in young-of-the year otoliths were also analyzed with isotope ratio mass spectrometry. Chemical signatures differed significantly among the distinct nurseries within Narragansett Bay and the coastal ponds across years. Significant differences were also observed within nurseries from year to year. Classification accuracy to each of the five tautog nursery areas ranged from 85% to 92% across years. Because accurate classification of juvenile tautog nursery sites was achieved, otolith chemistry can potentially be used as a natural habitat tag

Reducing Contamination in Forensic Science

The sensitivity of modern forensic techniques has drastically increased, with sensitive technology detecting even the smallest traces of DNA evidence left behind. This has made it possible to detect DNA profiles deposited through contamination. When DNA contamination occurs in forensic science, it has the potential to change the outcome of a criminal investigation and may have significant social and financial repercussions. A compilation of global research shows that DNA evidence transfer can occur during forensic product manufacturing, the fingerprinting process, or even autopsy and crime lab examinations. These vital areas of the forensic investigation are vulnerable to contamination, and national standards should address this susceptibility. Understanding the origins of contamination events provides the greatest insight into preventing their occurrence and maintaining the integrity of forensic evidence

Establishing Identity for International Protection: Challenges and Practices

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The legal life of objects : speaking evidence and mute subjects in Mark Twain’s Pudd’nhead Wilson

textIn this paper, I argue that legal authorities assign speaking power to objects and evidence in the courtroom in order to deny speaking power to racialized subjects and police racial identities. Mark Twain’s Pudd’nhead Wilson (1894) demonstrates how the law transverses the human/object boundary in order to regulate legal definitions of identity. I examine the legal animation of the textual document, as exemplified by the last will and testament; the knife, a material object that as a murder weapon is responsible for condemning the accused; and the fingerprint, a unique form of bodily evidence that merges the textual and the material, in order to understand how these objects blur the line between the living and the deceased, between human and nonhuman agency, and between body and text. My methodology brings object studies into conversation with a literature and the law approach in order to show not only how the nineteenth-century American literary imagination was concerned with testing and regulating racial boundaries, but also how fictions employed by the law produce subjects and objects. My investigation reminds us that when evidence appears to “speak for itself,” this speech act has been carefully orchestrated by human legal authorities who determine what the evidence can be understood to mean and for whom it speaks.Englis

GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics

How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromosome, plasmid, and phage) with farther divergences (much less or no homologous) over large size ranges (from Kbp to Mbp). We created a new method, GenomeFingerprinter, to unambiguously produce three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections to illustrate whole genome fingerprints. We further developed a set of concepts and tools and thereby established a new method, universal genome fingerprint analysis. We demonstrated their applications through case studies on over a hundred of genome sequences. Particularly, we defined the total genetic component configuration (TGCC) (i.e., chromosome, plasmid, and phage) for describing a strain as a system, and the universal genome fingerprint map (UGFM) of TGCC for differentiating a strain as a universal system, as well as the systematic comparative genomics (SCG) for comparing in-one-sitting a number of genomes crossing genetic category in diverse strains. By using UGFM, UGFM-TGCC, and UGFM-TGCC-SCG, we compared a number of genome sequences with farther divergences (chromosome, plasmid, and phage; bacterium, archaeal bacterium, and virus) over large size ranges (6Kbp~5Mbp), giving new insights into critical problematic issues in microbial genomics in the post-genomic era. This paper provided a new method for rapidly computing, geometrically visualizing, and intuitively comparing genome sequences at fingerprint level, and hence established a new method of universal genome fingerprint analysis for systematic comparative genomics.Comment: 63 pages, 15 figures, 5 table

Applications of Forensic Evidence in Criminal Cases

In 2003, Massachusetts governor Mitt Romney proposed a plan for an infallible death penalty that required irrefutable scientific evidence, effectively removing any doubt regarding potential innocence in death penalty cases. Forensic science encompasses many scientific disciplines including natural sciences and pattern analysis, but not all such areas experience equal amounts of general acceptance or influence in criminal cases. While DNA analysis and fingerprint identification using the Integrated Automated Fingerprint Identification System (IAFIS) are both widely accepted forensic applications, recent events expose concerns regarding the authenticity of other disciplines such as hair and bite mark comparison. Before policymakers address the issue of a reinstated death penalty, they must carefully consider the merits of forensic science as well as the potential dangers. Existing issues and a history of wrongful convictions aided by flawed forensic testimony necessitate further investigation and critical analysis of forensic disciplines and the application of forensic evidence in criminal cases

Molecular studies on intraspecific diversity and phylogenetic position of Coniothyrium minitans

Simple sequence repeat (SSR)±PCR amplification using a microsatellite primer (GACA)% and ribosomal RNA gene sequencing were used to examine the intraspecific diversity in the mycoparasite Coniothyrium minitans based on 48 strains, representing eight colony types, from 17 countries world-wide. Coniothyrium cerealis, C. fuckelii and C. sporulosum were used for interspecific comparison. The SSR±PCR technique revealed a relatively low level of polymorphism within C. minitans but did allow some differentiation between strains. While there was no relationship between SSR±PCR profiles and colony type, there was some limited correlation between these profiles and country of origin. Sequences of the ITS 1 and ITS 2 regions and the 5±8S gene of rRNA genes were identical in all twenty-four strains of C. minitans examined irrespective of colony type and origin. These results indicate that C. minitans is genetically not very variable despite phenotypic differences. ITS and 5±8S rRNA gene sequence analyses showed that C. minitans had similarities of 94% with C. fuckelii and C. sporulosum (which were identical to each other) and only 64% with C. cerealis. Database searches failed to show any similarity with the ITS 1 sequence for C. minitans although the 5±8S rRNA gene and ITS 2 sequences revealed an 87% similarity with Aporospora terricola. The ITS sequence including the 5±8S rRNA gene sequence of Coniothyrium cerealis showed 91% similarity to Phaeosphaeria microscopica. Phylogenetic analyses using database information suggest that C. minitans, C. sporulosum, C. fuckelii and A. terricola cluster in one clade, grouping with Helminthosporium species and 'Leptosphaeria' bicolor. Coniothyrium cerealis grouped with Ampelomyces quisqualis and formed a major cluster with members of the Phaeosphaeriacae and Phaeosphaeria microscopica