Closer to reality? The application of sequence analysis in crime linkage

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Jan-Martin Winter ◽  
Gina Rossi
Keyword(s):  
Sequence Analysis ◽  
Dimensional Space ◽  
Scaling Analysis ◽  
Sexual Assaults ◽  
Linkage Studies ◽  
Characteristic Analysis ◽  
Content Type ◽  
Discriminatory Accuracy ◽  
Sequence Of Events ◽  
Crime Linkage

Purpose Traditional crime linkage studies on serial sexual assaults have relied predominantly on a binary crime linkage approach that has yielded successful results in terms of linkage accuracy. Such an approach is a coarse reflection of reality by focussing mainly on the outcome of an offence, neglecting the forceful differences due to the intricate offender-victim interaction. Only few researchers have examined sexual assaults through the lens of a sequence analysis framework. This paper aims to present the first empirical test of offence sequence-based crime linkage, moving beyond exploratory analyses. Design/methodology/approach Offence accounts from 90 serial sexual assault and rape victims from the UK were analysed and sequentially coded. Sequence analysis allowed to compare all offences combinations regarding their underlying sequence of events. The resulting comparison was transformed and plotted in two-dimensional space by multidimensional scaling analysis for a visual inspection of linkage potential. The transformed proximities of all offences were used as predictors in a receiver operating characteristic analysis to actually test their discriminatory accuracy for crime linkage purpose. Findings Sequence analysis shows significant discriminatory accuracy for crime linkage purpose. However, the method does perform less well than previous binary crime linkage studies. Research limitations/implications Several limitations due to the nature of the data will be discussed. Practical implications The practical limitations are as follows: the study is a potential practical value for crime analysts; it is a complimentary methodology for statistical crime linkage packages; it requires automated coding to be useful; and it is very dependent on crime recoding standards. Originality/value The exploratory part of this study has been published in a book chapter in 2015. However, to the best of the authors’ knowledge, the succinct test of crime linkage accuracy is the first of its kind.

scholarly journals Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor

2011 ◽  
Vol 77 (19) ◽  
pp. 6972-6981 ◽  
Author(s):  
Ryan J. Newton ◽  
Jessica L. VandeWalle ◽  
Mark A. Borchardt ◽  
Marc H. Gorelick ◽  
Sandra L. McLellan
Keyword(s):  
Sequence Analysis ◽  
Genetic Marker ◽  
Microbial Community Composition ◽  
Fold Increase ◽  
Fecal Pollution ◽  
Plate Count ◽  
Rrna Gene ◽  
Fecal Indicators ◽  
Fecal Indicator ◽  
Content Type

ABSTRACTThe complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within theLachnospiraceaefamily, which was closely related to the genusBlautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for humanBacteroidales(based on the HF183 genetic marker), totalBacteroidalesspp., and enterococci and the conventionalEscherichia coliand enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and humanBacteroidalesincreased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE6013 Elements in Staphylococcus aureus

2017 ◽  
Vol 199 (8) ◽  
Author(s):  
Emily A. Sansevere ◽  
Xiao Luo ◽  
Joo Youn Park ◽  
Sunghyun Yoon ◽  
Keun Seok Seo ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Sequence Analysis ◽  
Integration Site ◽  
Consensus Sequence ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Site Preference ◽  
Conjugative Transfer ◽  
Content Type ◽  
Integrative Conjugative Elements

ABSTRACT ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus. Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA. The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013. Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci. IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013. A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.

scholarly journals Genetic Mechanisms behind the Spread of Reduced Susceptibility to Azithromycin in Shigella Strains Isolated from Men Who Have Sex with Men in Québec, Canada

2018 ◽  
Vol 63 (2) ◽  
pp. e01679-18 ◽  
Author(s):  
Khadidja Yousfi ◽  
Christiane Gaudreau ◽  
Pierre A. Pilon ◽  
Brigitte Lefebvre ◽  
Matthew Walker ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Shigella Flexneri ◽  
Complete Sequence ◽  
Shigella Sonnei ◽  
Content Type ◽  
Genetic Mechanisms ◽  
Sex With Men

ABSTRACT We analyzed 254 Shigella species isolates collected in Québec, Canada, during 2013 and 2014. Overall, 23.6% of isolates showed reduced susceptibility to azithromycin (RSA) encoded by mphA (11.6%), ermB (1.7%), or both genes (86.7%). Shigella strains with RSA were mostly isolated from men who have sex with men (68.8% or higher) from the Montreal region. A complete sequence analysis of six selected plasmids from Shigella sonnei and different serotypes of Shigella flexneri emphasized the role of IS26 in the dissemination of RSA.

An unusual presentation and resolution of syringomyelia after cervical spine injury

2005 ◽  
Vol 3 (6) ◽  
pp. 482-484 ◽  
Author(s):  
Joseph Cusick ◽  
Zvi Lidar
Keyword(s):  
Cervical Spine ◽  
Cervical Spine Injury ◽  
Spine Injury ◽  
Type I ◽  
Cervical Spine Trauma ◽  
Spine Trauma ◽  
Resonance Imaging ◽  
Chiari Malformation Type I ◽  
Content Type ◽  
Sequence Of Events

✓ The authors describe a case of noncommunicating syringomyelia associated with Chiari malformation Type I in a patient in whom acute symptomatic exacerbation occurred following cervical spine trauma. Surgical stabilization and realignment of the spine resulted in marked resolution of the neurological abnormalities, and subsequent magnetic resonance imaging demonstrated persistent collapse of the syrinx. The authors review the various factors in the pathogenesis of this unusual sequence of events.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals A Unique Urinary Metabolic Feature for the Determination of Bladder Cancer, Prostate Cancer, and Renal Cell Carcinoma

Metabolites ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 591
Author(s):  
Sujin Lee ◽  
Ja Yoon Ku ◽  
Byeong Jin Kang ◽  
Kyung Hwan Kim ◽  
Hong Koo Ha ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Renal Cell Carcinoma ◽  
Bladder Cancer ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clinical Signs ◽  
Analysis Of Covariance ◽  
Characteristic Analysis ◽  
Discriminatory Accuracy ◽  
Urological Cancers

Prostate cancer (PCa), bladder cancer (BCa), and renal cell carcinoma (RCC) are the most prevalent cancer among urological cancers. However, there are no cancer-specific symptoms that can differentiate them as well as early clinical signs of urological malignancy. Furthermore, many metabolic studies have been conducted to discover their biomarkers, but the metabolic profiling study to discriminate between these cancers have not yet been described. Therefore, in this study, we aimed to investigate the urinary metabolic differences in male patients with PCa (n = 24), BCa (n = 29), and RCC (n = 12) to find the prominent combination of metabolites between cancers. Based on 1H NMR analysis, orthogonal partial least-squares discriminant analysis was applied to find distinct metabolites among cancers. Moreover, the ranked analysis of covariance by adjusting a potential confounding as age revealed that 4-hydroxybenzoate, N-methylhydantoin, creatinine, glutamine, and acetate had significantly different metabolite levels among groups. The receiver operating characteristic analysis created by prominent five metabolites showed the great discriminatory accuracy with AUC > 0.7 for BCa vs. RCC, PCa vs. BCa, and RCC vs. PCa. This preliminary study compares the metabolic profiles of BCa, PCa, and RCC, and reinforces the exploratory role of metabolomics in the investigation of human urine.

scholarly journals Intra- and Interspecies Variability of Single-Cell Innate Fluorescence Signature of Microbial Cell

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Yutaka Yawata ◽  
Tatsunori Kiyokawa ◽  
Yuhki Kawamura ◽  
Tomohiro Hirayama ◽  
Kyosuke Takabe ◽  
...  
Keyword(s):  
Single Cell ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Population Level ◽  
Microbial Cell ◽  
Physiological Status ◽  
Growth Phases ◽  
Content Type ◽  
A Cell ◽  
Three Dimensional Space

ABSTRACT Here we analyzed the innate fluorescence signature of the single microbial cell, within both clonal and mixed populations of microorganisms. We found that even very similarly shaped cells differ noticeably in their autofluorescence features and that the innate fluorescence signatures change dynamically with growth phases. We demonstrated that machine learning models can be trained with a data set of single-cell innate fluorescence signatures to annotate cells according to their phenotypes and physiological status, for example, distinguishing a wild-type Aspergillus nidulans cell from its nitrogen metabolism mutant counterpart and log-phase cells from stationary-phase cells of Pseudomonas putida. We developed a minimally invasive method (confocal reflection microscopy-assisted single-cell innate fluorescence [CRIF] analysis) to optically extract and catalog the innate cellular fluorescence signatures of each of the individual live microbial cells in a three-dimensional space. This technique represents a step forward from traditional techniques which analyze the innate fluorescence signatures at the population level and necessitate a clonal culture. Since the fluorescence signature is an innate property of a cell, our technique allows the prediction of the types or physiological status of intact and tag-free single cells, within a cell population distributed in a three-dimensional space. Our study presents a blueprint for a streamlined cell analysis where one can directly assess the potential phenotype of each single cell in a heterogenous population by its autofluorescence signature under a microscope, without cell tagging. IMPORTANCE A cell’s innate fluorescence signature is an assemblage of fluorescence signals emitted by diverse biomolecules within a cell. It is known that the innate fluoresce signature reflects various cellular properties and physiological statuses; thus, they can serve as a rich source of information in cell characterization as well as cell identification. However, conventional techniques focus on the analysis of the innate fluorescence signatures at the population level but not at the single-cell level and thus necessitate a clonal culture. In the present study, we developed a technique to analyze the innate fluorescence signature of a single microbial cell. Using this novel method, we found that even very similarly shaped cells differ noticeably in their autofluorescence features, and the innate fluorescence signature changes dynamically with growth phases. We also demonstrated that the different cell types can be classified accurately within a mixed population under a microscope at the resolution of a single cell, depending solely on the innate fluorescence signature information. We suggest that single-cell autofluoresce signature analysis is a promising tool to directly assess the taxonomic or physiological heterogeneity within a microbial population, without cell tagging.

scholarly journals Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 23-29 ◽  
Author(s):  
Dominique Gueule ◽  
Gérard Fourny ◽  
Elisabeth Ageron ◽  
Anne Le Flèche-Matéos ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Great Lakes Region ◽  
The Novel ◽  
Content Type ◽  
African Great Lakes ◽  
Link Type

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea . By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea . Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).

scholarly journals Kinetics of Genetic Variation of the Mycoplasma genitalium MG192 Gene in Experimentally Infected Chimpanzees

2015 ◽  
Vol 84 (3) ◽  
pp. 747-753 ◽  
Author(s):  
Liang Ma ◽  
Jørgen S. Jensen ◽  
Miriam Mancuso ◽  
Leann Myers ◽  
David H. Martin
Keyword(s):  
Sequence Analysis ◽  
Sequence Variation ◽  
Variable Region ◽  
Mycoplasma Genitalium ◽  
Immune Selection ◽  
Content Type ◽  
Time Points ◽  
Single Colony ◽  
Nucleotide Sequence Variation ◽  
Kinetics Of

Mycoplasma genitalium, a human pathogen associated with sexually transmitted diseases, is capable of causing chronic infections, though mechanisms for persistence remain unclear. Previous studies have found that variation of the MgPa operon occurs by recombination of repetitive chromosomal sequences (known as MgPars) into the MG191 and MG192 genes carried on this operon, which may lead to antigenic variation and immune evasion. In this study, we determined the kinetics of MG192 sequence variation during the course of experimental infection using archived specimens from two chimpanzees infected withM. genitaliumstrain G37. The highly variable region of MG192 was amplified by PCR fromM. genitaliumisolates obtained at various time points postinfection (p.i.). Sequence analysis revealed that MG192 sequence variation began at 5 weeks p.i. With the progression of infection, sequence changes accumulated throughout the MG192 variable region. The presence of MG192 variants at specific time points was confirmed by variant-specific PCR assays and sequence analysis of single-colony clonedM. genitaliumorganisms. MG192 nucleotide sequence variation correlated with estimated recombination events, predicted amino acid changes, and time of seroconversion, a finding consistent with immune selection of MG192 variants. In addition, we provided evidence that MG192 sequence variation occurred during the process ofM. genitaliumsingle-colony cloning. Such spontaneous variation suggests that some MG192 variation is independent of immune selection but may form the basis for subsequent immune selection.

Sign in / Sign up

Export Citation Format

Share Document