A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

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A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types

Stem Cells ◽

10.1002/stem.2755 ◽

2017 ◽

Vol 36 (3) ◽

pp. 313-324 ◽

Cited By ~ 25

Author(s):

M. Joseph Phillips ◽

Peng Jiang ◽

Sara Howden ◽

Patrick Barney ◽

Jee Min ◽

...

Keyword(s):

Stem Cell ◽

Sequence Analysis ◽

Single Cell ◽

In Silico ◽

Pluripotent Stem Cell ◽

Cell Types ◽

Retinal Cell ◽

Human Pluripotent Stem Cell ◽

Rna Sequence ◽

Novel Approach

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Molecular Cloning, DNA Sequence Analysis, and Expression of cDNA Sequence of RNA Genomic Segment 6 (S6) that Encodes a Viral Outer Capsid Protein of Threadfin Aquareovirus (TFV)

Virus Genes ◽

10.1007/s11262-004-5629-7 ◽

2005 ◽

Vol 30 (2) ◽

pp. 209-221 ◽

Cited By ~ 3

Author(s):

Eng Khuan Seng ◽

Qin Fang ◽

Yoke Min Sin ◽

Toong Jin Lam

Keyword(s):

Sequence Analysis ◽

Molecular Cloning ◽

Capsid Protein ◽

Dna Sequence ◽

Cdna Sequence ◽

Dna Sequence Analysis ◽

Genomic Segment ◽

Outer Capsid Protein ◽

Outer Capsid

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Waypoint sequencing: simplifying behaviour sequence analysis for criminal cases

Journal of Criminal Psychology ◽

10.1108/jcp-08-2020-0035 ◽

2021 ◽

Vol 11 (1) ◽

pp. 72-82

Author(s):

David Keatley ◽

David D. Clarke

Keyword(s):

Sequence Analysis ◽

Temporal Analysis ◽

Serial Killer ◽

Criminal Cases ◽

Content Type ◽

Worked Example ◽

Criminological Research ◽

Novel Approach ◽

Novel Method ◽

Practical Implications

Purpose While behaviour sequence analysis (BSA) is popular, it is not without limitations, namely, the level of detail required and time taken to run analyses; therefore, this paper aims to outline a novel method, using 30 serial homicide cases as a worked example. Design/methodology/approach Temporal analysis methods are becoming increasingly popular in applied forensic and criminological research. In recent years, BSA has become a widely used approach. Findings Waypoint sequencing provides a streamlined version of the traditional BSA approach, allowing for fewer behaviours to be included and providing a clearer overview of the main behaviours of interest. Practical implications Waypoint sequencing is shown in the current paper through serial killer research to show how to conduct the analyses and how it is effective in current investigations by expediting the process and allowing quicker analysis to facilitate current investigations. Originality/value The current research provides a novel approach to sequence analysis that is more useful in applied settings as it requires fewer behaviours or events than traditional BSA.

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Behavior Sequencing Violent Episodes in Forensic Youth Populations

International Journal of Offender Therapy and Comparative Criminology ◽

10.1177/0306624x21988991 ◽

2021 ◽

pp. 0306624X2198899

Author(s):

David A. Keatley ◽

James Starritt ◽

Adrian Parke ◽

Tara Joyce ◽

David D. Clarke

Keyword(s):

Criminal Justice ◽

Sequence Analysis ◽

Criminal Justice System ◽

Justice System ◽

Research Literature ◽

Novel Approach ◽

Service Staff ◽

Children’S Homes ◽

Communal Areas ◽

Research Show

Every year, more children and youths are sent to Secure Children’s Homes while moving through the criminal justice system. Aggressive and violent incidents in these settings are common, and staff are often required to intervene and restrain violent individuals. The research literature has many examples of aggression and violence questionnaires and measures; however, for staff in communal areas it is the observable behaviors that they react to most. The current research, therefore, analyzed observable behaviors leading-up to violent episodes, and used Behavior Sequence Analysis to highlight the typical chains of behaviors that tend toward violence. The outcomes of this research show pathways to violence that staff can use to highlight potential spirals of aggression and violence. The current results show the links between non-confrontational behaviors (e.g., talking) through to more confrontational (staring, approaching, and pushing others). Overall, the research forms the foundation for future investigation into these and similar settings and outlines a novel approach to understanding violence escalation in a way that can be interpreted and used by service staff.

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