Evolution of the Hepatitis E virus hypervariable region

The presence of a hypervariable (HVR) region within the genome of hepatitis E virus (HEV) remains unexplained. Previous studies have described the HVR as a proline-rich spacer between flanking functional domains of the ORF1 polyprotein. Others have proposed that the region has no function, that it reflects a hypermutable region of the virus genome, that it is derived from the insertion and evolution of host sequences or that it is subject to positive selection. This study attempts to differentiate between these explanations by documenting the evolutionary processes occurring within the HVR. We have measured the diversity of HVR sequences within acutely infected individuals or amongst sequences derived from epidemiologically linked samples and, surprisingly, find relative homogeneity amongst these datasets. We found no evidence of positive selection for amino acid substitution in the HVR. Through an analysis of published sequences, we conclude that the range of HVR diversity observed within virus genotypes can be explained by the accumulation of substitutions and, to a much lesser extent, through deletions or duplications of this region. All published HVR amino acid sequences display a relative overabundance of proline and serine residues that cannot be explained by a local bias towards cytosine in this part of the genome. Although all published HVRs contain one or more SH3-binding PxxP motifs, this motif does not occur more frequently than would be expected from the proportion of proline residues in these sequences. Taken together, these observations are consistent with the hypothesis that the HVR has a structural role that is dependent upon length and amino acid composition, rather than a specific sequence

Hepatitis E virus mixed infection in immunocompetent patient

We detected 2 hepatitis E virus (HEV) strains in an acutely infected immunocompetent patient. Two populations of genotype 3 virus were observed in the hypervariable regions and open reading frames 2 and 3, indicating multiple infection with hepatitis E virus. Persons with mixed infections may provide the opportunity for virus recombination

Implementing The Prison Rape Elimination Act: A Toolkit for Jails

Minor edits. “The goal of this Toolkit is to provide jails of all sizes, political divisions, and geographic locations with a step-by-step guide for preventing, detecting, and eliminating sexual abuse of inmates in their custody – and for responding effectively to abuse when it occurs. Prison rape includes all forms of inmate sexual abuse within a correctional facility, including state and federal prisons, county and municipal jails, police lock-ups, holding facilities, inmate transportation vehicles, juvenile detention facilities, and community corrections facilities. Protecting arrestees, detainees, and inmates from sexual violence is part of a jail’s core mission. This toolkit will help assess your jail’s operations with an eye to improvements.” The Toolkit is divided into folders holding materials related to: introductory information about PREA [Prison Rape Elimination Act] and it Standards; a Self-Assessment Checklist with supporting forms “to provide a step-by-step process for jails to review and assess policies, procedures, and practices in light of the PREA Standards and accepted best practices”; and additional resources to assist you in PREA-readiness

Assessing changes to ecosystem structure and function following invasion by Spartina alterniflora and Phragmites australis: a meta-analysis [Supplemental Files]

Includes data and R codeBiological invasions resulting from anthropogenic activities are one of the greatest threats to maintaining ecosystem functioning and native biodiversity. Invasions are especially problematic when the invading species behaves as an ecosystem engineer that is capable of transforming ecosystem structure, function, and community dynamics. Of particular concern is the spread of emergent wetland grasses whose root systems alter hydrology and structural stability of soils, modify ecosystem functions, and change community dynamics and species richness. To address the threats posed to ecosystems across the globe, management practices focus on the control and removal of invasive grasses. However, it remains unclear how severely invasive grasses alter ecosystem functions and whether alterations persist after invasive grass removal, limiting our ability to determine if management practices are truly sufficient to fully restore ecosystems. Here, we conducted a meta-analysis to quantify ecological alterations and the efficacy of management following the invasion of Spartina alterniflora and Phragmites australis, two common and pervasive invaders in coastal wetlands. Our results indicate that S. alterniflora and P. australis significantly alter measures of ecosystem functioning and organismal abundance. Invaded ecosystems had significant elevations in abiotic carbon and nitrogen fixation and uptake in areas with invasive grasses, with differential photosynthetic pathways of these two grass species further explaining carbon fluxes. Moreover, evidence from our analyses indicates that management practices may not adequately promote recovery from invasion, but more data are needed to fully assess management efficacy. We call for future studies to conduct pairwise comparisons between uninvaded, invaded, and managed systems and provide research priorities

Implementing The Prison Rape Elimination Act: A Toolkit for Jails

Minor edits. “The goal of this Toolkit is to provide jails of all sizes, political divisions, and geographic locations with a step-by-step guide for preventing, detecting, and eliminating sexual abuse of inmates in their custody – and for responding effectively to abuse when it occurs. Prison rape includes all forms of inmate sexual abuse within a correctional facility, including state and federal prisons, county and municipal jails, police lock-ups, holding facilities, inmate transportation vehicles, juvenile detention facilities, and community corrections facilities. Protecting arrestees, detainees, and inmates from sexual violence is part of a jail’s core mission. This toolkit will help assess your jail’s operations with an eye to improvements.” The Toolkit is divided into folders holding materials related to: introductory information about PREA [Prison Rape Elimination Act] and it Standards; a Self-Assessment Checklist with supporting forms “to provide a step-by-step process for jails to review and assess policies, procedures, and practices in light of the PREA Standards and accepted best practices”; and additional resources to assist you in PREA-readiness

Implementing The Prison Rape Elimination Act: A Toolkit for Juvenile Agencies and Facilities

The goal of this Toolkit is to provide juvenile agencies and facilities of all sizes, political divisions, and geographic locations with a step-by-step guide for preventing, detecting, and eliminating sexual abuse of residents in their custody – and for responding effectively to abuse when it occurs. Prison rape includes all forms of resident sexual abuse within a correctional facility, including state and federal prisons, county and municipal jails, police lock-ups, holding facilities, resident transportation vehicles, juvenile facilities, and community corrections facilities. This toolkit will help assess your juvenile facility’s operations with an eye to improvements. The Toolkit is divided into folders holding materials related to: introductory information about PREA [Prison Rape Elimination Act] and it Standards; a Self-Assessment Checklist with supporting forms “to provide a step-by-step process for juvenile facilities to review and assess policies, procedures, and practices in light of the PREA Standards and accepted best practices”; and additional resources to assist you in PREA-readiness

Implementing The Prison Rape Elimination Act: A Toolkit for Juvenile Agencies and Facilities

The goal of this Toolkit is to provide juvenile agencies and facilities of all sizes, political divisions, and geographic locations with a step-by-step guide for preventing, detecting, and eliminating sexual abuse of residents in their custody – and for responding effectively to abuse when it occurs. Prison rape includes all forms of resident sexual abuse within a correctional facility, including state and federal prisons, county and municipal jails, police lock-ups, holding facilities, resident transportation vehicles, juvenile facilities, and community corrections facilities. This toolkit will help assess your juvenile facility’s operations with an eye to improvements. The Toolkit is divided into folders holding materials related to: introductory information about PREA [Prison Rape Elimination Act] and it Standards; a Self-Assessment Checklist with supporting forms “to provide a step-by-step process for juvenile facilities to review and assess policies, procedures, and practices in light of the PREA Standards and accepted best practices”; and additional resources to assist you in PREA-readiness