ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry

ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration

Vaccine confidence among people who use drugs: A cross-sectional survey

Adult immunization coverage remains low in the US, particularly for people who use drugs (PWUD), a population that experiences a disproportionate burden of vaccine-preventable diseases. The extent of and characteristics associated with vaccine confidence (VC) held by PWUD is poorly understood. As VC strongly correlates with vaccine uptake, this cross-sectional study identifies mutable factors associated with VC and quantifies its relationship to immunization status within a highly vulnerable, underimmunized population of PWUD. Using a community-engaged research strategy with select partner organizations hosting syringe exchange programs in Atlanta, Los Angeles, and Las Vegas, USA, we surveyed participants ages 18–69 years served by these organizations from 2019 to 2020. Survey measures included sociodemographics, health behavior including immunization receipt, and vaccine confidence in adult vaccinations using a modified Emory Vaccine Confidence Index (EVCI). The findings reflect relatively low VC among the 1,127 recruited participants, with 56% expressing low VC (EVCI 0–12), 35% medium (EVCI 13–20) and 10% high (EVCI 21–24). EVCI varied by city, with lowest confidence in Atlanta and highest in Las Vegas. VC was associated with past receipt of specific vaccines, including hepatitis A, MMR, Tdap, and influenza. VC varied by specific sociodemographic correlates such as housing insecurity (reduced confidence) and receipt of public benefits or disability (increased confidence). This study identified correlates associated with VC based on site and sociodemographic characteristics for this priority population, highlighting the need for specific interventions to raise VC among PWUD, especially among those experiencing housing insecurity and without public benefits

Study protocol for the Integra Initiative to assess the benefits and costs of integrating sexual and reproductive health and HIV services in Kenya and Swaziland.

BACKGROUND: In sub-Saharan Africa (SSA) there are strong arguments for the provision of integrated sexual and reproductive health (SRH) and HIV services. Most HIV transmissions are sexually transmitted or associated with pregnancy, childbirth, and breastfeeding. Many of the behaviours that prevent HIV transmission also prevent sexually transmitted infections and unintended pregnancies. There is potential for integration to increase the coverage of HIV services, as individuals who use SRH services can benefit from HIV services and vice-versa, as well as increase cost-savings. However, there is a dearth of empirical evidence on effective models for integrating HIV/SRH services. The need for robust evidence led a consortium of three organizations - International Planned Parenthood Federation, Population Council and the London School of Hygiene & Tropical Medicine - to design/implement the Integra Initiative. Integra seeks to generate rigorous evidence on the feasibility, effectiveness, cost and impact of different models for delivering integrated HIV/SRH services in high and medium HIV prevalence settings in SSA. METHODS/DESIGN: A quasi-experimental study will be conducted in government clinics in Kenya and Swaziland - assigned into intervention/comparison groups. Two models of service delivery are investigated: integrating HIV care/treatment into 1) family planning and 2) postnatal care. A full economic-costing will be used to assess the costs of different components of service provision, and the determinants of variations in unit costs across facilities/service models. Health facility assessments will be conducted at four time-periods to track changes in quality of care and utilization over time. A two-year cohort study of family planning/postnatal clients will assess the effect of integration on individual outcomes, including use of SRH services, HIV status (known/unknown) and pregnancy (planned/unintended). Household surveys within some of the study facilities' catchment areas will be conducted to profile users/non-users of integrated services and demand/receipt of integrated services, before-and-after the intervention. Qualitative research will be conducted to complement the quantitative component at different time points. Integra takes an embedded 'programme science' approach to maximize the uptake of findings into policy/practice. DISCUSSION: Integra addresses existing evidence gaps in the integration evaluation literature, building on the limited evidence from SSA and the expertise of its research partners. TRIAL REGISTRATION: Current Controlled Trials NCT01694862

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species