A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry.

Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism's proteome-even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database-as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a "species-specific" peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.

Prescription opioid injection among young people who inject drugs in New York City: a mixed-methods description and associations with hepatitis C virus infection and overdose.

AIM: Evidence is emerging that prescription opioid (PO) injection is associated with increased health risks. This mixed-methods study compares the mechanics of PO and heroin injection and examines the demographic and drug-related correlates of lifetime PO injection in a sample of young people who inject drugs (PWID) in New York City (NYC). METHODS: Qualitative analysis of 46 semi-structured interviews with young adult opioid users ages 18-32. Interview segments describing PO injection were analyzed for common themes. Quantitative analysis of structured interviews with 539 young adult opioid users ages 18-29 recruited via respondent-driven sampling (RDS). Analyses are based on the subsample of 353 participants (65%) who reported having ever injected drugs. All variables were assessed via self-report, except hepatitis C virus status, which was established via rapid antibody testing. RESULTS: Participants described injecting POs and reported that preparing abuse-deterrent pills for injection is especially cumbersome, requiring extended manipulation and large amounts of water. Injecting POs, in contrast to injecting heroin, requires repeated injections per injection episode. Among RDS-recruited participants, the majority of injectors reported injecting POs, sporadically (33%) or regularly (26%), but often infrequently (≤ 7 days/month). In separate multivariable analyses controlling for syringe- and cooker-sharing, ever injecting POs was a significant predictor of testing HCV antibody-positive (AOR = 2.97) and lifetime experience of non-fatal overdose (AOR = 2.51). Ever injecting POs was independently associated with lifetime homelessness (AOR = 2.93) and having grown up in a middle-income ($51,000-100,000/year vs. ≤ $50,000/year; AOR = 1.86) or a high-income household (> $100,000/year vs. ≤ $50,000/year; AOR = 2.54). CONCLUSIONS: Even in an urban environment like NYC with widespread heroin access, most young PWID have injected POs, although less frequently than heroin. PO injection involves practices that are known to increase risk for blood-borne viral infection (e.g., repeated injections) and predicted testing HCV-positive, as well as overdose. PO injection may also serve as a marker for a subgroup of PWID at elevated risk for multiple drug use-related comorbidities. Programs that provide prevention services to PWID need to tailor harm reduction measures and messaging to the specific practices and harms associated with the injection of POs.

Network Research Experiences in New York and Eastern Europe: Lessons for the Southern US in Understanding HIV Transmission Dynamics.

PURPOSE: This paper presents an overview of different kinds of risk and social network methods and the kinds of research questions each can address. RECENT FINDINGS: It also reviews what network research has discovered about how network characteristics are associated with HIV and other infections, risk behaviors, preventive behaviors, and care, and discusses some ways in which network-based public health interventions have been conducted. Based on this, risk and social network research and interventions seem both feasible and valuable for addressing the many public health and social problems raised by the widespread use of opioids in the US South.

Young adults' opioid use trajectories: From nonmedical prescription opioid use to heroin, drug injection, drug treatment and overdose.

INTRODUCTION: Recent research has begun to explore the transition from nonmedical use of prescription opioids (POs) to heroin and injection drug use, adding to earlier literature identifying factors that influence the transition from intranasal to injection use of heroin. However, little research has explored how these transitions are embedded within young people's broader opioid use trajectories - individual pathways that may also include experiences of nonfatal overdose and drug treatment. METHODS: Data are from a study of 539 18-29 year-old New York City residents, recruited via Respondent-Driven Sampling, who reported past-month nonmedical use of POs and/or heroin use. Participants completed structured, computer-assisted interviews that included assessment of their ages at a series of "benchmark" events and experiences, including first use of a drug or route of administration, the onset of "regular" use of a drug (i.e., 1 or more times a week for at least 1 month), first overdose and first drug treatment. RESULTS: Results suggest a predictable, ordered pathway by which opioid use tends to progress in this cohort of young adults. Participants initiated nonmedical PO use at age 16.8, on average, and most transitioned to heroin use (83%) and heroin injection (64%), generally within 4 years of first PO misuse. Drug treatment was not typically accessed until after participants had progressed to heroin use. First overdose occurred <1 year after first heroin use, on average. CONCLUSIONS: Findings may help inform the optimal timing for delivery of primary, secondary and tertiary prevention efforts targeting young opioid users.

High enhancer, downer, withdrawal helper: Multifunctional nonmedical benzodiazepine use among young adult opioid users in New York City.

BACKGROUND: Benzodiazepines are a widely prescribed psychoactive drug; in the U.S., both medical and nonmedical use of benzodiazepines has increased markedly in the past 15 years. Long-term use can lead to tolerance and dependence, and abrupt withdrawal can cause seizures or other life-threatening symptoms. Benzodiazepines are often used nonmedically in conjunction with other drugs, and with opioids in particular-a combination that can increase the risk for fatal and non-fatal overdose. This mixed-methods study examines nonmedical use of benzodiazepines among young adults in New York City and its relationship with opioid use. METHODS: For qualitative analysis, 46 90-minute semi-structured interviews were conducted with young adult opioid users (ages 18-32). Interviews were transcribed and coded for key themes. For quantitative analysis, 464 young adult opioid users (ages 18-29) were recruited using Respondent-Driven Sampling and completed structured interviews. Benzodiazepine use was assessed via a self-report questionnaire that included measures related to nonmedical benzodiazepine and opioid use. RESULTS: Participants reported using benzodiazepines nonmedically for a wide variety of reasons, including: to increase the high of other drugs; to lessen withdrawal symptoms; and to come down from other drugs. Benzodiazepines were described as readily available and cheap. There was a high prevalence (93%) of nonmedical benzodiazepine use among nonmedical opioid users, with 57% reporting regular nonmedical use. In bivariate analyses, drug-related risk behaviours such as polysubstance use, drug binging, heroin injection and overdose were strongly associated with regular nonmedical benzodiazepine use. In multivariate analysis, growing up in a middle-income household (earning between $51,000 and $100,000 annually), lifetime overdose experience, having ever used cocaine regularly, having ever been prescribed benzodiazepines, recent drug binging, and encouraging fellow drug users to use benzodiazepines to cope with opioid withdrawal were consistently strong predictors of regular nonmedical benzodiazepine use. CONCLUSION: Nonmedical benzodiazepine use may be common among nonmedical opioid users due to its drug-related multi-functionality. Harm reduction messages should account for the multiple functions benzodiazepines serve in a drug-using context, and encourage drug users to tailor their endorsement of benzodiazepines to peers to include safer alternatives.

Sexual Risk and Transmission Behaviors, Partnerships and Settings Among Young Adult Nonmedical Opioid Users in New York City.

Nonmedical prescription opioid use has become widespread. It can lead to heroin use, drug injection and HIV infection. We describe young adult opioid users' sexual risk behavior, partnerships and settings. 464 youth aged 18-29 who reported opioid use in the past 30 days were recruited using Respondent-Driven Sampling. Eligible participants completed a computer-assisted, interviewer-administered risk questionnaire and were tested for STIs and HIV. Participants (33% female; 66% white non-Hispanic) almost all had sex in the prior 90 days; 42% reported more than one partner. Same-sex sex was reported by 3% of men and 10% of women. Consistent condom use was rare. Seven percent reported group sex participation in the last 90 days but lifetime group sex was common among men and women. Young opioid users' unprotected sex, multiple partners and group sex puts them and others at high HIV and STI risk.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.

Genome-wide transcriptional profiling and enrichment mapping reveal divergent and conserved roles of Sko1 in the Candida albicans osmotic stress response.

Candida albicans maintains both commensal and pathogenic states in humans. Here, we have defined the genomic response to osmotic stress mediated by transcription factor Sko1. We performed microarray analysis of a sko1Δ/Δ mutant strain subjected to osmotic stress, and we utilized gene sequence enrichment analysis and enrichment mapping to identify Sko1-dependent osmotic stress-response genes. We found that Sko1 regulates distinct gene classes with functions in ribosomal synthesis, mitochondrial function, and vacuolar transport. Our in silico analysis suggests that Sko1 may recognize two unique DNA binding motifs. Our C. albicans genomic analyses and complementation studies in Saccharomyces cerevisiae showed that Sko1 is conserved as a regulator of carbohydrate metabolism, redox metabolism, and glycerol synthesis. Further, our real time-qPCR results showed that osmotic stress-response genes that are dependent on the kinase Hog1 also require Sko1 for full expression. Our findings reveal divergent and conserved aspects of Sko1-dependent osmotic stress signaling.