Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection.

The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.

Annexin A2 modulates phospholipid membrane composition upstream of Arp2 to control angiogenic sprout initiation.

The intersection of protein and lipid biology is of growing importance for understanding how cells address structural challenges during adhesion and migration. While protein complexes engaged with the cytoskeleton play a vital role, support from the phospholipid membrane is crucial for directing localization and assembly of key protein complexes. During angiogenesis, dramatic cellular remodeling is necessary for endothelial cells to shift from a stable monolayer to invasive structures. However, the molecular dynamics between lipids and proteins during endothelial invasion are not defined. Here, we utilized cell culture, immunofluorescence, and lipidomic analyses to identify a novel role for the membrane binding protein Annexin A2 (ANXA2) in modulating the composition of specific membrane lipids necessary for cortical F-actin organization and adherens junction stabilization. In the absence of ANXA2, there is disorganized cortical F-actin, reduced junctional Arp2, excess sprout initiation, and ultimately failed sprout maturation. Furthermore, we observed reduced filipin III labeling of membrane cholesterol in cells with reduced ANXA2, suggesting there is an alteration in phospholipid membrane dynamics. Lipidomic analyses revealed that 42 lipid species were altered with loss of ANXA2, including an accumulation of phosphatidylcholine (16:0_16:0). We found that supplementation of phosphatidylcholine (16:0_16:0) in wild-type endothelial cells mimicked the ANXA2 knock-down phenotype, indicating that ANXA2 regulated the phospholipid membrane upstream of Arp2 recruitment and organization of cortical F-actin. Altogether, these data indicate a novel role for ANXA2 in coordinating events at endothelial junctions needed to initiate sprouting and show that proper lipid modulation is a critical component of these events.

Characteristics of Students Participating in Collegiate Recovery Programs and the Impact of COVID-19: An Updated National Longitudinal Study.

The goals of the present study were to describe the development of the first national longitudinal study of collegiate recovery programs (CRP) students; provide an updated characterization of CRP students' demographics, past problem severity, and current recovery-related functioning; and examine the perceived impact of COVID-19 on CRP students' recovery. Universities and community colleges with CRPs across the United States and Ontario, Canada, were invited to partner on this project. Launched in fall 2020, three cohorts of participants were recruited. All participants who completed the baseline survey (N = 334 from 43 CRPs) were invited to complete follow-up surveys. The sample was composed of mostly undergraduate, White, cisgender women averaging 29 years old at baseline. They reported challenging backgrounds, including high levels of polysubstance use, alcohol/substance problem severity, mental health challenges, and involvement with the criminal legal system. Despite such adversity, they evidenced high levels of recovery-related functioning. Recovery capital and quality of life were high. Students reported an average of nearly four years in recovery, with most having between two and four years of abstinence from their primary substance of choice. COVID-19 represented a substantial source of stress for many, impacting some students' abstinence and recovery-related functioning. Results generally parallel findings from the only other national study of CRP students conducted a decade ago, providing a much-needed update and novel insights into CRP students. Findings can inform our understanding of the CRP student population and can be used to tailor CRP design and service offerings to students' backgrounds and needs.

Urinary phthalate metabolite concentrations and hot flash outcomes: Longitudinal associations in the Midlife Women's Health Study.

Midlife in women is an understudied time for environmental chemical exposures and menopausal outcomes. Recent cross-sectional research links phthalates with hot flashes, but little is known regarding such associations over time. Our objective was to estimate longitudinal associations between repeated measures of urinary phthalate metabolite concentrations and hot flash outcomes in midlife women. Using data from the Midlife Women's Health Study (MWHS), a prospective longitudinal study, we fit generalized linear mixed-effects models (GLMMs) and Cox proportional hazards regression models to repeated measures over a 4-year period. Recruitment occurred in Baltimore and surrounding counties, Maryland, USA between 2006 and 2015. Participants were premenopausal/perimenopausal women (n = 744) aged 45-54 years, who were not pregnant, not taking menopausal symptom medication or oral contraceptives, did not have hysterectomy/oophorectomy, and irrespective of hot flash experience. Baseline mean (SD) age was 48.4 (2.45), and 65% were premenopausal. Main outcome measures included adjusted odds ratios (ORs) for 4 self-reported hot flash outcomes (ever experienced, past 30 days experience, weekly/daily, and moderate/severe), and hazard ratios (HRs) for incident hot flashes. We observed mostly increased odds of certain hot flash outcomes with higher concentrations of metabolites of di (2-ethylhexyl) phthalate (DEHP), monoisobutyl phthalate (MiBP), and a molar summary measure of plasticizer phthalate metabolites (DEHP metabolites, mono-(3-carboxypropyl) phthalate (MCPP), monobenzyl phthalate (MBzP)). Some associations between exposures and outcomes indicated decreased odds. In conclusion, phthalate metabolites were associated with certain hot flash outcomes in midlife women. Midlife may be a sensitive period for higher phthalate metabolite concentrations with respect to menopausal symptoms.

A longitudinal study examining the associations between interpersonal trauma and romantic relationships among college students.

We examined the associations between the developmental timing of interpersonal trauma exposure (IPT) and three indicators of involvement in and quality of romantic relationships in emerging adulthood: relationship status, relationship satisfaction, and partner alcohol use. We further examined whether these associations varied in a sex-specific manner. In a sample of emerging adult college students (N = 12,358; 61.5% female) assessed longitudinally across the college years, we found precollege IPT increased the likelihood of being in a relationship, while college-onset IPT decreased the likelihood. Precollege and college-onset IPT predicted lower relationship satisfaction, and college-onset IPT predicted higher partner alcohol use. There was no evidence that associations between IPT and relationship characteristics varied in a sex-specific manner. Findings indicate that IPT exposure, and the developmental timing of IPT, may affect college students' relationship status. Findings also suggest that IPT affects their ability to form satisfying relationships with prosocial partners.

Risk of Legionellosis in residential areas around farms irrigating with municipal wastewater.

The conservation of freshwater is of both global and national importance, and in the United States, agriculture is one of the largest consumers of this resource. Reduction of the strain farming puts on local surface or groundwater is vital for ensuring resilience in the face of climate change, and one possible option is to irrigate with a combination of freshwater and reclaimed water from municipal wastewater treatment facilities. However, this wastewater can contain pathogens that are harmful to human health, such as Legionella pneumophila, which is a bacterium that can survive aerosolization and airborne transportation and cause severe pneumonia when inhaled. To assess an individual adult's risk of infection with L. pneumophila from a single exposure to agricultural spray irrigation, a quantitative microbial risk assessment was conducted for a scenario of spray irrigation in central Illinois, for the growing seasons in 2017, 2018, and 2019. The assessment found that the mean risk of infection for a single exposure exceeded the safety threshold of 10-6 infections/exposure up to 1 km from a low-pressure irrigator and up to 2 km from a high-pressure irrigator, although no median risk exceeded the threshold for any distance or irrigator pressure. These findings suggest that spray irrigation with treated municipal wastewater could be a viable option for reducing freshwater consumption in Midwest farming, as long as irrigation on windy days is avoided and close proximity to the active irrigator is limited.

The Associations of Polygenic Scores for Risky Behaviors and Parenting Behaviors with Adolescent Externalizing Problems.

The current study focused on longitudinal effects of genetics and parental behaviors and their interplay on externalizing behaviors in a panel study following individuals from adolescence to young adulthood. The nationally representative sample of Add Health participants of European ancestry included N = 4142 individuals, measured on three occasions. Parenting was operationalized as experiences with child maltreatment and maternal closeness. Externalizing problems were operationalized as alcohol use, cannabis use, and antisocial behaviors. Genetic effects were operationalized as a polygenic score (PGS) of risky behaviors. The results showed significant effects for child maltreatment, maternal closeness, and PGS, above and beyond other factors and previous levels of externalizing behaviors. Furthermore, maternal closeness was found to negatively correlate with PGS. No significant interaction effects of parenting and PGS were found. The results underscore the joint independent effects of parenting and genetics on the change in externalizing behaviors from adolescence to young adulthood.

Deriving a Measure of Social Recovery Capital From the Important People and Activities Instrument: Construction and Psychometric Properties.

AIM: This study presents a measure of Social Recovery Capital (SRC) derived from the Important People and Activities instrument (IPA). METHODS: The sample comprised young adults who participated in the Collaborative Study on the Genetics of Alcoholism, a high-risk family study of alcohol use disorder (N = 2472). Exploratory and confirmatory factor analysis identified influential items and factor structure, adjusting for family relatedness. The final scale was tested for reliability and validity. RESULTS: Factor analysis retained 10 items loading on three factors (Network Abstinence Behaviors, Basic Network Structure and Network Importance) that together explained 42% of the variance in SRC. The total model showed adequate fit (Comparative Fit Index = 0.95; Tucker Lewis Index = 0.93; Root Mean Square Error of Approximation = 0.06; Standardized Root Mean Squared Residual = 0.05) and acceptable reliability (α = 0.60; McDonald's ω = 0.73) and correlated with validation measures mostly in the weak to moderate range. Due to variable factor scores for reliability and validity, we only recommend using the total score. CONCLUSION: The SRC-IPA is a novel measure of SRC derived from the IPA that captures social network data and has applications in research and clinical work. Secondary data analyses using the SRC-IPA in studies that collected the IPA can further demonstrate the interaction of SRC with a wide variety of clinical indicators and demographic characteristics, making it a valuable addition to other measures of SRC.

Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees.

BACKGROUND: The number of cases of tick-borne diseases in humans is increasing rapidly within Illinois. The responsibility for increased surveillance of tick-borne disease cases and tick vectors is being placed on local health departments throughout the United States, but they often lack the funding, time, and/or training needed to perform said surveillance. The aims of this study were to develop, deliver, and determine the effectiveness of tick surveillance training workshops for local health department employees within Illinois. METHODS: We developed and delivered in-person training at local health department offices in each of six Illinois Department of Public Health Environmental Health Regions between April-May of 2019. Pre-, post-, and six-month follow-up questionnaires on knowledge, attitudes, and practices with regards to tick surveillance were administered to training participants. Paired student's t-test or Wilcoxon signed-rank test were used to compare knowledge, attitudes, and practices scores between questionnaires with Cohen's d being used to calculate effect sizes associated with t-tests. McNemar's and McNemar-Bowker tests were used to evaluate individual questions. Spearman's rank correlation was used to evaluate the relationship between knowledge, attitudes, and practices at pre-, post-, and six-month follow-up. RESULTS: Seventy-six employees from 40 local health departments that represent 44% (45/102) of Illinois counties attended at least one training workshop. Of these attendees, 81.5% (62/76) participated in at least one survey, 79% (60/76) in the in-person pre-training survey, 74% (56/76) in the in-person post-training survey, and 22% (17/76) in the online six-month follow-up survey. The average knowledge score was significantly increased by 8.21 (95% CI:7.28-9.14) points from pre-training to post-training. The average overall attitude score significantly increased by 5.29 (95% CI: 3.91-6.66) points from pre- to post-training. There were no significant differences in practice scores. CONCLUSIONS: Our study found the training was effective in increasing the knowledge of ticks, tick-borne diseases, and surveillance as well as promoting positive attitudes related to surveillance. While the training, by itself, was not associated with increases in surveillance practices, we were able to empower local public health officials with the knowledge and positive attitudes needed to enact change.

An Interdisciplinary Approach to One Health: Course Design, Development, and Delivery.

One Health is an approach to studying health by recognizing the interconnections between people, animals, plants, and their shared environment. This article describes the process of designing a new course on One Health at the University of Illinois at Urbana-Champaign (UIUC). We brought together faculty and students from across campus to develop a multidisciplinary course dedicated to One Health and infectious diseases. This group met over 9 months to brainstorm course goals, objectives, and ideas. The group also organized a workshop to explore One Health's existing knowledge and ongoing work on the UIUC campus. We solicited the help of experts throughout the university to co-teach the course. The course curriculum and course materials included 13 unique case studies. The course was offered in fall 2019, and its goals were to add to the existing training and coursework on One Health at the University of Illinois campus, offer a course that would be suitable for students from all fields of study, and develop helpful case studies to be made available to other educators. Student feedback highlights the course's successes as well as areas for future improvement. This article describes this entire process of course development, provides recommendations to guide improvements in the next offering of the course, and details our contributions to the field of One Health education.

Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection.

BACKGROUND: Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS: In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture. RESULTS: Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests. CONCLUSIONS: RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.

Evolutionary genomic and bacteria GWAS analysis of Mycobacterium avium subsp. paratuberculosis and dairy cattle Johne's disease phenotypes.

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle. The Regional Dairy Quality Management Alliance (RDQMA) project is a multistate research program involving MAP isolates taken from three intensively studied commercial dairy farms in the northeastern United States, which emphasized longitudinal data collection of both MAP isolates and animal health in three regional dairy herds for a period of about 7 years. This paper reports the results of a pan-GWAS analysis involving 318 MAP isolates and dairy cow Johne's disease phenotypes, taken from these three farms. Based on our highly curated accessory gene count the pan-GWAS analysis identified several MAP genes associated with bovine Johne's disease phenotypes scored from these three farms, with some of the genes having functions suggestive of possible cause/effect relationships to these phenotypes. This paper reports a pan-genomic comparative analysis between MAP and Mycobacterium tuberculosis, assessing functional Gene Ontology category enrichments between these taxa. Finally, we also provide a population genomic perspective on the effectiveness of herd isolation, involving closed dairy farms, in preventing MAP inter-farm cross infection on a micro-geographic scale.IMPORTANCE Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle, and enormous economic consequences for the dairy industry. Understanding which genes in this bacterium are correlated with key disease phenotypes can lead to functional experiments targeting these genes and ultimately lead to improved control strategies. This study represents a rare example of a prolonged longitudinal study of dairy cattle where the disease was measured and the bacteria were isolated from the same cows. The genome sequences of over 300 MAP isolates were analyzed for genes that were correlated with a wide range of Johne's disease phenotypes. A number of genes were identified that were significantly associated with several aspects of the disease and suggestive of further experimental follow-up.

Facial malformations, including cleft lip and palate, in wild primates in Paraguay.

Nine individual Alouatta caraya and Sapajus cay displaying facial malformations were observed across three sites in Paraguay. Six had cleft lip (with or without cleft palate), and three had malformations of the lower lip. This is the first record of cleft lip and/or palate in the genus Alouatta.

Using a developmental perspective to examine the moderating effects of marriage on heavy episodic drinking in a young adult sample enriched for risk.

Many studies demonstrate that marriage protects against risky alcohol use and moderates genetic influences on alcohol outcomes; however, previous work has not considered these effects from a developmental perspective or in high-risk individuals. These represent important gaps, as it cannot be assumed that marriage has uniform effects across development or in high-risk samples. We took a longitudinal developmental approach to examine whether marital status was associated with heavy episodic drinking (HED), and whether marital status moderated polygenic influences on HED. Our sample included 937 individuals (53.25% female) from the Collaborative Study on the Genetics of Alcoholism who reported their HED and marital status biennially between the ages of 21 and 25. Polygenic risk scores (PRS) were derived from a genome-wide association study of alcohol consumption. Marital status was not associated with HED; however, we observed pathogenic gene-by-environment effects that changed across young adulthood. Among those who married young (age 21), individuals with higher PRS reported more HED; however, these effects decayed over time. The same pattern was found in supplementary analyses using parental history of alcohol use disorder as the index of genetic liability. Our findings indicate that early marriage may exacerbate risk for those with higher polygenic load.

Quantification and Comparison of Risks Associated with Wastewater Use in Spray Irrigation.

In the U.S., spray irrigation is the most common method used in agriculture and supplementing with animal wastewater has the potential to reduce water demands. However, this could expose individuals to respiratory pathogens such as Legionella pneumophila and nontuberculosis Mycobacteria (NTM). Disinfection with methods like anaerobic digestion is an option but can increase concentrations of cytotoxic ammonia (personal communication). Our study aimed to model the annual risks of infection from these bacterial pathogens and the air concentrations of ammonia and determine if anaerobically digesting this wastewater is a safe option. Air dispersion modeling, conducted in AERMOD, generated air concentrations of water during the irrigation season (May-September) for the years 2013-2018. These values fed into the quantitative microbial risk assessments for the bacteria and allowed calculation of ammonia air concentrations. The outputs of these models were compared to the safety thresholds of 10-4 infections/year and 0.5 mg/m3 , respectively, to determine their potential for negative health outcomes. It was determined that infection from NTM was not a concern for individuals near active spray irrigators, but that infection with L. pneumophila could be a concern, with a maximum predicted annual risk of infection of 3.5 × 10-3 infections/year and 25.2% of parameter combinations exceeding the established threshold. Ammonia posed a minor risk, with 1.5% of parameter combinations surpassing the risk threshold of 0.5 mg/m3 . These findings suggest that animal wastewater should be anaerobically digested prior to use in irrigation to remove harmful pathogens.

A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands.

A limited set of T cell receptor (TCR) variable (V) gene segments are used to create a repertoire of TCRs that recognize all major histocompatibility complex (MHC) ligands within a species. How individual αßTCRs are constructed to specifically recognize a limited set of MHC ligands is unclear. Here we have identified a role for the differential pairing of particular V gene segments in creating TCRs that recognized MHC class II ligands exclusively, or cross-reacted with classical and nonclassical MHC class I ligands. Biophysical and structural experiments indicated that TCR specificity for MHC ligands is not driven by germline-encoded pairwise interactions.Rather, identical TCRß chains can have altered peptide-MHC (pMHC) binding modes when paired with different TCRα chains. The ability of TCR chain pairing to modify how V region residues interact with pMHC helps to explain how the same V genes are used to create TCRs specific for unique MHC ligands.

Bertiella sp. (Meyner, 1895) infection of Alouatta caraya (Humboldt, 1812) in urban and natural environments in Ñeembucú, southwest Paraguay.

Bertiella sp., a cestode known to infect a variety of hosts, including nonhuman primates and humans, was identified in Paraguay as early as 1895, but no systematic analysis of wild primates' gastrointestinal parasites has ever been carried out in Paraguay. Increased urbanization in southwest Paraguay has pushed the Paraguayan howler monkey (Alouatta caraya) into anthropogenic habitats, particularly in the city of Pilar (Ñeembucú department), giving rise to greater potential for zoonotic transmission between wild primates and humans. From July to December 2018, fecal samples were noninvasively collected from 48 howlers inside Pilar (urban environment), the Pilar Military Base (intermediate environment), and a ranch 27 km outside Pilar in the humid Chaco (natural environment) and analyzed for Bertiella eggs and proglottids using macro-analysis and formol-ether sedimentation. Howlers living in the urban environment had the highest rates of Bertiella infection (50% prevalence), with considerably lower infection rates in the intermediate environment (6.25% prevalence) and natural habitats (0% prevalence). A χ2 goodness-of-fit test indicated a significant difference between the three habitat types (p = .007, χ2 = 10.005, df = 2). While the habitat seems to impact the frequency of infection, Bertiella was not observed to select for other factors such as age or sex of the primate host. Here we identified a significant increase in the frequency of Bertiella infection in an urban environment, which can then be further transmitted to new hosts with more direct primate contact. Bertiella infection has already been documented in humans in Paraguay, all of which were associated with close primate contact. As howlers move into more urban habitats due to urbanization and habitat fragmentation, Bertiella could be introduced into this new ecosystem and has the potential to cause further infections in humans.

A QPCR ASSAY AND TESTING GUIDELINES FOR THE MOLECULAR DIAGNOSIS OF SYSTEMIC ISOSPOROSIS (FORMERLY ATOXPLASMOSIS) IN PASSERINE BIRDS.

Systemic isosporosis (formerly atoxoplasmosis), is a protozoal infection that causes death in nestling and fledgling passerine birds impacting ex situ breeding and reintroduction programs. Because current antemortem diagnostic tests lack sensitivity, a qPCR was developed for detection of Isospora spp. using primers and a fluorescent-tagged MGB probe targeting the large subunit (28s) ribosomal RNA gene (assay efficiency = >100%; sensitivity = <1 dsDNA copy). The assay was used to screen postmortem frozen or formalin-fixed paraffin-embedded tissue samples from passerine birds (n = 24; 12 with confirmed systemic isosporosis), whole blood and feces (n = 38) from live passerines, and other tissues infected with phylogenetically similar protozoa. The qPCR identified Isospora sp. DNA in tissues from 21/24 birds including 12/12 birds with cytologically-histologically confirmed infection (100% sensitivity) and 9/12 birds lacking microscopic organisms. The assay also amplified Eimeria sp. DNA; however, sequence analysis ruled out infection in the passerine cases. Blood and/or feces were positive in 30/38 birds, and in only 7/38 birds, blood and feces both contained Isospora sp. DNA. Finally, the qPCR was utilized to screen 30 consecutive daily fecal samples from live passerines (n = 20) to determine optimal sampling protocols. One or more of the daily fecal samples were positive in all 20 birds. In individual birds, the interval between positive qPCR amplification results ranged from 0 to 23 days, with an average of 5.85 days. Simulated application of 13 potential sample collection schedules was used to identify the sensitivity of repeated testing for identification of infected birds. Increased sampling days resulted in higher sensitivity but increased both cost and animal handling requirements. Based on statistical analysis and clinical considerations, the testing recommendation for detection of fecal shedding was collection and assay of five consecutive daily fecal samples, which had an average diagnostic sensitivity of 0.86.

Annot: a Django-based sample, reagent, and experiment metadata tracking system.

BACKGROUND: In biological experiments, comprehensive experimental metadata tracking - which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies - remains a challenge, especially when the experiment involves multiple laboratory scientists who execute different steps of the protocol. Here we describe Annot, a novel web application designed to provide a flexible solution for this task. RESULTS: Annot enforces the use of controlled vocabulary for sample and reagent annotation while enabling robust investigation, study, and protocol tracking. The cornerstone of Annot's implementation is a json syntax-compatible file format, which can capture detailed metadata for all aspects of complex biological experiments. Data stored in this json file format can easily be ported into spreadsheet or data frame files that can be loaded into R ( https://www.r-project.org/ ) or Pandas, Python's data analysis library ( https://pandas.pydata.org/ ). Annot is implemented in Python3 and utilizes the Django web framework, Postgresql, Nginx, and Debian. It is deployed via Docker and supports all major browsers. CONCLUSIONS: Annot offers a robust solution to annotate samples, reagents, and experimental protocols for established assays where multiple laboratory scientists are involved. Further, it provides a framework to store and retrieve metadata for data analysis and integration, and therefore ensures that data generated in different experiments can be integrated and jointly analyzed. This type of solution to metadata tracking can enhance the utility of large-scale datasets, which we demonstrate here with a large-scale microenvironment microarray study.

Genes, Roommates, and Residence Halls: A Multidimensional Study of the Role of Peer Drinking on College Students' Alcohol Use.

BACKGROUND: Peer drinking is one of the most robust predictors of college students' alcohol use and can moderate students' genetic risk for alcohol use. Peer effect research generally suffers from 2 problems: selection into peer groups and relying more on perceptions of peer alcohol use than peers' self-report. The goal of the present study was to overcome those limitations by capitalizing on a genetically informed sample of randomly assigned college roommates to examine multiple dimensions of peer influence and the interplay between peer effects and genetic predisposition on alcohol use, in the form of polygenic scores. METHODS: We used a subsample (n = 755) of participants from a university-wide, longitudinal study at a large, diverse, urban university. Participants reported their own alcohol use during fall and spring and their perceptions of college peers' alcohol use in spring. We matched individuals into their rooms and residence halls to create a composite score of peer-reported alcohol use for each of those levels. We examined multiple dimensions of peer influence and whether peer influence moderated genetic predisposition to predict college students' alcohol use using multilevel models to account for clustering at the room and residence hall level. RESULTS: We found that polygenic scores (ß = 0.12), perceptions of peer drinking (ß = 0.37), and roommates' self-reported drinking (ß = 0.10) predicted alcohol use (all ps < 0.001), while average alcohol use across residence hall did not (ß = -0.01, p = 0.86). We found no evidence for interactions between peer influence and genome-wide polygenic scores for alcohol use. CONCLUSIONS: Our findings underscore the importance of genetic predisposition on individual alcohol use and support the potentially causal nature of the association between peer influence and alcohol use.