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SARS-CoV-2 vaccines reduce the risk of COVID-19.1–3 However, some disease-modifying anti-rheumatic drugs (DMARDs), particularly glucocorticoids, methotrexate, mycophenolate mofetil and rituximab, may blunt the immunological response to COVID-19 vaccination.4 Little is known about the clinical efficacy of these vaccines at preventing COVID-19 infection in patients with systemic autoimmune rheumatic diseases (SARDs). Mass General Brigham (MGB) is a large multicentre healthcare system in the Boston, Massachusetts, USA area. Patients with SARDs with a positive SARS-CoV-2 PCR or antigen test between 30 January 2020 and 30 July 2021 at MGB were identified using diagnostic billing codes or were referred by physicians, as previously described.5 From this cohort, we identified breakthrough infections in fully vaccinated patients, defined as a positive test ≥14 days after the final vaccine dose.6 Of 786 SARD patients with COVID-19, 340 occurred after the initial emergency use authorisation for COVID-19 vaccination in the USA. Of these, 16 (4.7%) were breakthrough infections (online supplemental figure 1). Among the breakthrough infections, 12 (75%) were female, 11 (69%) were white, the median age was 50 years and 12 (75%) had ≥1 comorbidity (table 1). The most common SARDs included rheumatoid arthritis (6, 38%), inflammatory myositis (3, 19%) and systemic lupus erythematosus (3, 19%). Rituximab (5, …

BackgroundStaphylococcus aureusis a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carryS. aureusasymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influenceS. aureusacquisition and retention in early life.ResultsWe recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns ofS. aureuscarriage, positively associated withAcinetobacterspecies,Streptococcus parasanguinis,Streptococcus salivarius, andVeillonellaspecies and inversely associated with maternalDolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated withS. aureusin infants and mothers. In gene content-based strain profiling, infantS. aureusstrains are more similar to maternal strains.ConclusionsThis improved understanding ofS. aureuscolonization is an important first step toward the development of novel, ecological therapies for controllingS. aureuscarriage.

ObjectiveTo describe the characteristics of COVID-19 vaccine breakthrough infections among systemic autoimmune rheumatic disease (SARD) patients.MethodsWe identified SARDs patients in a large healthcare system with COVID-19 vaccination ≥14 days prior to a positive SARS-CoV-2 molecular test. Details of the patient’s SARD, vaccination status, and COVID-19 infection were extracted.ResultsOf 340 confirmed COVID-19 infections among SARDs patients between December 11th, 2020 (date of first COVID-19 vaccine approval in the US) and July 30th, 2021, we identified 16 breakthrough infections. Seven (44%) received the Pfizer-BioNtech vaccine, five (31%) received the Moderna vaccine, and four (25%) received the Janssen/Johnson & Johnson vaccine. The most common SARDs included rheumatoid arthritis (6, 38%), inflammatory myopathy (3, 19%), and systemic lupus erythematosus (3, 19%). Rituximab (5, 31%), glucocorticoids (4, 25%), and mycophenolate mofetil (4, 25%) were the most frequent treatments. Among the breakthrough infections, 15 (93%) were symptomatic, six (38%) were hospitalized, one (6%) required mechanical ventilation, and two (13%) died.ConclusionsSymptomatic, including severe, breakthrough infections were observed in SARDs patients; many were on treatments associated with attenuated antibody responses to vaccination. Further studies are needed to determine the rate of breakthrough infection associated with SARD treatments and other features.Key messagesWhat is already known about this subject?Breakthrough infections following COVID-19 vaccination are expected but some patients with systemic autoimmune rheumatic diseases (SARDs) may be at higher risk because of blunted antibody responses to vaccination associated with rheumatic disease treatments and other factors that remain poorly understood.What does this study add?We identify and describe 16 COVID-19 vaccine breakthrough infections within the Mass General Brigham system between December 11th, 2020 and June 26th, 2021. The vast majority of cases were symptomatic and two were fatal.How might this impact on clinical practice or future developments?This study complements observations regarding the attenuated antibody response to COVID-19 vaccination in patients with SARDs by identifying serious clinical outcomes from breakthrough infections in patients receiving DMARDs that have been reported to have blunted vaccine responses. Our study identifies characteristics of COVID-19 breakthrough infections that may guide the prioritization of booster vaccines and other risk-mitigating strategies in patients with SARDs.

© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ., Objectives: To determine factors associated with COVID-19-related death in people with rheumatic diseases. Methods: Physician-reported registry of adults with rheumatic disease and confirmed or presumptive COVID-19 (from 24 March to 1 July 2020). The primary outcome was COVID-19-related death. Age, sex, smoking status, comorbidities, rheumatic disease diagnosis, disease activity and medications were included as covariates in multivariable logistic regression models. Analyses were further stratified according to rheumatic disease category. Results: Of 3729 patients (mean age 57 years, 68% female), 390 (10.5%) died. Independent factors associated with COVID-19-related death were age (66-75 years: OR 3.00, 95% CI 2.13 to 4.22; >75 years: 6.18, 4.47 to 8.53; both vs ≤65 years), male sex (1.46, 1.11 to 1.91), hypertension combined with cardiovascular disease (1.89, 1.31 to 2.73), chronic lung disease (1.68, 1.26 to 2.25) and prednisolone-equivalent dosage >10 mg/day (1.69, 1.18 to 2.41; vs no glucocorticoid intake). Moderate/high disease activity (vs remission/low disease activity) was associated with higher odds of death (1.87, 1.27 to 2.77). Rituximab (4.04, 2.32 to 7.03), sulfasalazine (3.60, 1.66 to 7.78), immunosuppressants (azathioprine, cyclophosphamide, ciclosporin, mycophenolate or tacrolimus: 2.22, 1.43 to 3.46) and not receiving any disease-modifying anti-rheumatic drug (DMARD) (2.11, 1.48 to 3.01) were associated with higher odds of death, compared with methotrexate monotherapy. Other synthetic/biological DMARDs were not associated with COVID-19-related death. Conclusion: Among people with rheumatic disease, COVID-19-related death was associated with known general factors (older age, male sex and specific comorbidities) and disease-specific factors (disease activity and specific medications). The association with moderate/high disease activity highlights the importance of adequate disease control with DMARDs, preferably without increasing glucocorticoid dosages. Caution may be required with rituximab, sulfasalazine and some immunosuppressants.

Vaccines based on live attenuated viruses often induce broad, multifaceted immune responses. However, they also usually sacrifice immunogenicity for attenuation. It is particularly difficult to elicit an effective vaccine for herpesviruses due to an armament of immune evasion genes and a latent phase. Here, to overcome the limitation of attenuation, we developed a rational herpesvirus vaccine in which viral immune evasion genes were deleted to enhance immunogenicity while also attaining safety. To test this vaccine strategy, we utilized murine gammaherpesvirus-68 (MHV-68) as a proof-of-concept model for the cancer-associated human γ-herpesviruses, Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus. We engineered a recombinant MHV-68 virus by targeted inactivation of viral antagonists of type I interferon (IFN-I) pathway and deletion of the latency locus responsible for persistent infection. This recombinant virus is highly attenuated with no measurable capacity for replication, latency, or persistence in immunocompetent hosts. It stimulates robust innate immunity, differentiates virus-specific memory T cells, and elicits neutralizing antibodies. A single vaccination affords durable protection that blocks the establishment of latency following challenge with the wild type MHV-68 for at least six months post-vaccination. These results provide a novel approach to effective vaccination against cancer-associated herpesviruses through the elimination of latency and key immune evasion mechanisms from the pathogen.

Background:An increased risk of severe COVID-19 outcomes may be seen in patients with autoimmune diseases on moderate to high daily doses of glucocorticoids, as well as in those with comorbidities. However, specific information about COVID-19 outcomes in SLE is scarce.Objectives:To determine the characteristics associated with severe COVID-19 outcomes in a multi-national cross-sectional registry of COVID-19 patients with SLE.Methods:SLE adult patients from a physician-reported registry of the COVID-19 GRA were studied. Variables collected at COVID-19 diagnosis included age, sex, race/ethnicity, region, comorbidities, disease activity, time period of COVID-19 diagnosis, glucocorticoid (GC) dose, and immunomodulatory therapy. Immunomodulatory therapy was categorized as: antimalarials only, no SLE therapy, traditional immunosuppressive (IS) drug monotherapy, biologics/targeted synthetic IS drug monotherapy, and biologic and traditional IS drug combination therapy. We used an ordinal COVID-19 severity outcome defined as: not hospitalized/hospitalized without supplementary oxygen; hospitalized with non-invasive ventilation; hospitalized with mechanical ventilation/extracorporeal membrane oxygenation; and death. An ordinal logistic regression model was constructed to assess the association between demographic characteristics, comorbidities, medications, disease activity and COVID-19 severity. This assumed that the relationship between each pair of outcome groups is of the same direction and magnitude.Results:Of 1069 SLE patients included, 1047 (89.6%) were female, with a mean age of 44.5 (SD: 14.1) years. Patient outcomes included 815 (78.8%) not hospitalized/hospitalized without supplementary oxygen; 116 (11.2) hospitalized with non-invasive ventilation, 25 (2.4%) hospitalized with mechanical ventilation/extracorporeal membrane oxygenation and 78 (7.5%) died. In a multivariate model (n=804), increased age [OR=1.03 (1.01, 1.04)], male sex [OR =1.93 (1.21, 3.08)], COVID-19 diagnosis between June 2020 and January 2021 (OR =1.87 (1.17, 3.00)), no IS drug use [OR =2.29 (1.34, 3.91)], chronic renal disease [OR =2.34 (1.48, 3.70)], cardiovascular disease [OR =1.93 (1.34, 3.91)] and moderate/high disease activity [OR =2.24 (1.46, 3.43)] were associated with more severe COVID-19 outcomes. Compared with no use of GC, patients using GC had a higher odds of poor outcome: 0-5 mg/d, OR =1.98 (1.33, 2.96); 5-10 mg/d, OR =2.88 (1.27, 6.56); >10 mg/d, OR =2.01 (1.26, 3.21) (Table 1).Table 1.Characteristics associated with more severe COVID-19 outcomes in SLE. (N=804)OR (95% CI)Age, years1.03 (1.01, 1.04)Sex, Male1.93 (1.21, 3.08)Race/Ethnicity, Non-White vs White1.47 (0.87, 2.50)RegionEuropeRef.North America0.67 (0.29, 1.54)South America0.67 (0.29, 1.54)Other1.93 (0.85, 4.39)Season, June 16th 2020-January 8th 2021 vs January-June 15th 20201.87 (1.17, 3.00)Glucocorticoids0 mg/dayRef.0-5 mg/day1.98 (1.33, 2.96)5-10 mg/day2.88 (1.27, 6.56)=>10 mg/day2.01 (1.26, 3.21)Medication CategoryAntimalarial onlyRef.No IS drugs2.29 (1.34, 3.91)Traditional IS drugs as monotherapy1.17 (0.77, 1.77)b/ts IS drugs as monotherapy1.00 (0.37, 2.71)Combination of traditional and b/ts IS1.00 (0.55, 1.82)Comorbidity BurdenNumber of Comorbidities (excluding renal and cardiovascular disease)1.39 (0.97, 1.99)Chronic renal disease2.34 (1.48, 3.70)Cardiovascular disease1.93 (1.34, 3.91)Disease Activity, Moderate/ high vs Remission/ low 2.24 (1.46, 3.43)IS: immunosuppressive. b/ts: biologics/targeted syntheticsConclusion:Increased age, male sex, glucocorticoid use, chronic renal disease, cardiovascular disease and moderate/high disease activity at time of COVID-19 diagnosis were associated with more severe COVID-19 outcomes in SLE. Potential limitations include possible selection bias (physician reporting), the cross-sectional nature of the data, and the assumptions underlying the outcomes modelling.Acknowledgements:The views expressed here are those of the authors and participating members of the COVID-19 Global Rheumatology Alliance and do not necessarily represent the views of the ACR, EULAR) the UK National Health Service, the National Institute for Health Research (NIHR), or the UK Department of Health, or any other organization.Disclosure of Interests:Manuel F. Ugarte-Gil Grant/research support from: Pfizer, Janssen, Graciela S Alarcon: None declared, Andrea Seet: None declared, Zara Izadi: None declared, Cristina Reategui Sokolova: None declared, Ann E Clarke Consultant of: AstraZeneca, BristolMyersSquibb, GlaxoSmithKline, Exagen Diagnostics, Leanna Wise: None declared, Guillermo Pons-Estel: None declared, Maria Jose Santos: None declared, Sasha Bernatsky: None declared, Lauren Mathias: None declared, Nathan Lim: None declared, Jeffrey Sparks Consultant of: Bristol-Myers Squibb, Gilead, Inova, Janssen, and Optum unrelated to this work., Grant/research support from: Amgen and Bristol-Myers Squibb, Zachary Wallace Consultant of: Viela Bio and MedPace, Grant/research support from: Bristol-Myers Squibb and Principia/Sanofi, Kimme Hyrich Speakers bureau: Abbvie, Grant/research support from: MS, UCB, and Pfizer, Anja Strangfeld Speakers bureau: AbbVie, MSD, Roche, BMS, Pfizer, Grant/research support from: AbbVie, BMS, Celltrion, Fresenius Kabi, Lilly, Mylan, Hexal, MSD, Pfizer, Roche, Samsung, Sanofi-Aventis, and UCB, Laure Gossec Consultant of: Abbvie, Biogen, Celgene, Janssen, Lilly, Novartis, Pfizer, Sanofi-Aventis, UCB, Grant/research support from: Lilly, Mylan, Pfizer, Loreto Carmona: None declared, Elsa Mateus Grant/research support from: Pfizer, Abbvie, Novartis, Janssen-Cilag, Lilly Portugal, Sanofi, Grünenthal S.A., MSD, Celgene, Medac, Pharmakern, GAfPA, Saskia Lawson-Tovey: None declared, Laura Trupin: None declared, Stephanie Rush: None declared, Gabriela Schmajuk: None declared, Patti Katz: None declared, Lindsay Jacobsohn: None declared, Samar Al Emadi: None declared, Emily Gilbert: None declared, Ali Duarte-Garcia: None declared, Maria Valenzuela-Almada: None declared, Tiffany Hsu: None declared, Kristin D’Silva: None declared, Naomi Serling-Boyd: None declared, Philippe Dieudé Consultant of: Boerhinger Ingelheim, Bristol-Myers Squibb, Lilly, Sanofi, Pfizer, Chugai, Roche, Janssen unrelated to this work, Grant/research support from: Bristol-Myers Squibb, Chugaii, Pfizer, unrelated to this work, Elena Nikiphorou: None declared, Vanessa Kronzer: None declared, Namrata Singh: None declared, Beth Wallace: None declared, Akpabio Akpabio: None declared, Ranjeny Thomas: None declared, Suleman Bhana Consultant of: AbbVie, Horizon, Novartis, and Pfizer (all

Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.

Genes encoded close to one another on the chromosome are often coexpressed, by a mechanism and regulatory logic that remain poorly understood. We surveyed the yeast genome for tandem gene pairs oriented tail-to-head at which expression antisense to the upstream gene was conserved across species. The intergenic region at most such tandem pairs is a bidirectional promoter, shared by the downstream gene mRNA and the upstream antisense transcript. Genomic analyses of these intergenic loci revealed distinctive patterns of transcription factor regulation. Mutation of a given transcription factor verified its role as a regulator in trans of tandem gene pair loci, including the proximally initiating upstream antisense transcript and downstream mRNA and the distally initiating upstream mRNA. To investigate cis-regulatory activity at such a locus, we focused on the stress-induced NAD(P)H dehydratase YKL151C and its downstream neighbor, the metabolic enzyme GPM1. Previous work has implicated the region between these genes in regulation of GPM1 expression; our mutation experiments established its function in rich medium as a repressor in cis of the distally initiating YKL151C sense RNA, and an activator of the proximally initiating YKL151C antisense RNA. Wild-type expression of all three transcripts required the transcription factor Gcr2. Thus, at this locus, the intergenic region serves as a focal point of regulatory input, driving antisense expression and mediating the coordinated regulation of YKL151C and GPM1. Together, our findings implicate transcription factors in the joint control of neighboring genes specialized to opposing conditions and the antisense transcripts expressed between them.

High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring additional multi'omic data types that better capture community functional activity, such as transcriptomics, proteomics, and metabolomics; and combining multiple forms of multi'omic data in an integrated framework. We highlight studies in which the multi'omics approach has led to improved mechanistic models of microbial community structure and function.

Introduction In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal diseases. Campylobacter showae, an oral commensal that was historically linked to gingivitis and periodontitis, has recently been associated with newly diagnosed and established inflammatory bowel disease, hepatolithiasis, and colorectal cancer. The aim of this study was to generate robust genome sequence data for a number of clinical C. showae strains and identify functional properties that could explain their pathogenic potential. Method Genomes of eight C. showae strains were sequenced, assembled, annotated and compared including four strains from paediatric Crohn’s disease patients, three strains from colonic adenomas and one from a gastroenteritis patient. A series of functional analyses were also undertaken including adhesion and invasion assays, toxicity assays and inflammatory cytokine production assessment. Results The 8 new genome assemblies were of high contiguity and completeness and compared favourably with the existing 3 C. showae genomes. Functional analysis indicated that colonic strains could be classified into 2 groups - adherent/invasive vs non-adherent strains with differing virulence factors between the groups, which may be explained by specific genes. Overall, the 11 strains contained 4591 unique gene centroids. Adherent/invasive strains had 807 unique centroids, while non-adherent/non-invasive strains had 497 unique centroids (in 2 or more strains). The oral strain – RM3277 also contained 270 centroids not shared with the colonic strains. Adherent strains possessed a number of bacterial secretion system proteins including Type I and IV machinery that were absent in non-adherent strains. These differences may contribute to the distinct phenotypes observed between strains relating to motility, metal ion transport and host cell interaction. All strains contained unique plasmid sequences as well as a number of predicted genomic islands including some prophage clusters. Conclusion Our findings indicate that C. showae strains are phenotypically and genetically diverse, and suggest the genomes of this bacterium contain modifications in secretion systems that may play an important role in their virulence potential. Additionally, we have greatly added to the current C. showae resources with genome and plasmid assemblies of 8 strains. Disclosure of Interest None Declared

Fluoride has been added to drinking water and dental products since the 1950s. The beneficial effects of fluoride on oral health are due to its ability to inhibit the growth of bacteria that cause dental caries. Despite widespread human consumption of fluoride, there have been only two studies of humans that considered the effect of fluoride on human-associated microbial communities, which are increasingly understood to play important roles in health and disease. Notably, neither of these studies included a true cross-sectional control lacking fluoride exposure, as study subjects continued baseline fluoride treatment in their daily dental hygiene routines. To our knowledge, this work (in mice) is the first controlled study to assess the independent effects of fluoride exposure on the oral and gut microbial communities. Investigating how fluoride interacts with host-associated microbial communities in this controlled setting represents an effort toward understanding how common environmental exposures may potentially influence health., Fluoridation of drinking water and dental products prevents dental caries primarily by inhibiting energy harvest in oral cariogenic bacteria (such as Streptococcus mutans and Streptococcus sanguinis), thus leading to their depletion. However, the extent to which oral and gut microbial communities are affected by host fluoride exposure has been underexplored. In this study, we modeled human fluoride exposures to municipal water and dental products by treating mice with low or high levels of fluoride over a 12-week period. We then used 16S rRNA gene amplicon and shotgun metagenomic sequencing to assess fluoride’s effects on oral and gut microbiome composition and function. In both the low- and high-fluoride groups, several operational taxonomic units (OTUs) belonging to acidogenic bacterial genera (such as Parabacteroides, Bacteroides, and Bilophila) were depleted in the oral community. In addition, fluoride-associated changes in oral community composition resulted in depletion of gene families involved in central carbon metabolism and energy harvest (2-oxoglutarate ferredoxin oxidoreductase, succinate dehydrogenase, and the glyoxylate cycle). In contrast, fluoride treatment did not induce a significant shift in gut microbial community composition or function in our mouse model, possibly due to absorption in the upper gastrointestinal tract. Fluoride-associated perturbations thus appeared to have a selective effect on the composition of the oral but not gut microbial community in mice. Future studies will be necessary to understand possible implications of fluoride exposure for the human microbiome. IMPORTANCE Fluoride has been added to drinking water and dental products since the 1950s. The beneficial effects of fluoride on oral health are due to its ability to inhibit the growth of bacteria that cause dental caries. Despite widespread human consumption of fluoride, there have been only two studies of humans that considered the effect of fluoride on human-associated microbial communities, which are increasingly understood to play important roles in health and disease. Notably, neither of these studies included a true cross-sectional control lacking fluoride exposure, as study subjects continued baseline fluoride treatment in their daily dental hygiene routines. To our knowledge, this work (in mice) is the first controlled study to assess the independent effects of fluoride exposure on the oral and gut microbial communities. Investigating how fluoride interacts with host-associated microbial communities in this controlled setting represents an effort toward understanding how common environmental exposures may potentially influence health.

Uncommon renal disorders in pregnancy can be challenging to manage given limited evidence in the literature to guide management. We present a series of three uncommon renal disorders in pregnancy: Von Hippel–Lindau disease, Gitelman syndrome, and Nutcracker syndrome. Previously published case reports with differing outcomes offer some guidance to the management of these disorders in pregnancy. In this case series, we address the management of these syndromes during pregnancy and discuss the maternal and fetal outcomes. All three of our patients had good maternal and fetal outcomes, which will contribute to current data on maternal and fetal outcomes in these rare diseases, which is limited.

Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs., Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs. Author Video: An author video summary of this article is available.

Expression variation is widespread between species. The ability to distinguish regulatory change driven by natural selection from the consequences of neutral drift remains a major challenge in comparative genomics. In this work, we used observations of mRNA expression and promoter sequence to analyze signatures of selection on groups of functionally related genes in Saccharomycete yeasts. In a survey of gene regulons with expression divergence between Saccharomyces cerevisiae and S. paradoxus, we found that most were subject to variation in trans-regulatory factors that provided no evidence against a neutral model. However, we identified one regulon of membrane protein genes controlled by unlinked cis- and trans-acting determinants with coherent effects on gene expression, consistent with a history of directional, nonneutral evolution. For this membrane protein group, S. paradoxus alleles at regulatory loci were associated with elevated expression and altered stress responsiveness relative to other yeasts. In a phylogenetic comparison of promoter sequences of the membrane protein genes between species, the S. paradoxus lineage was distinguished by a short branch length, indicative of strong selective constraint. Likewise, sequence variants within the S. paradoxus population, but not across strains of other yeasts, were skewed toward low frequencies in promoters of genes in the membrane protein regulon, again reflecting strong purifying selection. Our results support a model in which a distinct expression program for the membrane protein genes in S. paradoxus has been preferentially maintained by negative selection as the result of an increased importance to organismal fitness. These findings illustrate the power of integrating expression- and sequence-based tests of natural selection in the study of evolutionary forces that underlie regulatory change.

The purpose of the study focused on how textbook authors in secondary school physical education used multicultural education concepts, using Banks’ (2006a) dimensions and Sleeter and Grant’s (1999) approaches. Data collection methods included examination of textbooks’ chapters, indexes, and references in five textbooks. Constant comparison method was used in data analysis. The findings of the study follow: 1) Most textbook authors treated multicultural education as an additive concept in the curriculum section and emphasized issues of gender and disability, 2) all of the textbook authors adopted either Banks’ or Sleeter and Grant’s multicultural education approaches, (3) Harrison, Blakemore, and Buck addressed issues of gender, disability and ethnicity in content objectives, and 4) Metzler addressed issues of gender and disability with Banks’ content integration and equity-based pedagogy concepts. An implication concerns incorporation of multicultural education concepts in curriculum and pedagogy in preparation of preservice teachers in secondary school physical education.

Nell-1 is a recently discovered secreted protein with the capacity to promote osteoblastic calvarial cell differentiation and mineralization and induce calvarial bone overgrowth and regeneration in various rodent models. However, the extent of Nell-1 osteoinductivity in large animal cells remains unknown. The objective of the study was to evaluate the feasibility of adenoviral encoding Nell-1 (AdNell-1) gene transfer into primary adult goat bone marrow stromal cells (BMSCs) in vitro and in vivo and to compare the osteoinductive effects with those produced by bone morphogenetic protein-2 (BMP-2), a well established osteoinductive molecule currently utilized for regional gene therapy. AdNell-1-transduced BMSCs expressed Nell-1 protein and underwent osteoblastic differentiation within 2 weeks in vitro, which is comparable to AdBMP-2. After intramuscular injection of nude mice, the AdNell-1- and AdBMP-2-transduced BMSCs revealed new bone formation, while untransduced or AdLacZ-transduced BMSCs showed mainly fibrotic tissue proliferation. At 4 weeks, BMP-2 induced significantly larger bone mass with a mature bone margin and central cavity filled with primarily fatty marrow tissue. Nell-1 samples had significantly less bone mass but were histologically similar to newly formed trabecular bone mixed with chondroid bone-like areas verified by type X collagen (ColX) immunohistochemistry. This distinct difference in histomorphology from the bone mass induced by BMP-2 suggests that there is a potential clinical role/advantage for Nell-1 in skeletal tissue engineering and regeneration.

Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen.

Protein O-GlcNAcylation has been shown to play a major role in the development of type 2 diabetes and diabetic complications. This study is investigating differences of gene expression of proteins ...

Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from expression data are at a premium in the field, and to date, phylogenetic approaches have not been well-suited to address the question in the small sets of taxa profiled in standard surveys of gene expression. We have developed a strategy to infer evolutionary histories from expression profiles by analyzing suites of genes of common function. In a manner conceptually similar to molecular evolution models in which the evolutionary rates of DNA sequence at multiple loci follow a gamma distribution, we modeled expression of the genes of an \emph{a priori}-defined pathway with rates drawn from an inverse gamma distribution. We then developed a fitting strategy to infer the parameters of this distribution from expression measurements, and to identify gene groups whose expression patterns were consistent with evolutionary constraint or rapid evolution in particular species. Simulations confirmed the power and accuracy of our inference method. As an experimental testbed for our approach, we generated and analyzed transcriptional profiles of four \emph{Saccharomyces} yeasts. The results revealed pathways with signatures of constrained and accelerated regulatory evolution in individual yeasts and across the phylogeny, highlighting the prevalence of pathway-level expression change during the divergence of yeast species. We anticipate that our pathway-based phylogenetic approach will be of broad utility in the search to understand the evolutionary relevance of regulatory change., 30 pages, 12 figures, 2 tables, contact authors for supplementary tables

Mitochondrial DNA Variants Mediate Energy Production and Expression Levels for CFH, C3 and EFEMP1 Genes: Implications for Age-Related Macular Degeneration M. Cristina Kenney 1 *, Marilyn Chwa 1 , Shari R. Atilano 1 , Janelle M. Pavlis 1 , Payam Falatoonzadeh 1 , Claudio Ramirez 1 , Deepika Malik 1 , Tiffany Hsu 1 , Grace Woo 1 , Kyaw Soe 1 , Anthony B. Nesburn 1,2 , David S. Boyer 3 , Baruch D. Kuppermann 1 , S. Michal Jazwinski 4 , Michael V. Miceli 4 , Douglas C. Wallace 5 , Nitin Udar 1 1 Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, United States of America, 2 Cedars-Sinai Medical Center, Los Angeles, California, United States of America, 3 Retina-Vitreous Associates Medical Group, Beverly Hills, California, United States of America, 4 Tulane Center for Aging and Department of Medicine, Tulane University, New Orleans, Louisiana, United States of America, 5 Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America Abstract Background: Mitochondrial dysfunction is associated with the development and progression of age-related macular degeneration (AMD). Recent studies using populations from the United States and Australia have demonstrated that AMD is associated with mitochondrial (mt) DNA haplogroups (as defined by combinations of mtDNA polymorphisms) that represent Northern European Caucasians. The aim of this study was to use the cytoplasmic hybrid (cybrid) model to investigate the molecular and biological functional consequences that occur when comparing the mtDNA H haplogroup (protective for AMD) versus J haplogroup (high risk for AMD). Methodology/Principal Findings: Cybrids were created by introducing mitochondria from individuals with either H or J haplogroups into a human retinal epithelial cell line (ARPE-19) that was devoid of mitochondrial DNA (Rho0). In cybrid lines, all of the cells carry the same nuclear genes but vary in mtDNA content. The J cybrids had significantly lower levels of ATP and reactive oxygen/nitrogen species production, but increased lactate levels and rates of growth. Q-PCR analyses showed J cybrids had decreased expressions for CFH, C3, and EFEMP1 genes, high risk genes for AMD, and higher expression for MYO7A, a gene associated with retinal degeneration in Usher type IB syndrome. The H and J cybrids also have comparatively altered expression of nuclear genes involved in pathways for cell signaling, inflammation, and metabolism. Conclusion/Significance: Our findings demonstrate that mtDNA haplogroup variants mediate not only energy production and cell growth, but also cell signaling for major molecular pathways. These data support the hypothesis that mtDNA variants play important roles in numerous cellular functions and disease processes, including AMD. Citation: Kenney MC, Chwa M, Atilano SR, Pavlis JM, Falatoonzadeh P, et al. (2013) Mitochondrial DNA Variants Mediate Energy Production and Expression Levels for CFH, C3 and EFEMP1 Genes: Implications for Age-Related Macular Degeneration. PLoS ONE 8(1): e54339. doi:10.1371/journal.pone.0054339 Editor: Walter Lukiw, Louisiana State University Health Sciences Center, United States of America Received October 1, 2012; Accepted December 10, 2012; Published January 24, 2013 Copyright: s 2013 Kenney et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funding provided by The Discovery Eye Foundation www.discoveryeye.org, Lincy Foundation lincyinstitute.unlv.edu/lincy.html, Beckman Macular Research Initiative www.beckmanmacular.org, The Henry Guenther Foundation, Polly and Michael Smith Foundation, Research to Prevent Blindness Foundation www.rpbusa.org, and the National Institute on Aging (AG006168). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mkenney@uci.edu specific SNP variants that have accumulated over tens of thousands of years and correspond to different geographic populations of the world. The H haplogroup is the most common European haplogroup, while the J haplogroup originates from the Northern European region and is defined by SNP variants that are associated with heat production as an adaptation to colder climates [4]. The mtDNA plays an important role in aging and diseases [4– 6]. Specific haplogroups are associated with a variety of eye diseases including age-related macular degeneration (AMD) [7– 10], diabetic retinopathy [11], pseudoexfoliation glaucoma [12,13], primary open-angle glaucoma [14], keratoconus [15], multiple sclerosis-related optic neuritis [16,17], and Leber Introduction Mitochondria provide critical cellular energy using the tricar- boxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and beta-oxidation of fatty acids for metabolism, cell division, production of reactive oxygen species (ROS), and apoptosis. Human mitochondrial (mt) DNA forms a circle of double stranded DNA with 16,569 nucleotide pairs. The non-coding mtDNA Dloop contains 1121 nucleotides and is important for replication and transcription. The coding region of mtDNA encodes for 37 genes including 13 protein subunits essential for OXPHOS, 2 ribosomal RNAs, and 22 transfer RNAs [1–3]. The mtDNA can be categorized into haplogroups that are defined by a set of PLOS ONE | www.plosone.org January 2013 | Volume 8 | Issue 1 | e54339

Introduction Emerging evidence links the gut microbiota to colonic inflammation and colorectal cancer (CRC). Studies have shown over-representation of oral bacterial species including Campylobacter spp. in CRC tissue and also njc-Campylobacter are over-represented in IBD wherein normal homeostasis has been lost. Understanding the role of njc-Campylobacter as an aetiological agent in CRC and elucidating their pathogenicity characteristics is of immense clinical importance. Aim To perform whole genome sequencing (WGS) of clinically derived njc-Campylobacter to compare/identify virulence traits potentially linked to disease presentation. Methods WGS of 21 unique clinically derived Campylobacter isolates was performed (7 Campylobacter showae, 3 Campylobacter ureolyticus and 11 Campylobacter concisus) from biopsy/faecal samples of subjects with malignancy, acute enteritis and IBD. DNA was extracted using the QIAamp DNA Mini Kit. Libraries were prepared using Illumina Nextera XT DNA Library Prep Kit and Nextera XT Index Kit v2, multiplexed, and paired-end sequenced on the Illumina MiSeq. De novo read assembly used the A5-miseq pipeline with QUAST. Genome annotation was performed using the rapid prokaryotic genome annotation tool Prokka. Results Genome assembly of C. showae strains resulted in 8 to 59 contigs per strain (mean number = 21; average genome size 2,199,446 nucleotides); C. concisus isolates had an average contig number of 72 and average genome size of 1,982,586 nucleotides. C. ureolyticus strains average contig number was 134 and average genome size of 1,608,008 nucleotides. Through Prokka annotation, the average number of coding sequences was 2215 for C. showae isolates (range 2050–2368) with function predicted for ~71.3%. For C. concisus the average number of coding sequences was 1985 (range 1833–2087) with function predicted for ~ 71.9%. C. ureolyticus had a lower number of coding sequences (average 1613) with function predicted for ~72.6%. We focused on the VirB4/D10 operon homologs, which are components of the Type IV secretion system. Contrary to previously published sequence data from oral strains, the majority of colonic C. showae isolated and 2 C. concisus strains possessed almost complete T4SS systems and additional virulence traits, including the exotoxin 9 gene. Conclusion The findings clearly demonstrate genetic differences among colonic Campylobacter isolates as compared to oral strains and sheds light on the pathogenic potential of these emerging colonic pathogens. The findings also further highlight the need for further sequencing studies to be undertaken. Disclosure of Interest None Declared

Osteogenesis is synergistically enhanced by the combined effect of complimentary factors. This study showed that Nell-1 and BMP-2 synergistically enhanced osteogenic differentiation of myoblasts and phosphorylated the JNK MAPK pathway. The findings are important because of the osteochondral specificity of Nell-1 signaling and the potential therapeutic effects of coordinated BMP-2 and Nell-1 delivery. Introduction: BMPs play an important role in the migration and proliferation of mesenchymal cells and have a unique ability to alter the differentiation of mesenchymal cells toward chondrogenic and osteogenic lineages. Signaling upstream of Cbfa1/Runx2, BMPs effects are not limited to cells of the osteoblast lineage. Thus, additional osteoblast-specific factors that could synergize with BMP-2 would be advantageous for bone regeneration procedures. NELL-1 (NEL-like molecule-1; NEL [a protein strongly expressed in neural tissue encoding epidermal growth factor like domain]) is a novel growth factor believed to preferentially target cells committed to the osteochondral lineage. Materials and Methods: C2C12 myoblasts were transduced with AdLacZ, AdNell-1, AdBMP-2, or AdNell-1+AdBMP-2 overexpression viruses. Effects were studied by cell morphology, alkaline phosphatase activity, osteopontin production, and MAPK signaling. Additionally, in a nude mouse model, viruses were injected into leg muscles, and new bone formation was examined after 2 and 8 wk. Results: C2C12 myoblasts co-transduced with AdNell-1+AdBMP-2 showed a synergistic effect on osteogenic differentiation as detected by alkaline phosphatase activity and osteopontin production. Nell-1 stimulation on AdNell-1 + AdBMP-2 preconditioned C2C12 cells revealed significant activation of the non-BMP-2 associated c-Jun N-terminal kinase (JNK) MAPK signaling pathway, but not the p38 or extracellular signal-regulated kinase (ERK1/2) MAPK pathways. Importantly Nell-1 alone did not induce osteogenic differentiation of myoblasts. In a nude mouse model, injection of AdNell-1 alone stimulated no bone formation within muscle; however, injection of AdNell-1+AdBMP-2 stimulated a synergistic increase in bone formation compared with AdBMP-2 alone. Conclusions: These findings are important because of the confirmed osteochondral specificity of Nell-1 signaling and the potential therapeutic effects of enhanced BMP-2 action with coordinated Nell-1 delivery.

A letter to the editor is presented in response to the article "Preventing infectious pulmonary tuberculosis among foreign-born residents of the United States" by A.L. Davidow, D. Katz, S. Ghosh and others and published in a 2015 issue of the journal.

Background context Recombinant growth factors bone morphogenetic protein-2 (BMP-2) and BMP-7 are currently approved for human use but are associated with various adverse effects including ectopic bone formation and local inflammatory reaction. The development of alternative growth factors may help minimize the adverse effects of current osteoinductive therapeutics. Nell-1 (Nel-like molecule-1; Nel [a protein strongly expressed in neural tissue encoding epidermal growth factor like domain]) is a novel secretory molecule that appears to act more specifically on osteoblasts than the BMPs, which can act on multiple cell types. From a molecular point of view, Nell-1 is directly regulated by runt-related transcription factor 2 (Runx2/Cbfa1), a master regulatory gene controlling bone formation. Previous studies showed that Nell-1 accelerates osteogenic differentiation in vitro and calvarial bone formation in vivo. We hypothesize that Nell-1 may also effectively form bone in spinal fusion. Purpose Our primary aim was to assess if direct adenoviral gene delivery with Nell-1 in a demineralized bone matrix (DBM) carrier can improve spinal fusion in a rat model. Because adenoviral vectors allow for sustained growth factor delivery, they were used for initial feasibility testing before protein studies. Study design/setting Two groups of 20 athymic rats underwent posterolateral intertransverse process spinal fusion at L4–L5 with implanted DBM carrier containing either adenovirus coding for Nell-1 (AdNell-1) or control, Lac Z (AdLacZ). No cells were implanted. The 20 rats were sacrificed at 6 weeks for evaluation of spinal fusion. Methods All animals underwent Faxitron radiographs at 2, 4, and 6 weeks, manual spine palpation at 6 weeks, and high-resolution micro computerized tomography (microCT) at 6 weeks. Spinal fusion rate was assessed by: 1) 6-week Faxitron images; 2) manual palpation by three independent observers; 3) microCT; and 4) histology. New bone formation was assessed by hematoxylin-eosin and Masson trichrome staining on decalcified, coronally sectioned spine segments. Results All differences achieved statistical significance. After 6 weeks, direct application of adenoviral Nell-1 in a DBM carrier achieved significantly higher rates of spinal fusion over Lac Z controls: 60% Nell-1 versus 20% Lac Z by manual palpation and 70% Nell-1 versus 20% Lac Z by microCT and histology. Histological assessment of bone quality and maturity revealed more mature, higher quality bone in all the Nell-1 treated specimens relative to Lac Z at 6 weeks. Conclusions Spinal fusion is more accurately assessed by microCT and histology than manual palpation. Direct application of adenoviral Nell-1 in a DBM carrier achieved significantly higher rates of spinal fusion over Lac Z controls at 6 weeks. Direct application of adenoviral Nell-1 in a DBM carrier also achieved significantly higher rates of spinal fusion over other reports in the literature using direct adenoviral BMP application. Direct application of adenoviral BMP in an allograft carrier achieved 8% fusion for BMP-2 and 16% fusion for BMP-7 at 8 weeks. These results indicate that Nell-1 may be a potent osteoinductive molecule. In addition, the regulation of Nell-1 by the master bone regulatory gene, Runx2 suggests that Nell-1 may exert its effects more specifically in osteoblastic cells than BMPs which affect multiple cell types. Overall, Nell-1 may fulfil a current need for an osteoinductive factor.

The converse piezoelectric effect in collagen type II fibrils, the main collagen constituent in cartilage, was investigated using piezoresponse force microscopy. The fibrils exhibited shear piezoelectric behavior similar to that previously reported in collagen type I fibrils and followed the same cantilever-fibril angle dependence present for type I. A uniform polarization directed from the amine to carboxyl termini, as seen for collagen type I, was observed in all type II fibrils studied. The shear piezoelectric coefficient, d 15, however, for type II was roughly 28–32% of the value measured for type I fibrils. Possible explanations for the reduced piezoelectric coefficient of type II collagen are provided. Science Foundation Ireland NANOREMEDIES Programme for Research in Third Level Institutions Cycle 5 European Regional Development Fund

Gene expression varies widely between individuals of a population, and regulatory change can underlie phenotypes of evolutionary and biomedical relevance. A key question in the field is how DNA sequence variants impact gene expression, with most mechanistic studies to date focused on the effects of genetic change on regulatory regions upstream of protein-coding sequence. By contrast, the role of RNA 3′-end processing in regulatory variation remains largely unknown, owing in part to the challenge of identifying functional elements in 3′ untranslated regions. In this work, we conducted a genomic survey of transcript ends in lymphoblastoid cells from genetically distinct human individuals. Our analysis mapped the cis-regulatory architecture of 3′ gene ends, finding that transcript end positions did not fall randomly in untranslated regions, but rather preferentially flanked the locations of 3′ regulatory elements, including miRNA sites. The usage of these transcript length forms and motifs varied across human individuals, and polymorphisms in polyadenylation signals and other 3′ motifs were significant predictors of expression levels of the genes in which they lay. Independent single-gene experiments confirmed the effects of polyadenylation variants on steady-state expression of their respective genes, and validated the regulatory function of 3′ cis-regulatory sequence elements that mediated expression of these distinct RNA length forms. Focusing on the immune regulator IRF5, we established the effect of natural variation in RNA 3′-end processing on regulatory response to antigen stimulation. Our results underscore the importance of two mechanisms at play in the genetics of 3′-end variation: the usage of distinct 3′-end processing signals and the effects of 3′ sequence elements that determine transcript fate. Our findings suggest that the strategy of integrating observed 3′-end positions with inferred 3′ regulatory motifs will prove to be a critical tool in continued efforts to interpret human genome variation., Author Summary Messenger RNAs carry the instructions necessary to synthesize proteins that do work for the cell. Extending beyond the protein-coding sequence of a given mRNA is an additional stretch of sequence, harboring signals that govern how much protein is made and how long the mRNA remains in the cell before it is broken down. The incorporation of this end region into mature mRNA is itself subject to change; for the vast majority of human genes, how and why cells use different mRNA ends remains largely unknown. In this work, we surveyed mRNA ends from ∼10,000 genes in immune cells from genetically distinct human individuals. We found that mRNA end positions were not randomly distributed, but rather preferentially flanked the locations of regulatory signals that govern mRNA fate. The usage of these mRNA length forms and regulatory elements varied across individuals and could be dissected molecularly. Our results uncover key mechanisms and regulatory effects of transcript end processing, particularly as these are perturbed by genetic differences between humans.

Author(s): Kim, Yong; Tong, Leming; Hsu, Tiffany; Shih, Evan; Leang, Ronika; Hwang, Seungmin; Sun, Ren; Wu, Ting-Ting