Psychometric properties of the mock interview rating scale for autistic transition-age youth.

Background: Employment is a major contributor to quality of life. However, autistic people are often unemployed and underemployed. One potential barrier to employment is the job interview. However, the availability of psychometrically-evaluated assessments of job interviewing skills is limited for autism services providers and researchers. Objective: We analyzed the psychometric properties of the Mock Interview Rating Scale that was adapted for research with autistic transition-age youth (A-MIRS; a comprehensive assessment of video-recorded job interview role-play scenarios using anchor-based ratings for 14 scripted job scenarios). Methods: Eighty-five transition-age youth with autism completed one of two randomized controlled trials to test the effectiveness of two interventions focused on job interview skills. All participants completed a single job interview role-play at pre-test that was scored by raters using the A-MIRS. We analyzed the structure of the A-MIRS using classical test theory, which involved conducting both exploratory and confirmatory factor analyzes, Rasch model analysis and calibration techniques. We then assessed internal consistency, inter-rater reliability, and test-retest reliability. Pearson correlations were used to assess the A-MIRS' construct, convergent, divergent, criterion, and predictive validities by comparing it to demographic, clinical, cognitive, work history measures, and employment outcomes. Results: Results revealed an 11-item unidimensional construct with strong internal consistency, inter-rater reliability, and test-retest reliability. Construct [pragmatic social skills (r = 0.61, p < 0.001), self-reported interview skills (r = 0.34, p = 0.001)], divergent [e.g., age (r = -0.13, p = 0.26), race (r = 0.02, p = 0.87)], and predictive validities [competitive employment (r = 0.31, p = 0.03)] received initial support via study correlations, while convergent [e.g., intrinsic motivation (r = 0.32, p = 0.007), job interview anxiety (r = -0.19, p = 0.08)] and criterion [e.g., prior employment (r = 0.22, p = 0.046), current employment (r = 0.21, p = 0.054)] validities were limited. Conclusion: The psychometric properties of the 11-item A-MIRS ranged from strong-to-acceptable, indicating it may have utility as a reliable and valid method for assessing the job interview skills of autistic transition-age youth.

Enhancing pre-employment transition services: A type 1 hybrid randomized controlled trial protocol for evaluating WorkChat: A Virtual Workday among autistic transition-age youth.

Autistic transition-age youth experience high rates of unemployment and underemployment, in part due to the social challenges they may face when having conversations in the workplace. In an effort to help enhance conversational abilities in the workplace, our collaborative team partnered to develop WorkChat: A Virtual Workday. Specifically, our team of scientists, community partners, and diversity and inclusion experts participated in a community-engaged process to develop WorkChat using iterative feedback from autistic transition-age youth and their teachers. With initial development complete, this study reports on the protocol that our collaborative team developed, reviewed, and approved to conduct a randomized controlled trial (RCT) to evaluate the real-world effectiveness and initial implementation process outcomes of WorkChat when integrated into post-secondary pre-employment transition services (Pre-ETS). Our aims are to: 1) evaluate whether services-as-usual in combination with WorkChat, compared to services-as-usual with an attention control, enhances social cognition and work-based social ability (between pre- and post-test); reduces anxiety about work-based social encounters (between pre- and post-test), and increases sustained employment by 9-month follow-up; 2) evaluate whether social cognitive ability and work-based social ability mediate the effect of WorkChat on sustained employment; and 3) conduct a multilevel, mixed-method process evaluation of WorkChat implementation.

Metabolically active bacteria detected with click chemistry in low organic matter rainwater.

Rain contains encapsulated bacteria that can be transported over vast distances during relatively short periods of time. However, the ecological significance of bacteria in "precontact" rainwater-rainwater prior to contact with non-atmospheric surfaces-remains relatively undefined given the methodological challenges of studying low-abundance microbes in a natural assemblage. Here, we implement single-cell "click" chemistry in a novel application to detect the protein synthesis of bacteria in precontact rainwater samples as a measure of metabolic activity. Using epifluorescence microscopy, we find approximately 103-104 bacteria cells mL-1 with up to 7.2% of the observed cells actively synthesizing protein. Additionally, our measurement of less than 30 µM total organic carbon in the samples show that some rainwater bacteria can metabolize substrates in very low organic matter conditions, comparable to extremophiles in the deep ocean. Overall, our results raise new questions for the field of rainwater microbiology and may help inform efforts to develop quantitative microbial risk assessments for the appropriate use of harvested rainwater.

Content and sentiment surveillance (CSI): A critical component for modeling modern epidemics.

Comprehensive surveillance systems are the key to provide accurate data for effective modeling. Traditional symptom-based case surveillance has been joined with recent genomic, serologic, and environment surveillance to provide more integrated disease surveillance systems. A major gap in comprehensive disease surveillance is to accurately monitor potential population behavioral changes in real-time. Population-wide behaviors such as compliance with various interventions and vaccination acceptance significantly influence and drive the overall epidemic dynamics in the society. Original infoveillance utilizes online query data (e.g., Google and Wikipedia search of a specific content topic such as an epidemic) and later focuses on large volumes of online discourse data about the from social media platforms and further augments epidemic modeling. It mainly uses number of posts to approximate public awareness of the disease, and further compares with observed epidemic dynamics for better projection. The current COVID-19 pandemic shows that there is an urgency to further harness the rich, detailed content and sentiment information, which can provide more accurate and granular information on public awareness and perceptions toward multiple aspects of the disease, especially various interventions. In this perspective paper, we describe a novel conceptual analytical framework of content and sentiment infoveillance (CSI) and integration with epidemic modeling. This CSI framework includes data retrieval and pre-processing; information extraction via natural language processing to identify and quantify detailed time, location, content, and sentiment information; and integrating infoveillance with common epidemic modeling techniques of both mechanistic and data-driven methods. CSI complements and significantly enhances current epidemic models for more informed decision by integrating behavioral aspects from detailed, instantaneous infoveillance from massive social media data.

Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.

Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.

Carbon limitation in response to nutrient loading in an eelgrass mesocosm: influence of water residence time.

Altered primary productivity associated with eutrophication impacts not only ecosystem structure but also the biogeochemical cycling of oxygen and carbon. We conducted laboratory experiments to empirically determine how residence time (1, 3, 10 d) influences eutrophication responses in a simplified Pacific Northwest Zostera marina-green macroalgal community. We expected long-residence time (RT) systems to exhibit eutrophication impairments. Instead, we observed an accumulation of nutrients at all RTs and a shift in the dissolved inorganic carbon speciation away from CO2 (aq) with unexpected consequences for eel grass plant condition, including shoot mortality. Most metrics responded more strongly to temperature treatments than to RT treatments. No dramatic shifts in the relative abundance of Z. marina and green macro algae were detected. Z. marina shoot density proliferated in cool temperatures (12°C) with a modest decline at 20°C. Eelgrass loss was associated with high total scale pH (pHT) and CO2 (aq) concentrations of <10 µmol kg-1 CO2 (aq), but not with high nutrients. Z. marina δ13C values support the hypo thesis that carbon availability was greater at short RT. Further, very low leaf sugar concentrations are consistent with extreme photosynthetic CO2 (aq) limitation. We suggest that the effects of extremely low environ mental car bon concentrations (CO2 (aq)) and increased respiration at warm temperatures (20°C) and other physiological processes can lead to internal carbon limitation and shoot mortality. Eutrophication responses to nutrient loading are more nuanced than just light limitation of eelgrass and require additional research on the interaction of the biogeochemical environment and plant physiology to better understand estuarine ecosystem disruption.

"Not all groups come together, but this one just clicks": Ten Tips for Sustaining an Engagement Panel.

In 2017, ten veteran patients with the shared experience of living with chronic pain united to form a Veteran Engagement Panel (VEP) to support the Patient-Centered Outcomes Research Institute® (PCORI®)funded Veterans Pain Care Organizational Improvement Comparative Effectiveness (VOICE) Study. The study, conducted at ten Veterans Affairs (VA) sites, compares two team-based approaches to improve pain management and reduce potential harms of opioid therapy. The panel shares ten best practices for sustaining a successful engagement partnership.

Management pathways for the successful reduction of nonpoint source nutrients in coastal ecosystems.

Eutrophication remains a threat to coastal habitats and water quality worldwide. The U.S. Clean Water Act resulted in reductions of nutrient loading from point sources but management of nonpoint sources (NPS) of nutrients remains challenging despite efforts over at least three decades. The hydrological factors, best management practices (BMPs) and regulatory mechanisms that target nutrient NPS and improve coastal ecosystem function are poorly understood. We identified three case study sites in the U.S. with sufficient NPS management and monitoring history to quantify changes in estuarine habitat and water quality following BMP implementation and regulation targeting nutrient NPS. Utilizing publicly available data, we compared sites that are geographically distant and hydrologically distinct. We found that BMPs targeting NPS loads from surface waters into Roberts Bay (Florida) and Newport Bay (California) significantly reduced nutrient concentrations and harmful algal blooms within ~20 years. Improvements occurred despite concurrent human population growth within both watersheds. Conversely, we found that the majority of BMPs implemented within the Peconic Estuary (New York) watershed targeted surface waters despite a dominance of nitrogen inputs (97%) from groundwater and atmospheric sources. Declines in habitat and water quality in Peconic Estuary may be due to a failure to control the dominant nutrient sources and the long residence time of nitrogen in groundwater. Compared to surface water, reducing groundwater and atmospheric nutrients face greater technical and financial challenges. Improvements to Peconic Estuary may occur with further reductions in surface water inputs and as nutrients leach out of the groundwater. Although the effectiveness of specific NPS BMPs has been examined at small spatial scales, our study is the first to quantify improvements at a watershed scale. We showed that successful NPS management pathways are those which targeted the dominant sources of nutrients to coastal ecosystems and applied multiple BMPs within watersheds.

Integrating High-Resolution Coastal Acidification Monitoring Data Across Seven United States Estuaries.

Beginning in 2015, the United States Environmental Protection Agency's (EPA's) National Estuary Program (NEP) started a collaboration with partners in seven estuaries along the East Coast (Barnegat Bay; Casco Bay), West Coast (Santa Monica Bay; San Francisco Bay; Tillamook Bay), and the Gulf of Mexico (GOM) Coast (Tampa Bay; Mission-Aransas Estuary) of the United States to expand the use of autonomous monitoring of partial pressure of carbon dioxide (pCO2) and pH. Analysis of high-frequency (hourly to sub-hourly) coastal acidification data including pCO2, pH, temperature, salinity, and dissolved oxygen (DO) indicate that the sensors effectively captured key parameter measurements under challenging environmental conditions, allowing for an initial characterization of daily to seasonal trends in carbonate chemistry across a range of estuarine settings. Multi-year monitoring showed that across all water bodies temperature and pCO2 covaried, suggesting that pCO2 variability was governed, in part, by seasonal temperature changes with average pCO2 being lower in cooler, winter months and higher in warmer, summer months. Furthermore, the timing of seasonal shifts towards increasing (or decreasing) pCO2 varied by location and appears to be related to regional climate conditions. Specifically, pCO2 increases began earlier in the year in warmer water, lower latitude water bodies in the GOM (Tampa Bay; Mission-Aransas Estuary) as compared with cooler water, higher latitude water bodies in the northeast (Barnegat Bay; Casco Bay), and upwelling-influenced West Coast water bodies (Tillamook Bay; Santa Monica Bay; San Francisco Bay). Results suggest that both thermal and non-thermal influences are important drivers of pCO2 in Tampa Bay oxygen, National Estuary Program and Mission-Aransas Estuary. Conversely, non-thermal processes, most notably the biogeochemical structure of coastal upwelling, appear to be largely responsible for the observed pCO2 values in West Coast water bodies. The co-occurrence of high salinity, high pCO2, low DO, and low temperature water in Santa Monica Bay and San Francisco Bay characterize the coastal upwelling paradigm that is also evident in Tillamook Bay when upwelling dominates freshwater runoff and local processes. These data demonstrate that high-quality carbonate chemistry observations can be recorded from estuarine environments using autonomous sensors originally designed for open-ocean settings.

Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease.

There has been much interest in the ability of regulatory T cells (Treg) to switch function in vivo, either as a result of genetic risk of disease or in response to environmental and metabolic cues. The relationship between levels of FOXP3 and functional fitness plays a significant part in this plasticity. There is an emerging role for Treg in tissue repair that may be less dependent on FOXP3, and the molecular mechanisms underpinning this are not fully understood. As a result of detailed, high-resolution functional genomics, the gene regulatory networks and key functional mediators of Treg phenotype downstream of FOXP3 have been mapped, enabling a mechanistic insight into Treg function. This transcription factor-driven programming of T-cell function to generate Treg requires the switching on and off of key genes that form part of the Treg gene regulatory network and raises the possibility that this is reversible. It is plausible that subtle shifts in expression levels of specific genes, including transcription factors and non-coding RNAs, change the regulation of the Treg gene network. The subtle skewing of gene expression initiates changes in function, with the potential to promote chronic disease and/or to license appropriate inflammatory responses. In the case of autoimmunity, there is an underlying genetic risk, and the interplay of genetic and environmental cues is complex and impacts gene regulation networks frequently involving promoters and enhancers, the regulatory elements that control gene expression levels and responsiveness. These promoter-enhancer interactions can operate over long distances and are highly cell type specific. In autoimmunity, the genetic risk can result in changes in these enhancer/promoter interactions, and this mainly impacts genes which are expressed in T cells and hence impacts Treg/conventional T-cell (Tconv) function. Genetic risk may cause the subtle alterations to the responsiveness of gene regulatory networks which are controlled by or control FOXP3 and its target genes, and the application of assays of the 3D organization of chromatin, enabling the connection of non-coding regulatory regions to the genes they control, is revealing the direct impact of environmental/metabolic/genetic risk on T-cell function and is providing mechanistic insight into susceptibility to inflammatory and autoimmune conditions.

Isolation and Characterization of vB_PagP-SK1, a T7-Like Phage Infecting Pantoea agglomerans.

Background: Pantoea is a genus within the Enterobacterales whose members encompass free-living and host-associated lifestyles. Despite our growing understanding of the role of mobile genetic elements in the biology, ecology, and evolution of this bacterial group, few Pantoea bacteriophages have been identified and characterized. Materials and Methods: A bacteriophage that could infect Pantoea agglomerans was isolated from barnyard soil. We used electron microscopy and complete genome sequencing to identify the viral family, and evaluated its host range across 10 different Pantoea species groups using both bacterial lawn and phage lawn assays. The latter assays were carried out using a scalable microplate assay to increase throughput and enable spectrophotometric quantitation. We also performed a phylogenetic analysis to determine the closest relatives of our phage. Results: Phage vB_PagP-SK1 belongs to the genus Teseptimavirus of the Podoviridae family in the order Caudovirales. The 39,938 bp genome has a modular structure with early, middle, and late genes, along with the characteristic direct terminal repeats of 172 bp. Genome composition and synteny were similar to that of the Erwinia amylovora phage, vB_EamP-L1, with the exception of a few loci that are most similar to genes of phage infecting other members of the Enterobacteriaceae. A total of 94 Pantoea strains were surveyed and vB_PagP-SK1 was found to infect 15 Pantoea strains across three species, predominantly P. agglomerans, along with one Erwinia billingiae strain. Conclusions: vB_PagP-SK1 belongs to the Teseptimavirus genus and has a host range that spans multiple species groups, and is most closely related to the E. amylovora phage, vB_EamP-L1. The presence of xenologous genes in its genome indicates that the genome is a mosaic of multiple Teseptimavirus phages that infect members of the Enterobacteriaceae.

Peptidase inhibitor 16 identifies a human regulatory T-cell subset with reduced FOXP3 expression over the first year of recent onset type 1 diabetes.

CD4+ T-cell subsets play a major role in the host response to infection, and a healthy immune system requires a fine balance between reactivity and tolerance. This balance is in part maintained by regulatory T cells (Treg), which promote tolerance, and loss of immune tolerance contributes to autoimmunity. As the T cells which drive immunity are diverse, identifying and understanding how these subsets function requires specific biomarkers. From a human CD4 Tconv/Treg cell genome wide analysis we identified peptidase inhibitor 16 (PI16) as a CD4 subset biomarker and we now show detailed analysis of its distribution, phenotype and links to Treg function in type 1 diabetes. To determine the clinical relevance of Pi16 Treg, we analysed PI16+ Treg cells from type 1 diabetes patient samples. We observed that FOXP3 expression levels declined with disease progression, suggesting loss of functional fitness in these Treg cells in Type 1 diabetes, and in particular the rate of loss of FOXP3 expression was greatest in the PI16+ve Treg. We propose that PI16 has utility as a biomarker of functional human Treg subsets and may be useful for tracking loss of immune function in vivo. The ability to stratify at risk patients so that tailored interventions can be applied would open the door to personalised medicine for Type 1 diabetes.

Choice Architecture in Appalachian High Schools: Evaluating and Improving Cafeteria Environments.

School meals are a primary source of nutrition for many adolescents. Determining factors that influence the selection of various foods can provide insight on strategies to improve students' cafeteria choices. This evaluation and observation was conducted at three Appalachian high schools to assess the cafeteria environment. The study developed and implemented an assessment tool created using principles of choice architecture and behavioral economics building on the work of the Cornell Center for Behavioral Economics in Child Nutrition Programs (BEN Center). The assessment tool scored eight components of the lunchroom-the exterior, hot serving area, cold serving area, salad bar, beverage area, payment station, dining area and grab-n-go, where a higher score equals healthier components offered. High school (HS) #1 earned 73/128 points (57%), HS #2 earned 69/128 (54%), and HS #3 earned 53/102 (52%). HS #3 did not have a grab-n-go option and the final score was out of 102. Video observation was used to collect data on lunchroom activity during mealtimes. Each school received reports that highlight the results and suggest improvements to raise their score. The scoring tool represents a novel way to assess the health of school lunches, provide insights on how to improve the healthfulness of students' lunch choice, and improve overall nutrition status.

Privacy-preserving techniques of genomic data-a survey.

Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regarding the collection, storage and analysis of such sensitive human data. Recent results show that given some background information, it is possible for an adversary to reidentify an individual from a specific genomic data set. This can reveal the current association or future susceptibility of some diseases for that individual (and sometimes the kinship between individuals) resulting in a privacy violation. Regardless of these risks, our genomic data hold much importance in analyzing the well-being of us and the future generation. Thus, in this article, we discuss the different privacy and security-related problems revolving around human genomic data. In addition, we will explore some of the cardinal cryptographic concepts, which can bring efficacy in secure and private genomic data computation. This article will relate the gaps between these two research areas-Cryptography and Genomics.

Benchmarking forensic volume crime performance in Australia between 2011 and 2015.

In 2011, the Australia New Zealand Policing Advisory Agency National Institute of Forensic Science Australia New Zealand (ANZPAA NIFS) ran the End to End Forensic Identification Process Project: Phase 1 (E2E1) to identify bottlenecks and inefficiencies across the end-to-end forensic process in Australia and make recommendations as to how these might be addressed. The study concentrated on the analysis of DNA and fingerprint evidence in burglary offences, benchmarking current forensic processes and performance across all eight Australian States and Territories (jurisdictions). Following a positive response, overwhelming support was given for the project to be repeated four years later in order to measure any improvements. End to End Phase 2 (E2E2) was conducted in the same eight Australian jurisdictions with the same sampling areas, across the same length of time as E2E1. The aim was to enable agencies to compare their own data from the previous phase and establish, amongst other things, whether implemented recommendations from E2E1 project had any significant impact. Data was collected for over 7,500 burglaries nationally. This paper presents the findings of the 2015 study as well as comparative analyses between 2011 and 2015. Finally, we discuss the measures taken, whether legal, technological or organisational, that are likely contributors to the performance improvements.

Statistical models of fecal coliform levels in Pacific Northwest estuaries for improved shellfish harvest area closure decision making.

There is a substantial need for tools that effectively predict spatial and temporal fecal pollution patterns in estuarine waters. In this study, statistical models of exceedances of shellfish fecal coliform (FC) water quality criteria were developed using a 10-year dataset of FC levels and environmental data. Performance (sensitivity, specificity, and predictive capacity) of five different types of models was tested (MLR regression, Tobit (censored) regression, Firth's binary logistic regression (BLR), classification trees, and mixed-effects regression) for each of three conditionally managed shellfish-harvesting areas in Tillamook Bay, Oregon (USA). The most influential variables were related to precipitation and river stage height in the wet season and wind and tidal-stage in the dry season. Classification tree and Firth's BLR approaches better explained exceedances of shellfish water quality standards than the current closure thresholds. Findings demonstrate the utility of statistical modeling approaches for improved management of shellfish harvesting waters.

FOXP3 and miR-155 cooperate to control the invasive potential of human breast cancer cells by down regulating ZEB2 independently of ZEB1.

Control of oncogenes, including ZEB1 and ZEB2, is a major checkpoint for preventing cancer, and loss of this control contributes to many cancers, including breast cancer. Thus tumour suppressors, such as FOXP3, which is mutated or lost in many cancer tissues, play an important role in maintaining normal tissue homeostasis. Here we show for the first time that ZEB2 is selectively down regulated by FOXP3 and also by the FOXP3 induced microRNA, miR-155. Interestingly, neither FOXP3 nor miR-155 directly altered the expression of ZEB1. In breast cancer cells repression of ZEB2, independently of ZEB1, resulted in reduced expression of a mesenchymal marker, Vimentin and reduced invasion. However, there was no de-repression of E-cadherin and migration was enhanced. Small interfering RNAs targeting ZEB2 suggest that this was a direct effect of ZEB2 and not FOXP3/miR-155. In normal human mammary epithelial cells, depletion of endogenous FOXP3 resulted in de-repression of ZEB2, accompanied by upregulated expression of vimentin, increased E-cadherin expression and cell morphological changes. We suggest that FOXP3 may help maintain normal breast epithelial characteristics through regulation of ZEB2, and loss of FOXP3 in breast cancer cells results in deregulation of ZEB2.

Seagrass habitat metabolism increases short-term extremes and long-term offset of CO2 under future ocean acidification.

The role of rising atmospheric CO2 in modulating estuarine carbonate system dynamics remains poorly characterized, likely due to myriad processes driving the complex chemistry in these habitats. We reconstructed the full carbonate system of an estuarine seagrass habitat for a summer period of 2.5 months utilizing a combination of time-series observations and mechanistic modeling, and quantified the roles of aerobic metabolism, mixing, and gas exchange in the observed dynamics. The anthropogenic CO2 burden in the habitat was estimated for the years 1765-2100 to quantify changes in observed high-frequency carbonate chemistry dynamics. The addition of anthropogenic CO2 alters the thermodynamic buffer factors (e.g., the Revelle factor) of the carbonate system, decreasing the seagrass habitat's ability to buffer natural carbonate system fluctuations. As a result, the most harmful carbonate system indices for many estuarine organisms [minimum pHT, minimum Ωarag, and maximum pCO2(s.w.)] change up to 1.8×, 2.3×, and 1.5× more rapidly than the medians for each parameter, respectively. In this system, the relative benefits of the seagrass habitat in locally mitigating ocean acidification increase with the higher atmospheric CO2 levels predicted toward 2100. Presently, however, these mitigating effects are mixed due to intense diel cycling of CO2 driven by aerobic metabolism. This study provides estimates of how high-frequency pHT, Ωarag, and pCO2(s.w.) dynamics are altered by rising atmospheric CO2 in an estuarine habitat, and highlights nonlinear responses of coastal carbonate parameters to ocean acidification relevant for water quality management.

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis.

To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.