Biology subjects

Williams, A.

Publications and source records attributed to Williams, A..

123 records · Page 7Linked to original sources

bioRxiv2020

Importance of polymorphic SNPs, short tandem repeats and structural variants for differential gene expression among inbred C57BL/6 and C57BL/10 substrains

Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with 8 C57BL/6 and 5 C57BL/10 closely related inbred substrains. Whole genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 INDELs, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs) and 2,826 differentially expressed genes (DEGenes) among these 14 strains. 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs and frameshifting INDELs that were associated with DEGenes. Our results can be used for both forward and reverse genetic approaches, and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.

genomics↗

bioRxiv2020

Phylogenomic analysis of Clostridiodes difficile ribotype 106 strains reveals novel genetic islands and emergent phenotypes

BackgroundClostridioides difficile RT106 has emerged as a dominant molecular type in the USA in recent years, but the underlying factors contributing to its predominance remain undefined. As part of our ongoing C. difficile infection (CDI) surveillance in Arizona, we monitored RT106 frequency and characterized the genomic and phenotypic properties of the recovered isolates. ResultsFrom 2015-2018, RT106 was the second-most prevalent molecular type isolated from CDI patients in our surveillance. A representative RT106 strain displayed robust virulence and 100% lethality in the hamster model of acute CDI. We identified a unique 46 KB genomic island (GI1) in all RT106 strains, including those in public databases. GI1 was not found in its entirety in any other C. difficile clade, or indeed in any other microbial genome; however, smaller segments were detected in select Enterococcus faecium strains. Molecular clock analyses suggest that GI1 was horizontally acquired and sequentially assembled over time. Consistent with the presence of genes encoding homologs of VanZ and a SrtB-anchored collagen-binding adhesin in GI1, all tested RT106 strains had increased teicoplanin resistance and a majority displayed collagen-dependent biofilm formation. Two additional genomic islands (GI2 and GI3) were also present in a subset of RT106 strains. All three islands have features of mobile genetic elements and encode several putative virulence factors. ConclusionsConsistent with the known genetic plasticity of C. difficile, strains belonging to the RT106 clade harbor unique genetic islands. Correspondingly, emergent phenotypic properties may contribute to the relatively rapid shifts of strain distribution in patient populations.

genomics↗

bioRxiv2019

Short-term circulating tumor cell dynamics in mouse xenograft models and implications for liquid biopsy.

MotivationCirculating tumor cells (CTCs) are widely studied using liquid biopsy methods that analyze single, fractionally-small peripheral blood (PB) samples. However, little is known about fluctuations in CTC numbers that occur over short timescales in vivo, and how these may affect accurate enumeration from blood samples. MethodsWe recently developed an instrument called diffuse in vivo flow cytometry (DiFC) that allows continuous, non-invasive counting of rare, green fluorescent protein expressing CTCs in large deeply-seated blood vessels in mice. Here, we used DiFC to study short-term changes in CTC numbers in multiple myeloma and Lewis lung carcinoma xenograft models. We analyzed 35- to 50-minute data sets, with intervals corresponding to approximately 1, 5, 10 and 20% of the PB volume, as well as changes over 24-hour periods. ResultsFor rare CTCs, the use of short DiFC intervals (corresponding to small PB samples) frequently resulted in no detections. For more abundant CTCs, CTC numbers frequently varied by an order of magnitude or more over the time-scales considered. This variability far exceeded that expected by Poisson statistics, and instead was consistent with rapidly changing mean numbers of CTCs in the PB. ConclusionsBecause of these natural temporal changes, accurately enumerating CTCs from fractionally small blood samples is inherently problematic. The problem is likely to be compounded for multicellular CTC clusters or specific CTC subtypes. However, we also show that enumeration can be improved by averaging multiple samples, analysis of larger volumes, or development of new methods for enumeration of CTCs directly in vivo.

bioengineering↗

bioRxiv2019

A modular high-density 294-channel μECoG system on macaque vlPFC for auditory cognitive decoding

OBJECTIVEA fundamental goal of the auditory system is to parse the auditory environment into distinct perceptual representations. Auditory perception is mediated by the ventral auditory pathway, which includes the ventrolateral prefrontal cortex (vlPFC) late. Because large-scale recordings of auditory signals are quite rare, the spatiotemporal resolution of the neuronal code that underlies vlPFCs contribution to auditory perception has not been fully elucidated. Therefore, we developed a modular, chronic, high-resolution, multi-electrode array system with long-term viability.\n\nAPPROACHWe molded three separate ECoG arrays into one and implanted this system in a non-human primate. A custom 3D-printed titanium chamber was mounted on left hemisphere. The molded 294-contact ECoG array was implanted subdurally over vlPFC. ECoG activity was recorded while the monkey participated in a \"hearing-in-noise\" task in which they reported hearing a \"target\" vocalization from a background \"chorus\" of vocalizations. We titrated task difficulty by varying the sound level of the target vocalization, relative to the chorus (target-to-chorus ratio, TCr).\n\nMAIN RESULTSWe decoded the TCr and the monkeys behavioral choices from the ECoG signal. We analyzed decoding capacity as a function of neuronal frequency band, spatial resolution, and time from implantation. Over a one-year period, we were successfully able to record ECoG signals. Although we found significant decoding with as few as two electrodes, we found near-perfect decoding with [~]16 electrodes. Decoding further improved when we included more electrodes. Finally, because the decoding capacity of individual electrodes varied on a day-by-day basis, high-density electrode arrays ensure robust decoding in the long term.\n\nSIGNIFICANCEOur results demonstrate the utility and robustness of high-resolution chronic {micro}ECoG recording. We developed a new high-resolution surface electrode array that can be scaled to cover larger cortical areas without increasing the chamber footprint.

neuroscience↗

bioRxiv2019

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

RNA has been classically known to play central roles in biology, including maintaining telomeres1, protein synthesis2, and in sex chromosome compensation in certain species3,4. At the center of these important biological systems are noncoding RNAs. While thousands of long noncoding RNAs (lncRNAs) have been identified in mammalian genomes5-8, attributing RNA-based roles to lncRNA loci requires an assessment of whether the observed effect could be due to DNA regulatory elements, the act of transcription, or the lncRNA transcript. Here, we use the syntenically conserved lncRNA locus, Functional intergenic repeating RNA element (Firre), that is located on the X chromosome as a model to discriminate between DNA- and RNA-mediated effects in vivo. To this end, we generated genetically defined loss-of-function, gain-of-function, and rescue mouse models for Firre and provide genetic evidence that the Firre locus produces a trans-acting RNA. We report that: (i) Firre mutant mice have cell-specific defects during hematopoiesis and changes in gene expression that can be rescued by induction of Firre RNA from a transgene in the Firre knockout background, (ii) mice overexpressing Firre from a transgene exhibit increased levels of pro-inflammatory cytokines and impaired survival upon exposure to lipopolysaccharide, and (iii) deletion of the Firre locus did not result in changes in local gene expression on the X chromosome in 9 different biological contexts, suggesting that Firre does not function by cis-acting RNA or DNA elements. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis and immune function.

immunology↗

bioRxiv2018

Activation of the endoplasmic reticulum unfolded protein response reverses an inflammation-like response to cytoplasmic DNA

Innate immune responses protect organisms against various insults, but may lead to tissue damage when aberrantly activated. In higher organisms, cytoplasmic DNA can trigger inflammation that can lead to tissue degeneration. Simpler in vivo models could shed new mechanistic light on how inflammatory responses to cytoplasmic DNA lead to pathology. Here we show that in DNase II-deficient Caenorhabditis elegans, persistent foreign cytoplasmic DNA leads to systemic tissue degeneration, and we identify impaired protein homeostasis as an inflammatory pathomechanism. This pathological outcome can be alleviated by improving protein homeostasis, either via ectopic induction of the endoplasmic reticulum unfolded protein response (UPRER) or by treatment with N-acetylglucosamine. Our results establish C. elegans as an ancestral metazoan model for studying outcomes of inflammation-like conditions caused by persistent cytoplasmic DNA and provide insight into potential therapies for conditions involving chronic inflammation.

cell biology↗

bioRxiv2018

AgriSeqDB: an online RNA-Seq database for functional studies in agriculturally relevant plant species

BackgroundThe genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for datasets from major agricultural crops.\n\nDescriptionAgriSeqDB (https://expression.latrobe.edu.au/agriseqdb), is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome datasets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into datasets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications.\n\nConclusionPowered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their datasets, promoting research collaborations and dataset reuse.

genomics↗

bioRxiv2018

Economic evaluation of a healthy lifestyle intervention for chronic low back pain: a randomised controlled trial

We performed an economic evaluation of a healthy lifestyle intervention targeting weight loss, physical activity and diet for patients with chronic low back pain, who are overweight or obese. Eligible patients with chronic low back pain (n=160) were randomised to an intervention or usual care control group. The intervention included brief advice, a clinical consultation and referral to a 6-month telephone-based healthy lifestyle coaching service. The primary outcome was quality-adjusted life years (QALYs). Secondary outcomes were pain intensity, disability, weight, and body mass index. Costs included intervention costs, healthcare utilisation costs and work absenteeism costs. An economic analysis was performed from the societal perspective. Mean total costs were lower in the intervention group than the control group (-$614; 95%CI: -3133 to 255). The intervention group had significantly lower healthcare costs (-$292; 95%CI: -872 to -33), medication costs (-$30; 95%CI: -65 to -4) and absenteeism costs (-$1000; 95%CI: -3573 to -210). For all outcomes, the intervention was on average less expensive and more effective than usual care, and the probability of the intervention being cost-effective compared to usual care was relatively high (i.e. 0.81) at a willingness-to-pay of $0/unit of effect. However, the probability of cost-effectiveness was not as favourable among sensitivity analyses. The healthy lifestyle intervention seems to be cost-effective from the societal perspective. However, variability in the sensitivity analyses indicates caution is needed when interpreting these findings.

clinical trials↗

bioRxiv2018

Causal mechanisms of a healthy lifestyle intervention for patients with musculoskeletal pain who are overweight or obese

We assessed the causal mechanisms of a healthy lifestyle intervention for patients with chronic low back pain and knee osteoarthritis (OA), who are overweight or obese. We conducted causal mediation analyses of aggregated data from two RCTs; which included 160 patients with chronic low back pain, and 120 patients with knee OA. Participants were randomised via one central randomisation schedule, to the intervention, or usual care. The intervention consisted of brief advice and referral to a 6-month telephone-based healthy lifestyle coaching service. Participants in the back pain trial were also offered a single physiotherapy consultation. The hypothesised primary mediator was self-reported weight, and alternative mediators were diet, physical activity, and pain beliefs. Outcomes were pain intensity, disability, and quality of life (QoL). Data were analysed using causal mediation analyses with sensitivity analyses for sequential ignorability. All mediation models were specified a priori. The intervention had no effect on pain intensity, disability or physical QoL. The intervention significantly improved mental QoL, however, the intervention effect was not channelled via the selected mediators. The intervention did not reduce weight, or the alternative mediators (diet, physical activity, pain beliefs), and these mediators were not associated with the outcomes (with one exception; poor diet was associated with lower mental QoL). The sensitivity analyses showed that our estimates were stable across all possible levels of residual confounding. Our findings show that the intervention did not cause a meaningful change in the hypothesised mediators, and these mediators were not associated with patient outcomes.

clinical trials↗

bioRxiv2018

Cost-effectiveness of telephone-based weight loss support for patients with knee osteoarthritis: a pragmatic randomised controlled trial

BackgroundTelephone-based support offers a promising option to provide widely accessible and cost-effective weight loss care to the people with knee osteoarthritis who are overweight. While telephone-based interventions targeting weight loss are used routinely in the general populations, the cost-effectiveness of referring patients with knee osteoarthritis to these is unknown. The aim of this study was to assess the cost-effectiveness of referral to a telephone-based weight management and healthy lifestyle service for patients with knee osteoarthritis, who are overweight or obese, compared to usual care. MethodsWe randomised 120 patients with knee osteoarthritis to an intervention or usual care control group in a 1:1 ratio. Participants in the intervention group received a referral to an existing non-disease specific 6-month telephone-based weight management and healthy lifestyle service. The primary outcome of the study was quality-adjusted life years (QALYs). Secondary outcomes included pain intensity, disability, weight, and body mass index (BMI). Costs included intervention costs, healthcare utilisation costs (healthcare services and medication use) and absenteeism costs due to knee pain. The primary cost-effectiveness analysis was performed from the societal perspective. ResultsMean cost differences between groups (intervention minus control) were, $454 (95%CI: -2735 to 4206) for healthcare costs, $-36, (95%CI: -73 to 2) for medication costs, and $-13 (95%CI: -225 to 235) for absenteeism costs. The total mean difference in societal costs was $1022 (95%CI: -2201 to 4771). For all outcomes, the probability of the intervention being cost-effective compared with usual care was less than 0.33 at all willingness-to-pay values. ConclusionFrom a societal perspective, telephone-based weight loss support, provided using an existing non-disease specific 6-month weight management and healthy lifestyle service was not cost-effective in comparison with usual care for overweight and obese patients with knee osteoarthritis for QALYs, pain intensity, disability, weight, and BMI.

clinical trials↗

bioRxiv2018

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

Using machine learning (ML), we interrogated the function of all human-chimpanzee variants in 2,645 Human Accelerated Regions (HARs), some of the fastest evolving regions of the human genome. We predicted that 43% of HARs have variants with large opposing effects on chromatin state and 14% on neurodevelopmental enhancer activity. This pattern, consistent with compensatory evolution, was confirmed using massively parallel reporter assays in human and chimpanzee neural progenitor cells. The species-specific enhancer activity of assayed HARs was accurately predicted from the presence and absence of transcription factor footprints in each species. Despite these striking cis effects, activity of a given HAR sequence was nearly identical in human and chimpanzee cells. These findings suggest that HARs did not evolve to compensate for changes in the trans environment but instead altered their ability to bind factors present in both species. Thus, ML prioritized variants with functional effects on human neurodevelopment and revealed an unexpected reason why HARs may have evolved so rapidly.

evolutionary biology↗

bioRxiv2018

Open access policies of high impact medical journals: a cross-sectional study

ObjectivesAcademic and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use. We set out to clarify the open access variants provided by leading medical journals for research in general and industry-funded research in particular, and record the availability of the CC BY licence for commercially funded research.\n\nMethodsWe identified medical journals with a 2015 impact factor of at least 15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journals open access policies from their websites and/or by email contact. We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.\n\nResultsThirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access with varying embargo periods of up to 12 months. Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (e.g. to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organizations and one offered this option to funders who required it.\n\nConclusionsMost leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material. The journals policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academic funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.\n\nStrengths and limitations of this studyO_LIThis manuscript includes a systematic analysis of open access policies of journals with a high impact factor, including society-owned journals, from multiple publishers.\nC_LIO_LIThe open access policies of all journals analysed were clarified, and confirmation of our findings was received by email from 97% of the contacted journals.\nC_LIO_LIOpen access policies of the journals and publishers analysed are subject to change, so the information presented here may not be current.\nC_LIO_LIBy selecting journals with a high impact factor, our analysis does not include prestigious journals from specialized therapy areas and regional or non-English language journals, which may have lower impact factors.\nC_LIO_LIAlthough our study covers only a small number of journals, extending such a manual analysis to a greater number of journals without loss of detail and verification of all results would be cumbersome and inefficient by relying on traditional analysis tools.\nC_LI

scientific communication and education↗

bioRxiv2017

Transcriptome Analysis of Adult C. elegans Cells Reveals Tissue-specific Gene and Isoform Expression

The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are critical for understanding molecular mechanisms that control their phenotypes. We used adult cell-specific isolation to identify the transcriptomes of C. elegans four major tissues (or \"tissue-ome\"), identifying ubiquitously expressed and tissue-specific \"super-enriched\" genes. These data newly reveal the hypodermis metabolic character, suggest potential worm-human tissue orthologies, and identify tissue-specific changes in the Insulin/IGF-1 signaling pathway. Tissue-specific alternative splicing analysis identified a large set of collagen isoforms and a neuron-specific CREB isoform. Finally, we developed a machine learning-based prediction tool for 70 sub-tissue cell types, which we used to predict cellular expression differences in IIS/FOXO signaling, stage-specific TGF-b activity, and basal vs. memory-induced CREB transcription. Together, these data provide a rich resource for understanding the biology governing multicellular adult animals

genomics↗

bioRxiv2017

Components Of Alcohol Use And All-Cause Mortality

ImportanceCurrent recommendations for low-risk drinking are based on drinking quantity: up to one drink daily for women and two drinks daily for men. Drinking frequency has not been independently examined for its contribution to mortality.\n\nObjectiveTo evaluate the impact of drinking frequency on all-cause mortality after adjusting for drinks per day and binge drinking behavior.\n\nDesignTwo independent observational studies with self-reported alcohol use and subsequent all-cause mortality: the National Health Interview Survey (NHIS), and data from Veterans Health Administration clinics (VA).\n\nSettingEpidemiological sample (NHIS) and VA outpatient database (VA Corporate Data Warehouse).\n\nParticipants208,661 individuals from the NHIS interviewed between 1997 and 2009 at the age of 30 to 70 with mortality follow-up in the last quarter of 2011; 75,515 VA outpatients born between 1948 and 1968 who completed an alcohol survey in 2008 with mortality follow-up in June 2016.\n\nExposuresQuantity of alcohol use when not binging (1-2 drinks on typical day, 3-4 drinks on typical day), frequency of non-binge drinking (never, weekly or less, 2-3 times weekly, 4 or more times weekly), and frequency of binge drinking (never, less than weekly, 1-3 times weekly, 4 or more times weekly). Covariates included age, sex, race, and comorbidity.\n\nMain Outcomes and MeasuresAll-cause mortality.\n\nResultsAfter adjusting for binge drinking behavior, survival analysis showed an increased risk for all-cause mortality among people who typically drink 1-2 drinks four or more times weekly, relative to people who typically drink 1-2 drinks at a time weekly or less (NHIS dataset HR=1.15, 95% CI 1.06-1.26; VA dataset HR=1.31, 95% CI 1.15-1.49).\n\nConclusions and RelevanceDrinking four or more times weekly increased risk of all-cause mortality, even among those who drank only 1 or 2 drinks daily. This was seen in both a large epidemiological database and a large hospital-based database, suggesting that the results can be generalized.

epidemiology↗

bioRxiv2017

Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers; we also outline important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

bioinformatics↗