Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications

This is the author accepted manusript. The final version is available from American Chemical Society via the DOI in this recordAccession Codes: The sequence data for the four Geobacillus spp. used in this study have been submitted to the NCBI Sequence Read Archive and are available under the accession number PRJNA521450.Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space

eHealth Literacy and Web 2.0 Health Information Seeking Behaviors Among Baby Boomers and Older Adults

Background: Baby boomers and older adults, a subset of the population at high risk for chronic disease, social isolation, and poor health outcomes, are increasingly utilizing the Internet and social media (Web 2.0) to locate and evaluate health information. However, among these older populations, little is known about what factors influence their eHealth literacy and use of Web 2.0 for health information. Objective: The intent of the study was to explore the extent to which sociodemographic, social determinants, and electronic device use influences eHealth literacy and use of Web 2.0 for health information among baby boomers and older adults. Methods: A random sample of baby boomers and older adults (n=283, mean 67.46 years, SD 9.98) participated in a cross-sectional, telephone survey that included the eHealth literacy scale (eHEALS) and items from the Health Information National Trends Survey (HINTS) assessing electronic device use and use of Web 2.0 for health information. An independent samples t test compared eHealth literacy among users and non-users of Web 2.0 for health information. Multiple linear and logistic regression analyses were conducted to determine associations between sociodemographic, social determinants, and electronic device use on self-reported eHealth literacy and use of Web 2.0 for seeking and sharing health information. Results: Almost 90% of older Web 2.0 users (90/101, 89.1%) reported using popular Web 2.0 websites, such as Facebook and Twitter, to find and share health information. Respondents reporting use of Web 2.0 reported greater eHealth literacy (mean 30.38, SD 5.45, n=101) than those who did not use Web 2.0 (mean 28.31, SD 5.79, n=182), t217.60=−2.98, P=.003. Younger age (b=−0.10), more education (b=0.48), and use of more electronic devices (b=1.26) were significantly associated with greater eHealth literacy (R2 =.17, R2adj =.14, F9,229=5.277, P<.001). Women were nearly three times more likely than men to use Web 2.0 for health information (OR 2.63, Wald= 8.09, df=1, P=.004). Finally, more education predicted greater use of Web 2.0 for health information, with college graduates (OR 2.57, Wald= 3.86, df =1, P=.049) and post graduates (OR 7.105, Wald= 4.278, df=1, P=.04) nearly 2 to 7 times more likely than non-high school graduates to use Web 2.0 for health information. Conclusions: Being younger and possessing more education was associated with greater eHealth literacy among baby boomers and older adults. Females and those highly educated, particularly at the post graduate level, reported greater use of Web 2.0 for health information. More in-depth surveys and interviews among more diverse groups of baby boomers and older adult populations will likely yield a better understanding regarding how current Web-based health information seeking and sharing behaviors influence health-related decision making

Intracellular sodium elevation reprograms cardiac metabolism

Intracellular Na elevation in the heart is a hallmark of pathologies where both acute and chronic metabolic remodelling occurs. Here, we assess whether acute (75 μM ouabain 100 nM blebbistatin) or chronic myocardial Nai load (PLM3SA mouse) are causally linked to metabolic remodelling and whether the failing heart shares a common Na-mediated metabolic ‘fingerprint’. Control (PLMWT), transgenic (PLM3SA), ouabain-treated and hypertrophied Langendorff-perfused mouse hearts are studied by 23Na, 31P, 13C NMR followed by 1H-NMR metabolomic profiling. Elevated Nai leads to common adaptive metabolic alterations preceding energetic impairment: a switch from fatty acid to carbohydrate metabolism and changes in steady-state metabolite concentrations (glycolytic, anaplerotic, Krebs cycle intermediates). Inhibition of mitochondrial Na/Ca exchanger by CGP37157 ameliorates the metabolic changes. In silico modelling indicates altered metabolic fluxes (Krebs cycle, fatty acid, carbohydrate, amino acid metabolism). Prevention of Nai overload or inhibition of Na/Camito may be a new approach to ameliorate metabolic dysregulation in heart failure

Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii.

Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations

Proximate Kitaev quantum spin liquid behaviour in a honeycomb magnet.

Quantum spin liquids (QSLs) are topological states of matter exhibiting remarkable properties such as the capacity to protect quantum information from decoherence. Whereas their featureless ground states have precluded their straightforward experimental identification, excited states are more revealing and particularly interesting owing to the emergence of fundamentally new excitations such as Majorana fermions. Ideal probes of these excitations are inelastic neutron scattering experiments. These we report here for a ruthenium-based material, α-RuCl3, continuing a major search (so far concentrated on iridium materials) for realizations of the celebrated Kitaev honeycomb topological QSL. Our measurements confirm the requisite strong spin-orbit coupling and low-temperature magnetic order matching predictions proximate to the QSL. We find stacking faults, inherent to the highly two-dimensional nature of the material, resolve an outstanding puzzle. Crucially, dynamical response measurements above interlayer energy scales are naturally accounted for in terms of deconfinement physics expected for QSLs. Comparing these with recent dynamical calculations involving gauge flux excitations and Majorana fermions of the pure Kitaev model, we propose the excitation spectrum of α-RuCl3 as a prime candidate for fractionalized Kitaev physics.Research using ORNL’s HFIR and SNS facilities was sponsored by the US Department of Energy, Office of Science, Basic Energy Sciences (BES), Scientific User Facilities Division. A part of the synthesis and the bulk characterization performed at ORNL was supported by the US Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division (C.A.B. and J.-Q.Y.). The work at University of Tennessee was funded in part by the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4416 (D.G.M. and L.L.). The work at Dresden was in part supported by DFG grant SFB 1143 (J.K. and R.M.), and by a fellowship within the Postdoc-Program of the German Academic Exchange Service (DAAD) (J.K.). D.L.K. is supported by EPSRC Grant No. EP/M007928/1. The collaboration as a whole was supported by the Helmholtz Virtual Institute ‘New States of Matter and their Excitations’ initiative.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nmat460

Dynamical Properties of one dimensional Mott Insulators

At low energies the charge sector of one dimensional Mott insulators can be described in terms of a quantum Sine-Gordon model. Using exact results derived from integrability it is possible to determine dynamical properties like the frequency dependent optical conductivity. We compare the exact results to perturbation theory and renormalisation group calculations. We also discuss the application of our results to experiments on quasi-1D organic conductors.Comment: 17 pages, 5 figures, to appear in the proceedings of the NATO ASI/EC summer school "New Theoretical Approaches to Strongly Correlated Systems" Newton Institute for Mathematical Sciences, Cambridge UK, April 200

In-situ sequencing reveals the effect of storage on lacustrine sediment microbiome demographics and functionality

This is the final version. Available from BMC via the DOI in this record. Availability of data and materials: The datasets generated and analysed during the current study are available in the NCBI SRA repository under BioProject ID PRJNA548524.The sediment microbiome is a demographically diverse and functionally active biosphere. Ensuring that data acquired from sediment is truly representative of the microbiome is critical to achieving robust analyses. Sample storage and the processing and timing of nucleic acid purification after environmental sample extraction may fundamentally affect the detectable microbial community and thereby significantly alter resultant data. Direct sequencing of environmental samples is increasingly commonplace due to the advent of the portable Oxford Nanopore MinION sequencing device. Here we demonstrate that storing sediment subsamples at −20 °C or storing the cores at 4 °C for 10 weeks prior to analysis, has a significant effect on the sediment microbiome analysed using sedimentary DNA (sedDNA), especially for Alpha-, Beta- and Deltaproteobacteria species. Furthermore, these significant differences are observed regardless of sediment type. We show that the taxa which are predominantly affected by storage are Proteobacteria, and therefore recommend on-site purifications are performed to ensure an accurate representation of these taxa are observed in the microbiome. Comparisons of sedimentary RNA (sedRNA) analyses, revealed substantial differences between samples purified and sequenced immediately on-site, samples that were frozen before transportation, and cores that were stored at 4 °C prior to analysis. Our data therefore suggest that a more accurate representation of the sediment microbiome demography and functionality may be achieved by environmental sequencing as rapidly as possible to minimise confounding effects of storage.University of Exete

Draft Genome Sequence of Weissella paramesenteroides STCH-BD1, Isolated from Ensiled Sorghum bicolor

This is the final version. Available on open access from the American Society for Microbiology via the DOI in this recordData availability. The draft genome sequence of W. paramesenteroides STCH-BD1 is deposited in GenBank under the accession numbers CP065045 and CP065046. Oxford Nanopore and Illumina DNA sequence reads have been deposited in the NCBI Sequence Read Archive under accession numbers SRR13083241 and SRR13083242, respectivelyWeissella paramesenteroides has potential as an industrial biocatalyst due to its ability to produce lactic acid. A novel strain of W. paramesenteroides was isolated from ensiled sorghum. The genome was sequenced using a hybrid assembly of Oxford Nanopore and Illumina data to produce a 2-Mbp genome and 22-kbp plasmid sequence.Shell International Exploration and Production, In

Excitations in the field-induced quantum spin liquid state of α-RuCl3

The celebrated Kitaev quantum spin liquid (QSL) is the paradigmatic example of a topological magnet with emergent excitations in the form of Majorana Fermions and gauge fluxes. Upon breaking of time-reversal symmetry, for example in an external magnetic field, these fractionalized quasiparticles acquire non-Abelian exchange statistics, an important ingredient for topologically protected quantum computing. Consequently, there has been enormous interest in exploring possible material realizations of Kitaev physics and several candidate materials have been put forward, recently including α-RuCl3. In the absence of a magnetic field this material orders at a finite temperature and exhibits low-energy spin wave excitations. However, at moderate energies, the spectrum is unconventional and the response shows evidence for fractional excitations. Here we use time-of-flight inelastic neutron scattering to show that the application of a sufficiently large magnetic field in the honeycomb plane suppresses the magnetic order and the spin waves, leaving a gapped continuum spectrum of magnetic excitations. Our comparisons of the scattering to the available calculations for a Kitaev QSL show that they are consistent with the magnetic field induced QSL phase.The work at ORNL’s Spallation Neutron Source and the High Flux Isotope Reactor was supported by the United States Department of Energy (US-DOE), Office of Science - Basic Energy Sciences (BES), Scientific User Facilities Division. Part of the research was supported by the US-DOE, Office of Science - BES, Materials Sciences and Engineering Division (P.K., C.A.B. and J-Q.Y.). D.M. and P.K. acknowledge support from the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4416. The work at Dresden was in part supported by DFG grant SFB 1143 (J.K. and R.M.). J.K. is supported by the Marie Curie Programme under EC Grant agreements No.703697

Positive and negative well-being and objectively measured sedentary behaviour in older adults: evidence from three cohorts

Background: Sedentary behaviour is related to poorer health independently of time spent in moderate to vigorous physical activity. The aim of this study was to investigate whether wellbeing or symptoms of anxiety or depression predict sedentary behaviour in older adults. Method: Participants were drawn from the Lothian Birth Cohort 1936 (LBC1936) (n = 271), and the West of Scotland Twenty-07 1950s (n = 309) and 1930s (n = 118) cohorts. Sedentary outcomes, sedentary time, and number of sit-to-stand transitions, were measured with a three-dimensional accelerometer (activPAL activity monitor) worn for 7 days. In the Twenty-07 cohorts, symptoms of anxiety and depression were assessed in 2008 and sedentary outcomes were assessed ~ 8 years later in 2015 and 2016. In the LBC1936 cohort, wellbeing and symptoms of anxiety and depression were assessed concurrently with sedentary behaviour in 2015 and 2016. We tested for an association between wellbeing, anxiety or depression and the sedentary outcomes using multivariate regression analysis. Results: We observed no association between wellbeing or symptoms of anxiety and the sedentary outcomes. Symptoms of depression were positively associated with sedentary time in the LBC1936 and Twenty-07 1950s cohort, and negatively associated with number of sit-to-stand transitions in the LBC1936. Meta-analytic estimates of the association between depressive symptoms and sedentary time or number of sit-to-stand transitions, adjusted for age, sex, BMI, long-standing illness, and education, were β = 0.11 (95% CI = 0.03, 0.18) and β = − 0.11 (95% CI = − 0.19, −0.03) respectively. Conclusion: Our findings indicate that depressive symptoms are positively associated with sedentary behavior. Future studies should investigate the causal direction of this association