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Journal articleRosini R, Nicchi S, Pizza M, et al., 2020,
Vaccines Against Antimicrobial Resistance (vol 11, 1048, 2020)
, FRONTIERS IN IMMUNOLOGY, Vol: 11, ISSN: 1664-3224 -
Journal articleSethi S, Jones NS, Fulcher B, et al., 2020,
Characterising soundscapes across diverse ecosystems using a universal acoustic feature set
, Proceedings of the National Academy of Sciences of USA, Vol: 117, Pages: 17049-17055, ISSN: 0027-8424Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labor-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we have developed a generalizable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed soundscapes from a variety of ecosystems into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, providing a potential route for real-time automated detection of irregular environmental behavior including illegal logging and hunting. Our highly generalizable approach, and the common set of features, will enable scientists to unlock previously hidden insights from acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.
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Journal articleAaij R, Beteta CA, Ackernley T, et al., 2020,
Precision measurement of the B-c(+) meson mass
, The Journal of High Energy Physics, Vol: 2020, Pages: 1-21, ISSN: 1029-8479A precision measurement of the B+c meson mass is performed using proton- proton collision data collected with the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV, corresponding to a total integrated luminosity of 9.0 fb−1. The B+c mesons are reconstructed via the decays B+c→ J/ψπ+, B+c→ J/ψπ+π−π+, B+c→J/ψpp¯¯¯π+, B+c→J/ψD+s, B+c→ J/ψ D0K+ and B+c→B0sπ+. Combining the results of the individual decay channels, the B+c mass is measured to be 6274.47 ± 0.27 (stat) ± 0.17 (syst) MeV/c2. This is the most precise measurement of the B+c mass to date. The difference between the B+c and B0s meson masses is measured to be 907.75 ± 0.37 (stat) ± 0.27 (syst) MeV/c.
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Journal articleGraystock P, Ng WH, Parks K, et al., 2020,
Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities
, Nature Ecology and Evolution, Vol: 4, Pages: 1358-1367, ISSN: 2397-334XPollinator reductions can leave communities less diverse and potentially at increased risk of infectious diseases. Species-rich plant and bee communities have high species turnover, making the study of disease dynamics challenging. To address how temporal dynamics shape parasite prevalence in plant and bee communities, we screened >5,000 bees and flowers over an entire growing season for five common bee microparasites (Nosema ceranae, Nosema bombi, Crithidia bombi, Crithidia expoeki and neogregarines). Over 110 bee species and 89 flower species were screened, revealing that 42% of bee species (12.2% individual bees) and 70% of flower species (8.7% individual flowers) had at least one parasite in or on them, respectively. Some common flowers (for example, Lychnis flos-cuculi) harboured multiple parasite species whilst others (for example, Lythrum salicaria) had few. Significant temporal variation of parasite prevalence in bees was linked to bee diversity, bee and flower abundance and community composition. Specifically, we found that bee communities had the highest prevalence late in the season, when social bees (Bombus spp. and Apis mellifera) were dominant and bee diversity was lowest. Conversely, prevalence on flowers was lowest late in the season when floral abundance was highest. Thus turnover in the bee community impacted community-wide prevalence, and turnover in the plant community impacted when parasite transmission was likely to occur at flowers. These results imply that efforts to improve bee health will benefit from the promotion of high floral numbers to reduce transmission risk, maintaining bee diversity to dilute parasites and monitoring the abundance of dominant competent hosts.
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Journal articleHantson S, Kelley DI, Arneth A, et al., 2020,
Quantitative assessment of fire and vegetation properties in simulations with fire-enabled vegetation models from the Fire Model Intercomparison Project
, Geoscientific Model Development, Vol: 13, Pages: 3299-3318, ISSN: 1991-959XGlobal fire-vegetation models are widely used to assess impacts of environmental change on fire regimes and the carbon cycle and to infer relationships between climate, land use and fire. However, differences in model structure and parameterizations, in both the vegetation and fire components of these models, could influence overall model performance, and to date there has been limited evaluation of how well different models represent various aspects of fire regimes. The Fire Model Intercomparison Project (FireMIP) is coordinating the evaluation of state-of-the-art global fire models, in order to improve projections of fire characteristics and fire impacts on ecosystems and human societies in the context of global environmental change. Here we perform a systematic evaluation of historical simulations made by nine FireMIP models to quantify their ability to reproduce a range of fire and vegetation benchmarks. The FireMIP models simulate a wide range in global annual total burnt area (39–536 Mha) and global annual fire carbon emission (0.91–4.75 Pg C yr−1) for modern conditions (2002–2012), but most of the range in burnt area is within observational uncertainty (345–468 Mha). Benchmarking scores indicate that seven out of nine FireMIP models are able to represent the spatial pattern in burnt area. The models also reproduce the seasonality in burnt area reasonably well but struggle to simulate fire season length and are largely unable to represent interannual variations in burnt area. However, models that represent cropland fires see improved simulation of fire seasonality in the Northern Hemisphere. The three FireMIP models which explicitly simulate individual fires are able to reproduce the spatial pattern in number of fires, but fire sizes are too small in key regions, and this results in an underestimation of burnt area. The correct representation of spatial and seasonal patterns in vegetation appears
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Journal articleKoufopanou V, 2020,
Population size, sex and purifying selection: comparative genomics of two sister taxa of the wild yeast Saccharomyces paradoxus
, Genome Biology and Evolution, Vol: 12, Pages: 1636-1645, ISSN: 1759-6653This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.
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Journal articleKoufopanou V, Lomas S, Pronina O, et al., 2020,
Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus
, Genome biology and evolution, Vol: 12, Pages: 1636-1645, ISSN: 1759-6653Abstract This study uses population genomic data to estimate demographic and selection parameters in two sister lineages of the wild yeast Saccharomyces paradoxus and compare their evolution. We first estimate nucleotide and recombinational diversities in each of the two lineages to infer their population size and frequency of sex and then analyze the rate of mutation accumulation since divergence from their inferred common ancestor to estimate the generation time and efficacy of selection. We find that one of the lineages has significantly higher silent nucleotide diversity and lower linkage disequilibrium, indicating a larger population with more frequent sexual generations. The same lineage also shows shorter generation time and higher efficacy of purifying selection, the latter consistent with the finding of larger population size and more frequent sex. Similar analyses are also performed on the ancestries of individual strains within lineages and we find significant differences between strains implying variation in rates of mitotic cell divisions. Our sample includes some strains originating in the Chernobyl nuclear-accident exclusion zone, which has been subjected to high levels of radiation for nearly 30 years now. We find no evidence, however, for increased rates of mutation. Finally, there is a positive correlation between rates of mutation accumulation and length of growing period, as measured by latitude of the place of origin of strains. Our study illustrates the power of genomic analyses in estimating population and life history parameters and testing predictions based on population genetic theory.
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Journal articleZhang Y, Matthews S, Munroe P, et al., 2020,
Effect of particle pre-oxidation on Ni and Ni20Cr splat formation during plasma spraying
, SURFACE & COATINGS TECHNOLOGY, Vol: 393, ISSN: 0257-8972- Cite
- Citations: 17
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Journal articleLima DO, BanksLeite C, Lorini ML, et al., 2020,
Anthropogenic effects on the occurrence of medium‐sized mammals on the Brazilian Pampa biome
, Animal Conservation, ISSN: 1367-9430 -
Journal articleCraven GB, Affron DP, Kösel T, et al., 2020,
Multiparameter kinetic analysis for covalent fragment optimization using quantitative irreversible tethering (qIT)
, ChemBioChem: a European journal of chemical biology, Vol: 21, Pages: 3417-3422, ISSN: 1439-4227Covalent fragments are increasingly being implemented to develop chemical probes but the complex relationship between fragment structure and binding kinetics makes optimization uniquely challenging. We describe a new technique in covalent probe discovery that enables data driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing methods for covalent fragment hit identification by facilitating rapid multiparameter kinetic analysis of covalent structure-activity relationships through simultaneous determination of Ki, kinact and intrinsic reactivity. We apply this approach to develop novel probes against electrophile sensitive kinases and showcase how multiparameter kinetic analysis enabled a successful fragment merging strategy.
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Journal articleYi L, Rebollo-Ramirez S, Larrouy-Maumus G, 2020,
Metabolomics reveals that the cAMP receptor protein regulates nitrogen and peptidoglycan synthesis in Mycobacterium tuberculosis
, RSC Advances: an international journal to further the chemical sciences, Vol: 10, Pages: 26212-26219, ISSN: 2046-2069Mycobacterium tuberculosis requires extensive sensing and response to environment for its successful survival and pathogenesis, and signalling by cyclic adenosine 3′,5′-monophosphate (cAMP) is an important mechanism. cAMP regulates expression of target genes via interaction with downstream proteins, one of which is cAMP receptor protein (CRP), a global transcriptional regulator. Previous genomic works had identified regulon of CRP and investigated transcriptional changes in crp deletion mutant, however a link to downstream metabolomic events were lacking, which would help better understand roles of CRP. This work aims at investigating changes at metabolome level in M. tuberculosis crp deletion mutant combining untargeted LC-MS analysis and 13C isotope tracing analysis. The results were compared with previously published RNA sequencing data. We identified increasing abundances of metabolites related to nitrogen metabolism including ornithine, citrulline and glutamate derivatives, while 13C isotope labelling analysis further showed changes in turnover of these metabolites and amino acids, suggesting regulatory roles of CRP in nitrogen metabolism. Upregulation of diaminopimelic acid and its related genes also suggested role of CRP in regulation of peptidoglycan synthesis. This study provides insights on metabolomic aspects of cAMP-CRP regulatory pathway in M. tuberculosis and links to previously published transcriptomic data drawing a more complete map.
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Journal articleCator L, Johnson LR, Mordecai EA, et al., 2020,
The role of vector trait variation in vector-borne disease dynamics
, Frontiers in Ecology and Evolution, Vol: 8, ISSN: 2296-701XMany important endemic and emerging diseases are transmitted by vectorsthat are biting arthropods. The functional traits of vectors can affect pathogen transmission ratesdirectly andalso through their effect on vector population dynamics. Increasing empirical evidence shows that vector traits vary significantlyacross individuals, populations, and environmental conditions, andat time scales relevant to disease transmission dynamics. Here, we review empirical evidence for variation invector traits and how this trait variation is currentlyincorporated into mathematical modelsof vector-borne disease transmission. We argue that mechanistically incorporating trait variationinto these models, by explicitly capturingits effects on vector fitness and abundance, can improve the reliability oftheir predictions in a changing world. We provide a conceptual framework for incorporating trait variation into vector-borne disease transmission models,and highlight key empirical and theoretical challenges.This framework provides a means to conceptualize how traits can be incorporated in Vector Borne Disease systems,and identifies key areas in which trait variation can be explored. Determining when and to what extent it is important to incorporate trait variation into vector borne disease models remainsan important, outstanding question.
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Working paperZhang S, Contini C, Hindley J, et al., 2020,
Engineering motile aqueous phase-separated droplets via liposome stabilisation
<title>Abstract</title> <p>There are increasing efforts to engineer functional compartments that mimic aspects of cellular behaviour in a drive to construct an artificial cell from the bottom-up. One behaviour that is receiving particular attention is motility, due to its biotechnological potential and the fact that movement of discrete cells is a ubiquitous feature of living systems. Many existing platforms make use of the Marangoni effect to achieve motion in water/oil (w/o) droplet systems. However, most of these systems are unsuitable for biological applications due to issues with biocompatibility caused by the presence of oil phases. Here we report a biocompatible all aqueous (w/w) PEG/dextran Pickering-like emulsion system consisting of liposome-stabilized cell-sized droplets, where the stability can be easily tuned by adjusting liposome composition and concentration. We demonstrate that the compartments are capable of negative chemotaxis: if water is introduced into the emulsion system, these droplets can respond through directional motion away from PEG in the continuous phase and down to the polymer gradient with a velocity change proportional to the rearrangement of liposome stabilisers in the PEG/dextran interface. The biocompatibility, motility and partitioning abilities of this novel droplet system offers new directions to pursue research in motion-related biological processes.</p>
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Journal articleStorch M, Haines MC, Baldwin GS, 2020,
DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology
, Synthetic Biology, Vol: 5, Pages: ysaa010-ysaa010, ISSN: 2397-7000Multi-part DNA assembly is the physical starting point for many projects in Synthetic and Molecular Biology. The ability to explore a genetic design space by building extensive libraries of DNA constructs is essential for creating programmed biological systems. With multiple DNA assembly methods and standards adopted in the Synthetic Biology community, automation of the DNA assembly process is now receiving serious attention. Automation will enable larger builds using less researcher time, while increasing the accessible design space. However, these benefits currently incur high costs for both equipment and consumables. Here, we address this limitation by introducing low-cost DNA assembly with BASIC on OpenTrons (DNA-BOT). For this purpose, we developed an open-source software package and demonstrated the performance of DNA-BOT by simultaneously assembling 88 constructs composed of 10 genetic parts, evaluating the promoter, ribosome binding site and gene order design space for a three-gene operon. All 88 constructs were assembled with high accuracy, at a consumables cost of $1.50-$5.50 per construct. This illustrates the efficiency, accuracy and affordability of DNA-BOT, making it accessible for most labs and democratizing automated DNA assembly.
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Journal articleJoos F, Spahni R, Stocker BD, et al., 2020,
N2O changes from the Last Glacial Maximum to the preindustrial - Part 2: terrestrial N2O emissions and carbon-nitrogen cycle interactions
, Biogeosciences, Vol: 17, Pages: 3511-3543, ISSN: 1726-4170Carbon–nitrogen (C–N) interactions regulate N availability for plant growth and for emissions of nitrous oxide (N2O) and the uptake of carbon dioxide. Future projections of these terrestrial greenhouse gas fluxes are strikingly divergent, leading to major uncertainties in projected global warming. Here we analyse the large increase in terrestrial N2O emissions over the past 21 000 years as reconstructed from ice-core isotopic data and presented in part 1 of this study. Remarkably, the increase occurred in two steps, each realized over decades and within a maximum of 2 centuries, at the onsets of the major deglacial Northern Hemisphere warming events. The data suggest a highly dynamic and responsive global N cycle. The increase may be explained by an increase in the flux of reactive N entering and leaving ecosystems or by an increase in N2O yield per unit N converted. We applied the LPX-Bern dynamic global vegetation model in deglacial simulations forced with Earth system model climate data to investigate N2O emission patterns, mechanisms, and C–N coupling. The N2O emission changes are mainly attributed to changes in temperature and precipitation and the loss of land due to sea-level rise. LPX-Bern simulates a deglacial increase in N2O emissions but underestimates the reconstructed increase by 47 %. Assuming time-independent N sources in the model to mimic progressive N limitation of plant growth results in a decrease in N2O emissions in contrast to the reconstruction. Our results appear consistent with suggestions of (a) biological controls on ecosystem N acquisition and (b) flexibility in the coupling of the C and N cycles during periods of rapid environmental change. A dominant uncertainty in the explanation of the reconstructed N2O emissions is the poorly known N2O yield per N lost through gaseous pathways and its sensitivity to soil conditions. The deglacial N2O record provides a constraint for future studies.
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Journal articleVincent C, Simoes da Silva C, Wadhawan A, et al., 2020,
Origins of metabolic pathology in Francisella-infected Drosophila
, Frontiers in Immunology, Vol: 11, ISSN: 1664-3224The origins and causes of infection pathologies are often not understood. Despite this, the study of infection and immunity relies heavily on the ability to discern between potential sources of pathology. Work in the fruit fly has supported the assumption that mortality resulting from bacterial invasion is largely due to direct host-pathogen interactions, as lower pathogen loads are often associated with reduced pathology, and bacterial load upon death is predictable. However, the mechanisms through which these interactions bring about host death are complex. Here we show that infection with the bacterium Francisella novicida leads to metabolic dysregulation and, using treatment with a bacteriostatic antibiotic, we show that this pathology is the result of direct interaction between host and pathogen. We show that mutants of the immune deficiency immune pathway fail to exhibit similar metabolic dysregulation, supporting the idea that the reallocation of resources for immune-related activities contributes to metabolic dysregulation. Targeted investigation into the cross-talk between immune and metabolic pathways has the potential to illuminate some of this interaction.
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Journal articleFulcher B, Lubba C, Sethi S, et al., 2020,
A self-organizing, living library of time-series data
, Scientific Data, Vol: 7, ISSN: 2052-4463Time-series data are measured across the sciences, from astronomy to biomedicine, but meaningful cross-disciplinary interactions are limited by the challenge of identifying fruitful connections. Here we introduce the web platform, CompEngine, a self-organizing, living library of time-series data, that lowers the barrier to forming meaningful interdisciplinary connections between time series. Using a canonical feature-based representation, CompEngine places all time series in a common feature space, regardless of their origin, allowing users to upload their data and immediately explore diverse data with similar properties, and be alerted when similar data is uploaded in future. In contrast to conventional databases which are organized by assigned metadata, CompEngine incentivizes data sharing by automatically connecting experimental and theoretical scientists across disciplines based on the empirical structure of the data they measure. CompEngine’s growing library of interdisciplinary time-series data also enables the comprehensive characterization of time-series analysis algorithms across diverse types of empirical data.
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Journal articleSlater S, Frankel G, 2020,
Advances and challenges in studying type III secretion effectors of attaching and effacing pathogens
, Frontiers in Cellular and Infection Microbiology, Vol: 10, Pages: 1-7, ISSN: 2235-2988 -
Journal articleLarburu N, Adams C, Chen C, et al., 2020,
Mechanism of Hsp70 specialised interactions in protein translocation and the unfolded protein response
, Open Biology, Vol: 10, Pages: 1-9, ISSN: 2046-2441Hsp70 chaperones interact with substrate proteins in a coordinated fashion that is regulated by nucleotides and enhanced by assisting cochaperones. There are numerous homologues and isoforms of Hsp70 that participate in a wide variety of cellular functions. This diversity can facilitate adaption or specialisation based on particular biological activity and location within the cell. In this review, we highlight two specialised binding partner proteins, Tim44 and IRE1, that interact with Hsp70 at the membrane in order to serve their respective roles in protein translocation and UPR signaling. Recent mechanistic data suggest analogy in the way the two Hsp70 homologues (BiP and mtHsp70) can bind and release from IRE1 and Tim44 upon substrate engagement. These shared mechanistic features may underlie how Hsp70 interacts with specialised binding partners and may extend our understanding of the mechanistic repertoire that Hsp70 chaperones possess.
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Journal articleWest K, Kanu C, Maric T, et al., 2020,
Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery
, Gut, Vol: 69, Pages: 1452-1459, ISSN: 0017-5749Due to the global increase in obesity rates and success of bariatric surgery in weight reduction, an increasing number of women now present pregnant with a previous bariatric procedure. This study investigates the extent of bariatric-associated metabolic and gut microbial alterations during pregnancy and their impact on fetal development.DesignA parallel metabonomic (1H NMR spectroscopy) and gut bacterial (16S rRNA gene amplicon sequencing) profiling approach was used to determine maternal longitudinal phenotypes associated with malabsorptive/mixed (n=25) or restrictive (n=16) procedures, compared to women with similar early pregnancy body mass index but without bariatric surgery (n=70). Metabolic profiles of offspring at birth were also analysed.ResultsPrevious malabsorptive, but not restrictive, procedures induced significant changes in maternal metabolic pathways involving branched-chain and aromatic amino acids with decreased circulation of leucine, isoleucine and isobutyrate, increased excretion of microbial-associated metabolites of protein putrefaction (phenylacetlyglutamine, p-cresol sulfate, indoxyl sulfate and p-hydroxyphenylacetate), and a shift in the gut microbiota. Urinary concentration of phenylacetylglutamine was significantly elevated in malabsorptive patients relative to controls (P=0.001) and was also elevated in urine of neonates born from these mothers (P=0.021). Furthermore, the maternal metabolic changes induced by malabsorptive surgery were associated with reduced maternal insulin resistance and fetal/birth weight.ConclusionMetabolism is altered in pregnant women with a previous malabsorptive bariatric surgery. These alterations may be beneficial for maternal outcomes, but the effect of elevated levels of phenolic and indolic compounds on fetal and infant health should be investigated further.
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Journal articleSanchez-Garrido J, Shenoy A, 2020,
Regulation and repurposing of nutrient sensing and autophagy in innate immunity
, Autophagy, Vol: 17, Pages: 1571-1591, ISSN: 1554-8627Nutrients not only act as building blocks but also as signaling molecules. Nutrient-availability promotes cell growth and proliferation and suppresses catabolic processes, such as macroautophagy/autophagy. These effects are mediated by checkpoint kinases such as MTOR (mechanistic target of rapamycin kinase), which is activated by amino acids and growth factors, and AMP-activated protein kinase (AMPK), which is activated by low levels of glucose or ATP. These kinases have wide-ranging activities that can be co-opted by immune cells upon exposure to danger signals, cytokines or pathogens. Here, we discuss recent insight into the regulation and repurposing of nutrient-sensing responses by the innate immune system during infection. Moreover, we examine how natural mutations and pathogen-mediated interventions can alter the balance between anabolic and autophagic pathways leading to a breakdown in tissue homeostasis and/or host defense.
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Journal articleBroncel M, Dominicus C, Vigetti L, et al., 2020,
Profiling of myristoylation in <i>Toxoplasma</i> <i>gondii</i> reveals an <i>N</i>-myristoylated protein important for host cell penetration
, ELIFE, Vol: 9, ISSN: 2050-084X- Cite
- Citations: 23
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Journal articleAaij R, Beteta CA, Adeva B, et al., 2020,
Updated measurement of time-dependent CP-violating observables in B-s(0) -> J/psi K+ K- decays (vol 79, 706, 2019)
, European Physical Journal C: Particles and Fields, Vol: 80, Pages: 1-8, ISSN: 1124-1861 -
Working paperTossell K, Yu X, Soto BA, et al., 2020,
Sleep deprivation triggers somatostatin neurons in prefrontal cortex to initiate nesting and sleep via the preoptic and lateral hypothalamus
, Publisher: bioRxivAnimals undertake specific behaviors before sleep. Little is known about whether these innate behaviors, such as nest building, are actually an intrinsic part of the sleep-inducing circuitry. We found, using activity-tagging genetics, that mouse prefrontal cortex (PFC) somatostatin/GABAergic (SOM/GABA) neurons, which become activated during sleep deprivation, induce nest building when opto-activated. These tagged neurons induce sustained global NREM sleep if their activation is prolonged metabotropically. Sleep-deprivation-tagged PFC SOM/GABA neurons have long-range projections to the lateral preoptic (LPO) and lateral hypothalamus (LH). Local activation of tagged PFC SOM/GABA terminals in LPO and the LH induced nesting and NREM sleep respectively. Our findings provide a circuit link for how the PFC responds to sleep deprivation by coordinating sleep preparatory behavior and subsequent sleep.
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Journal articleJohri S, Dunn N, Chapple TK, et al., 2020,
Mitochondrial genome of the Silvertip shark, Carcharhinus albimarginatus, from the British Indian Ocean Territory
, Mitochondrial DNA Part B: Resources, Vol: 5, Pages: 2085-2086, ISSN: 2380-2359The Chagos archipelago in the British Indian Ocean Territory (BIOT) has been lacking in detailed genetic studies of its chondrichthyan populations. Chondrichthyes in Chagos continue to be endangered through illegal fishing operations, necessitating species distribution and abundance studies to facilitate urgent monitoring and conservation of the species. Here, we present a complete mitochondrial genome of the Silvertip Shark, Carcharhinus albimarginatus sampled in the Chagos archipelago. The mitochondrial genome of C. albimarginatus was 16,706 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, a replication origin and a D-loop region. GC content was at 38.7% and the control region was 1,065 bp in length. We expect that mitogenomes presented here will aid development of molecular assays for species distribution studies. Overall these studies will promote effective conservation of marine ecosystemes in the BIOT.
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Journal articleAaij R, Beteta CA, Ackernley T, et al., 2020,
Measurement of CP-averaged observables in the B-0 -> K-star 0 mu(+)mu(-) decay
, Physical Review Letters, Vol: 125, Pages: 011802 – 1-011802 – 13, ISSN: 0031-9007An angular analysis of the B0→K*0(→K+π−)μ+μ− decay is presented using a dataset corresponding to an integrated luminosity of 4.7 fb−1 of pp collision data collected with the LHCb experiment. The full set of CP-averaged observables are determined in bins of the invariant mass squared of the dimuon system. Contamination from decays with the K+π− system in an S-wave configuration is taken into account. The tension seen between the previous LHCb results and the standard model predictions persists with the new data. The precise value of the significance of this tension depends on the choice of theory nuisance parameters.
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Journal articleCohen EJ, Nakane D, Kabata Y, et al., 2020,
Campylobacter jejuni motility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella
, PLoS Pathogens, Vol: 16, Pages: 1-24, ISSN: 1553-7366Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.
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ReportWaring B, Neumann M, Prentice IC, et al., 2020,
What role can forests play in tackling climate change?
, What role can forests play in tackling climate change?, www.imperial.ac.uk/grantham, Publisher: Grantham Institute, Discussion paper 6This discussion paper consolidates knowledge on the potential environmental, economic and societal benefits of using trees to reduce the concentration of carbon dioxide in the atmosphere. It highlights areas for further research and defines the limits of trees’ ability to halt the progress of climate change.
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Journal articleGhosh M, Rihel J, 2020,
Hierarchical compression reveals sub-second to day-long structure in larval zebrafish behavior
, eNeuro, Vol: 7, ISSN: 2373-2822Animal behavior is dynamic, evolving over multiple timescales from milliseconds to days and even across a lifetime. To understand the mechanisms governing these dynamics, it is necessary to capture multi-timescale structure from behavioral data. Here, we develop computational tools and study the behavior of hundreds of larval zebrafish tracked continuously across multiple 24-h day/night cycles. We extracted millions of movements and pauses, termed bouts, and used unsupervised learning to reduce each larva's behavior to an alternating sequence of active and inactive bout types, termed modules. Through hierarchical compression, we identified recurrent behavioral patterns, termed motifs. Module and motif usage varied across the day/night cycle, revealing structure at sub-second to day-long timescales. We further demonstrate that module and motif analysis can uncover novel pharmacological and genetic mutant phenotypes. Overall, our work reveals the organization of larval zebrafish behavior at multiple timescales and provides tools to identify structure from large-scale behavioral datasets.
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Journal articleCohen EJ, Nakane D, Kabata Y, et al., 2020,
Campylobacter jejunimotility integrates specialized cell shape, flagellar filament, and motor, to coordinate action of its opposed flagella
, PLoS Pathogens, Vol: 16, Pages: 1-24, ISSN: 1553-7366Campylobacter jejuni rotates a flagellum at each pole to swim through the viscous mucosa of its hosts’ gastrointestinal tracts. Despite their importance for host colonization, however, how C. jejuni coordinates rotation of these two opposing flagella is unclear. As well as their polar placement, C. jejuni’s flagella deviate from the norm of Enterobacteriaceae in other ways: their flagellar motors produce much higher torque and their flagellar filament is made of two different zones of two different flagellins. To understand how C. jejuni’s opposed motors coordinate, and what contribution these factors play in C. jejuni motility, we developed strains with flagella that could be fluorescently labeled, and observed them by high-speed video microscopy. We found that C. jejuni coordinates its dual flagella by wrapping the leading filament around the cell body during swimming in high-viscosity media and that its differentiated flagellar filament and helical body have evolved to facilitate this wrapped-mode swimming.
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