bluuebunny/crossref_metadata_2025_split huggingface dataset:
A shared alarmone-GTP switch underlies triggered and spontaneous persistence
Authors: Fung Danny K. , Barra Jessica T. , Schroeder Jeremy W. , Ying David , Wang Jue D. 
Published: March 2020

SummaryPhenotypically-switched, antibiotic-refractory persisters may prevent pathogen eradication. Although how triggered persistence via starvation-induced (p)ppGpp is well characterized, generation of persisters without starvation are poorly understood. Here we visualized the formation of spontaneous persisters in a small fraction of cells from growing wild type bacteria, revealing a striking single cell rapid switch from growth to dormancy. This switch-like entrance is triggered by GTP dropping beneath a threshold due to stochastic production and self-amplification of (p)ppGpp via allosteric enzyme activation. In addition, persisters are induced by lethal and sublethal concentrations of cell wall antibiotics by inducing (p)ppGpp via cell wall stress response. Thus spontaneous, triggered and antibiotic-induced persisters can all stem from a common metabolic switch: GTP depletion by (p)ppGpp induction, and each pathway of persister formation is activated by different (p)ppGpp synthetases. These persistence pathways are likely conserved in pathogens which may be exploited to potentiate antibiotic efficacy.
Using directed attenuation to enhance vaccine immunity
Authors: Antia Rustom , Ahmed Hasan , Bull James J 
Published: March 2020

AbstractMany viral infections can be prevented by immunizing with live, attenuated vaccines. Early methods of attenuation were hit-and-miss, and these are now much improved by genetic engineering. But even current attenuation methods operate on the principle of genetic harm, reducing the virus’s ability to grow, which in turn limits the host immune response below that of infection by wild-type. We use mathematical models of the dynamics of virus and its control by innate and adaptive immunity to explore the tradeoff between attenuation of virus growth and the generation of immunity. Our analysis suggests that directed attenuation that disables key viral defenses against the host immune responses may attenuate viral growth without compromising, and potentially even enhancing the generation of immunity. We explore which immune evasion pathways should be attenuated and how attenuating multiple pathways could lead to robust attenuation of pathology with enhancement of immunity.Author summaryLive attenuated virus vaccines are among the most effective interventions to combat viral infections. Historically, the mechanism of attenuation has been one of genetically reduced viral growth rate, often achieved by adapting the virus to grow in a novel cells. More recent attenuation methods use genetic engineering but also are thought to impair viral growth rate. These classical attenuations typically result in a tradeoff whereby attenuation depresses the within-host viral load and pathology (which is beneficial to vaccine design), but reduces immunity (which is not beneficial). We use models to explore ways of directing the attenuation of a virus to avoid this tradeoff. We show thatdirected attenuationby interfering with (some) viral immune-evasion pathways can yield a mild infection but elicit higher levels of immunity than of the wild-type virus.
Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site
Authors: Davidson Andrew D. , Williamson Maia Kavanagh , Lewis Sebastian , Shoemark Deborah , Carroll Miles W. , Heesom Kate , Zambon Maria , Ellis Joanna , Lewis Phillip A. , Hiscox Julian A. , Matthews David A. 
Published: March 2020

ABSTRACTDirect RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
Genetic analysis identifies theOstrea stentina/aupouria/equestrisoyster species complex in Hawai‘i, and resolves its lineage as the western PacificO. equestris
Authors: Sutton Jolene T. , Nishimoto Jared , Schrader Jeremy , Agonias Keinan , Antonio Nicole , Bautista Brandi , Cabarloc Riley , Fakasieiki Maata , Gonong Noreen Aura Mae , Ramangmou Torey , Uehara Lavin , Wong Jade , Wilkie Daniel , Littrell David , Rem-McGeachy Marni , Chandler-‘Īao Rhiannon , Haws Maria 
Published: March 2020

AbstractBackgroundExtensive phenotypic plasticity in oysters makes them difficult to identify based on morphology alone, but their identities can be resolved by applying genetic and genomic technologies. In this study, we collected unknown oyster specimens from Hawaiian waters for genetic identification.MethodsWe sequenced two partial gene fragments, mitochondrial 16S ribosomal RNA (16S) and cytochrome c oxidase subunit I (COI), in 48 samples: 27 unidentified oyster specimens collected from two locations on O‘ahu, 13 known specimens from a hatchery in Hilo, Hawai‘i Island, and 8 known specimens from Hilo Bay, Hawai‘i Island.ResultsMolecular data identified approximately 85% of unknown samples as belonging to theOstrea stentina/aupouria/equestrisspecies complex, a globally distributed group with a history of uncertain and controversial taxonomic status. The remaining unknown samples were the nativeDendostrea sandvichensis(G. B. Sowerby II, 1871), and nonnativeCrassostrea gigas(Thunberg, 1793), the latter of which is a commercial species that was introduced to Hawai‘I from multiple sources during the 20th century. Phylogenetic analysis placed Hawai‘iOstreaalongside samples from China, Japan, and New Zealand, grouping them within the recently classified western PacificO. equestris. Until now, four extant species of true oyster have been documented in Hawai‘i. This study expands the known range ofO. equestrisby providing the first verification of its occurrence in Hawai‘i.
Integrative Epigenomic and Transcriptomic Analysis Reveals Robust Metabolic Switching in the Brain During Intermittent Fasting
Authors: Ng Gavin Yong-Quan , Sheng Dominic Paul Lee Kok , Kang Sung Wook , Fann David Yang-Wei , Kim Joonki , Alli-Shaik Asfa , Cho Yoon Suk , Han Jihoon , Sul Jae Hoon , Karamyan Vardan , Okun Eitan , Dheen Thameem , Hande M. Prakash , Vemuganti Raghu , Mallilankaraman Karthik , Kennedy Brian K. , Drummond Grant , Sobey Christopher G. , Gunaratne Jayantha , Mattson Mark P. , Foo Roger Sik-Yin , Jo Dong-Gyu , Arumugam Thiruma V. 
Published: March 2020

AbstractIntermittent fasting (IF) is a lifestyle intervention comprising a dietary regimen in which energy intake is restricted via alternating periods of fasting andad libitumfood consumption, without compromising nutritional composition. While epigenetic modifications can mediate effects of environmental factors on gene expression, no information is yet available on potential effects of IF on the epigenome. In this study, we found that IF causes modulation of histone H3 lysine 9 trimethylation (H3K9me3) epigenetic mark in the cerebellum of male C57/BL6 mice, which in turn orchestrates a plethora of transcriptomic changes involved in the robust metabolic switching processes commonly observed during IF. Interestingly, both epigenomic and transcriptomic modulation continued to be observed after refeeding, suggesting that memory of the IF-induced epigenetic change is maintained at the locus. Notably though, we found that termination of IF results in a loss of H3K9me3regulation of the transcriptome. Collectively, our study characterizes a novel mechanism of IF in the epigenetic-transcriptomic axis, which controls myriad metabolic process changes. In addition to providing a valuable and innovative resource, our systemic analyses reveal molecular framework for understanding how IF impacts the metaboloepigenetics axis of the brain.Highlights○ Intermittent fasting (IF) and refeeding modifies epigenome in the cerebellum○ Integrative epigenomic and transcriptomic analyses revealed metabolic switching○ IF affects the metaboloepigenetics axis in regulating metabolic processes○ Integrative analyses revealed a loss of epigenetic reprogramme following refeeding
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells
Authors: Liu Shang , Zhou Biaofeng , Wu Liang , Sun Yan , Chen Jie , Liu Shiping 
Published: March 2020

AbstractRecent advances in single-cell RNA sequencing (scRNA-seq), enriched the knowledge of the heterogeneity of the tumor-infiltrating lymphocytes (TIL) for understanding the mechanisms of cancer initiation and progression. However, alternative splicing (AS), as one of the important regulatory factors of heterogeneity, has been poorly investigated. Here, we proposed a computational tool, DESJ-detection, which could fast and accurately detect the differentially expressed splicing junction (DESJ) between cell groups at single-cell level. We analyzed 5,063 T cells of hepatocellular carcinoma (HCC) and identified 1,176 DESJs across 11 T cell subtypes. Cell subtypes with a similar function clustered closer rather than the lineage at the AS level. Meanwhile, we identified two novel cell states, pre-exhaustion and pre-activation with the marker isoform CD103-201 and ARHGAP15-205. In summary, we presented a comprehensive investigation of alternative splicing differences, which provided novel insights for heterogeneity of T cells and can be applied in other full-length scRNA-seq datasets.
Improved segmentation of the intracranial and ventricular volumes in populations with cerebrovascular lesions and atrophy using 3D CNNs
Authors: Ntiri Emmanuel E. , Holmes Melissa F. , Forooshani Parisa M. , Ramirez Joel , Gao Fuqiang , Ozzoude Miracle , Adamo Sabrina , Scott Christopher J.M. , Dowlatshahi Dar , Lawrence-Dewar Jane M. , Kwan Donna , Lang Anthony E. , Symons Sean , Bartha Robert , Strother Stephen , Tardif Jean-Claude , Masellis Mario , Swartz Richard H. , Moody Alan , Black Sandra E. , Goubran Maged 
Published: March 2020

AbstractSuccessful segmentation of the total intracranial vault (ICV) and ventricles is of critical importance when studying neurodegeneration through neuroimaging. We present iCVMapper and VentMapper, robust algorithms that use a convolutional neural network (CNN) to segment the ICV and ventricles from both single and multi-contrast MRI data. Our models were trained on a large dataset from two multi-site studies (N=528 subjects for ICV, N=501 for ventricular segmentation) consisting of older adults with varying degrees of cerebrovascular lesions and atrophy, which pose significant challenges for most segmentation approaches. The models were tested on 238 participants, including subjects with vascular cognitive impairment and high white matter hyperintensity burden. Two of the three test sets came from studies not used in the training dataset. We assessed our algorithms relative to four state-of-the-art ICV extraction methods (MONSTR, BET, Deep Extraction, FreeSurfer), as well as a ventricular segmentation tool (FreeSurfer). Our multi-contrast models outperformed other methods across all evaluation metrics, with average Dice coefficients of 0.98 and 0.94 for ICV and ventricular segmentation respectively. Both models were also the most time efficient, segmenting the structures in orders of magnitude faster than some of the other available methods. Our networks showed an increased accuracy with the use of a conditional random field (CRF) as a post-processing step. We further validated both segmentation models, highlighting their robustness to images with lower resolution and signal-to-noise ratio, compared to tested techniques. The pipeline and models are available at:https://icvmapp3r.readthedocs.ioandhttps://ventmapp3r.readthedocs.ioto enable further investigation of the roles of ICV and ventricles in relation to normal aging and neurodegeneration in large multi-site studies.
Elucidating the mechanism ofTrypanosoma cruziacquisition by triatomine insects: evidence from a large field survey ofTriatoma infestans
Authors: Tustin Aaron W. , Castillo-Neyra Ricardo , Tamayo Laura D. , Borini-Mayorí Katty , Salazar Renzo , Levy Michael Z. 
Published: March 2020

AbstractBlood-sucking triatomine bugs transmit the protozoan parasiteTrypanosoma cruzi, the etiologic agent of Chagas disease. We measured the prevalence ofT. cruziinfection in 58,519Triatoma infestanscaptured in residences in and near Arequipa, Peru. Among bugs from infected colonies,T. cruziprevalence increased with stage from 12% in second instars to 36% in adults. Regression models demonstrated a linear relationship between infection prevalence and developmental stage. Prevalence increased by 5.4 percentage points with each additional stage. We postulate that the probability of acquiring the parasite may be related to the number of feeding events. Transmission of the parasite does not appear to be correlated with the amount of blood ingested during feeding. Similarly, other hypothesized transmission routes such as coprophagy fail to explain the observed pattern of prevalence. Our results could have implications for the feasibility of late-acting control strategies that preferentially kill older insects.
Natural and synthetic potential inhibitors of endoribonuclease Nsp15 encoded by Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Computer modelingin silicoexperiments.p-Coumaric acid, Curcumin and their Boronic acid derivatives compared to Hydroxychloroquine and its Boronic acid derivative
Authors: Barquero Juan F. 
Published: March 2020

AbstractBased on the structural and biochemical characterization of endoribonuclease Nsp15 in crystal structure PDB code 5YVD, I am providing plausible inhibitors of this enzyme. In this report I intent to signal that is possible to inhibit this enzyme by the use of natural occurring compounds and their boronic acid derivatives, compounds with borono B(OH)2groups. Boronic acids are atracted to serine side chains in the active site of serine proteases, in this case an endoribonuclease. Actual lab tests need to be conducted, nevertheless I venture here to propose four compounds:p-coumaric acid, Curcumin and their boronic acid derivatives with the use of computer modeling,in silicoexperiments. I also compared the above mentioned compounds to Hydroxychloroquine and its boronic acid derivative. I usedAutoDock Vina, UCSF Chimera1.12,DeepView / Swiss-Pdb Viewer4 1.0,Sulp3.0,PubChem, MDL Isis Draw2.5,OpenBabelGUI2.2.3, andMicrosoft WordPad. As hardware I used a VAIO loptop with Intel Core i5 withMicrosoft Windows8.0, and a Dell loptop Inspiron E 1405 with an Intel Core Duo withMicrosoft WindowsXp (off line).
Ultra-Low-Cost Integrated Silicon-based Transducer for On-Site, Genetic Detection of Pathogens
Authors: Nunez-Bajo Estefania , Kasimatis Michael , Cotur Yasin , Asfour Tarek , Collins Alex , Tanriverdi Ugur , Grell Max , Kaisti Matti , Senesi Guglielmo , Stevenson Karen , Güder Firat 
Published: March 2020

AbstractRapid screening and low-cost diagnosis play a crucial role in choosing the correct course of interventione.g.,drug therapy, quarantine, no action etc. when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2 (the pathogen causing COVID-19), and shows no or similar symptoms to other common infections. We report a silicon-based integrated Point-of-Need (PoN) transducer (TriSilix) that can chemically-amplify and detect pathogen-specific sequences of nucleic acids (NA) quantitatively in real-time. Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. TriSilix is, therefore, resilient to disruptions in the global supply chain as the devices can be produced anywhere in the world. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e.thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically. A single 4-inch Si wafer yields 37 TriSilix chips of 10×10×0.65 mm in size and can be produced in 7 hours, costing ~US $0.35 per device. The system is operated digitally, portable and low power – capable of running up to 35 tests with a 4000 mAh battery (a typical battery capacity of a modern smartphone). We were able to quantitatively detect a 563-bp fragment (Insertion Sequence IS900) of the genomic DNA ofM. aviumsubsp.paratuberculosis(extracted from cultured field samples) through PCR in real-time with a Limit-of-Detection of 20 fg, equivalent to a single bacterium, at the 30thcycle. Using TriSilix, we also detected the cDNA from SARS-CoV-2 (1 pg), through PCR, with high specificity against SARS-CoV (2003).
Grain number and genotype drive nitrogen-dependent yield response in the C4 modelSetaria italica(L.) P. Beauv
Authors: Bandyopadhyay Tirthankar , Swarbreck Stéphanie M , Jaiswal Vandana , Gupta Rajeev , Bentley Alison R. , Griffiths Howard , Prasad Manoj 
Published: March 2020

AbstractFertiliser nitrogen (N) drives crop yields and requires the breeding and selection of cultivars that are inherently highly N responsive. For major cereal crops such as wheat (Triticum aestivumL.) breeding over time has led to enhanced N use in modern cultivars however there remains a gap in understanding the N responsiveness of minor cereals grains, many of which are highly relevant to global food security. Here we investigate response to increasing N availability in a diverse population ofSetaria italica(L., foxtail millet) accessions demonstrating that N-driven yield increase is dependent on grain number rather than individual grain weight. Within the population, some accessions responded strongly to increased N availability while others show little yield improvement under high N. Genetic markers were generated to enable investigation of N responsiveness at a genome-wide level, highlighting likely underlying causal loci, especially for grains per plant. Despite the lack of response in terms of yield increase, a non-responsive accession shows a strong transcriptional response suggesting different metabolic functioning under high vs low N. Our results show major differences in N responsiveness inS. italicaand provide novel insight into the genetic and molecular basis for this variation.One sentence summaryNitrogen dependent yield response inSetaria italicaL. is driven by grain number and genotypes with low N yield responsive genotypes being more transcriptionally dynamic under varied N levels post-flowering compared to high N yield responsive genotypes.
CATH functional families predict protein functional sites
Authors: Das Sayoni , Scholes Harry M. , Orengo Christine A. 
Published: March 2020

AbstractMotivationIdentification of functional sites in proteins is essential for functional characterisation, variant interpretation and drug design. Several methods are available for predicting either a generic functional site, or specific types of functional site. Here, we present FunSite, a machine learning predictor that identifies catalytic, ligand-binding and protein-protein interaction functional sites using features derived from protein sequence and structure, and evolutionary data from CATH functional families (FunFams).ResultsFunSite’s prediction performance was rigorously benchmarked using cross-validation and a holdout dataset. FunSite outperformed all publicly-available functional site prediction methods. We show that conserved residues in FunFams are enriched in functional sites. We found FunSite’s performance depends greatly on the quality of functional site annotations and the information content of FunFams in the training data. Finally, we analyse which structural and evolutionary features are most predictive for functional sites.AvailabilityThe datasets and prediction models are available on request.Contactc.orengo@ucl.ac.ukSupplementary informationSupplementary data are available atBioinformaticsonline.