bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of library preparation and sequencing depths for direct sequencing ofBordetella pertussispositive samples
Authors: Fong Winkie , Pey Keenan , Rockett Rebecca , Sadsad Rosemarie , Sintchenko Vitali , Timms Verlaine 
Published: February 2021

AbstractWhooping cough, or pertussis, is a highly transmissible respiratory infection caused byBordetella pertussis. Due to the high burden of pertussis, vaccine programmes were introduced internationally and in Australia since the 1950s. This has resulted in a significant decrease of pertussis infections. However, since the 1990s the number of pertussis notifications has increased considerably. Currently circulatingB. pertussisstrains differ in vaccine antigen composition compared to strains that circulated in the pre-vaccination era. These genetic differences are thought to contribute, in part, to the re-emergence of pertussis in Australia and around the world. Whole genome sequencing (WGS) can resolve minute differences in circulating strains and provides unparalleled resolution of vaccine antigens. This high-resolution snapshot can provide clues that enable more targeted public health interventions. However, pertussis is primarily diagnosed with culture-independent diagnostic assays which offer fast turnaround result times and reduced laboratory costs, eliminating the need to culture isolates. Current WGS methods require a cultured isolate, resulting in an absence ofB. pertussisgenome sequences in the post vaccination era. This scarcity has, in turn, limited understanding of currently circulating strains and respective vaccine antigen compositions.Recent advancements of WGS technologies have allowed direct sequencing of clinical specimens without the need for a cultured isolate. However, recovering reliable sequence data from clinical samples of low bacterial load infections such asB. pertussisis a pressing challenge. We sought to increase the yield ofB. pertussissequences direct from a clinical sample by evaluating widely available WGS library preparation methods.We report that the Illumina DNA prep library preparation kit combined with deep sequencing allowed the detection of important surveillance information such as allelic variations in theB. pertussisvaccine antigens. Further, our method generates high coverage over the 23S ribosomal RNA ofB. pertussisenabling macrolide resistance to be easily determined. Overall, this method can improve surveillance ofB. pertussis, by monitoring changes in vaccine antigens, detecting antimicrobial resistance and guiding Public Health control interventions.
Microbiota-derived metabolites inhibitSalmonellavirulent subpopulation development by acting on single-cell behaviors
Authors: Hockenberry Alyson M , Micali Gabriele , Takács Gabriella , Weng Jessica , Hardt Wolf-Dietrich , Ackermann Martin 
Published: February 2021

AbstractSalmonella spp.expressSalmonellapathogenicity island 1 (SPI-1) genes to mediate the initial phase of interaction with host cells. Prior studies indicate short-chain fatty acids, microbial metabolites at high concentrations in the gastrointestinal tract, limit SPI-1 gene expression. A number of reports show only a subset ofSalmonellacells in a population express these genes, suggesting short-chain fatty acids could decrease SPI-1 population-level expression by acting on per-cell expression and/or the proportion of expressing cells. Here, we combine single-cell, theoretical, and molecular approaches to address the effect of short-chain fatty acids on SPI-1 expression. Our results show short-chain fatty acids do not repress SPI-1 expression by individual cells. Rather, these compounds act to selectively slow the growth of SPI-1 expressing cells, ultimately decreasing their frequency in the population. Further experiments indicate slowed growth arises from short-chain fatty acid-mediated depletion of the proton motive force. By influencing the SPI-1 cell-type proportions, our findings imply gut microbial metabolites act on cooperation between the two cell-types and ultimately influenceSalmonella’s capacity to establish within a host.Significance StatementEmergence of distinct cell-types in populations of genetically identical bacteria is common. Furthermore, it is becoming increasingly clear that cooperation between cell-types can be beneficial. This is the case duringSalmonellainfection, in which cooperation between inflammation-inducing virulent and fast-growing avirulent cell-types occurs during infection to aid in colonization of the host gut. Here, we show gut microbiota-derived metabolites slow growth by the virulent cell-type. Our study implies microbial metabolites shape cooperative interactions between the virulent and avirulent cell types, a finding that can help explain the wide array of clinical manifestations ofSalmonellainfection.
Quantifying and Mitigating Motor Phenotypes Induced by Antisense Oligonucleotides in the Central Nervous System
Authors: Moazami Michael P. , Rembetsy-Brown Julia M. , Wang Feng , Krishnamurthy Pranathi Meda , Weiss Alexandra , Marosfoi Miklos , King Robert M. , Motwani Mona , Gray-Edwards Heather , Fitzgerald Katherine A. , Brown Robert H. , Watts Jonathan K. 
Published: February 2021

ABSTRACTAntisense oligonucleotides (ASOs) are emerging as a promising class of therapeutics for neurological diseases. When injected directly into the cerebrospinal fluid, ASOs distribute broadly across brain regions and exert long-lasting therapeutic effects. However, many phosphorothioate (PS)-modified gapmer ASOs show transient motor phenotypes when injected into the cerebrospinal fluid, ranging from reduced motor activity to ataxia or acute seizure-like phenotypes. The effect of sugar and phosphate modifications on these phenotypes has not previously been systematically studied. Using a behavioral scoring assay customized to reflect the timing and nature of these effects, we show that both sugar and phosphate modifications influence acute motor phenotypes. Among sugar analogues, PS-DNA induces the strongest motor phenotype while 2’-substituted RNA modifications improve the tolerability of PS-ASOs. This helps explain why gapmer ASOs have been more challenging to develop clinically relative to steric blocker ASOs, which have a reduced tendency to induce these effects. Reducing the PS content of gapmer ASOs, which contain a stretch of PS-DNA, improves their toxicity profile, but in some cases also reduces their efficacy or duration of effect. Reducing PS content improved the acute tolerability of ASOs in both mice and sheep. We show that this acute toxicity is not mediated by the major nucleic acid sensing innate immune pathways. Formulating ASOs with calcium ions before injecting into the CNS further improved their tolerability, but through a mechanism at least partially distinct from the reduction of PS content. Overall, our work identifies and quantifies an understudied aspect of oligonucleotide toxicology in the CNS, explores its mechanism, and presents platform-level medicinal chemistry approaches that improve tolerability of this class of compounds.
What are housekeeping genes?
Authors: Joshi Chintan J. , Ke Wenfan , Drangowska-Way Anna , O’Rourke Eyleen J. , Lewis Nathan E. 
Published: February 2021

AbstractThe concept of “housekeeping genes” has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as “essential for cellular existence regardless of their specific function in the tissue or organism”, and “stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal”. However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens, bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 12 other animal species that include primates, chicken, andC. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we here present a quantitative and experimentally validated definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics.
Calling differential DNA methylation at cell-type resolution: addressing misconceptions and best practices
Authors: Rahmani Elior , Jew Brandon , Schweiger Regev , Rhead Brooke , Criswell Lindsey A. , Barcellos Lisa F. , Eskin Eleazar , Rosset Saharon , Sankararaman Sriram , Halperin Eran 
Published: February 2021

AbstractWe benchmarked two approaches for the detection of cell-type-specific differential DNA methylation: Tensor Composition Analysis (TCA) and a regression model with interaction terms (CellDMC). Our experiments alongside rigorous mathematical explanations show that TCA is superior over CellDMC, thus resolving recent criticisms suggested by Jing et al. Following misconceptions by Jing and colleagues with modelling cell-type-specificity and the application of TCA, we further discuss best practices for performing association studies at cell-type resolution. The scripts for reproducing all of our results and figures are publicly available at github.com/cozygene/CellTypeSpecificMethylationAnalysis.
Spatially Interacting Phosphorylation Sites and Mutations in Cancer
Authors: Huang Kuan-lin , Scott Adam D. , Zhou Daniel Cui , Wang Liang-Bo , Weerasinghe Amila , Elmas Abdulkadir , Liu Ruiyang , Wu Yige , Wendl Michael C. , Wyczalkowski Matthew A. , Baral Jessika , Sengupta Sohini , Lai Chin-Wen , Ruggles Kelly , Payne Samuel H. , Raphael Benjamin , Fenyö David , Chen Ken , Mills Gordon , Ding Li 
Published: February 2021

ABSTRACTAdvances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1,255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1,000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.
Unravelling processes between phenotypic plasticity and population dynamics in migratory birds
Authors: Liu Jin , Lei Weipan , Mo Xunqiang , Hassell Chris J. , Zhang Zhengwang , Coulson Tim 
Published: February 2021

AbstractPopulations can rapidly respond to environmental change via adaptive phenotypic plasticity, which can also modify interactions between individuals and their environment, affecting population dynamics. Bird migration is a highly plastic resource-tracking strategy in seasonal environments. However, the link between the population dynamics of migratory birds and migration strategy plasticity is not well understood.The quality of staging habitats affects individuals’ migration timing and energy budgets in the course of migration, and can consequently affect individuals’ breeding and overwintering performance, and impact population dynamics. Given staging habitats being lost in many parts of the world, our goal is to investigate responses of individual migration strategies and population dynamics in the face of loss of staging habitat, and to identify the key processes connecting them.We started by constructed and analysed a general full-annual-cycle individual-based model with a stylized migratory population to generate hypotheses on how changes in the size of staging habitat might drive changes in individual stopover duration and population dynamics, and to identify the key processes connecting them. Next, through the interrogation of census data, we tested these hypotheses by analysing population trends and stopover duration of migratory waterbirds experiencing loss of staging habitat.We found empirical support for our modelling-identified hypotheses: the loss of staging habitat generates plasticity in migration strategies, with individuals remaining on the staging habitat for longer to obtain food due to a reduction in per capita food availability. The subsequent increasing population density on the staging habitat has knock on effects on population dynamics in the breeding and overwintering stage.Our results demonstrate how environmental change that impacts one energetically costly life history stage in migratory birds can have population dynamics impacts across the entire annual cycle via phenotypic plasticity.
The hippocampus shows an own-age bias during unfamiliar face viewing
Authors: Koen Joshua D. , Hauck Nedra , Rugg Michael D. 
Published: February 2021

AbstractThe present study investigated the neural correlates of the own-age bias for face recognition in a repetition suppression paradigm. Healthy young and older adults viewed upright and inverted unfamiliar faces. Some of the upright faces were repeated following one of two delays (lag 0 or lag 11). Repetition suppression effects were observed in bilateral fusiform cortex. However, there were no significant effects indicating an own-age bias in repetition suppression. The absence of these effects is arguably inconsistent with perceptual expertise accounts of own-age biases in face processing. By contrast, the right anterior hippocampus showed an own-age bias (greater activity for own-than other-age faces) when viewing an unfamiliar face for the first time. Given the importance of the hippocampus for episodic memory encoding, we conjecture that the increased hippocampal activity for own-age relative to other-age faces reflects differential engagement of neural processes supporting the episodic encoding of faces and might provide insight into the neural underpinnings of own-age biases in face recognition memory.
A new field instrument for leaf volatiles reveals an unexpected vertical profile of isoprenoid emission capacities in a tropical forest
Authors: Taylor Tyeen C. , Wisniewski Wit T. , Alves Eliane G. , de Oliveira Raimundo C. , Saleska Scott R. 
Published: February 2021

AbstractBoth plant physiology and atmospheric chemistry are substantially altered by the emission of volatile isoprenoids (VI), such as isoprene and monoterpenes, from plant leaves. Yet, since gaining scientific attention in the 1950’s, empirical research on leaf VI has been largely confined to laboratory experiments and atmospheric observations. Here, we introduce a new field instrument designed to bridge the scales from leaf to atmosphere, by enabling precision VI detection in real time from plants in their natural ecological setting. With a field campaign in the Brazilian Amazon, we reveal an unexpected distribution of leaf emission capacities (EC) across the vertical axis of the forest canopy, with EC peaking in the mid-canopy instead of the sun-exposed canopy surface, and high emissions occurring in understory specialist species. Compared to the simple interpretation that VI protect leaves from heat stress at the hot canopy surface, our results encourage a more nuanced view of the adaptive role of VI in plants. We infer that forest emissions to the atmosphere depend on the dynamic microenvironments imposed by canopy structure, and not simply on canopy surface conditions. We provide a new emissions inventory from 51 tropical tree species, revealing moderate consistency in EC within taxonomic groups. Our self-contained, portable instrument provides real-time detection and live measurement feedback with precision and detection limits better than 0.5 nmol m-2leafs-1. We call the instrument ‘PORCO’ based on the gas detection method: photoionization of organic compounds. We provide a thorough validation of PORCO and demonstrate its capacity to detect ecologically driven variation in leaf emission rates and thus accelerate a nascent field of science: the ecology and ecophysiology of plant volatiles.Type of paperMethod
AAV-MediatedIn VivoCAR Gene Therapy for Targeting Human T Cell Leukemia
Authors: Nawaz Waqas , Huang Bilian , Xu Shijie , Li Yanlei , Zhu Linjing , Wu Zhiwei , Wu Xilin 
Published: February 2021

AbstractChimeric antigen receptor (CAR) T cell therapy is the most active field in immuno-oncology and brings substantial benefit to patients with B cell malignancies. However, the complex procedure for CAR T cell generation hampers its widespread applications. Here, we describe a novel approach in which human CAR T cells can be generated within the host upon injecting an Adeno-associated virus (AAV)vector carrying the CAR gene, which we call AAV delivering CAR gene therapy (ACG). Upon single infusion into a humanized NCG tumor mouse model of human T cell leukemia, AAV generates sufficient numbers of potentin vivoCAR cells, resulting in tumor regression; these in vivo generated CAR cells produce antitumor immunological characteristics. This instantaneous generation ofin vivoCAR T cells may bypass the need for patient lymphodepletion, as well as theex vivoprocesses of traditional CAR T cell production, which may make CAR therapy simpler and less expensive. It may allow the development of intricate, individualized treatments in the form of on-demand and diverse therapies.Significance StatementAAV can generate enough CAR cells within the host. That act as a living drug, distributed throughout the body, and persist for weeks, with the ability to recognize and destroy tumor cells.
Identification of salt tolerant genotypes in wheat using stress tolerance indices
Authors: Bakhshi Behnam , Taghi Tabatabaei Seyed Mohammad , Naroui Rad Mohammad Reza , Masoudi Bahram 
Published: February 2021

AbstractSalinity is one of the most important causes of yield loss in agricultural products, especially wheat. Wheat cultivation, on the other hand, is carried out on a wide range of agricultural land in saline lands. Therefore, wheat breeding for tolerance to salinity can be an effective way to improve yield and yield stability under these conditions. In this study, twenty wheat genotypes were studied in a randomized complete block design with three replications in two normal and salinity stress conditions in order to identify suitable indices of wheat stress tolerance and also to identify genotypes tolerant to salinity stress. Genotypes were evaluated based on tolerance index (TOL), stress tolerance index (STI), mean productivity (MP), susceptibility to stress (SSI), geometric mean productivity (GMP), harmonic mean productivity (HM), yield stability (YS) and yield index (YS). The results showed that MP, GMP, HM and STI indices are suitable indices because of their positive and highly significant correlation with yield in both normal and salinity stress conditions and it was found that these indices were suitable tools to achieve high yield genotypes in both environments. The results also showed that genotypes 10, 4, 9, 3 and 8 are resistant to salt stress with acceptable yield. Genotypes 5, 11, 12, 14, 16, 17, 18 and 20 were also identified as the most susceptible genotypes.
Nutrient copper signaling promotes protein turnover by allosteric activation of ubiquitin E2D conjugases
Authors: Opazo C.M. , Lotan A. , Xiao Z. , Zhang B. , Greenough M.A. , Lim C.M. , Trytell H. , Ramírez A. , Ukuwela A.A. , Mawal C.H. , McKenna J. , Saunders D.N. , Burke R. , Gooley P.R. , Bush A.I. 
Published: February 2021

SUMMARYNutrient copper supply is critical for cell growth and differentiation, and its disturbance is associated with major pathologies including cancer and neurodegeneration. Although increasing copper bioavailability in late Precambrian facilitated emergence of novel cuproproteins, their intricate regulation by this essential trace element remains largely cryptic. We found that subtle rises in cellular copper strikingly increase polyubiquitination and accelerate protein degradation within 30 minutes in numerous mammalian cell lines. We track this surprising observation to allostery induced in the UBE2D ubiquitin conjugase clade through a conserved CXXXC sub-femtomolar-affinity Cu+binding motif. Thus, physiologic fluctuation in cytoplasmic Cu+is coupled to the prompt degradation of UBE2D protein targets, including p53. InDrosophilaharboring a larval-lethal knockdown of the nearly identical fly orthologue UbcD1, complementation with human UBE2D2 restored near-normal development, but mutation of its CXXXC Cu+binding motif profoundly disrupted organogenesis. Nutrient Cu+emerges as a trophic allosteric modulator of UBE2D activity through a structural motif whose evolution coincides with animal multicellularity.One Sentence SummaryModulation of nutrient copper impacts protein turnover and animal morphogenesis through conserved allostery of ubiquitin E2D conjugases.HilightsNutrient copper supply is critical for cell growth and differentiationThe E2D clade of ubiquitin conjugases contains a sub-femtomolar-affinity Cu+binding motifAllosteric activation by Cu+markedly accelerates protein polyubiquitinationThis sensor couples physiologic fluctuations in cytoplasmic Cu+with the degradation rate of E2D targets, including p53This metazoan signaling mechanism is critical fordrosophilamorphogenesisIn BriefConserved allostery of ubiquitin E2D conjugases links nutrient copper signaling to protein degradation and animal morphogenesis.Abstract FigureGraphical Abstract