bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential effects of antibiotic treatment with piperacillin/tazobactam or ceftriaxone on the murine gut microbiota
Authors: Venturini Carola , Bowring Bethany , Fajardo-Lubian Alicia , Devine Carol , Iredell Jonathan 
Published: May 2020

AbstractEffective antimicrobial stewardship requires a better understanding of the impact of different antibiotics on the gut microflora. Studies in humans are confounded by large inter-individual variability and difficulty in identifying control cohorts. However, controlled murine models can provide valuable information. We examined the impact of a penicillin-like antibiotic (piperacillin/tazobactam, TZP) or a third-generation cephalosporin (ceftriaxone, CRO) on the murine gut microbiota. We analyzed gut microbiome composition by 16S-rRNA amplicon sequencing and effects on the Enterobacteriaceae by qPCR and standard microbiology. Colonization resistance to multidrug resistantEscherichia coliST131 andKlebsiella pneumoniaeST258 was also tested. Changes in microbiome composition and a significant (p<0.001) decrease in diversity occurred in all treated mice, but were more marked and longer lasting after CRO exposure with a persistent rise in Proteobacteria levels. Increases in the Enterobacteriaceae occurred in all antibiotic treated mice, but were transient and associated with direct antibiotic pressure. Co-habitation of treated and untreated mice attenuated the detrimental effect of antibiotics on treated animals, but also caused disturbance in untreated co-habitants. At the height of dysbiosis after antibiotic termination, the murine gut was highly susceptible to colonization with both multidrug resistant pathogens. The administration of a third-generation cephalosporin caused a significantly prolonged dysbiosis in the murine gut microflora, when compared to a penicillin/β-lactam inhibitor combination with comparable activity against medically important virulent bacteria. At the height of dysbiosis, both antibiotic treatments equally led to microbial imbalance associated with loss of resistance to gut colonization by antibiotic-resistant pathogens.
“Association of Poor Housing Conditions with COVID-19 Incidence and Mortality Across US Counties.”
Authors: Ahmad Khansa , Erqou Sebhat , Shah Nishant , Nazir Umair , Morrison Alan , Choudhary Gaurav , Wu Wen-Chih 
Published: May 2020

AbstractObjectivePoor housing conditions have been linked with worse health outcomes and infectious spread in communities but its relationship with incidence and mortality of COVID-19 is unknown. Therefore, we undertook this study to determine the association between poor housing condition and COVID-19 incidence and mortality in US counties.MethodsWe conducted cross-sectional analysis of county-level data from the US Centers for Disease Control, US Census Bureau and John Hopkins Coronavirus Resource Center for 3141 US counties. The exposure of interest was percentage of households with poor housing conditions (one or more of: overcrowding, high housing cost, incomplete kitchen facilities, or incomplete plumbing facilities). Outcomes were incidence rate ratios (IRR) and mortality rate ratios (MRR) of COVID-19 across US counties through 4/21/2020. Multilevel generalized linear modeling was utilized with adjustment for population density and county characteristics including demographics, income, education, prevalence of medical comorbidities, access to healthcare insurance and emergency rooms, and state-level COVID-19 test density.ResultsAcross 3135 US counties, the mean percentage of households with poor housing conditions was 14.2% (range 2.7% to 60.2%). The mean (SD) incidence and mortality of COVID-19 were 255.68 (2877.03) cases and 13.90 (272.22) deaths per county, respectively. In the fully adjusted models, with each 5% increase in percent households with poor housing conditions, there was a 50% higher risk of COVID-19 incidence (IRR 1.50, 95% CI: 1.38 – 1.62) and a 42% higher risk of COVID-19 mortality (MRR 1.42, 95% CI: 1.25 – 1.61). Results remained similar using earlier timepoints (3/31/2020 and 4/10/2020).Conclusions and RelevanceCounties with a higher percentage of households with poor housing had higher incidence of, and mortality associated with, COVID-19. These findings suggest targeted health policies to support individuals living in poor housing conditions should be considered in further efforts to mitigate adverse outcomes associated with COVID-19.
Lineage tracing of human embryonic development and foetal haematopoiesis through somatic mutations
Authors: Chapman Michael Spencer , Ranzoni Anna Maria , Myers Brynelle , Williams Nick , Coorens Tim , Mitchell Emily , Butler Timothy , Dawson Kevin J , Hooks Yvette , Moore Luiza , Nangalia Jyoti , Robinson Philip S , Hook Elizabeth , Campbell Peter J , Cvejic Ana 
Published: May 2020

AbstractTo date, ontogeny of the human haematopoietic system during foetal development has been characterized mainly through careful microscopic observations. Here we used whole-genome sequencing (WGS) of 511 single-cell derived haematopoietic colonies from healthy human foetuses of 8 and 18 post-conception weeks (pcw) coupled with deep targeted sequencing of tissues of known embryonic origin to reconstruct a phylogenetic tree of blood development. We found that in healthy foetuses, individual haematopoietic progenitors acquire tens of somatic mutations by 18 pcw. Using these mutations as barcodes, we timed the divergence of embryonic and extra-embryonic tissues during development and estimated the number of blood antecedents at different stages of embryonic development. Our analysis has shown that ectoderm originates from a smaller set of blood antecedents compared to endoderm and mesoderm. Finally, our data support a hypoblast origin of the extra-embryonic mesoderm and primitive blood in humans.
SYBR green one-step qRT-PCR for the detection of SARS-CoV-2 RNA in saliva
Authors: Ganguly DR , Rottet S , Yee S , Hee WY , Smith AB , Khin NC , Millar AA , Fahrer AM 
Published: May 2020

AbstractWe describe our efforts at developing a one-step quantitative reverse-transcription (qRT)-PCR protocol to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA directly from saliva samples, without RNA purification. We find that both heat and the presence of saliva impairs the ability to detect synthetic SARS-CoV-2 RNA. Buffer composition (for saliva dilution) was also crucial to effective PCR detection. Using the SG2 primer pair, designed by Sigma-Aldrich, we were able to detect the equivalent of 1.7×106viral copies per mL of saliva after heat inactivation; approximately equivalent to the median viral load in symptomatic patients. This would make our assay potentially useful for rapid detection of high-shedding infected individuals. We also provide a comparison of the PCR efficiency and specificity, which varied considerably, across 9 reported primer pairs for SARS-CoV-2 detection. Primer pairs SG2 and CCDC-N showed highest specificity and PCR efficiency. Finally, we provide an alternate primer pair to use as a positive control for human RNA detection in SARS-CoV-2 assays, as we found that the widely used US CDC primers (targeting humanRPP30) do not span an exon-exon junction and therefore does not provide an adequate control for the reverse transcription reaction.
Tumor-Immune Partitioning and Clustering (TIPC) algorithm reveals distinct signatures of tumor-immune cell interactions within the tumor microenvironment
Authors: Lau Mai Chan , Borowsky Jennifer , Väyrynen Juha P. , Haruki Koichiro , Zhao Melissa , Costa Andressa Dias , Gu Simeng , Silva Annacarolina da , Arima Kota , Yeong Joe , Felt Kristen D. , Hamada Tsuyoshi , Nishihara Reiko , Lennerz Jochen K. , Fuchs Charles S. , Wu Catherine J. , Ogino Shuji , Nowak Jonathan A. 
Published: May 2020

AbstractGrowing evidence supports the importance of understanding tumor-immune spatial relationship in the tumor microenvironment in order to achieve precision cancer therapy. However, existing methods, based on oversimplistic cell-to-cell proximity, are largely confounded by immune cell density and are ineffective in capturing tumor-immune spatial patterns. Here we developed a novel computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), to offer an effective solution for spatially informed tumor subtyping. Our method could measure the extent of immune cell partitioning between tumor epithelial and stromal areas as well as the degree of immune cell clustering. Using a U.S. nation-wide colorectal cancer database, we showed that TIPC could determine tumor subtypes with unique tumor-immune spatial patterns that were significantly associated with patient survival and key tumor molecular features. We also demonstrated that TIPC was robust to parameter settings and readily applicable to different immune cell types. The capability of TIPC in delineating clinically relevant patient subtypes that encapsulate tumor-immune spatial relationship, immune density, and tumor morphology is expected to shed light on underlying immune mechanisms. Hence, TIPC can be a useful bioinformatics tool for effective characterization of the spatial composition of the tumor-immune microenvironment to inform precision immunotherapy.
Indigenous plants promote insect biodiversity in urban greenspaces
Authors: Mata Luis , Andersen Alan N. , Morán-Ordóñez Alejandra , Hahs Amy K. , Backstrom Anna , Ives Christopher D. , Bickel Daniel , Duncan David , Palma Estibaliz , Thomas Freya , Cranney Kate , Walker Ken , Shears Ian , Semeraro Linda , Malipatil Mallik , Moir Melinda L. , Plein Michaela , Porch Nick , Vesk Peter A. , Smith Tessa R. , Lynch Yvonne 
Published: May 2020

AbstractThe contribution of urban greenspaces to support biodiversity and provide benefits for people is increasingly recognised. However, ongoing management practices still favour (1) vegetation oversimplification, often limiting greenspaces to lawns and tree canopy rather than multi-layered vegetation that includes under and midstorey; and (2) the use of nonnative plant species. These practices likely hinder the potential of greenspaces to sustain indigenous biodiversity, particularly for taxa like insects, that rely on plants for food and habitat. Yet, little is known about which plant species may maximise positive outcomes for taxonomically and functionally diverse insect communities in urban greenspaces. Additionally, while urban environments are expected to experience high rates of introductions, quantitative assessments of the relative occupancy of indigenous vs. introduced insect species in greenspace are rare – hindering understanding of how greenspace management may promote indigenous biodiversity while limiting the establishment of introduced insects. Using a hierarchically replicated study design across 15 public parks, we recorded occurrence data from 552 insect species on 133 plant species – differing in planting design element (lawn, midstorey and tree canopy), midstorey growth form (forbs, lilioids, graminoids and shrubs) and origin (nonnative, native and indigenous) – to assess: (1) the relative contributions of indigenous and introduced insect species and (2) which plant species sustained the highest number of indigenous insects. Our data indicates that the insect community was predominately composed of indigenous rather than introduced species. Our findings further highlight the core role of multi-layered vegetation in sustaining high insect biodiversity in urban areas, with indigenous midstorey and canopy representing key elements to maintain rich and functionally diverse indigenous insect communities. Intriguingly, graminoids supported the highest indigenous insect richness across all studied growth forms by plant origin groups. Taken together, our study emphasise the opportunity posed by indigenous understory and midstorey plants, particularly indigenous graminoids in our study area, to promote indigenous insect biodiversity in urban greenspaces. Our work provides a blueprint and stimulus for built-environment professionals to incorporate into their practice plant species palettes that foster a larger presence of indigenous over regionally native or nonnative plant species, whilst incorporating a broader mixture of midstorey growth forms.
Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth
Authors: Poidevin Laetitia , Forment Javier , Unal Dilek , Ferrando Alejandro 
Published: May 2020

ABSTRACTPlant reproduction is one key biological process very sensitive to heat stress and, as a consequence, enhanced global warming poses serious threats to food security worldwide. In this work we have used a high-resolution ribosome profiling technology to study how heat affects both the transcriptome and the translatome ofArabidopsis thalianapollen germinatedin vitro. Overall, a high correlation between transcriptional and translational responses to high temperature was found, but specific regulations at the translational level were also present. We show thatbona fideheat shock genes are induced by high temperature indicating thatin vitrogerminated pollen is a suitable system to understand the molecular basis of heat responses. Concurrently heat induced significant down-regulation of key membrane transporters required for pollen tube growth, thus uncovering heat-sensitive targets. We also found that a large subset of the heat-repressed transporters is specifically up-regulated, in a coordinated manner, with canonical heat-shock genes in pollen tubes grownin vitroandsemi in vivo, based on published transcriptomes fromArabidopsis thaliana. Ribosome footprints were also detected in gene sequences annotated as non-coding, highlighting the potential for novel translatable genes and translational dynamics.
Physical constraints on early blastomere packings
Authors: Giammona James , Campàs Otger 
Published: May 2020

AbstractAt very early embryonic stages, when embryos are composed of just a few cells, establishing the correct packing arrangements (contacts) between cells is essential for the proper development of the organism. As early as the 4-cell stage, the observed cellular packings in different species are distinct and, in many cases, differ from the equilibrium packings expected for simple adherent and deformable particles. It is unclear what are the specific roles that different physical parameters, such as the forces between blastomeres, their division times, orientation of cell division and embryonic confinement, play in the control of these packing configurations. Here we simulate the non-equilibrium dynamics of cells in early embryos and systematically study how these different parameters affect embryonic packings at the 4-cell stage. In the absence of embryo confinement, we find that cellular packings are not robust, with multiple packing configurations simultaneously possible and very sensitive to parameter changes. Our results indicate that the geometry of the embryo confinement determines the packing configurations at the 4-cell stage, removing degeneracy in the possible packing configurations and overriding division rules in most cases. Overall, these results indicate that physical confinement of the embryo is essential to robustly specify proper cellular arrangements at very early developmental stages.Author summaryAt the initial stages of embryogenesis, the precise arrangement of cells in the embryo is critical to ensure that each cell gets the right chemical and physical signals to guide the formation of the organism. Even when the embryo is made of only four cells, different species feature varying cellular arrangements: cells in mouse embryos arrange as a tetrahedron, in the nematode wormC. eleganscells make a diamond and in sea urchins cells arrange in a square configuration. How do cells in embryos of different species control their arrangements? Using computer simulations, we studied how cell divisions, physical contacts between cells and the confinement of the embryo by an eggshell affect the arrangements of cells when the embryos have only 4 cells. We find that the shape of the confining eggshell plays a key role in controlling the cell arrangements, removing unwanted arrangements and robustly specifying the proper contacts between cells. Our results highlight the important roles of embryonic confinement in establishing the proper cell-cell contacts as the embryo starts to develop.
Total mercury concentrations in invasive lionfish (Pterois volitans/miles) from the Atlantic coast of Florida
Authors: Johnson Eric G. , Dichiera Angelina , Goldberg Danielle , Swenarton MaryKate , Gelsleichter James 
Published: May 2020

ABSTRACTInvasive lionfish (Pterois volitans/miles) pose a serious threat to marine ecosystems throughout the western Atlantic Ocean and Caribbean Sea. The development of a fishery for lionfish has been proposed as a strategy for controlling populations; however, there is concern about consumption of this species by humans due to its high trophic position and potential for bioaccumulation of mercury. We analyzed total mercury (THg) in tissues of lionfish from two locations on the east coast of Florida. THg in lionfish increased with size and differed by location and sex. THg was highest in muscle tissue and was strongly positively correlated among tissues. THg in lionfish was lower than other commonly consumed marine fishes, and falls into Florida’s least restrictive advisory level. Consumption of lionfish poses a low risk and concerns over mercury bioaccumulation should not present a significant barrier to lionfish harvest.
Method for Zero-Waste Circular Economy using worms for plastic agriculture: Augmenting polystyrene consumption and plant growth
Authors: Gan Samuel Ken-En , Phua Ser-Xian , Yeo Joshua Yi , Heng Zealyn Shi-Lin , Xing Zhenxiang 
Published: May 2020

AbstractPolystyrene (PS) is one of the major plastics contributing to environmental pollution with its durability and resistance to natural biodegradation. Recent research showed that meal-worms (Tenebrio molitor) and superworms (Zophobas morio) are naturally able to consume PS as a carbon food source and degrade them without observable toxic effects. In this study, we explored the effects of possible food waste contamination and use of worm frass as potential plant fertilizers. We found that small amounts of sucrose and bran increased PS consumption and that the worm frass alone could support dragon fruit cacti (Hylocereus undatus) growth, with superworm frass in particular, supporting better growth and rooting than mealworm frass and control media over a fortnight. As known fish and poultry feed, these finding present worms as a natural solution to simultaneously tackle both the global plastic problem and urban farming issue in a zero-waste sustainable bioremediation cycle.
Non-canonical glutamate-cysteine ligase activity protects against ferroptosis
Authors: Kang Yun Pyo , Mockabee-Macias Andrea , Jiang Chang , Harris Isaac S. , DeNicola Gina M. 
Published: May 2020

AbstractCysteine is required for maintaining cellular redox homeostasis in both normal and transformed cells. Deprivation of cysteine induces the iron-dependent form of cell death known as ferroptosis; however, the metabolic consequences of cysteine starvation beyond impairment of glutathione synthesis are uncharacterized. Here, we find that cystine starvation promotes ferroptosis not only through the inhibition of glutathione (GSH) synthesis, but also through the accumulation of glutamate. Surprisingly, we find that glutamate-cysteine ligase catalytic subunit (GCLC) prevents glutamate accumulation through the generation of alternative γ-glutamyl peptides. Further, inhibition of GCLC accelerates ferroptosis under cystine starvation in a GSH-independent manner. These results indicate that GCLC has an additional, non-canonical role in the protection against ferroptosis to maintain glutamate homeostasis under cystine starvation.
Tim29 is required for stem cell activity during regeneration in the flatwormMacrostomum lignano
Authors: Mouton Stijn , Ustyantsev Kirill , Beltman Frank , Glazenburg Lisa , Berezikov Eugene 
Published: May 2020

AbstractDomain of Unknown Function (DUF) genes are broadly conserved in metazoa but have an unknown biological function. Previously, we established transcriptional profiles of the germline and stem cells of the flatwormMacrostomum lignano(Grudniewska et al., 2016). Here, we used this information to probe the function of DUF genes inM. lignano. Recently, Kang et al. (2016) found that DUF2366 is a mitochondrial inner membrane protein that interacts with the protein import complex TIM22. DUF2366 was renamed TIM29, and shown to stabilize the TIM22 complex, but its biological role remained largely unknown. We now demonstrate that DUF2366/TIM29 is dispensable in the homeostatic condition inM. lignano, but is essential to adapt to a highly proliferative state required for regeneration. Our results show that ‘de-DUFing’ the function of DUF genes might require special biological conditions, such as regeneration, and establishesM. lignanoas an informative platform to study DUF genes.
A target enrichment probe set for resolving the flagellate plant tree of life
Authors: Breinholt Jesse W. , Carey Sarah B. , Tiley George P. , Davis E. Christine , Endara Lorena , McDaniel Stuart F. , Neves Leandro G. , Sessa Emily B. , von Konrat Matt , Chantanaorrapint Sahut , Fawcett Susan , Ickert-Bond Stefanie M. , Labiak Paulo H. , Larraín Juan , Lehnert Marcus , Lewis Lily R. , Nagalingum Nathalie S. , Patel Nikisha , Rensing Stefan A. , Testo Weston , Vasco Alejandra , Villarreal Juan Carlos , Williams Evelyn Webb , Burleigh J. Gordon 
Published: May 2020

ABSTRACTPremise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms.Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa.ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.