bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing top-down hyperspectral imaging for monitoring genotype and growth conditions in maize
Authors: Tirado Sara B. , St Dennis Susan , Enders Tara A. , Springer Nathan M. 
Published: January 2020

AbstractThere is significant enthusiasm about the potential for hyperspectral imaging to document variation among plant species, genotypes or growing conditions. However, in many cases the application of hyperspectral imaging is performed in highly controlled situations that focus on a flat portion of a leaf or side-views of plants that would be difficult to obtain in field settings. We were interested in assessing the potential for applying hyperspectral imaging to document variation in genotypes or abiotic stresses in a fashion that could be implemented in field settings. Specifically, we focused on collecting top-down hyperspectral images of maize seedlings similar to a view that would be collected in a typical maize field. A top-down image of a maize seedling includes a view into the funnel-like whorl at the center of the plant with several leaves radiating outwards. There is substantial variability in the reflectance profile of different portions of this plant. To deal with the variability in reflectance profiles that arises from this morphology we implemented a method that divides the longest leaf into 10 segments from the center to the leaf tip. We show that using these segments provides improved ability to discriminate different genotypes or abiotic stress conditions (heat, cold or salinity stress) for maize seedlings. We also found substantial differences in the ability to successfully classify abiotic stress conditions among different inbred genotypes of maize. This provides an approach that can be implemented to help classify genotype and environmental variation for maize seedlings that could be implemented in field settings.Significance StatementThis study describes the importance of using spatial information for the analysis of hyperspectral images of maize seedling. The segmentation of maize seedling leaves provides improved resolution for using hyperspectral variation to document genotypic and environmental variation in maize.
BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs
Authors: Luhmann Nina , Holley Guillaume , Achtman Mark 
Published: January 2020

AbstractBlastFrost is a highly efficient method for querying 100,000s of genome assemblies. It builds on Bifrost, a recently developed dynamic data structure for compacted and colored de Bruijn graphs from bacterial genomes. BlastFrost queries a Bifrost data structure for sequences of interest, and extracts local subgraphs, thereby enabling the efficient identification of the presence or absence of individual genes or single nucleotide sequence variants. Here we describe the algorithms and implementation of BlastFrost. We also present two exemplar practical applications. In the first, we determined the presence of the individual genes within the SPI-2Salmonellapathogenicity island within a collection of 926 representative genomes in minutes. In the second application, we determined the existence of known single nucleotide polymorphisms associated with fluoroquinolone resistance in the genesgyrA, gyrBandparEamong 190, 209 Salmonella genomes. BlastFrost is available for download athttps://github.com/nluhmann/BlastFrost.
Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks
Authors: Lanuza Jose B. , Bartomeus Ignasi , Ashman Tia Lynn , Rader Romina 
Published: January 2020

SUMMARYPollinator sharing can have negative consequences for plant fitness with the arrival of foreign pollen, yet responses are often variable among species. Plant traits and relatedness of donor and recipient species have been suggested to drive the variations in plant fitness, but how they shape the structure of pollen competition networks has been overlooked at the community level.To understand the importance of traits and relatedness we conducted a controlled glasshouse experiment with an artificial co-flowering community. We performed 900 reciprocal crosses by experimentally transferring pollen among 10 species belonging to three different plant families.We found a significant reduction in seed set for 67% of the crosses, driven largely by recipient traits and the interaction between recipient-donor traits under specific circumstances of trait-matching. These traits and their asymmetries among species led to a hierarchical (or transitive) structure of pollen competition with clear winners and losers depending on specific combination of traits.A greater understanding of the importance of trait matching and asymmetries among donor and recipient plant species will facilitate knowledge of the mechanisms underlying foreign pollen impacts upon plant reproductive fitness. This will require a shift from pairwise to community level interactions.
Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D inDrosophilaneurons
Authors: Insolera Ryan , Lőrincz Péter , Wishnie Alec J , Juhász Gábor , Collins Catherine A 
Published: January 2020

AbstractA healthy population of mitochondria, maintained by proper fission, fusion, and degradation, is critical for the long-term survival and function of neurons. Here, our discovery of mitophagy intermediates in fission-impairedDrosophilaneurons brings new perspective into the relationship between mitochondrial fission and mitophagy. Neurons lacking either the ataxia disease gene Vps13D or the dynamin related protein Drp1 contain enlarged mitochondria that are engaged with autophagy machinery and also lack matrix components due to rupture. Reporter assays combined with genetic studies imply that mitophagy both initiates and is completed in Drp1 impaired neurons, but fails to complete in Vps13D impaired neurons, which accumulate compromised mitochondria within stalled mito-phagophores. Our findings imply that in fission-defective neurons, mitophagy becomes induced, and that the lipid channel containing protein Vps13D has separable functions in mitochondrial fission and phagophore elongation.
Megafauna decline have reduced pathogen dispersal which may have increased emergent infectious diseases
Authors: Doughty Christopher E. , Prys-Jones Tomos , Faurby Søren , Abraham Andrew , Hepp Crystal , Leshyk Victor , Fofanov Viacheslav Y. , Nieto Nathan C. , Svenning Jens-Christian , Galetti Mauro 
Published: January 2020

AbstractThe Late Quaternary extinctions of megafauna (defined as animal species >44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body-mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven-fold reduction in the movement of gut-transported microbes, such asEscherichia coli(3.3 km2/day to 0.5 km2/day). Similarly, the extinctions led to a seven-fold reduction in the mean home ranges of vector-borne pathogens (7.8 km2to 1.1 km2). To understand the impact of this, we created an individual-based model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4-fold after 20,000 years. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.
Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs that facilitate the evolution of drug resistance
Authors: Bettauer V , Massahi S , Khurdia S , Costa ACBP , Omran RP , Khosravi N , Simpson S , Harb M , Dumeaux V , Whiteway M , Hallett MT 
Published: January 2020

AbstractWe developed a modified protocol for nanolitre droplet-based single cell sequencing appropriate for fungal settings, and used it to transcriptionally profiled several thousands cells from a prototrophicCandida albicanspopulation and several drug exposed colonies (incl. fluconazole, caspofungin and nystatin). Thousands of cells from each colony were profiled both at early and late time points post-treatment in order to infer survival trajectories from initial drug tolerance to drug resistance. We find that prototrophicC. albicanspopulations differentially and stochastically express cytoprotective epigenetic programs. For all drugs, there is evidence that tolerant individuals partition into distinct subpopulations, each with a unique survival strategy involving different regulatory programs. These responses are weakly related to changes in morphology (shift from white to opaque forms, or shift from yeast to filamentous forms). In turn, those subpopulations that successfully reach resistance each have a distinct multivariate epigenetic response that coordinates the expression of efflux pumps, chaperones, transport mechanisms, and cell wall maintenance. Live cell fluorescent imaging was used to validate predictions of which molecular responses most often led to survival after drug exposure. Together our findings provide evidence thatC. albicanshas a robust toolkit of short-term epigenetic cytoprotective responses designed to “buy time” and increase the chance of acquiring long-term resistance.
Remodeling of pre-existing myelinated axons and oligodendrocyte differentiation is stimulated by environmental enrichment in the young adult brain
Authors: Nicholson Madeline , Wood Rhiannon J , Fletcher Jessica L , Gonsalvez David G , Hannan Anthony J , Murray Simon S , Xiao Junhua 
Published: January 2020

AbstractOligodendrocyte production and central nervous system (CNS) myelination is a protracted process, extending into adulthood. While stimulation of neuronal circuits has been shown to enhance oligodendrocyte production and myelination during development, the extent to which physiological stimuli induces activity-dependent plasticity within oligodendrocytes and myelin is unclear, particularly in the adult CNS. Here, we find that using environmental enrichment (EE) to physiologically stimulate neuronal activity for 6-weeks during young adulthood in C57Bl/6 mice results in an enlargement of callosal axon diameters, with a corresponding increase in thickness of pre-existing myelin sheaths. Additionally, EE uniformly promotes the direct differentiation of pre-existing oligodendroglia in both corpus callosum and somatosensory cortex, while differentially impeding OPC homeostasis in these regions. Furthermore, results of this study indicate that physiologically relevant stimulation in young adulthood exerts little influence upon thede novogeneration of new myelin sheaths on previously unmyelinated segments and does not enhance OPC proliferation. Rather in this context, activity-dependent plasticity involves the coincident structural remodeling of axons and pre-existing myelin sheaths and increases the direct differentiation of pre-existing oligodendroglia, implying constraints on maximalde novoproduction in the adult CNS. Together, our findings of myelinated axon remodeling and increased pre-existing oligodendroglial differentiation constitute a previously undescribed form of adaptive myelination that likely contributes to neuronal circuit maturation and the maintenance of optimum cognitive function in the young adult CNS.Main pointsEnvironmental enrichment induces the plasticity of myelinated axons, resulting in axon caliber enlargement and increased thickness of pre-existing myelin sheathsEnvironmental enrichment increases the direct differentiation of pre-existing oligodendrogliaEnvironmental enrichment alters OPC homeostasis
Moderate episodic prenatal alcohol does not impact female offspring fertility in rats
Authors: McReight Elizabeth K , Liew Seng H , Steane Sarah E , Hutt Karla J , Moritz Karen M , Akison Lisa K 
Published: January 2020

AbstractPrenatal alcohol exposure (PAE) has been associated with reproductive dysfunction in offspring. However, studies in females, particularly examining long-term infertility or impacts on ovarian reserve, are lacking. The current study utilised a moderate, episodic exposure model in rats to mimic ‘special occasion’ drinking, which is reported to be common during pregnancy. Our objective was to examine the consequences of this prenatal alcohol exposure on reproductive parameters in female offspring. Pregnant Sprague Dawley rats were treated with either an ethanol gavage (1g EtOH/kg body weight), or an equivalent volume of saline, on embryonic days 13.5 and 14.5 of pregnancy, resulting in a peak blood alcohol concentration of ∼0.04%. Neonatal female offspring were examined for molecular markers regulating early follicle numbers in the ovary and unbiased stereology used to quantify primordial and early growing follicle numbers. Puberty onset (age at vaginal opening and first estrous) was measured post-weaning and estrous cycles, reproductive hormones (progesterone and estradiol) and pregnancy success measured in adults (5-6 months of age). We found no evidence that any of these reproductive parameters were significantly altered by PAE in this model. This animal study provides some reassurance for women who may have consumed a small amount of alcohol during their pregnancy. However, previously published effects on offspring metabolism using this model reinforce avoidance of alcohol during pregnancy.
Structural insight into tanapoxvirus mediated inhibition of apoptosis
Authors: Suraweera Chathura D. , Anasir Mohd Ishtiaq , Chugh Srishti , Javorsky Airah , Impey Rachael E. , Zadeh Mohammad Hasan , Soares da Costa Tatiana P. , Hinds Mark G. , Kvansakul Marc 
Published: January 2020

AbstractPremature programmed cell death or apoptosis of cells is a strategy utilized by multicellular organisms to counter microbial threats. Tanapoxvirus (TANV) is a large double-stranded DNA virus belonging to thepoxviridaethat causes mild Monkeypox-like infections in humans and primates. TANV encodes for a putative apoptosis inhibitory protein 16L. We show that TANV16L is able to bind to a range of peptides spanning the BH3 motif of human pro-apoptotic Bcl-2 proteins, and is able to counter growth arrest of yeast induced by human Bak and Bax. We then determined the crystal structures of TANV16L bound to three identified interactors, Bax, Bim and Puma BH3. TANV16L adopts a globular Bcl-2 fold comprising 7 α-helices, and utilizes the canonical Bcl-2 binding groove to engage pro-apoptotic host cell Bcl-2 proteins. Unexpectedly, TANV16L is able to adopt both a monomeric as well as a domain-swapped dimeric topology where the α1 helix from one protomer is swapped into a neighbouring unit. Despite adopting two different oligomeric forms, the canonical ligand binding groove in TANV16L remains unchanged from monomer to domain-swapped dimer. Our results provide a structural and mechanistic basis for tanapoxvirus mediated inhibition of host cell apoptosis, and reveal the capacity of Bcl-2 proteins to adopt differential oligomeric states whilst maintaining the canonical ligand binding groove in an unchanged state.
A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations
Authors: De Micheli Andrea J. , Spector Jason A. , Elemento Olivier , Cosgrove Benjamin D. 
Published: January 2020

AbstractSingle-cell RNA-sequencing (scRNA-seq) facilitates the unbiased reconstruction of multicellular tissue systems in health and disease. Here, we present a curated scRNA-seq dataset of human muscle samples from 10 adult donors with diverse anatomical locations. We integrated ∼22,000 single-cell transcriptomes using Scanorama to account for technical and biological variation and resolved 16 distinct populations of muscle-resident cells using unsupervised clustering of the data compendium. These cell populations included muscle stem/progenitor cells (MuSCs), which bifurcated into discrete “quiescent” and “early-activated” MuSC subpopulations. Differential expression analysis identified transcriptional profiles altered in the activated MuSCs including genes associated with ageing, obesity, diabetes, and impaired muscle regeneration, as well as long non-coding RNAs previously undescribed in human myogenic cells. Further, we modeled ligand-receptor cell-communication interactions and observed enrichment of the TWEAK-FN14 pathway in activated MuSCs, a characteristic signature of muscle wasting diseases. In contrast, the quiescent MuSCs have enhanced expression of theEGFRreceptor, a recognized human MuSC marker. This work provides a new technical resource to examine human muscle tissue heterogeneity and identify potential targets in MuSC diversity and dysregulation in disease contexts.
Evidence of Absence Regression: A Binomial N-Mixture Model for Estimating Fatalities at Wind Energy Facilities
Authors: McDonald Trent , Bay Kimberly , Studyvin Jared , Leckband Jesse , Schorg Amber , McIvor Jennifer 
Published: January 2020

AbstractEstimating bird and bat fatalities caused by wind-turbine facilities is challenging when carcass counts are rare and produce counts that are either exactly zero or very near zero. The rarity of found carcasses is exacerbated when live members of a particular species are rare and when carcasses degrade quickly, are removed by scavengers, or are not detected by observers. With few observed carcass counts, common statistical methods like logistic, Poisson, or negative binomial regression are unreliable (statistically biased) and often fail to provide answers (i.e., fail to converge). Here, we propose a binomial N-mixture model that estimates fatality rates as well as the total number of carcass counts when these rates are expanded. Our model extends the ‘evidence of absence’ model (Huso et al., 2015; Dalthorp, Huso, and Dail, 2017) by relating carcass deposition rates to study covariates and by incorporating terms that naturally scale counts from facilities of different sizes. Our model, which we call Evidence of Absence Regression (EoAR), can estimate the total number of birds or bats killed at a single wind energy facility or a fleet of wind energy facilities based on covariate values. Furthermore, with accurate prior distributions the model’s results are extremely robust to sparse data and unobserved combinations of covariate values. In this paper, we describe the model, show its low bias and high precision via computer simulation, and apply it to bat carcass counts observed at 21 wind energy facilities in Iowa.
Use of high-refractive index hydrogels and tissue clearing for large biological sample imaging
Authors: Richardson Alexander , Fok Sandra , Lee Victoria , Rye Kerry-Anne , Di Girolamo Nick , Cochran Blake J. 
Published: January 2020

ABSTRACTRecent advances in tissue clearing and light sheet fluorescence microscopy have improved insights into and understanding of tissue morphology and disease pathology by imaging large samples without the requirement of histological sectioning. However, sample handling and conservation of sample integrity during lengthy staining and acquisition protocols remains a challenge. This study overcomes these challenges with acrylamide hydrogels synthesised to match the refractive index of solutions typically utilised in aqueous tissue clearing protocols. These hydrogels have a high-water content (82.0±3.7% by weight). The gels are stable over time and FITC-IgG readily permeated into, and effluxed out of them. Whilst the gels deformed and/or swelled over time in some commonly used solutions, this was overcome by using a previously described custom refractive index matched solution. To validate their use, CUBIC cleared mouse tissues and whole embryos were embedded in hydrogels, stained using fluorescent small molecule dyes, labels and antibodies and successfully imaged using light sheet fluorescence microscopy. In conclusion, the high-water content, high refractive index hydrogels described in this study have a broad applicability to research that delves into pathophysiological processes by stabilising and protecting large and fragile samples.
Independent evolution of transcript abundance and gene regulatory dynamics
Authors: Krieger Gat , Lupo Offir , Levy Avraham A. , Barkai Naama 
Published: January 2020

AbstractChanges in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels, but providing limited information about variations in gene regulation. To close this gap, we profiled gene expression of related yeast species in hundreds of conditions, and used co-expression analysis to distinguish variations in transcription regulation from variations in expression levels or environmental perception. The majority of genes whose expression varied between the species maintained a conserved transcriptional regulation. Profiling the interspecific hybrid provided insights into the basis of variations, showed thattrans-varying alleles interact dominantly, and revealed complementation ofcis-variations by variations intrans. Our data suggests that gene expression diverges primarily through changes in promoter strength that do not alter gene positioning within the transcription network.
Lipid accumulation promotes scission of caveolae
Authors: Hubert Madlen , Larsson Elin , Gayathri Vegesna Naga Venkata , Ahnlund Maria , Johansson Annika I. , Moodie Lindon W. K. , Lundmark Richard 
Published: January 2020

ABSTRACTCaveolae, bulb-shaped invaginations of the plasma membrane (PM), show distinct behaviors of scission and fusion at the cell surface. Although it is known that caveolae are enriched in cholesterol and sphingolipids, exactly how lipid composition influences caveolae surface stability has not yet been elucidated. Accordingly, we inserted specific lipids into the PM of cells via membrane fusion and studied acute effects on caveolae dynamics. We demonstrate that cholesterol and glycosphingolipids specifically accumulate in caveolae, which decreases their neck diameter and drives their scission from the cell surface. The lipid-induced scission was counteracted by the ATPase EHD2. We propose that lipid accumulation in caveolae generates an intrinsically unstable domain prone to scission if not balanced by the restraining force of EHD2 at the neck. Our work advances the understanding of how lipids contribute to caveolae dynamics, providing a mechanistic link between caveolae and their ability to sense the PM lipid composition.SUMMARYCaveolae serve as mechanoprotectors and membrane buffers but their specific role in sensing plasma membrane lipid composition remains unclear. Hubert et al. show that cholesterol and glycosphingolipids accumulate in caveolae and drive subsequent scission from the cell surface. These results provide new insight into how lipids contribute to budding and scission of membrane domains in cells.