bluuebunny/crossref_metadata_2025_split huggingface dataset:
The most widespread phage in animals: Genomics and taxonomic classification of Phage WO
Authors: Bordenstein Sarah R. , Bordenstein Seth R. 
Published: November 2021

AbstractWolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to assign taxonomic classification of the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages that includes distinguishable genera of phage WO, a family of non-Wolbachia phages from aquatic environments, and an order that captures the collective relatedness of these viruses.
Digital twin predicting diet response before and after long-term fasting
Authors: Silfvergren Oscar , Simonsson Christian , Ekstedt Mattias , Lundberg Peter , Gennemark Peter , Cedersund Gunnar 
Published: November 2021

SummaryToday, there is great interest in diets proposing new combinations of macronutrient compositions and fasting schedules. Unfortunately, there is little consensus regarding the impact of these different diets, since available studies measure different sets of variables in different populations, thus only providing partial, non-connected insights. We lack an approach for integrating all such partial insights into a useful and interconnected big picture. Herein, we present such an integrating tool. The tool uses a novel mathematical model that describes mechanisms regulating diet-response and fasting metabolic fluxes, both for organ-organ crosstalk, and inside the liver. The tool can mechanistically explain and integrate data from several clinical studies, and correctly predict new independent data, including data from a new clinical study. Using this model, we can predict non-measured variables, e.g. hepatic glycogen and gluconeogenesis, and we can quantify personalized expected differences in outcome for any diet. This constitutes a new digital twin technology.
Correlative microscopy reveals the nanoscale morphology of E. coli-derived supported lipid bilayers
Authors: Bali Karan , Mohamed Zeinab , Pappa Anna-Maria , Daniel Susan , Kaminski Clemens F. , Owens Róisín M. , Mela Ioanna 
Published: November 2021

AbstractSupported lipid bilayers (SLBs) made from reconstituted lipid vesicles are an important tool in molecular biology. A breakthrough in the field has come with the use of vesicles derived from cell membranes to form SLBs. These new supported bilayers, consisting both of natural and synthetic components, provide a physiologically relevant system on which to study protein-protein interactions as well as protein-ligand interactions and other lipid membrane properties. These complex bilayer systems hold promise but have not yet been fully characterised in terms of their composition, ratio of natural to synthetic component and membrane protein content. Here, we describe a method of correlative atomic force (AFM) with structured illumination microscopy (SIM) for the accurate mapping of complex lipid bilayers that consist of a synthetic fraction and a fraction of lipids derived from Escherichia coli outer membrane vesicles (OMVs). We exploit the enhanced resolution and molecular specificity that SIM can offer to identify areas of interest in these bilayers and the atomic scale resolution that the AFM provides to create detailed topography maps of the bilayers. We are thus able to understand the way in which the two different lipid fractions (natural and synthetic) mix within the bilayers, quantify the amount of bacterial membrane incorporated in the bilayer and directly visualise the interaction of these bilayers with bacteria-specific, membrane-binding proteins. Our work sets the foundation for accurately understanding the composition and properties of OMV-derived SLBs and establishes correlative AFM/ SIM as a method for characterising complex systems at the nanoscale.
The Human Eye Transcriptome Atlas: A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue
Authors: Wolf Julian , Boneva Stefaniya , Schlecht Anja , Lapp Thabo , Auw-Haedrich Claudia , Lagrèze Wolf , Agostini Hansjürgen , Reinhard Thomas , Schlunck Günther , Lange Clemens 
Published: November 2021

ABSTRACTThe applications of deep sequencing technologies in life science research and clinical diagnostics have increased rapidly over the last decade. Although fast algorithms for data processing exist, intuitive, portable solutions for data analysis are still rare. For this purpose, we developed a web-based transcriptome database, which provides a platform-independent, intuitive solution to easily explore and compare ocular gene expression of 100 diseased and healthy human tissue samples from 15 different tissue types collected at the Eye Center of the University of Freiburg. To ensure comparability of expression between different tissues, reads were normalized across all 100 samples. Differentially expressed genes were calculated between each tissue type to determine tissue-specific genes. Unsupervised analysis of all 100 samples revealed an accurate clustering according to different tissue types. Cluster analysis based on known cell type-specific marker genes allowed differentiation of respective tissues. Several tissue-specific marker genes were identified. These genes were involved in tissue- or disease-specific processes, such as myelination for the optic nerve, visual perception for retina, keratinocyte differentiation for conjunctival carcinoma, as well as endothelial cell migration for choroidal neovascularization membranes. The results are accessible at the Human Eye Transcriptome Atlas website at https://www.eye-transcriptome.com. In summary, this searchable transcriptome database enables easy exploration of ocular gene expression in healthy and diseased human ocular tissues without bioinformatics expertise. Thus, it provides rapid access to detailed insights into the molecular mechanisms of various ocular tissues and diseases, as well as the rapid retrieval of potential new diagnostic and therapeutic targets.
A multivariate view of cognitive performance reveals positive correlation in the Trinidadian Guppy (Poecilia reticulata)
Authors: Prentice Pamela M , Thorton Alex , Wilson Alastair J 
Published: November 2021

AbstractCognitive variation is common among-individuals and can be consistent across time and context. From an evolutionary perspective, among-individual variation is important as a pre-requisite for natural selection and adaptive evolution. Selection is widely hypothesized to favor high cognitive performance but directional selection should erode variation over time, how then is cognitive variation maintained? As selection does not act on traits in isolation, covariance among specific cognitive traits and/or other aspects of phenotype (e.g. personality) could result in fitness trade-offs that are important in shaping evolutionary dynamics. Here we test this using Trinidadian guppies (Poecilia reticulata), using a multivariate approach by characterising the correlation structure among task-specific cognitive performance measures and a personality trait. We estimate the among-individual correlation matrix (ID) in performance across three cognitive tasks; colour association learning task; motor learning task; reversal learning task, and the personality trait ‘boldness’ measured as emergence time from a shelter. We found no support for trade-offs among performance in these tasks. Nor do we find evidence of hypothesised speed-accuracy trade-offs within the association learning task. Rather we find strong positive correlation structure inID,with 57% of variation explained by the leading eigen vector. While noting that non-cognitive factors and assay composition may affect the structure ofID, we suggest our findings are consistent with theg-model of cognitive performance variation, in which a dominant axis of variation loads positively on all performance measures. Thus, we add to a growing body of support for general variation among individuals in animal cognitive ability.
No Correlation Between Pollen Fertility and Viability: Differential Measures of Male Gametophytic Fitness inCannabis sativaL.
Authors: Wizenberg Sydney B. , Dang Michelle , Campbell Lesley G. 
Published: November 2021

AbstractPollen grains are male gametophytes, an ephemeral haploid generation of plants, commonly engaging in competition for a limited supply of ovules. Since differential male fertility may influence the direction and pace of population evolution, the relative fitness of pollen is regularly estimated as either pollen viability, the proportion of pollen containing intact cytoplasm’s and regenerative nuclei, or pollen fertility, the frequency of pollen germinating under standardized conditions. Here, we estimated the relative fitness of pollen in a dioecious, wind-pollinated model system,Cannabis sativa, by characterizing pollen fertility and viability from multiple sires. Pollen fertility quickly declined within two weeks of anther dehiscence, and pollen stored under freezer conditions did not germinate regardless of storage time. In contrast, pollen viability declined slowly and persisted longer than the lifetime of a sporophyte plant under both room temperature and freezer conditions. Pollen samples that underwent both fertility and viability analysis displayed no significant correlation, implying researchers cannot predict pollen fertility from pollen viability, nor infer male gametophytic fitness from a single measure. Our work demonstrates two approaches to measure proxies of male fitness inC. sativa, and identifies new questions around what are valuable estimates of male fitness in plants.
Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species
Authors: Wilkerson Dustin G. , Taskiran Bircan , Carlson Craig H. , Smart Lawrence B. 
Published: November 2021

ABSTRACTWithin the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing six Salix species (S. viminalis, S. suchowensis, S. integra, S. koriyanagi, S. udensis, and S. alberti) to common male and female S. purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S. suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.
Parental environmental effects are common and strong, but unpredictable, in Arabidopsis thaliana
Authors: Latzel Vít , Fischer Markus , Groot Maartje , Gutzat Ruben , Lampei Christian , Ouborg Joop , Parepa Madalin , Schmid Karl , Vergeer Philippine , Zhang Yuanye , Bossdorf Oliver 
Published: November 2021

AbstractThe phenotypes of plants can be influenced by the environmental conditions experienced by their parents. In some cases, such parental effects have been found to be adaptive, which has led to much speculation about their ecological and evolutionary significance. However, there is still much uncertainty about how common and how predictable parental environmental effects really are. We carried out a comprehensive test for parental effects of different environmental stresses in the model plant Arabidopsis thaliana. We subjected plants of three Arabidopsis genotypes to a broad range of biotic or abiotic stresses, or combinations thereof, and compared their offspring phenotypes in a common environment. The majority of environmental stresses (16 out of 24 stress treatments) caused significant parental effects, in particular on plant biomass and reproduction, with positive or negative effects ranging from −35% to +38% changes in offspring fitness. The expression of parental effects was strongly genotype-dependent, with some effects only present in some genotypes but absent, or even in the opposite direction, in others. Parental effects of multiple environmental stresses were often non-additive, and their effects can thus not be predicted from what we know about the effects of individual stresses. Intriguingly, the direction and magnitude of parental effects were unrelated to the direct effects on the parents: some stresses did not affect the parents but caused substantial effects on offspring, while for others the situation was reversed. In summary, parental environmental effects are common and often strong in A. thaliana, but they are genotype-dependent and difficult to predict.SignificanceStress experienced by plants can alter the phenotypes of their offspring. To understand the ecological and evolutionary significance of such parental effects, we must know how common and how predictable they are. In a large experiment with Arabidopsis thaliana, we show that the majority of 24 environmental stresses cause significant, and often strong, positive or negative parental effects. However, we also find that parental effects are genotype-specific and unrelated to the direct effect of individual stresses, and that multiple stresses often act in non-additive ways across generations. Thus, parental effects appear to be common and strong, but difficult to predict. Our findings have important implications for the study of plant responses to environmental change, and the design of stress experiments.
FISHFactor: A Probabilistic Factor Model for Spatial Transcriptomics Data with Subcellular Resolution
Authors: Walter Florin C. , Stegle Oliver , Velten Britta 
Published: November 2021

AbstractMotivationFactor analysis is a widely used tool for unsupervised dimensionality reduction of high-throughput data sets in molecular biology, with recently proposed extensions designed specifically for spatial transcriptomics data. However, these methods expect (count) matrices as data input and are therefore not directly applicable to single molecule resolution data, which are in the form of coordinate lists annotated with genes and provide insight into subcellular spatial expression patterns. To address this, we here propose FISHFactor, a probabilistic factor model that combines the benefits of spatial, non-negative factor analysis with a Poisson point process likelihood to explicitly model and account for the nature of single molecule resolution data. In addition, FISHFactor shares information across a potentially large number of cells in a common weight matrix, allowing consistent interpretation of factors across cells and yielding improved latent variable estimates.ResultsWe compare FISHFactor to existing methods that rely on aggregating information through spatial binning and cannot combine information from multiple cells, and show that our method leads to more accurate results on simulated data. We demonstrate on a real data set that FISHFactor is able to identify major subcellular expression patterns and spatial gene clusters in a data-driven manner.Availability and ImplementationThe model implementation, data simulation and experiment scripts are available under https://www.github.com/bioFAM/FISHFactor.Contactb.velten@dkfz.de
The Effect of A1/A2 Reactive Astrocyte Expression on Hydrocephalus Shunt Failure
Authors: Khodadadei Fatemeh , Arshad Rooshan , Morales Diego M. , Gluski Jacob , Marupudi Neena I. , McAllister James P. , Limbrick David D. , Harris Carolyn A. 
Published: November 2021

AbstractUnderstanding the composition characteristics of the glial scar contributing to the high failure rate of neuroprosthetic devices implanted in the brain has been limited, to date, with the evaluation of cells, tissue, and biomarkers obstructing the implant. However, there remains a critical knowledge gap in gene expression profiles of the obstructing cells. This first-time study investigates the phenotypic expression specific to astrocyte scarring from those cells on hydrocephalus shunt surfaces at the time of failure, aimed at the development of therapeutic approaches to target reactive astrocytes for improved functional outcome. Recent evidence has indicated that the tissue obstructing shunts is over 80% inflammatory, with a more exaggerated astrocytic response. To understand how to mitigate the astrocyte immune response to shunts, we performed gene expression profiling of the C3 and EMP1 genes to quantify if astrocytes were classically activated and pro-inflammatory (A1) or alternatively activated and anti-inflammatory (A2), respectively. Shunt catheters were removed from patients at the time of failure and categorized by obstructed vs non-obstructed shunts. RNAscope fluorescent in situ hybridization and quantitative PCR analysis of the C3 and EMP1 expressed genes revealed that a heterogeneous mixed population of both the A1 and A2 reactive phenotype exist on the shunt surface. However, the number of A2 reactive astrocytes are significantly higher on obstructed shunts compared to A1 reactive astrocytes. ELISA data also confirmed higher levels of IL-6 for obstructed shunts involved in A2 reactive astrocyte proliferation and glial scar formation on the shunt surface. Since TNF-α and IL-1β propel resting astrocytes into an A2 reactive state, by simply blocking the secretion or action of these cytokines, astrocyte activation and attachment on obstructing shunts could be inhibited.
Prioritising the eradication of invasive species from island archipelagos with high reinvasion risk
Authors: Kumar Viney , Nunez Andre , Brown Kaitlyn , Agarwal Kanupriya , Hall Samuel , Bode Michael 
Published: November 2021

AbstractEradicating invasive species from islands is a proven method for safeguarding threatened and endangered species from extinction. Island eradications can deliver lasting benefits, but require large up-front expenditure of limited conservation resources. The choice of islands must therefore be prioritised. Numerous tools have been developed to prioritise island eradications, but none fully account for the risk of those eradicated species later returning to the island: reinvasion. In this paper, we develop a prioritisation method for island eradications that accounts for the complexity of the reinvasion process. By merging spatially-explicit metapopulation modelling with stochastic dynamic optimisation techniques, we construct a decision-support tool that optimises conservation outcomes in the presence of reinvasion risk. We applied this tool to two different case studies – rat (Rattus rattus) invasions in the Seaforth archipelago in New Zealand, and cane toad (Rhinella marina) invasions in the Dampier archipelago in Australia – to illustrate how state-dependent optimal policies can maximise expected conservation gains. In both case studies, incorporating reinvasion risk dramatically altered the optimal order of island eradications, and improved the potential conservation benefits. The increase in benefits was larger in Dampier than Seaforth (42% improvement versus 6%), as a consequence of both the characteristics of the invasive species, and the arrangement of the islands. Our results illustrate the potential consequences of ignoring reinvasion risk, and demonstrate that including reinvasion in eradication prioritisation can dramatically improve conservation outcomes.
Salidroside protects lipopolysaccharide-induced acute lung injury by regulating miR-145/ cytosolic phospholipase A2
Authors: Gu Lanxin , Shi Zhaoling 
Published: November 2021

AbstractSalidroside is one of the main active components from the root ofRhodiola rosea. Previous reports showed that salidroside exhibits anti-inflammatory properties, but the underlying mechanisms are not fully understood. Here, we observed the effects of salidroside on lipopolysaccharide (LPS)-induced acute lung injury (ALI) bothin vivoandin vitro. As revealed by survival study, salidroside reduced mortality of rats and prolonged their survival time. Meanwhile, salidroside significantly improved LPS-induced lung histopathologic changes, decreased lung wet-to-dry and lung-to-body weight ratios, inhibited lung myeloperoxidase (MPO) activity. Salidroside also suppressed the expression of cytosolic PLA2(cPLA2), the activity of phospholipase A2(PLA2) in LPS-treated rats and the metabolites of PLA2in bronchoalveolar lavage fluid (BALF), which was confirmed by results of prostaglandin E2(PGE2), leukotriene B4(LTB4) and thromboxane B2(TXB2) detection. And the expression of microRNA-145 in LPS-treated rats was up-regulated by salidroside. Besides, salidroside raised the level of miR-145and reduced PLA2activity in LPS-induced A549 cells in a concentration-dependent manner, which was obviously reversed by miR-145 inhibition. In conclusion, the current study demonstrated that salidroside exhibited a protective effect on LPS-induced ALI by inhibiting of the inflammatory response, which may involve in the up-regulation of miR-145 and the suppression of cPLA2.HighlightsSalidroside reduces acute lung injury by inhibiting the increment and metabolism of phospholipase A2;Salidroside inhibits LPS-induced PLA2 increase dependent on miR-145;The inhibitory effect of Salidroside on Phospholipases A2 provides a link between the identification of new targets and potential new therapeutic agents for the treatment of acute lung injury.