bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell RNA-seq differential expression tests within a sample should use pseudo-bulk data of pseudo-replicates
Authors: Hafemeister Christoph , Halbritter Florian 
Published: March 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) has become a standard approach to investigate molecular differences between cell states. Comparisons of bioinformatics methods for the count matrix transformation (normalization) and differential expression (DE) analysis of these data have already highlighted recommendations for effective between-sample comparisons and visualization. Here, we examine two remaining open questions: (i) What are the best combinations of data transformations and statistical test methods, and (ii) how do pseudo-bulk approaches perform in single-sample designs? We evaluated the performance of 343 DE pipelines (combinations of eight types of count matrix transformations and ten statistical tests) on simulated and real-world data, in terms of precision, sensitivity, and false discovery rate. We confirm superior performance of pseudo-bulk approaches without prior transformation. For within-sample comparisons, we advise the use of three pseudo-replicates, and provide a simple R packageDElegateto facilitate application of this approach.
Identification of Differentially Expressed Genes in Wheat NILs in Response to Leaf Rust Infection using In Silico Analysis
Authors: Kumar Rahul 
Published: March 2023

AbstractIn this study, the molecular basis of leaf rust resistance was investigated by examining the differential gene expression of wheat cultivar Thatcher, both with and without a leaf rust resistance gene, in response to rust infection. unigenes/ESTs databases were utilized belonging to three near-isogenic lines (NILs) of Thatcher, including Thatcher, Thatcher + Lr10, and Thatcher + Lr1, to identify differentially expressed unigenes (DEUs) in response to leaf rust. Sixty-eight DEUs were identified using a data mining tool called Digital Differential Display (DDD). Among these DEUs were specific unigenes associated with Lr1 and/or Lr10-mediated resistance, as well as unigenes expressed exclusively in compatible interactions. Our results suggest that photosynthesis, lignin, and antifungal proteins play a role in the leaf rust resistance mechanism, as indicated by the overexpression of Ribulose-1,5-bisphosphate carboxylase/oxygenase, caffeic acid O-methyltransferase, and Glutathione S-transferase unigenes, respectively. Our findings demonstrate both common and distinctive genetic pathways involved in rust resistance in the Lr1 and Lr10 NILs. The expression of most DEUs was found to be high in leaves, moderate in sheath, stem, and inflorescence, and low in seed, root, flower, crown, callus, and cell culture, indicating their role in leaf rust. Using high-throughput microarray gene expression data, a subset of DEUs was validated, and as a result, eleven unigenes were mapped to deletion bins on individual wheat chromosomes. These key genes may be used as molecular markers for genome editing, which could facilitate the development of leaf rust-resistant wheat cultivars.
Distinct sources and behavioral correlates of macaque motor cortical low and high beta
Authors: Nougaret Simon , López-Galdo Laura , Caytan Emile , Poitreau Julien , Barthelemy Frederic V , Kilavik Bjørg Elisabeth 
Published: March 2023

SUMMARYHIGHLIGHTSThe low beta rhythm is dominant in M1 and the high beta rhythm in PMdThe beta rhythms correlate with task-instructed and uninstructed behaviorLow beta reflects movement preparation and spontaneous postural dynamicsHigh beta reflects temporal task prediction and dynamical visuospatial attentionLow and high beta frequency rhythms were observed in the motor cortex, but their respective sources and behavioral correlates remain unknown. We studied local field potentials during pre-cued reaching behavior in macaques. They contained a low beta band (<20Hz) dominant in primary motor cortex and a high beta band (>20Hz) dominant in dorsal premotor cortex. Low beta correlated positively with reaction time from visual cue onset, and negatively with uninstructed hand postural micro-movements throughout the trial. High beta reflected temporal task prediction, with selective modulations before and during cues, which were enhanced in moments of increased focal attention when the gaze was on the work area. This double-dissociation in sources and behavioral correlates of motor cortical low and high beta, with respect to both task-instructed and spontaneous behavior, reconciles the largely disparate roles proposed for the beta rhythm, by suggesting band-specific roles in both movement control and spatio-temporal attention.
A kernel integral method to remove biases in estimating trait turnover
Authors: Latombe Guillaume , Boittiaux Paul , Hui Cang , McGeoch Melodie 
Published: March 2023

AbstractTrait diversity, including trait turnover, that differentiates the roles of species and communities according to their functions, is a fundamental component of biodiversity. Accurately capturing trait diversity is crucial to better understand and predict community assembly, as well as the consequences of global change on community resilience. Existing methods to compute trait turnover have limitations. Trait space approaches based on minimum convex polygons only consider species with extreme trait values. Tree-based approaches using dendrograms consider all species but distort trait distance between species. More recent trait space methods using complex polytopes try to harmonise the advantages of both methods, but their current implementation have mathematical flaws.We propose a new kernel integral method (KIM) to compute trait turnover, based on the integration of kernel density estimators (KDEs) rather than using polytopes. We explore how this difference and the computational aspects of the KDE computation can influence the estimates of trait turnover. We compare our novel method to existing ones using justified theoretical expectations for a large number of simulations in which we control the number of species and the distribution of their traits. We illustrate the practical application of KIM using plant species introduced to the Pacific Islands of French Polynesia.Analyses on simulated data show that KIM generates results better aligned with theoretical expectations than other methods and is less sensitive to the total number of species. Analyses for French Polynesia data also show that different methods can lead to different conclusions about trait turnover, and that the choice of method should be carefully considered based on the research question.Mathematical aspects for computing trait turnover are crucial as they can have important effects on the results and therefore lead to different conclusions. Our novel kernel integral method generates values that better reflect the distribution of species in the trait space than other existing methods. We therefore recommend using KIM in future studies on trait turnover. In contrast, tree-based approaches should be kept for phylogenetic diversity, as phylogenetic trees will then reflect the constrained speciation process.
Synthesis and validation of click-modified of NOD1/2 agonists
Authors: Bharadwaj Ravi , Anonick Madison V. , Mashayekh Siavash , Brown Ashley , Wodzanowski Kimberly A. , Okuda Kendi , Silverman Neal , Grimes Catherine L. 
Published: March 2023

AbstractNOD1 and NOD2 sense small bacterial peptidoglycan fragments often called muropeptides. These muropeptides include iE-DAP and MDP, the minimal agonists for NOD1 and NOD2, respectively. Here, we synthesized and validated alkyne-modified muropeptides, iE-DAP-Alk and MDP-Alk, for use in click-chemistry reactions. While it has long been known that many cell types respond to extracellular exposure to muropeptides, it is unclear how these innate immune activators access their cytosolic innate immune receptors, NOD1 and NOD2. The subcellular trafficking and transport mechanisms by which muropeptides access these cytosolic innate immune receptors are a major gap in our understanding of these critical host responses. The clickchemistry-enabled agonists developed here will be particularly powerful to decipher the underlying cell biology and biochemistry of NOD1 and NOD2 innate immune sensing.
Long-term evolution of proliferating cells using the eVOLVER platform
Authors: García-Ruano Daniel , Jain Akanksha , Heins Zachary J , Wong Brandon G , Wolle Ezira Yimer , Khalil Ahmad S , Coudreuse Damien 
Published: March 2023

ABSTRACTExperimental evolution using fast-growing unicellular organisms is a unique strategy for deciphering the principles and mechanisms underlying evolutionary processes as well as the architecture and wiring of basic biological functions. Over the past decade, this approach has benefited from the development of powerful systems for the continuous control of the growth of independently evolving cultures. While the first devices compatible with multiplexed experimental evolution remained challenging to implement and required constant user intervention, the recently-developed eVOLVER framework represents a fully automated closed-loop system for laboratory evolution assays. However, it remained difficult to maintain and compare parallel evolving cultures in tightly controlled environments over long periods of time using eVOLVER. Furthermore, a number of tools were lacking to cope with the various issues that inevitably occur when conducting such long-term assays. Here we present a significant upgrade of the eVOLVER framework, providing major modifications of the experimental methodology, hardware and software as well as a new standalone protocol. Altogether, these adaptations and improvements make the eVOLVER a versatile and unparalleled setup for long-term experimental evolution.
Spatiotemporal transcriptomic map of ischemic brain injury
Authors: Zucha Daniel , Abaffy Pavel , Kirdajova Denisa , Jirak Daniel , Anderova Miroslava , Kubista Mikael , Valihrach Lukas 
Published: March 2023

AbstractThe role of non-neuronal cells in the resolution of cerebral ischemia remains to be fully understood. To decode key cellular processes that occur after ischemia, we performed spatial and single-cell transcriptomic profiling of mouse brain tissue during the first week of injury. Cortical gene expression was severely disrupted, being defined by inflammation and cell death in the lesion core, and glial scar formation on the periphery. For each of the three major glial populations, an inflammatory-responsive state, resembling the reactive states observed in neurodegenerative contexts, was documented. The recovered spectrum of ischemia-induced oligodendrocyte states supports the emerging hypothesis that oligodendrocytes actively respond to and modulate the neuroinflammatory stimulus. Thus, we present a landmark transcriptomic dataset that provides a comprehensive view of spatiotemporal organization of processes in the post-ischemic brain and documents the conservation of glial response in CNS pathology.
Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography
Authors: Rahmani Shahrokh , Jafree Daniyal J , Lee Peter D , Tafforeau Paul , Brunet Joseph , Nandanwar Sonal , Jacob Joseph , Bellier Alexandre , Ackermann Maximilian , Jonigk Danny D , Shipley Rebecca J , Long David A , Walsh Claire L 
Published: March 2023

ABSTRACTThe architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.
SimuCell3D: 3D Simulation of Tissue Mechanics with Cell Polarization
Authors: Runser Steve , Vetter Roman , Iber Dagmar 
Published: March 2023

AbstractThe 3D organisation of cells determines tissue function and integrity, and changes dramatically in development and disease. Cell-based simulations have long been used to define the underlying mechanical principles. However, large computational costs have so far limited simulations to either simplified cell geometries or small tissue patches. Here, we present SimuCell3D, a highly efficient open-source program to simulate large tissues in 3D with subcellular resolution, growth, proliferation, extracellular matrix, fluid cavities, nuclei, and non-uniform mechanical properties, as found in polarised epithelia. Spheroids, vesicles, sheets, tubes, and other tissue geometries can readily be imported from microscopy images and simulated to infer biomechanical parameters. Doing so, we show that 3D cell shapes in layered and pseudostratified epithelia are largely governed by a competition between surface tension and intercellular adhesion. SimuCell3D enables the large-scalein silicostudy of 3D tissue organization in development and disease at an unprecedented level of detail.
The Primacy of Temporal Dynamics in Driving Spatial Self-organization of Soil Redox Patterns
Authors: Dong Xiaoli , Richter Daniel de , Thompson Aaron , Wang Junna 
Published: March 2023

AbstractIn this study, we investigate mechanisms that generate regularly-spaced, iron banding in upland soils. These redoximorphic features appear in soils worldwide, but their genesis has been heretofore unresolved. Upland soils are highly redox dynamic, with significant redox fluctuations driven by rainfall, groundwater changes, or irrigation. Pattern formation in these highly dynamic systems provides an opportunity to investigate the temporal dimension of spatial self-organization, which is not often explored. By comparing multiple alternative mechanisms, we find that regular redox patterns in upland soils are formed by coupling two sets of scale-dependent feedbacks (SDF), the general framework underlying Turing instability. The first set of SDF is based on clay aggregation and disaggregation. The second set is realized by threshold-dependent, negative root responses to aggregated crystalline Fe(III). The former SDF amplifies Fe(III) aggregation and crystallinity to trigger the latter SDF. Neither set of SDF alone is sufficient to reproduce observed patterns. Redox oscillations driven by environmental variability play an indispensable role in pattern formation. Environmental variability creates a range of conditions at the same site for various processes in SDF to occur, albeit in different temporal windows of differing durations. In effect, environmental variability determines mean rates of pattern-forming processes over the timescale relevant to pattern formation and modifies the likelihood that pattern formation will occur. As such, projected climate change might significantly alter many self-organized systems, as well as the ecological consequences associated with the striking patterns they present. This temporal dimension of pattern formation is previously unreported and merits close attention.Statement of SignificanceIron reactions create redox features in soils around the world. This study investigates mechanisms forming regularly-spaced iron stripes in upland soils. Upland soil redox conditions, driven by environmental variability, are highly dynamic. We show that two sets of scale-dependent feedbacks are coupled to form redox patterns and environmental variability plays a critical role in both. Significantly, environmental variability creates opportunities for various pattern-forming processes to occur at the same site in different temporal windows and determines mean process rates over the timescale relevant to pattern formation. Hence, environmental variability dictates the likelihood of pattern formation. Such a critical role of the temporal dimension in spatial self-organization has rarely been reported and has great potential for application in other self-organized ecosystems.
Bite force transmission and mandible shape in grasshoppers, crickets, and allies is largely dependent on phylogeny, not diet
Authors: Edel Carina , Rühr Peter T. , Frenzel Melina , van de Kamp Thomas , Faragó Tomáš , Hammel Jörg U. , Wilde Fabian , Blanke Alexander 
Published: March 2023

AbstractAlthough organ systems evolve in response to many intrinsic and extrinsic factors, frequently one factor has a dominating influence. For example, mouthpart shape and mechanics are thought to correlate strongly with aspects of the diet. Within insects, this paradigm of a shape-diet connection is advocated for decades but the relationship has so far never been quantified and is mostly based on qualitative observations. Orthoptera (grasshoppers, crickets, and allies) are a prominent case, for which mandible shape and dietary preference are thought to correlate strongly and even lead to predictions of feeding preferences. Here, we analysed mandible shape, biting efficiency, and their potential correlation with dietary categories in a phylogenetic framework for a broad sampling of several hundred extant Orthoptera covering nearly all families. The mandibular mechanical advantage was used as a descriptor of gnathal edge shape and bite force transmission efficiency. We aimed to understand how mandible shape is linked to biting efficiency and diet, and how these traits are influenced by phylogeny and allometry. The investigation reveals that feeding ecology is not the unequivocal predictor of mandible shape that it was assumed to be. There is a strong phylogenetic signal suggesting that phylogenetic history does have a much more prevalent influence on gnathal edge shape and distal mechanical advantage, than, e.g., feeding guilds or the efficiency of the force transmission to the food. Being ancestrally phytophagous, Orthoptera evolved in an environment with abundant food sources so that selective pressures leading to more specialized mouthpart shapes and force transmission efficiencies were low.
The Role of Experience in Prioritizing Hippocampal Replay
Authors: Gorriz M. Huelin , Takigawa M. , Bendor D. 
Published: March 2023

SUMMARYDuring sleep, recent memories are consolidated, whereby behavioral episodes first encoded by the hippocampus get transformed into long-term memories. However, the brain cannot consolidate every experience and much like the triage of an emergency room, the hippocampus is hypothesized to give precedence to more important memories first, and deprioritize or even skip over less relevant memories if needed. Here we examine two factors that are postulated to influence this memory triage process- 1)repetition, arising from the number of times a behavioral episode is repeated,increasing the priority to consolidateand 2)familiarity, resulting from previously experiencing a similar behavioral episode, in turndecreasing the need for further consolidation. Recording from large ensembles of hippocampal place cells while rats ran repeated spatial trajectories, and afterwards during periods of sleep, we examined how these two factors influencedreplay, a hypothesized mechanism of consolidation involving the offline spontaneous reactivation of memory traces. We observed that during sleep, the rate of replay events for a given trackincreasedproportionally with the number of spatial trajectories run by the rat. In contrast to this, the rate of sleep replay eventsdecreasedif the rat was more familiar with the track, arising from previously running on the same track before its most recent sleep session. Furthermore, we find that thecumulative number of awakereplay events that occur during behavior, influenced by both the novelty and duration of an experience, predicts which memories are prioritized for sleep replay, and provides a more parsimonious mechanism for the selectively strengthening and triaging of memories.
Mrc1Claspinis essential for heterochromatin maintenance inSchizosaccharomyces pombe
Authors: Kawakami Kei , Ueno Yukari , Hayama Nao , Tanaka Katsunori 
Published: March 2023

AbstractHeterochromatin is a highly condensed chromatin structure that represses gene expression. In eukaryotes, maintenance of the heterochromatin structure during cell proliferation is essential for guaranteeing cell identity. However, how heterochromatin is maintained and transmitted to the daughter cells remains largely unknown. In this study, we constructed a reporter system to study the maintenance of heterochromatin in the subtelomeric region of the fission yeast,Schizosaccharomyces pombe. We demonstrated that once subtelomeric heterochromatin was established, it tended to be maintained as a metastable structure through cell proliferation. Using this system, we screened anS. pombegenome-wide gene deletion library and identified 57 factors required for the maintenance of subtelomeric heterochromatin. We focused on Mrc1Claspin, a mediator of DNA replication checkpoint. We found that Mrc1 maintains heterochromatin structure not only at the subtelomeres but also at other heterochromatic loci, such as the pericentromeres and mating-type regions. Furthermore, we showed that Mrc1 facilitates the hypoacetylation state of histone H3K14 by recruiting the Snf2/Hdac-containing Repressor Complex (SHREC), via physical interaction. In addition, depletion of Mst2, an H3K14 acetyltransferase, restored heterochromatin integrity inmrc1mutants. This is the first report to show a link between DNA replication factors and H3K14 deacetylation in heterochromatin.
mRNA capping enzyme exports to cytoplasm, localizes to stress granules and maintains cap homeostasis of the target mRNAs
Authors: Gayen Anakshi , Mukherjee Avik , Majumder Shubhra , Mukherjee Chandrama 
Published: March 2023

AbstractmRNA decapping is believed to trigger RNA degradation until the identification of cytoplasmic capping that has changed the epitome of RNA stability. Unlike nuclear capping machinery that includes RNA polymerase II bound mRNA Capping Enzyme (CE), N-7 RNA methyl transferase and RNMT activating protein RAM, cytoplasmic capping complex consist of cytoplasmic pool of CE (cCE) and N-7 RNA methyl transferase-RAM along with a few cytoplasmic proteins of various functions. Cytoplasmic capping has been shown to recap selective uncapped mRNAs and maintains cap homeostasis by a cyclic process of decapping and recapping. Thus, it acts as post-transcriptional nexus for the target transcripts. Our data show nuclear export of mammalian CE is regulated by Exportin1 (XPO1) pathway via a conserved Nuclear Export Signal sequence. In order to examine biological function of cCE, we show cCE forms granules during stress and majority of these granules co-localize with SGs. In order to identify how cCE regulates cap homeostasis during stress and recovery, we measured the cap status of specific cCE targeted mRNA transcripts along with non-targeted transcripts during non-stress, stress and recovery phase using Xrm1 susceptibility assay. Our data show cCE targeted mRNA transcripts lost their caps in stress condition when cCE is sequestered in granules. After removal of stress, when cCE is released, the cap status has been restored for these transcripts pointing towards the role of cCE in altering cap homeostasis and thus promoting cellular recovery from stress.