bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome assembly and annotation ofCorallium rubrum: a Mediterranean coral threatened by overharvesting and climate change
Authors: Ledoux Jean-Baptiste , Gomez-Garrido Jessica , Cruz Fernando , Camara Ferreira Francisco , Matos Ana , Sarropoulou Xenia , Ramirez-Calero Sandra , Aurelle Didier , Lopez-Sendino Paula , Grayson Natalie , Moore Bradley , Antunes Agostinho , Aguilera Laura , Gut Marta , Salces-Ortiz Judit , Fernández Rosa , Linares Cristina , Garrabou Joaquim , Alioto Tyler 
Published: July 2024

AbstractReference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral,Corallium rubrum(Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management ofC. rubrum.Significance StatementThe Mediterranean red coral,Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly,C. rubrumis increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated toC. rubrum.
Insights into theforagingGene’s Influence on Mating Investments of MaleDrosophila
Authors: Li Wengjing , Huang Yongwen , Kim Woo Jae 
Published: July 2024

ABSTRACTTheforaginggene is a key genetic factor that modulates social behavior in insects, primarily by governing the trade-off between individual foraging and group-related activities. It has been associated with various behaviors associated with food search and resource exploitation, thereby playing a crucial role in determining the efficiency of foraging and the overall success of the collective. In this study, we investigate the critical role of theforaginggene in mediating complex interval timing behaviors, particularly mating duration, in the fruit flyDrosophila melanogaster. By examining two distinct variant phenotypes, rover and sitter, we observe specific deficiencies in longer (LMD) and shorter mating duration (SMD) behaviors, respectively, suggesting the gene’s crucial influence on these interval timing mechanisms. Utilizing single-cell RNA sequencing and knockdown experiments, we identify the gene’s significant expression in key neurons involved in learning and memory. However, its impact on mating duration is not observed in these brain regions. Instead, our data reveal the gene’s crucial role in specific neurons expressing Pdfr, a critical regulator of circadian rhythms. Furthermore, the study uncovers sexually dimorphic expression patterns in the brain and highlights the necessity of the gene’s dosage in specific cell populations within the ellipsoid body for normal mating duration. These findings underscore theforaginggene’s pivotal role in mediating complex interval timing behaviors inDrosophila, providing valuable insights into the intricate interplay between genetics, environment, and behavior. This research contributes to a deeper understanding of the genetic and neural mechanisms underlying complex interval timing behaviors, with broader implications for unraveling the function offoraginggene.
Predicting future patterns of land cover from climate projections using machine learning
Authors: Stepinski Tomasz F. 
Published: July 2024

AbstractVegetation plays a crucial role in the Earth’s system, and its characteristics are strongly influenced by climate. Previous studies have investigated the climate-vegetation relationship, often attempting to predict vegetation types based on climate data. Many of them have utilized biome types as proxies for different vegetation forms. Biomes, although widely used, are not always optimal for this task. They are broadly defined, a priori linked to climate, and subject to change over time. This study proposes a novel approach by using the local composition of land cover (LC) categories as descriptors of vegetation types and examines the feasibility of modeling such compositions based on climate data. The investigation focuses on the Sahel region of Africa, which is tessellated into 5 × 5 km square tiles, serving as the basic units of analysis. The independent variable comprises a set of bioclimatic variables assigned to each tile, while the dependent variable consists of shares of each LC category within the tile. The modeling framework involves a set ofnregressions, one for each LC category. The K-nearest neighbors (KNN) algorithm is employed to ensure that interdependently predicted shares sum up to 100%. The model’s performance is validated using 2010 data, where both climate and LC information are available. The mean absolute value of residuals ranges from 1% to 11%, depending on the LC category. Subsequently, future predictions of LC patterns are made for 2040, 2070, and 2100 using climate projections under IPCC scenarios 370 and 585. A novel visualization technique called synthetic landscape is introduced to visually compare the temporal sequence of predicted LC maps from 2010 to 2100 with similar sequences of biome maps and Köppen-Geiger climate type maps. This comparison highlights overall similarities across all sequences but also reveals some significant differences.
Optimum Push-off During Uneven Walking for Just-in-Time Strategy; Delayed Push-off Exertion is Mechanically Costly
Authors: Hosseini-Yazdi Seyed Saleh 
Published: July 2024

AbstractIt is shown that step mechanical work roughly describes walking energetics, and optimal walking economy is achieved by pre-emptive step work. We suggest this is also true for uneven walking. Using a simple powered walking model, we estimated the preferred pre-emptive push-offs to cover the entire step energy. The maximum push-off is exerted when the subsequent heel-strike dissipation is zero, setting an upper bound for step-up amplitude achievable with pre-emptive push-off. For instance, at a walking speed of 1.4 m · s−1, the maximum step-up is 0.106 m. Conversely, for any step-up amplitude, there is a minimum walking speed. For a step-up height (Δh) of 0.06 m, the minimum walking speed is 1.06 m · s−1. The importance of pre-emptive push-off and optimal timing of push-off and collision is widely discussed. However, there are cases where this timing is undermined, such as during uneven walking, necessitating post-transition mechanical energy compensation. The ankle (via delayed push-off) or hip can provide mid-flight energy, but no mechanical determinant prefers one source over the other. Our modeling demonstrates that delayed push-off entails mechanical energy waste, likely converted to heat by stretching the stance leg. This stretch may also release energy stored during the heel-strike (e.g., in the Achilles tendon), exacerbating the required mechanical work performance in the subsequent step transition. Hence, we propose that during the double support phase, when the stance leg is switched, hip actuation becomes mechanically preferable. Physiological observations also support our proposition.
Grape extract and resveratrol mitigate sleep fragmentation, Aβ accumulation, and abnormal neuronal excitability in aDrosophilamodel of Alzheimer’s disease
Authors: Yu Ziqi , Xu Yangkun , Ping Yong 
Published: July 2024

AbstractConsumption of red wine and grape extracts may offer a range of health benefits, largely attributable to the grapes’ rich content of vitamins, fiber, and antioxidant compounds, such as polyphenols. To determine if resveratrol (RES) present in grape extracts is responsible for these benefits, we conducted a study on the effects of red grape skin extract (GSKE), seed extract (GSEE), and RES on sleep patterns, amyloid-beta (Aβ) deposition, neuronal excitability, and lifespan in aDrosophilamodel expressing Aβ42. Aβ42 flies experienced significant sleep fragmentation at night, yet their overall sleep duration was unaffected. Dietary GSKE significantly enhanced sleep duration and mitigated sleep fragmentation in these flies, whereas GSEE only increased the duration of sleep bouts during the day. RES demonstrated a similar effect, albeit to a lesser extent compared to GSKE. All three dietary interventions led to a reduction in Aβ42 levels and an extension of the lifespan in Aβ42 flies, with GSEE showing the least pronounced effects. Furthermore, GSEE and RES were able to reverse the hyperexcitability of mushroom body neurons (MBNs) caused by Aβ42 expression. These results suggest that GSKE and RES are potent promoters of sleep and have the potential to ameliorate sleep disturbances. Additionally, the study highlights that other bioactive component in GSKE, beyond RES, may contribute to its diverse pharmacological activities, which could differ from those of GSEE or RES alone. This underscores the multifaceted nature of grape extracts and their potential therapeutic applications in addressing sleep disorders and neurodegenerative conditions associated with Aβ deposition.
Large-Scale Maps of Altered Cortical Dynamics in Early-Stage Psychosis Are Related to GABAergic and Glutamatergic Neurotransmission
Authors: Arazi Ayelet , Toso Alessandro , Grent-‘t-Jong Tineke , Uhlhaas Peter J. , Donner Tobias H. 
Published: July 2024

AbstractPsychotic disorders present a challenge for research and clinical practice. Their pathogenesis is poorly understood, symptoms vary widely between patients, and there is a lack of objective biomarkers. Evidence points to a distributed nature of the underlying synaptic alterations in the cerebral cortex. Using magnetoencephalography source imaging, we mapped alterations of neural population dynamics in psychosis across the human cortex. Individuals with early-stage psychosis exhibited characteristic patterns of changes in neural dynamics, in opposite directions for different cortical areas. These patterns were similar for first-episode psychosis and clinical high-risk for psychosis. Different components of these large-scale patterns resembled the effects produced in the healthy brain by pharmacological manipulations of either GABA-A or glutamate (NMDA) receptors. The expression of the GABA-A-component in first-episode psychosis patients was related to positive symptoms, and the expression of the NMDA-component to negative symptoms. Our study opens a window on the large-scale pathophysiology of psychosis.TeaserCortex-wide changes in neural dynamics in early-stage psychosis relate to GABA-A or NMDA receptors and clinical symptoms.
A Mathematical Exploration of SDH-b Loss in Chromaffin Cells
Authors: Vera-Sigüenza Elías , Rana Himani , Nashebi Ramin , Cloete Ielyaas , Kl’učková Katarína , Spill Fabian , Tennant Daniel A. 
Published: July 2024

AbstractThe succinate dehydrogenase (SDH) is a four-subunit enzyme complex (SDH-a, SDH-b, SDH-c, and SDH-d) central to cell carbon metabolism. The SDH bridges the tricarboxylic acid cycle to the electron transport chain. A pathological loss of the SDH-b subunit leads to a cell-wide signalling cascade that shifts the cell’s metabolism into a pseudo-hypoxic state akin to the so-called Warburg effect (or aerobic glycolysis). This trait is a hallmark of phaeochromocytomas, a rare tumour arising from chromaffin cells; a type of cell that lies in the medulla of the adrenal gland.In this study, we leverage the insights from a mathematical model constructed to underpin the metabolic implications of SDH-b dysfunction in phaeochromocytomas. We specifically investigate why chromaffin cells seemingly have the ability to maintain electron transport chain’s (ETC) Complex I function when confronted with the loss of the SDH-b subunit while other cells do not. Our simulations indicate that retention of Complex I is associated with cofactor oxidation, which enables cells to manage mitochondrial swelling and limit the reversal of the adenosine triphosphate (ATP) synthase, supporting cell fitness, without undergoing lysis. These results support previous hypotheses that point at mitochondrial proton leaks as a critical factor of future research. Moreover, the model asserts that control of the proton gradient across the mitochondrial inner membrane is rate-limiting upon fitness management of SDH-b deficient cells.
Generation and application of novel hES cell reporter lines for the differentiation and maturation of hPS cell-derived islet-like clusters
Authors: Zanfrini Elisa , Bandral Manuj , Jarc Luka , Ramirez-Torres Maria Alejandra , Pezzolla Daniela , Kufrin Vida , Rodriguez-Aznar Eva , Avila Ana Karen Mojica , Cohrs Christian , Speier Stephan , Neumann Katrin , Gavalas Anthony 
Published: July 2024

ABSTRACTThe significant advances in the differentiation of human pluripotent stem (hPS) cells into pancreatic endocrine cells, including functional β-cells, have been based on a detailed understanding of the underlying developmental mechanisms. However, the final differentiation steps, leading from endocrine progenitors to mono-hormonal and mature pancreatic endocrine cells, remain to be fully understood and this is reflected in the remaining shortcomings of the hPS cell-derived islet cells (SC-islet cells), which include a lack of β-cell maturation and variability among different cell lines. Additional signals and modifications of the final differentiation steps will have to be assessed in a combinatorial manner to address the remaining issues and appropriate reporter lines would be useful in this undertaking.Here we report the generation and functional validation of human pluripotent stem cell reporter lines that can monitor the generation of INS+and GCG+cells and their resolution into mono-hormonal cells (INSeGFP, INSeGFP/ GCGmCHERRY) as well as β-cell maturation (INSeGFP/ MAFAmCHERRY) and function (INSGCaMP6). The reporter hPS cell lines maintained strong and widespread expression of pluripotency markers and differentiated efficiently into definitive endoderm and pancreatic progenitor (PP) cells. PP cells from all lines differentiated efficiently into islet cell clusters that robustly expressed the corresponding reporters and contained glucose-responsive, insulin-producing cells.To demonstrate the applicability of these hES cell reporter lines in a high-content live imaging approach for the identification of optimal differentiation conditions, we adapted our differentiation procedure to generate SC-islet clusters in microwells. This allowed the live confocal imaging of multiple SC-islets for a single condition and, using this approach, we found that the use of the N21 supplement in the last stage of the differentiation increased the number of monohormonal β-cells without affecting the number of α-cells in the SC-islets.The hPS cell reporter lines and the high-content live imaging approach described here will enable the efficient assessment of multiple conditions for the optimal differentiation and maturation of SC-islets.
Human FASTK preferentially binds single-stranded and G-rich RNA
Authors: Dawidziak Daria M. , Dzadz Dawid A. , Kuska Mikołaj I. , Kanavalli Madhuri , Klimecka Maria M. , Merski Matthew , Bandyra Katarzyna J. , Górna Maria W. 
Published: July 2024

AbstractFas-activated serine/threonine kinase (FASTK) is the founding member of the FASTKD protein family, which was shown to regulate the fate of mRNA molecules on multiple levels. The mitochondrial variant of FASTK co-localizes with mitochondrial RNA granules and regulates degradation of mitochondrial mRNAs, whereas the cytoplasmic and nuclear forms of FAST are involved in regulation of alternative splicing, cytoplasmic RNA granule formation and mRNA translation. Despite these multiple roles of FASTK in mRNA biology, the exact rules of RNA recognition by this protein remained undetermined. Here, we demonstrate direct RNA binding by purified human FASTK and show its preference for single-stranded G-rich sites and RNA G-quadruplexes. Addition of FASTK alone was sufficient to achieve protection of mitochondrial mRNAs from degradation by the degradosome. Structural characterization by SAXS showed that FASTK in solution is a monomer with an extended conformation. Point mutagenesis studies supported the structural predictions of an exposed RNA-binding interface in the central helical region, preceded by a smaller, flexibly attached, helical N-terminal domain. We provide the first such extensivein vitrocharacterization of the RNA binding properties for a representative of the FASTKD protein family, and suggest how these intrinsic properties may underly FASTK function in mRNA metabolism.
Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations
Authors: Conte Mattia , Abraham Alex , Esposito Andrea , Yang Liyan , Gibcus Johan H. , Parsi Krishna M. , Vercellone Francesca , Fontana Andrea , Pierno Florinda Di , Dekker Job , Nicodemi Mario 
Published: July 2024

AbstractHere, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb wide genomic region encompassing the humanLTN1gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in-silico the ensemble of single-moleculeLTN13D structures, which we benchmark against recent in-situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.
Cortical layer-specific and cell type-specific dendritic expression of Arc (Arg 3.1) in anin vitromodel of slow-wave sleep
Authors: Hartnell Iain J. , Simon Anna , Hall Stephen P. , Ducotterd Fiona , Whittington Miles A. , Chawla Sangeeta 
Published: July 2024

AbstractAn abundance of evidence shows sleep homeostatically regulates synaptic plasticity and memory consolidation but the underlying molecular regulators of this important function of sleep have been difficult to directly elucidate. Arc is an immediate early gene that has a fundamental role in several aspects of synaptic plasticity including regulation and maintenance. Using a physiological brain slice model of slow-wave sleep, here we show that Arc protein has a characteristic spatial and cell-type specific distribution during persistent sleep-related delta oscillations in neocortical slices, which may correlate with aspects of sleep-dependent regulation of synaptic plasticity in cortical regions. In delta oscillating slices, Arc is highly expressed in layer 2/3 dendrites of the primary and secondary association cortex and this dendritic localisation is specific to intrinsically bursting cells (IB) whose cell bodies are in layer 5. Moreover, Arc immunopositive dendrites are clustered together arranged in a quasi hexagonal arrangement with a spacing of ∼ 50 µm between clusters. The cytoarchitectural distribution of Arc across the association cortex has implications for the mechanisms of sleep and for the synaptic homeostasis hypothesis regarding the function of sleep.
Constraining MeV to 10 GeV Majorons by big bang nucleosynthesis
Authors: Chang Sanghyeon , Ganguly Sougata , Jung Tae Hyun , Park Tae-Sun , Shin Chang Sub 
Published: July 2024

We estimate the big bang nucleosynthesis (BBN) constraint on the majoron in the mass range between 1 MeV to 10 GeV which dominantly decays into the standard model neutrinos. When the Majoron lifetime is shorter than 1 sec, the injected neutrinos mainly heat up background plasma, which alters the relation between photon temperature and background neutrino temperature. For a lifetime longer than 1 sec, most of the injected neutrinos directly contribute to the protons-to-neutrons conversion. In both cases, deuterium and helium abundances are enhanced, while the constraint from the deuterium is stronger than that from the helium. Li7 abundance gets decreased as a consequence of additional neutrons, but the parameter range that fits the observed Li7 abundance is excluded by the deuterium constraint. We also estimate other cosmological constraints and compare them with the BBN bound.

Published by the American Physical Society
2024
Derivation of the nonequilibrium generalized Langevin equation from a time-dependent many-body Hamiltonian
Authors: Netz Roland R. 
Published: July 2024

It has become standard practice to describe systems that remain far from equilibrium even in their steady state by Langevin equations with colored noise which is chosen independently from the friction contribution. Since these Langevin equations are typically not derived from first-principle Hamiltonian dynamics, it is not clear whether they correspond to physically realizable scenarios. By exact Mori projection in phase space we derive the nonequilibrium generalized Langevin equation (GLE) for an arbitrary phase-space dependent observable A from a generic many-body Hamiltonian with a time-dependent external force h(t) acting on the same observable A. This is the same Hamiltonian from which the standard fluctuation-dissipation theorem is derived, which reflects the generality of our approach. The observable A could, for example, be the position of an atom, of a molecule or of a macroscopic object, the distance between two such entities or a more complex phase-space function such as the reaction coordinate of a chemical reaction or of the folding of a protein. The Hamiltonian could, for example, describe a fluid, a solid, a viscoelastic medium, or even a turbulent inhomogeneous environment. The GLE, which is a closed-form equation of motion for the observable A, is obtained in explicit form to all orders in h(t) and without restrictions on the type of many-body Hamiltonian or the observable A. If the dynamics of the observable A corresponds to a Gaussian process, the resultant GLE has a similar form as the equilibrium Mori GLE, and in particular the friction memory kernel is given by the two-point autocorrelation function of the sum of the complementary and the external force h(t). This is a nontrivial and useful result, as many observables that characterize nonequilibrium systems display Gaussian statistics. For non-Gaussian nonequilibrium observables correction terms appear in the GLE and in the relation between the force autocorrelation and the friction memory kernel, which are explicitly given in terms of cubic correlation functions of A. Interpreting the external force h(t) as a stochastic process, we derive nonequilibrium corrections to the fluctuation-dissipation theorem and present methods to extract all GLE parameters from experimental or simulation time-series data, thus making our nonequilibrium GLE a practical tool to study and model general nonequilibrium systems.

©2024 American Physical Society
2024
American Physical Society