bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do sapling and adult demography explain beech predominance along environmental gradients in Central European forests?
Authors: Heiland Lukas , Kunstler Georges , Hülsmann Lisa 
Published: November 2023

AbstractUnderstanding how species abundances are driven by biotic interactions along environmental gradients is a fundamental question in ecology. For abundances at competitive equilibria in Central European forests, a classical ecological theory formulated by Ellenberg (1963) predicts that beech (Fagus sylvaticaL.) outcompetes other tree species within a mesic range of soil pH and water levels, while other species prevail under less favorable conditions. While the theory is generally accepted in forest ecology, only certain aspects of it have been substantiated by empirical evidence. Moreover, the demographic processes driving the turnover from beech to other tree species at the extremes of the soil gradients remain mostly unexplained.To address this, we inversely calibrated a parsimonious forest model (JAB model) with a sapling stage and interacting populations with short time series of observed tree abundances from the German national forest inventory. By modelling how demographic rates vary along pH and soil water gradients, we were able to test the prediction that beech naturally predominates only at favorable soil conditions. Moreover, we tested with simulations how the environmental response of demographic rates explainsFagus’ changing relative abundance along the soil gradients.Our results largely confirm thatFagusout competes other species in a central environmental range. Environmental change ofFagus’ relative abundance is primarily explained by environmental variation of its net basal area increment, followed by its competition response at the overstory and at the sapling stage. We found that even though sapling tolerance to shading is the primary mechanism forFaguspredominance, it only plays a secondary role for the environmental variation of its relative abundance.Synthesis:By inverse calibration of a forest population model with demographic rates that respond to the environment, we confirm the predictions of Ellenberg’s classical, albeitonlypartially-evidenced, theory onF. sylvatica’s predominance in Central European forests. Furthermore, for thefirsttime, we substantiate the theory by elucidating how the environmental variation in species composition is based in demographic processes. This demonstrates that our approach can be utilized to predict distributions of interacting species and to explain the dynamics between species, as influenced by their environment.
Fluorescent human RPA to track assembly dynamics on DNA
Authors: Kaushik Vikas , Chadda Rahul , Kuppa Sahiti , Pokhrel Nilisha , Vayyeti Abhinav , Grady Scott , Arnatt Chris , Antony Edwin 
Published: November 2023

AbstractDNA metabolic processes including replication, repair, recombination, and telomere maintenance occur on single-stranded DNA (ssDNA). In each of these complex processes, dozens of proteins function together on the ssDNA template. However, when double-stranded DNA is unwound, the transiently open ssDNA is protected and coated by the high affinity heterotrimeric ssDNA binding Replication Protein A (RPA). Almost all downstream DNA processes must first remodel/remove RPA or function alongside to access the ssDNA occluded under RPA. Formation of RPA-ssDNA complexes trigger the DNA damage checkpoint response and is a key step in activating most DNA repair and recombination pathways. Thus, in addition to protecting the exposed ssDNA, RPA functions as a gatekeeper to define functional specificity in DNA maintenance and genomic integrity. RPA achieves functional dexterity through a multi-domain architecture utilizing several DNA binding and protein-interaction domains connected by flexible linkers. This flexible and modular architecture enables RPA to adopt a myriad of configurations tailored for specific DNA metabolic roles. To experimentally capture the dynamics of the domains of RPA upon binding to ssDNA and interacting proteins we here describe the generation of active site-specific fluorescent versions of human RPA (RPA) using 4-azido-L-phenylalanine (4AZP) incorporation and click chemistry. This approach can also be applied to site-specific modifications of other multi-domain proteins. Fluorescence-enhancement through non-canonical amino acids (FEncAA) and Förster Resonance Energy Transfer (FRET) assays for measuring dynamics of RPA on DNA are also described.HighlightsRPA is an essential protein for most DNA metabolic processes including replication, repair, and recombination.RPA is a ssDNA binding protein made of six domains situated across RPA70, RPA32 and RPA14 subunits. Four high affinity DNA binding domains engage the DNA.Site-specific fluorescent probes were incorporated into two domains of RPA and report on ssDNA binding dynamics.Bulk-level kinetic and single-molecule assays are described to monitor the binding and remodeling of individual RPA domains on ssDNA.
The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis
Authors: Reimão-Pinto Madalena M. , Castillo-Hair Sebastian M. , Seelig Georg , Schier Alex F. 
Published: November 2023

SummaryThe 5′ UTRs of mRNAs are critical for translation regulation, but theirin vivoregulatory features are poorly characterized. Here, we report the regulatory landscape of 5′ UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5′ UTR is sufficient to confer temporal dynamics to translation initiation, and identified 86 motifs enriched in 5′ UTRs with distinct ribosome recruitment capabilities. A quantitative deep learning model, DaniO5P, revealed a combined role for 5′ UTR length, translation initiation site context, upstream AUGs and sequence motifs onin vivoribosome recruitment. DaniO5P predicts the activities of 5′ UTR isoforms and indicates that modulating 5′ UTR length and motif grammar contributes to translation initiation dynamics. This study provides a first quantitative model of 5′ UTR-based translation regulation in early vertebrate development and lays the foundation for identifying the underlying molecular effectors.HighlightsIn vivoMPRA systematically interrogates the regulatory potential of endogenous 5′ UTRsThe 5′ UTR alone is sufficient to regulate the dynamics of ribosome recruitment during early embryogenesisThe MPRA identifies 5′ UTRcis-regulatory motifs for translation initiation control5′ UTR length, upstream AUGs and motif grammar contribute to the differential regulatory capability of 5′ UTR switching isoforms
Male boldness and female parental care predict reproductive success in a bi-parental cichlid, the rainbow krib (Pelvicachromis pulcher)
Authors: Scherer U. , Niemelä P.T. , Schuett W. 
Published: November 2023

ABSTRACTAnimal personality differences, i.e. consistent among-individual behavioural differences within populations, are prevalent across the animal kingdom. However, we are just beginning to understand the adaptive significance of the observed behavioural variation. We are particularly in need of empirical studies testing hypotheses of proposed theoretical frameworks aiming to understand the existence animal personality differences. In this study, we investigated a hypothesis derived from a framework suggesting that sexual selection may generate and maintain personality variation. The authors of this framework propose parental care as a mechanism linking animal personality and reproductive fitness.We repeatedly measured individual boldness in male and female rainbow kribs,Pelvicachromis pulcher, a West African cichlid known for territorial cave breeding and shared parental care. We then formed 54 breeding pairs with varying behavioural contrasts in boldness. For pairs that produced offspring (N = 20), we repeatedly recorded parental care behaviour (parental boldness and brood guarding) of both parents over one month. Reproductive success was measured as the likelihood to reproduce, the number of offspring, and offspring size at the end of breeding.In both sexes, we found consistent among-individual differences in boldness before breeding and in parental care behaviours. Bolder males were less likely to reproduce but, when breeding was successful, produced bigger broods compared to less bold males. Female parental boldness positively correlated with the number of offspring produced. However, individual boldness before breeding did not predict parental care behaviour in either sex and we found no effects of the pairs’ contrast in prebreeding boldness on parental care coordination or reproductive success.The outcomes of our study may suggest that among-individual variation in male boldness is maintained by males with different behavioural types playing different reproductive strategies of equal average fitness. Future research should delve into understanding the intricate link between male boldness and reproductive success, exploring for instance underlying genetic mechanisms and interactions with environmental conditions.
Causes of Autoimmune Psoriasis and Associated Cardiovascular Disease: Roles of Human Endogenous Retroviruses and Antihypertensive Drugs—A Systematic Review and Meta-analysis
Authors: Rezabakhsh Aysa , Manjili Masoud H. , Hosseinifard Hossein , Reza Sadaie M. 
Published: November 2023

AbstractCurrent treatments are ineffective to cure or prevent occurrences of autoimmune psoriasis and psoriatic cardiovascular disease/CVD. Psoriasis is associated with deregulated expressions of human endogenous retroviruses (ERVs) variants. ERV transcripts and proteins are detected in lesioned biopsies—without assembled viral particles—in addition to antibody and T-cell responses against ERV-K dUTPase. In persons living with HIV-1, manifestations of psoriasis are exacerbated variably. These may depend on multiple factors, differences in ERVs expressions, subtypes of HIV-1, and/or epigenetics. This article represents a quantitative risk assessment and meta-analysis approach with an attempt to assess causality. We surmise that mutated ERVs trigger aberrant proliferation and differentiation of keratinocytes, which in turn induce proinflammatory polarization. Independent risk factors and/or covariates with a range of relative risk/RR ratios appear to significantly impact the development of autoimmune psoriasis or immune intolerance, plausibly through ERVs genes activity. Given the antihypertensive drug’s potential in psoriasis development, a probable role in promising either ERVs activation or perturbations in epigenetic factors is questionable. Although the correlational nature of the data based on RR ratios prevents making robust conclusions, we reckon that the likelihood of attributable risk factors for certain antihypertensive drugs may stem from their pleiotropic effects or potentials for inducing ERV-mediated dysregulation of keratinocytes and/or endothelial cells. These findings expand our knowledge regarding ERV activations and HIV-1, antihypertensive drugs use, and incidents of psoriatic disease, and call for exploring cell-specific therapies aimed at blocking or reversing mutated ERVs gene activity toward attaining stable remissions in psoriasis and associated CVD.
BdNRT2A and BdNRT3.2 are the major components of the High-Affinity nitrate Transport System inBrachypodium distachyon
Authors: David Laure C. , Grégoire Mathilde , Berquin Patrick , Marmagne Anne , Dalmais Marion , Bendahmane Abdelhafid , Miller Anthony J. , Krapp Anne , Daniel-Vedele Françoise , Girin Thomas , Ferrario-Méry Sylvie 
Published: November 2023

SummaryAn efficient nitrate uptake system contributes to the improvement of crop nitrogen use efficiency under low nitrogen availability. TheHighAffinity nitrateTransportSystem (HATS) in plants is active in low external nitrate and is mediated by a two-component system [high affinity transporters NRT2 associated to a partner protein NRT3 (NAR2)].In Brachypodium, the model plant for C3 cereals, we investigated the role ofBdNRT2AandBdNRT3.2through various experimental approaches including gene expression profiling, functional characterisation in heterologous system, intracellular localization by imaging, and reverse genetics via gene silencing.Expression ofBdNRT2.AandBdNRT3.2genes in response to nitrate availability fits with the characteristics of the HATS components. Co-expression ofBdNRT2AandBdNRT3.2is required for an effective nitrate transport in the heterologous expression system Xenopus oocytes. Functional interaction between BdNRT2A-GFP and BdNRT3.2-RFP fusion proteins has been observed at the plasma membrane in Arabidopsis protoplasts in transient expression experiments. BdNRT3.2 appeared to be necessary for the plasma membrane localization of BdNRT2A.15Nitrate influx measurements withbdnrt2amutants (two amiRNA mutants and one NaN3induced mutant with a truncated NRT2A protein), confirmed that BdNRT2A is a major contributor of the HATS in Brachypodium.Directed mutagenesis in BdNRT2A of a conserved Ser residue (S461) specific to monocotyledons has been performed to mimic a non-phosphorylated S461A or a constitutively phosphorylated S461D, in order to evaluate its potential role in the BdNRT2A and BdNRT3.2 interaction leading to plasma membrane targeting. Interestingly, the phosphorylation status of S461 did not modify the interaction, suggesting on a more complex mechanism.In conclusion, our data show that BdNRT2A and BdNRT3.2 are the main components of the nitrate HATS activity in Brachypodium (Bd21-3) and allow an optimal growth in low N conditions.
Antiviral protection in the Pacific oysterCrassostrea (Magallana) gigasagainst OsHV-1 infection using UV-inactivated virus
Authors: Morga Benjamin , Mège Mickäel , Faury Nicole , Dégremont Lionel , Petton Bruno , Pépin Jean-François , Renault Tristan , Montagnani Caroline 
Published: November 2023

AbstractThe increase of the frequency and severity of marine diseases affecting farmed marine mollusks are currently threatening the sustainability of this aquaculture sector, with few available prophylactic or therapeutic solutions. Recent advances have shown that the innate immune system of invertebrates can develop memory mechanisms allowing for efficient protection against pathogens. These properties have been called innate immune memory, immune priming or trained immunity. Previous results demonstrated the possibility to elicit antiviral immune priming to protect Pacific oysters against the ostreid herpes virus 1 (OsHV-1), currently plaguingM. gigasproduction worldwide. Here, we demonstrate that UV-inactivated OsHV-1 is also a potent elicitor of immune priming. Previous exposure to the inactivated virus was able to efficiently protect oysters against OsHV-1, significantly increasing oyster survival. We demonstrate that this exposure blocked viral replication and was able to induce antiviral gene expression potentially involved in controlling the infection. Finally, we show that this phenomenon can persist for at least 3 months, suggesting the induction of innate immune memory mechanisms. This study unravels new ways to train the Pacific oyster immune system that could represent an opportunity to develop new prophylactic strategies to improve health and to sustain the development of marine mollusk aquaculture.
Mating preferences act independently on different elements of visual signals inHeliconiusbutterflies
Authors: Smith S. H. , Queste L. , Wright D.S. , Bacquet C.N. , Merrill R.M. 
Published: November 2023

AbstractMating cues are often comprised of several elements, which can act independently, or in concert to attract a suitable partner. Individual elements may also function in other contexts, such as anti-predator defense or camouflage. InHeliconiusbutterflies, wing patterns comprise several individual color pattern elements, which advertise the butterflies’ toxicity to predators. These wing patterns are also mating cues, and males predominantly court females that possess the same wing pattern as their own. However, it is not known whether male preference is based on the full wing pattern or only individual pattern elements. We compared preferences of maleH. erato lativittabetween female models with the full wing pattern and those with some pattern elements removed. We found no differences in preference between the full wing pattern model and a model with pattern elements removed, indicating that the complete composition of all elements is not essential to the mating signal. Wing pattern preferences also contribute to pre-mating isolation between two otherHeliconiustaxa,H. erato cyrbiaandH. himera, therefore, we next compared preferences for the same models in these species.H. erato cyrbiaandH. himerastrongly differed in preferences for the models, potentially providing a mechanism for how pre-mating isolation acts between these species. These findings suggest that contrasting levels of selective constraint act on elements across the wing pattern.
Transcription termination by RNA polymerase I
Authors: Turowski Tomasz W. , Petfalski Elisabeth , Winz Marie-Luise , Tollervey David 
Published: November 2023

ABSTRACTTranscription elongation is stochastic and driven by a Brownian ratchet mechanism, making it subject to changes in velocity. However, on regions occupied by multiple polymerases, notably the rDNA, DNA rotation plus torsion constrain polymerase molecules to proceed at the same rate generating “torsional entrainment”. We report that release of entrainment, by co-transcriptional 3’-end cleavage, is permissive for relative movement between polymerases, promoting pausing and backtracking. Subsequent termination (polymerase release) is facilitated by the 5’-exonuclease Rat1 (Xrn2) and backtracked transcript cleavage by RNAPI subunit Rpa12. These activities were reproducedin vitro. Short nascent transcripts close to the transcriptional start site, combined with nascent transcript folding energy, similarly facilitate RNAPI pausing. Nascent, backtracked transcripts at pause sites, are targeted by both the exosome cofactor TRAMP and Rat1, promoting termination. Topoisomerase 2 localizes adjacent to RNAPI pause sites, potentially allowing continued elongation by downstream polymerases. Biophysical modeling supported substantial (∼10%) premature termination.HighlightsNascent pre-rRNA 3’ cleavage promotes RNAPI deceleration and termination RNAPI undergoes early, start-site proximal termination at sites of polymerase pausing Biophysical modeling indicates ∼10% early termination – or ∼100 events per minute Model presented for overall organization of pre-rRNA transcription
All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq
Authors: Csillag Veronika , Noble JC , Calvigioni Daniela , Reinius Björn , Fuzik János 
Published: November 2023

AbstractNeuronal pathways recruit large postsynaptic populations and maintain connections via distinct postsynaptic response types (PRTs). Until recently, PRTs were only accessible as a selection criterion for single-cell RNA-sequencing (scRNA-seq) through probing by low-throughput whole-cell electrophysiology. To overcome these limitations and target neurons based on specific PRTs for soma collection and subsequent scRNA-seq, we developed Voltage-Seq. An on-site analysis tool, VoltView, was created to guide soma harvesting of specific PRTs using a classifier based on a previously acquired connectome database from multiple animals.Here, we present a detailed step-by-step protocol, including setting up the optical path, the imaging setup, detailing the imaging procedure, and analysis, the reagents and protocols, complete procedure for sequencing library preparation, and provide other tips and pitfalls to assist researchers in conducting high-throughput all-optical voltage imaging, and to obtain the single-cell transcriptomic data from selected postsynaptic neurons.Voltage-seq workflow can be completed in ∼6 weeks including 4-5 weeks of viral expression of the Voltron sensor. The approach allows researchers to resolve the connectivity ratio of a specific pathway and explore the diversity of PRTs within that connectome. Furthermore, the high throughput in conjunction with quick analysis gives unique access to find specific connections within a large postsynaptic connectome. Voltage-seq also allows the investigation of correlations between connectivity and gene expression changes in a postsynaptic cell-type-specific manner in both excitatory and inhibitory connections.
Crosstalk between Gut Sensory Ghrelin Signaling and Adipose Tissue Sympathetic Outflow Regulates Metabolic Homeostasis
Authors: Thomas M. Alex , Cui Xin , Artinian Liana R. , Cao Qiang , Jing Jia , Silva Felipe C. , Wang Shirong , Zigman Jeffrey M. , Sun Yuxiang , Shi Hang , Xue Bingzhong 
Published: November 2023

AbstractThe stomach-derived orexigenic hormone ghrelin is a key regulator of energy homeostasis and metabolism in humans. The ghrelin receptor, growth hormone secretagogue receptor 1a (GHSR), is widely expressed in the brain and gastrointestinal vagal sensory neurons, and neuronal GHSR knockout results in a profoundly beneficial metabolic profile and protects against diet-induced obesity (DIO) and insulin resistance. Here we show that in addition to the well characterized vagal GHSR, GHSR is robustly expressed in gastrointestinal sensory neurons emanating from spinal dorsal root ganglia. Remarkably, sensory neuron GHSR deletion attenuates DIO through increased energy expenditure and sympathetic outflow to adipose tissue independent of food intake. In addition, neuronal viral tract tracing reveals prominent crosstalk between gut non-vagal sensory afferents and adipose sympathetic outflow. Hence, these findings demonstrate a novel gut sensory ghrelin signaling pathway critical for maintaining energy homeostasis.
Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud
Authors: Shen Liangying , Qi Zewen , Li Shuwen , Wang Mengdi , Chen Jiabao , Zhang Jiahang , Xu Lixin , Han Liebao , Chao Yuehui 
Published: November 2023

AbstractHighlightIntegration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance inZoysia japonicaSteud.The warm-season turfgrass Zoysia japonica is renowned for its drought resistance and serves as an exceptional domestic turfgrass in China. In order to unlock the potential of this native grass, identify drought-resistant genes, enhance the genetic transformation system, and maximize its utilization benefits, we conducted physiological characterization, multi-omics analysis, and RT-qPCR experimental verification in Zoysia japonica. This study suggested that 63 high-confidence genes related to drought stress and 6 motifs regulating drought responses were identified using a combined omics approach and RT-qPCR validation. The study discovered a positive correlation between ATAC-Seq peak intensity and gene expression levels. The expression of high-confidence genes was linked toZoysia japonicaresistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related genes inZoysia japonica, elucidating the grass’s adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork forZoysia japonicaimprovement and breeding.