bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs
Authors: Minařík Martin , Modrell Melinda S. , Andrew Gillis J. , Campbell Alexander S. , Fuller Isobel , Lyne Rachel , Micklem Gos , Gela David , Pšenička Martin , Baker Clare V. H. 
Published: April 2023

AbstractIn electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related ’sister cell type’ to hair cells. We previously identified only one transcription factor gene,Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 23 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Twelve are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Six are electrosensory-restricted on the head(Irx5,Insm1,Sp5,Satb2,MafAandRorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1,Sox8,Isl1,Hmx2andRorb). However, as previously reported,Sox8is expressed in ampullary organs as well as neuromasts in a shark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
Ultrastructure of the brain waste-clearance pathway
Authors: Grubb Søren 
Published: April 2023

AbstractEfficient metabolic waste clearance is essential for optimal brain function. Waste accumulation can cause inflammation, tissue damage, and potentially lead to dementia and other neurological disorders. The primary waste exit route is debated, with evidence suggesting the lymphatic system or arachnoid villi/granulations as possible pathways.This study uses an ultrastructural dataset to emphasize the potential underestimation of macrophages and arachnoid villi/granulations in waste removal.Based on brain surface ultrastructure analysis of the MICrONS dataset, waste clearance may occur through a transcellular route involving astrocytes to the perivascular space. Waste is then either phagocytosed by perivascular macrophages or directed to the subarachnoid space for meningeal macrophage phagocytosis.Evidence is provided that macrophages transport non-degradable waste in lysosomes to arachnoid villi for exocytosis into the villus lumen and venous system routing. Additionally, the study investigates fibroblast-macrophage interactions via primary cilia, potentially optimizing waste clearance. The role of astrocytes in brain water homeostasis and GFAP’s potential significance in water filtration are also examined. This study offers valuable insights into waste clearance mechanisms in the brain, potentially aiding dementia understanding and treatment.
Declining food availability and habitat shifts drive community responses to marine hypoxia
Authors: Duskey E , Casini M , Limburg KE , Gårdmark A 
Published: April 2023

AbstractWorsening marine hypoxia has had severe negative consequences for fish communities across the globe. While individual­ and population­level impacts of deoxygenation have been identified, it is unknown how they interact to drive changes in food webs. To address this, we incorporated several major impacts of hypoxia, including declines in benthic re­ sources, habitat shifts, increasing mortality, and changes to rates of feeding, assimilation, and reproductive efficiency, into an existing size spectrum food web modeling framework. We used this structure to ask the following questions: which of these direct effects are most critical to capturing population and community dynamics in a representative hypoxic system, how do they interact to result in community responses to deoxygenation, and what are the potential consequences of these effects in the context of accelerating deoxygenation? We tested the effect of different combinations of oxygen­dependent processes, driven by observed oxygen levels, on the food web model’s ability to explain time series of observed somatic growth, diets, biomass, and fishery yields of commercially relevant species in the Baltic Sea. Model results suggest that food availability is most critical to capturing observed dynamics. There is also some evidence for oxygen­dependent habitat use and physological rates as drivers of observed dynamics. Deoxygenation results in declining growth both of benthic and benthopelagic fish species, as the latter are unable to compensate for the loss of benthic resources by consuming more pelagic fish and resources. Analysis of scenarios of ideal, declining, and degraded oxygen conditions show that deoxygenation results in a decline in somatic growth of predators, an altered habitat occupancy resulting in changing species interactions, and a shift in energy flow to benthopelagic predators from benthic to pelagic resources. This may have important implications for management as oxygen declines or improves.
ANP rescues the preeclamptic symptoms inAxlknockout mice by improving trophoblast function ANP rescues the preeclamptic symptoms
Authors: Zhou Chan , Zhu Yunqing , Zhang Liang , Li Xuexiang , Yao Jiatong , Zhao Miaomiao , Chen Zi-jiang , Zhang Cong 
Published: April 2023

AbstractPre-eclampsia (PE) is characterized by maternal hypertension and/or proteinuria after 20 weeks of gestation. Shallow trophoblast invasion into spiral artery (SpA) and defective decidualization have been implicated in the pathogenesis of PE. However, the underlying mechanisms remain unclear. AXL receptor tyrosine kinase is a biomarker and therapeutic target for a variety of metastatic cancers while tumorigenesis and placentation share many features. In this study, a new function of AXL in promoting SpA remodeling and trophoblast invasion were demonstrated. The pregnantAxlknockout (Axl−/−) mice exhibited typical PE symptoms, including increased blood pressure and proteinuria. Artificially induced decidualization experiments showed that appeared normal, however, RNA-seq results ofAxl−/−deciduoma revealed abnormal expression of a number of transcripts, includingCorin, which encodes a cardiac protease that activates atrial natriuretic peptide (ANP). Treatment with ANP reversed the PE symptoms. Moreover, in decidua from women afflicted with PE, AXL level was significantly lower than that in normal pregnancies. These data show that the abnormality of decidua-derived AXL-CORIN-ANP affects maternal-fetal crosstalk and contributes to PE.
Spt5 interacts genetically with Myc and is limiting for brain tumor growth in Drosophila
Authors: Hofstetter Julia , Ogunleye Ayoola , Kutschke André , Buchholz Lisa Marie , Wolf Elmar , Raabe Thomas , Gallant Peter 
Published: April 2023

AbstractThe transcription factor SPT5 physically interacts with MYC oncoproteins and is essential for efficient transcriptional activation of MYC targets in cultured cells. Here we useDrosophilato address the relevance of this interaction in a living organism. Spt5 displays moderate synergy with Myc in fast proliferating young imaginal disc cells. During later development, Spt5-knockdown has no detectable consequences on its own, but strongly enhances eye defects caused by Myc-overexpression. Similarly, Spt5-knockdown in larval type 2 neuroblasts has only mild effects on brain development and survival of control flies, but dramatically shrinks the volumes of experimentally induced neuroblast tumors and significantly extends the lifespan of tumor-bearing animals. This beneficial effect is still observed when Spt5 is knocked down systemically and after tumor initiation, highlighting SPT5 as a potential drug target in human oncology.
Migratory herbivorous waterfowl track multiple resource waves during spring migration
Authors: Xu Fei , Wu Wei , Wei Jie , Xin Qinchuan , Wielstra Ben , La Sorte Frank A. , Ma Zhijun , Lei Guangchun , Lei Jialin , Wu Wenzhao , Yang Yongchuan , Gong Peng , Xu Bing , Si Yali 
Published: April 2023

AbstractEast Asian herbivorous waterfowl intensively use farmland in spring, next to their natural habitat. Accordingly, they might have expanded their migration strategy from merely tracking the green wave of newly emerging vegetation to also incorporating the availability of post-harvest agricultural seeds (here dubbed the seed wave). However, if and how waterfowl use multiple food resources to time their seasonal migration is still unknown. We test this migration strategy using 167 spring migration tracks of five East Asian herbivorous waterfowl species and mixed-effect resource selection function models. We find all study species arrive at their core stopover sites in the Northeast China Plain after agricultural seeds become available, extend their stay after spring vegetation emerges, and arrive at breeding sites around the emergence of vegetation. Moreover, the cue used in exploiting the availability of both food resources varies in different regions and among species. At the core stopover sites, larger-bodied species use the seed wave and smaller-bodied ones adopt the green wave. At the breeding sites, the former follow the green wave, and the latter track the snow-free time. Our findings suggest that waterfowl track multiple resource waves to finetune their migration, highlighting new opportunities for conservation.
Honeybee flight dynamics and pair separation in windy conditions near the hive entrance
Authors: Hejazi Bardia , Antigny Hugo , Huellstrunk Sophia , Bodenschatz Eberhard 
Published: April 2023

AbstractAnimals and living organisms are continuously adapting to changes in their environment. How do animals, especially those that are critical to their ecosystem, respond to rapidly changing conditions in their environment? Here, we report on the three-dimensional trajectories of flying honeybees under calm and windy conditions in front of the hive entrance. We also investigate the pitch and yaw in our experiments. We find that the mean velocities, accelerations and angular velocities of honeybees increase with increasing wind speeds. We observed that pair separation between honeybees is highly controlled and independent of wind speeds. Our results on the coordination used by honeybees may have potential applications for coordinated flight of unmanned aerial vehicles.
Production of sterile Atlantic salmon by germ cell ablation with antisense oligonucleotides
Authors: Tveiten Helge , Andersen Øivind , Swain Jaya Kumari , Johnsen Hanne , Mommens Maren , Slanchev Krasimir 
Published: April 2023

AbstractCultivation of sterile-only fish in aquaculture offers multiple benefits of environmental, economical, and social value. A reliable method for efficient sterilization without affecting fish welfare and performance traits would have significant impact on fish production practices. Here, we demonstrate sterilization of Atlantic salmon embryos by targeting thedead endgene with antisense oligonucleotides. Successful gene knock down and sterilization was achieved only when using Gapmer oligonucleotides and not with morpholino oligos. Germ cell-depleted embryos developed into morphologically normal male and female salmon with rudimentary gonads devoid of gametes.
Cross-subject Mapping of Neural Activity with Restricted Boltzmann Machines
Authors: Yang Haoming , Angjelichinoski Marko , Wu Suya , Putney Joy , Sponberg Simon , Tarokh Vahid 
Published: April 2023

AbstractSubject-to-subject variability is a common challenge in generalizing neural data models across subjects. While many methods exist that map one subject to another, it remains challenging to combine many subjects in a computationally efficient manner, especially with features that are highly non-linear such as when considering populations of spiking neurons or motor units. Our objective is to transfer data from one or more target subjects to the data space of one or more source subject(s) such that the neural decoder of the source subject can directly decode the target data when the source(s) is not available during test time. We propose to use the Gaussian-Bernoulli Restricted Boltzmann Machine (RBM); once trained over the entire set of subjects, the RBM allows the mapping of target features on source feature spaces using Gibbs sampling. We also consider a novel computationally efficient training technique for RBMs based on the minimization of the Fisher divergence, which allows the gradients of the RBM to be computed in closed form, in contrast to the more traditional contrastive divergence. We apply our methods to decode turning behaviors from a comprehensive spike-resolved motor program – neuromuscular recordings of spike trains from the ten muscles that control wing motion in an agile flying Manduca sexta. The dataset consists of the comprehensive motor program recorded from nine subjects driven by six discrete visual stimuli. The evaluations show that the target features can be decoded using the source classifier with an accuracy of up to 95% when mapped using an RBM trained by Fisher divergence.Significant StatementIn this study, we address the variability of neural data across subjects, which is a significant obstacle in developing models that can generalize across subjects. Our objective is to create a task-specific representation of the target subject signal in the feature space of the source subject. Our proposed RBM architectures achieve highly flexible and accurate cross-subject mapping with few assumptions. Our Fisher RBM improved the previous state of the art method by 300%. Our methods show promise in generalizing features of complex neural datasets across individuals, tuning neural interfaces to subject-specific features, and leveraging data across multiple subjects when experiments are limited in time or completeness.
Arabidopsis NF-YCs interact with CRY2 and PIF4/5 to repress blue light-mediated hypocotyl growth
Authors: Wang Wei , Gao Lin , Zhao Tianliang , Chen Jiamei , Chen Ting , Lin Wenxiong 
Published: April 2023

AbstractPlants can not move automatically, thus they have to perceive the changing environment (light, temperate and so on) by developing the adapted phenotypes. Light-induced hypocotyl length is an ideal phenotype for studying how plants response to light. So far, many signaling components in light-induced hypocotyl growth have been reported. Here, we focused on identifying transcription factors (TFs) involved in blue light-induced hypocotyl growth by constructing Arabidopsis TFs overexpressing lines and screening blue light-induced hypocotyl length. Finally, we found that three NF-YC proteins, NF-YC7, NF-YC5 and NF-YC8 (NF-YCs as short name), develop longer hypocotyls than the wild type under blue light. While deficient mutants,nf-yc5nf-yc7andnf-yc7nf-yc8, fail to promote the hypocotyl elongation under blue light.NF-YCs physically interacted with CRY2 and PIF4/5, while the NF-YCs-PIF4/5 interactions were repressed by CRY2. Moreover, overexpression of CRY2 or deficiency of PIF4/5 repressed the hypocotyl elongation induced by NF-YC7 under blue light. Further investigation revealed that NF-YC7 increased the blue light-induced CRY2 degradation and regulated the activities of PIF4/5.Taking together, this study provided a new insight into that NF-YCs function as CRY2-and PIF4/5-interacting proteins and modulate their stabilization to repress the blue light-mediated hypocotyl growth.Author SummaryLight is an essential environmental factor for plants growth and development. Plants response to light signaling by displaying short hypocotyls, green leaves, and so on. The mechanisms of light responding to light have aroused extensive attention. In this study, we clarified that NF-YC family members NF-YC5/7/8 interact with CRY2, PIF4/5 and modulate their stabilization to repress the blue light-mediated hypocotyl growth. It was the first time for reporting NF-Y family members function as CRY2-and PIF4/5-interacting proteins. Therefore, this study provides a novel understanding how plants adapt to light.
Stochastic characterization of navigation strategies in an automated variant of the Barnes maze
Authors: Lee Ju-Young , Jung Dahee , Royer Sébastien 
Published: April 2023

AbstractAnimals can use a repertoire of strategies to navigate in an environment, and it remains an intriguing question how these strategies are selected based on the nature and familiarity of environments. To investigate this question, we developed a fully automated variant of the Barnes maze, characterized by 24 vestibules distributed along the periphery of a circular arena, and monitored the trajectories of mice over 15 days as they learned to navigate towards a goal vestibule from a random start vestibule. We show that the patterns of vestibule visits can be reproduced by the combination of three stochastic processes reminiscent of random, serial and spatial strategies. The processes randomly selected vestibules based on either uniform (random) or biased (serial and spatial) probability distributions. They closely matched experimental data across a range of statistical distributions characterizing the length, distribution, step size, direction, and stereotypy of vestibule sequences, revealing a shift from random to spatial and serial strategies over time, with a strategy switch occurring approximately every six vestibule visits. Our study provides a novel apparatus and analysis toolset for tracking the repertoire of navigation strategies and demonstrates that a set of stochastic processes can largely account for exploration patterns in the Barnes maze.
Assessing the quality of comparative genomics data and results with thecogeqcR/Bioconductor package
Authors: Almeida-Silva Fabricio , Van de Peer Yves 
Published: April 2023

ABSTRACTComparative genomics has become an indispensable part of modern biology due to the advancements in high-throughput sequencing technologies and the accumulation of genomic data in public databases. However, the quality of genomic data and the choice of parameters used in software tools used for comparative genomics can greatly impact the accuracy of results. To address these issues, we presentcogeqc, an R/Bioconductor package that provides researchers with a toolkit to assess genome assembly and annotation quality, orthogroup inference, and synteny detection. The package offers context-guided assessments of assembly and annotation statistics by comparing observed statistics to those of closely-related species on NCBI. To assess orthogroup inference,cogeqccalculates a protein domain-aware orthogroup score that aims at maximizing the number of shared protein domains within the same orthogroup. The assessment of synteny detection consists in representing anchor gene pairs as a synteny network and analyzing its graph properties, such as clustering coefficient, node count, and scale-free topology fit. The application of cogeqc to real data sets allowed for an evaluation of multiple parameter combinations for orthogroup inference and synteny detection, providing researchers with guidelines to aid in the selection of the most appropriate tools and parameters for their specific data.
The airborne transmission of viruses causes tight transmission bottlenecks
Authors: Sinclair Patrick , Zhao Lei , Beggs Clive , Illingworth Christopher J. R. 
Published: April 2023

AbstractThe transmission bottleneck describes the number of viral particles that found an infection in a new host. Previous studies have used genome sequence data to suggest that transmission bottlenecks for influenza and SARS-CoV-2 involve few viral particles, but the general principles underlying these bottlenecks are not fully understood. Here we show that, across a broad range of circumstances, tight transmission bottlenecks arise as a consequence of the physical process underlying airborne viral transmission. We use a mathematical model to describe the process of infectious particles being emitted by an infected individual and inhaled by others nearby. The extent to which exposure to particles translates into infection is determined by an effective viral load, which is calculated as a function of the epidemiological parameter R0. Across multiple scenarios, including those present at a superspreading event, our model suggests that the great majority of transmission bottlenecks involve few viral particles, with a high proportion of infections being caused by a single viral particle. Our results provide a physical explanation for previous inferences of bottleneck size and predict that tight transmission bottlenecks prevail more generally in respiratory virus transmission.
Y-linked copy number polymorphism of target of rapamycin (TOR) is associated with sexual size dimorphism in seed beetles
Authors: Kaufmann Philipp , Wiberg R. Axel W. , Papachristos Konstantinos , Scofield Douglas G. , Tellgren-Roth Christian , Immonen Elina 
Published: April 2023

AbstractThe Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetleCallosobruchus maculatussegregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here we assembleC. maculatussex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the genetarget of rapamycin(TOR), males carry an additionalTORcopy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linkedTORprovides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation forTOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additionalTORcopies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation ofTORfollowed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbour adaptive potential as a male-limited supergene.