bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ongoing hybridisation among clownfishes: the genomic architecture of the Kimbe Bay hybrid zone
Authors: Schmid Sarah , Hartasánchez Diego A. , Gainsford Ashton , Jones Geoffrey P. , Salamin Nicolas 
Published: March 2024

ABSTRACTHybrid zones – locations where genetically distinct lineages interact and reproduce – are remarkable resources for exploring the evolutionary trajectory of species. Not only can we learn from hybrid zones about the mechanisms of speciation and how reproductive isolation is maintained, but we can also study their impact on evolutionary processes. Thanks to the advent of next-generation sequencing, we are now able to gain new insight into the structure of hybrid genomes and the factors influencing the outcome of hybridisation. Here, we focus on the Kimbe Bay hybrid zone, a narrow region in the Pacific Ocean where two species of clownfish –Amphiprion chrysopterusandA. sandaracinos– hybridise and give rise to the hybridA. leucokranos. Based on whole-genome sequencing, we found that the hybrid zone is mainly composed of first-generation hybrids, the first evidence of F2 hybrids in the wild and early backcrosses withA. sandaracinos. The recurrent backcrossing with one of the parental species might lead to adaptive introgression, with few adaptive introgressed loci fromA. chrysopterusintegrated into theA. sandaracinosgenomic background. This study builds upon the growing literature body relative to the evolutionary outcomes of hybridisation and its importance in the evolution of many species.
A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level
Authors: He Mengyu , Zhao Ni 
Published: March 2024

AbstractBackgroundRecent studies have highlighted the importance of human microbiota in our health and diseases. However, in many areas of research, individual microbiome studies often offer inconsistent results due to the limited sample sizes and the heterogeneity in study populations and experimental procedures. This inconsistency underscores the necessity for integrative analysis of multiple microbiome datasets. Despite the critical need, statistical methods that incorporate multiple microbiome datasets and account for the study heterogeneity are not available in the literature.MethodsIn this paper, we develop a mixed effect similarity matrix regression (SMRmix) approach for identifying community level microbiome shifts between outcomes. SMRmix has a close connection with the microbiome kernel association test, one of the most popular approaches for such a task but is only applicable when we have a single study. SMRmix enables researchers to consolidate findings from diverse microbiome studies.ResultsVia extensive simulations, we show that SMRmix has well-controlled type I error and higher power than some potential competitors. We applied the SMRmix to two real-world datasets. The first, from the HIV-reanalysis consortium, integrated data from 17 studies on gut dysbiosis in HIV. Our analysis confirmed consistent associations between the gut microbiome and HIV infection as well as MSM (men who have sex with men) status, demonstrating greater power than competing methods. The second dataset involved 11 studies on the gut microbiome in colorectal cancer; analysis with SMRmix confirmed significant dysbiosis in affected individuals compared to healthy controls.ConclusionThe development of SMRmix enables the integration of multiple studies and effectively managing study heterogeneity, and provides a powerful tool for uncovering consistent associations between diseases and community-level microbiome data.
Whole organism snRNA-seq reveals systemic peripheral changes in Alzheimer’s Disease fly models
Authors: Park Ye-Jin , Lu Tzu-Chiao , Jackson Tyler , Goodman Lindsey D. , Ran Lindsey , Chen Jiaye , Liang Chung-Yi , Harrison Erin , Ko Christina , Hsu Ao-Lin , Yamamoto Shinya , Qi Yanyan , Bellen Hugo J. , Li Hongjie 
Published: March 2024

AbstractPeripheral tissues become disrupted in Alzheimer’s Disease (AD). However, a comprehensive understanding of how the expression of AD-associated toxic proteins, Aβ42 and Tau, in neurons impacts the periphery is lacking. UsingDrosophila, a prime model organism for studying aging and neurodegeneration, we generated the Alzheimer’s Disease Fly Cell Atlas (AD-FCA): whole-organism single-nucleus transcriptomes of 219 cell types from adult flies neuronally expressing human Aβ42 or Tau. In-depth analyses and functional data reveal impacts on peripheral sensory neurons by Aβ42 and on various non-neuronal peripheral tissues by Tau, including the gut, fat body, and reproductive system. This novel AD atlas provides valuable insights into potential biomarkers and the intricate interplay between the nervous system and peripheral tissues in response to AD-associated proteins.
CatPred: A comprehensive framework for deep learning in vitro enzyme kinetic parameterskcat,KmandKi
Authors: Boorla Veda Sheersh , Maranas Costas D. 
Published: March 2024

AbstractQuantification of enzymatic activities still heavily relies on experimental assays, which can be expensive and time-consuming. Therefore, methods that enable accurate predictions of enzyme activity can serve as effective digital twins. A few recent studies have shown the possibility of training machine learning (ML) models for predicting the enzyme turnover numbers (kcat) and Michaelis constants (Km) using only features derived from enzyme sequences and substrate chemical topologies by training onin vitromeasurements. However, several challenges remain such as lack of standardized training datasets, evaluation of predictive performance on out-of-distribution examples, and model uncertainty quantification. Here, we introduce CatPred, a comprehensive framework for ML prediction ofin vitroenzyme kinetics. We explored different learning architectures and feature representations for enzymes including those utilizing pretrained protein language model features and pretrained three-dimensional structural features. We systematically evaluate the performance of trained models for predictingkcat,Km, and inhibition constants (Ki) of enzymatic reactions on held-out test sets with a special emphasis on out-of-distribution test samples (corresponding to enzyme sequences dissimilar from those encountered during training). CatPred assumes a probabilistic regression approach offering query-specific standard deviation and mean value predictions. Results on unseen data confirm that accuracy in enzyme parameter predictions made by CatPred positively correlate with lower predicted variances. Incorporating pre-trained language model features is found to be enabling for achieving robust performance on out-of-distribution samples. Test evaluations on both held-out and out-of-distribution test datasets confirm that CatPred performs at least competitively with existing methods while simultaneously offering robust uncertainty quantification. CatPred offers wider scope and larger data coverage (∼23k, 41k, 12k data-points respectively forkcat, Kmand Ki). A web-resource to use the trained models is made available at:https://tiny.cc/catpred
Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variant JN.1 in critically ill COVID-19 patients: a prospective, multicenter cohort study
Authors: de Prost Nicolas , Audureau Etienne , Guillon Antoine , Handala Lynda , Préau Sébastien , Guigon Aurélie , Uhel Fabrice , Hingrat Quentin Le , Delamaire Flora , Grolhier Claire , Tamion Fabienne , Moisan Alice , Darreau Cédric , Thomin Jean , Contou Damien , Henry Amandine , Daix Thomas , Hantz Sébastien , Saccheri Clément , Giordanengo Valérie , Pham Tài , Chaghouri Amal , Bay Pierre , Pawlotsky Jean-Michel , Fourati Slim 
Published: March 2024

ABSTRACTA notable increase in severe cases of COVID-19, with significant hospitalizations due to the emergence and spread of JN.1 was observed worldwide in late 2023 and early 2024. During the study period (November 2022-January 2024), 56 JN.1- and 126 XBB-infected patients were prospectively enrolled in 40 French intensive care units. JN.1-infected patients were more likely to be obese (35.7% vs 20.8%; p=0.033) and less frequently immunosuppressed than others (20.4% vs 41.4%; p=0.010). JN.1-infected patients required invasive mechanical ventilation support in 29.1%, 87.5% of them received dexamethasone, 14.5% tocilizumab and none received monoclonal antibodies. Day-28 mortality of JN.1-infected patients was 14.6%.
Bicuspid Aortic Valve Disease With Early Onset Complications: Characteristics And Aortic Outcomes
Authors: Selbst Maximilian A. , Laughlin Megan K. , Ward Colin R. , Michelena Hector , Sabate-Rotes Anna , Bianco Lisa , De Backer Julie , Mosquera Laura Muiño , Yetman Anji T. , Bissell Malenka M , Andreassi Maria Grazia , Foffa Ilenia , Hui Dawn S. , Caffarelli Anthony , Kim Yuli Y. , Guo Dongchuan , Citro Rodolfo , De Marco Margot , Tretter Justin T. , Morris Shaine A. , McBride Kim L. , Body Simon C. ,   EBAV Investigators, Prakash Siddharth K. 
Published: March 2024

AbstractBicuspid aortic valve (BAV) is the most common congenital heart malformation in adults but can also cause childhood-onset complications. In multicenter study, we found that adults who experience significant complications of BAV disease before age 30 are distinguished from the majority of BAV cases that manifest after age 50 by a relatively severe clinical course, with higher rates of surgical interventions, more frequent second interventions, and a greater burden of congenital heart malformations. These observations highlight the need for prompt recognition, regular lifelong surveillance, and targeted interventions to address the significant health burdens of patients with early onset BAV complications.
Common cuckoo female host selection is not determined by host quality but can affect cuckoo nestling growth when parasitising Common redstarts
Authors: Abaurrea Teresa , Moreras Angela , Tolvanen Jere , Thomson Robert L. , Thorogood Rose 
Published: March 2024

ABSTRACTCommon cuckoo (Cuculus canorus) females lay their eggs in the nests of other avian hosts, relying on parental care provided by parasitised hosts. Therefore, it would benefit cuckoo females to target high-quality individual hosts, able to provide optimal parental care. Attempts at testing cuckoo female host selection have so far shown mixed results. However, this might be because studies have rarely considered the host nests that are available in space and time during each cuckoo egg-laying event, as well as the implications of host choice on the cuckoo nestling growth. Here we combined long-term monitoring data with an experiment to test whether cuckoo females parasitising Common redstarts (Phoenicurus phoenicurus) target individual hosts to optimise their nestlingś growth. Making use of data collected between 2013 and 2022 from 350+ nest boxes in Oulu (Finland), we first explored whether there is a range of available host nests for the cuckoo female to choose from. Second, we tested if hosts are targeted according to individual quality (using clutch size as a proxy). And third, we investigated the outcomes of cuckoo female host-selection on nestling growth (mass, tarsus length, and wing length) between 2014 and 2019. We conducted a cross-fostering experiment where we either left cuckoo eggs to hatch and be raised in the nest their mother originally chose for them or moved cuckoo eggs to non-parasitised nests. Additionally, we conducted an exploratory analysis to test the quality of the parents caring for the cross-fostered cuckoo nestlings. After accounting for how many host nests were available to the cuckoo female to choose from, we found that nests with bigger clutches were not more likely to be parasitised, and cross-fostering did not affect mass and tarsus length growth. However, both in the wing length growth and in our exploratory analysis of host parental care on cuckoo nestling growth we found that cuckoo nestlings that grew in the nest selected by their mothers, reached higher asymptotic growth at a slower rate. This suggests that while cuckoos may not choose redstart hosts based on their individual quality when parasitising common redstarts, cuckoo female host selection might improve cuckoo nestling growth and thus, have an adaptive significance.
A systematic exploration of unexploited genes for oxidative stress in Parkinson’s disease
Authors: Suzuki Takayuki , Bono Hidemasa 
Published: March 2024

ABSTRACTHuman disease-associated gene data are accessible through databases, including the Open Targets Platform, DisGeNET, miRTex, RNADisease, and PubChem. However, missing data entries in such databases are anticipated because of factors, such as errors/biases by curators and text mining failures. Additionally, the extensive research on human diseases has resulted in challenges to register comprehensive data. The lack of essential data in databases hinders knowledge sharing and should be addressed. Therefore, we propose an analysis pipeline to explore missing entries of unexploited genes in the human disease-associated gene databases. To demonstrate this, we used the pipeline for genes in Parkinson’s disease with oxidative stress, which revealed two unexploited genes: nuclear protein 1 (NUPR1) and ubiquitin-like with PHD and ring finger domains 2 (UHRF2). The proposed methodology and findings facilitate the identification of disease-associated genes that are not completely represented in existing databases, thereby facilitating easier access to the potential human disease-related functional genes.
Negative impact of mild arid conditions in natural rodent populations revealed using markers of physiological condition in natura
Authors: Keilani Hamilcar , Avenant Nico , Caminade Pierre , Pillay Neville , Ganem Guila 
Published: March 2024

AbstractUnderstanding how organisms respond to seasonal variations in their environment can be a window to their potential adaptability, a classical problem in evolutionary ecology. In the context of climate change, inducing increased aridity and disruption of seasonality, it is crucial to study the extent and limits of species responsiveness.Here, the physiological response to food and water shortage during seasonally dry conditions were investigated. We studied populations of two rodent species of the genusRhabdomys, one arid and one mesic, in a semi-arid zone where their range overlap in South Africa. We measured blood concentrations of markers of kidney and liver function, as well as body condition, at the onset and the end of the dry season.We found similar shifts in blood metabolite levels, in the semi-arid populations of the two species, indicating malnutrition consistent with the observed degradation of habitat quality between the start and the end of the dry season. Furthermore, regardless of the period, differences between the two species in blood metabolite concentrations (e.g. amylase, sodium, alkaline phosphatase) were observed, suggesting contrasting diets and water conservation abilities.Overall, we show that, as seasonal dry conditions worsen, organisms are increasingly affected by reduced food availability, and local adaptation to arid conditions may provide the arid species with an advantage to cope with semi-arid conditions. Our study suggests that even mild arid conditions could have a negative impact and questions resilience of animals to harsher arid conditions.
Beyond blooms: A novel time series analysis framework predicts seasonal keystone species and sheds light on Arctic pelagic ecosystem stability
Authors: Oldenburg Ellen , Kronberg Raphael M. , Metfies Katja , Wietz Matthias , von Appen Wilken-Jon , Bienhold Christina , Popa Ovidiu , Ebenhöh Oliver 
Published: March 2024

ABSTRACTA thorough understanding of ecosystem functioning in the Arctic Ocean, a region under severe threat by climate change, requires detailed studies on linkages between biodiversity and ecosystem stability. The identification of keystone species with special relevance for ecosystem stability is of great importance, yet difficult to achieve with established community assessments. In the case of microbes, metabarcoding and metagenomics offer fundamental insights into community structure and function, yet remain limited regarding the ecological relevance of individual taxa. To overcome this limitation, we have developed an analytical approach based on three different methods: Co-Occurrence Networks, Convergent Cross Mapping, and Energy Landscape Analysis. These methods enable the identification of seasonal communities in microbial ecosystems, elucidate their interactions, and predict potential stable community configurations under varying environmental conditions. Combining the outcomes of these three methods allowed us to define 38 keystone species in the Arctic Fram Strait that represent different trophic modes within the food web, and might signify indicator for ecosystem functionality under the impact of environmental change. Our research reveals a clear seasonal pattern in phytoplankton composition, with distinct assemblages characterizing the phases of carbon fixation (polar day) and consumption (polar night). Species interactions exhibited strong seasonality, with significant influence of summer communities on winter communities but not vice versa. Spring harbored two distinct groups: consumers (heterotrophs), strongly linked to polar night, and photoautotrophs (mainly Bacillariophyta). These groups are not causally related, suggesting a “winter reset” with selective effects that facilitates a new blooming period, allowing survivors of the dark phase to emerge. Energy Landscape Analysis showed that winter communities are more stable than summer communities. In summary, the ecological landscape of the Fram Strait can be categorized into two distinct phases: a production phase governed by specialized organisms that are highly responsive to environmental variability, and a heterotrophic phase dominated by generalist species with enhanced resilience.
Phylogenetically distant enzymes localized in cytosol and plastids drive citral biosynthesis in lemongrass
Authors: Gupta Priyanka , Sharma Anuj , Kiran N.R. , Pranav Raj T.K. , Krishna Ram , Nagegowda Dinesh A. 
Published: March 2024

AbstractExcept for the genetic basis of citral-forming alcohol dehydrogenases (ADHs) inLitsea cubebatree, and biochemical studies on citral-forming enzymes from select plants, knowledge regardingin-plantabiosynthesis of citral and its metabolic origin remains limited. Here, we have elucidated the functions of an ADH (CfADH1) and an aldoketo-reductase (CfAKR2b) in citral biosynthesis in lemongrass (Cymbopogon flexuosus), one of the most cultivated aromatic crops for its citral-rich essential oil. Expression of bothCfADH1andCfAKR2bshowed correlation with citral accumulation in different developmental stages. Recombinant CfADH1 and CfAKR2b, despite their sequence unrelatedness, exhibited similar kinetic properties and formed citral from geraniol with NADP cofactor. Virus-induced gene silencing in lemongrass, and transient expression in lemon balm (Melissa officinalis), demonstrated thein-plantainvolvement ofCfADH1andCfAKR2bin citral biosynthesis. While CfADH1 exhibited a dual cytosolic/plastidial localization, CfAKR2b was localized to cytosol. Moreover, feeding lemongrass seedlings with mevalonate- and methylerythritol-phosphate-pathway specific inhibitors combined with volatile profiling supported the role of both pathways in citral formation. Our results demonstrate phylogenetically distant enzymes localized in cytosol and plastids drive citral biosynthesis in lemongrass, indicating an evolutionary scenario aimed at maximizing the utilization of precursor pools from both cytosolic and plastidial pathways for high citral production.
Astrocytes control quiescent NSC reactivation via GPCR signaling-mediated F-actin remodeling
Authors: Lin Kun-Yang , Gujar Mahekta R. , Lin Jiaen , Ding Wei Yung , Huang Jiawen , Gao Yang , Tan Ye Sing , Teng Xiang , Christine Low Siok Lan , Kanchanawong Pakorn , Toyama Yusuke , Wang Hongyan 
Published: March 2024

AbstractThe transitioning of neural stem cells (NSCs) between quiescent and proliferative states is fundamental for brain development and homeostasis. Defects in NSC reactivation are associated with neurodevelopmental disorders.Drosophilaquiescent NSCs extend an actin-rich primary protrusion toward the neuropil. However, the function of the actin cytoskeleton during NSC reactivation is unknown. Here, we reveal the fine F-actin structures in the protrusions of quiescent NSCs by expansion and super-resolution microscopy. We show that F-actin polymerization promotes the nuclear translocation of Mrtf, a microcephaly-associated transcription factor, for NSC reactivation and brain development. F-actin polymerization is regulated by a signaling cascade composed of G-protein-coupled receptor (GPCR) Smog, G-protein αq subunit, Rho1 GTPase, and Diaphanous (Dia)/Formin during NSC reactivation. Further, astrocytes secrete a Smog ligand Fog to regulate Gαq-Rho1-Dia-mediated NSC reactivation. Together, we establish that the Smog-Gαq-Rho1 signaling axis derived from astrocytes, a NSC niche, regulates Dia-mediated F-actin dynamics in NSC reactivation.
Freshwater fish egg dispersal by attaching to waterbirds
Authors: Yao Akifumi , Mashiko Miyuki , Toquenaga Yukihiko 
Published: March 2024

ABSTRACTDispersal over geographic barriers plays an essential role in colonization, gene flow, metapopulation dynamics, and invasion (Bowler and Benton 2005). Since dry lands strictly separate freshwater habitats, as expressed by the phrase “islands of water in a sea of dry land” (Faulks, Gilligan, and Beheregaray 2010), dispersal among freshwater waterbodies by themselves is challenging of aquatic organisms. Rumors have existed worldwide that freshwater fish eggs are dispersed by attaching to (ectozoochory) or excretion from (endzoochory) waterbirds (Hirsch et al. 2018). It is well documented that waterbirds disperse aquatic plants, zooplankton, and various aquatic invertebrates, which are co-distributed with fishes (Green et al. 2023). However, there is only two reported cases of empirical evidence of endzoochory in freshwater fishes and no scientific evidence of ectozoochory (Hirsch et al. 2018; Silva et al. 2019; Lovas-Kiss et al. 2020; Green et al. 2023). Here, we show that the southern medaka (Oryzias latipes, hereafter medaka) egg can travel passively by attaching to waterbirds.