bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular basis of arthropod appendage diversity
Authors: Bruce Heather S. , Patel Nipam H. 
Published: January 2025

ABSTRACTArthropods have an incredible diversity of limbs that are modified for walking, chewing, cleaning, mating, grasping, sensing, and more. Understanding the relationships and evolutionary histories of different limbs is a central task, but their sheer diversity makes this a daunting if not impossible task using morphology alone. Here, the in situ expression patterns and CRISPR-Cas9 phenotypes for the five best-studied leg-patterning genes –Distal-less,Sp6-9,dachshund,extradenticle, andhomothorax– are described for all limbs of the crustaceanParhyale.Crustaceans are well-suited for this task because their limbs are more diverse than those of other arthropods, and each individual possesses a wide range of limb types that are relevant to many other arthropods, living and extinct. These results will a) provide a template for understanding the genetic basis of limb construction in arthropods more generally based on the strong phenotypes that can be obtained with CRISPR-Cas9, and b) contribute to our understanding of the evolution and affinities of highly modified legs like mouthparts and genitalia using molecular methods to complement previous morphological and embryological approaches.
Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry
Authors: Boatman Anna K. , Chappel Jessie R. , Kirkwood-Donelson Kaylie I. , Fleming Jonathon F. , Reif David M. , Schymanski Emma L. , Rager Julia E. , Baker Erin S. 
Published: January 2025

AbstractOver the last decade, global contamination from per- and polyfluoroalkyl substances (PFAS) has become apparent due to their detection in countless matrices worldwide, from consumer products to human blood to drinking water. As researchers implement non-targeted analyses (NTA) to more fully understand the PFAS present in the environment and human bodies, clear guidance is needed for consistent and objective reporting of the identified molecules. While confidence levels for small molecules analyzed and identified with high-resolution mass spectrometry (HRMS) have existed since 2014, unification and automation of these levels is needed due to inconsistencies in reporting and continuing innovations in analytical methods. Here, we (i) investigate current practices for confidence level reporting of PFAS identified with liquid chromatography (LC), gas chromatography (GC), and/or ion mobility spectrometry (IMS) coupled with high resolution mass spectrometry (HRMS) and (ii) propose a simple, unified confidence level guidance that incorporates both PFAS-specific attributes and IMS collision cross section (CCS) values.SynopsisUnified and simplified requirements guide confidence level assignment in non-targeted PFAS identification efforts with ion mobility spectrometry.
Phylo-HS: A phylogenetic hierarchical softmax for taxonomic classification
Authors: Menegaux Romain 
Published: January 2025

AbstractTaxonomic binning –assigning taxonomic labels to DNA sequencing reads – is a core component of metagenomics data analysis. While machine learning approaches offer competitive speed and accuracy, their scalability is hindered by the growing number of referenced genomes and species. A major bottleneck lies in the final softmax layer of neural network models, which computes probabilities and gradients for all outcome classes. To address this, we proposePhylo-HS, a hierarchical softmax method that leverages the taxonomic tree to group classes into meaningful clusters. Phylo-HS achieves an order of magnitude speed improvement on a dataset with 5,000 classes and improves classification accuracy compared to frequency-based hierarchical softmax methods. By integrating phylogenetic structure into the model, Phylo-HS effectively balances scalability and accuracy for large-scale metagenomic analysis.
Antioxidant supplementation blunts the proteome response to three weeks of sprint interval training preferentially in human type 2 muscle fibres
Authors: Wyckelsma Victoria L , Murgia Marta , Kamandulis Sigitas , Gastaldello Stefano , Brazaitis Marius , Snieckus Audrius , Eimantas Nerijus , Pääsuke Mati , Edman Sebastian , Apro William , Andersson Daniel C , Westerblad Håkan , Venckunas Tomas 
Published: January 2025

ABSTRACTSprint interval training (SIT) is a time-efficient type of endurance training that involves large type 2 muscle fibre recruitment. Effiective antioxidant supplementation may mitigate positive training adaptations by limiting the oxidant challenge. Our aim was to test whether SIT affiects type 2 more than type 1 muscle fibres, and whether the training response is mitigated by antioxidant treatment. Young men performed three SIT sessions (6 × 30 s all-out cycling) per week for three weeks while treated with antioxidants (vitamin C, 1 g/day; vitamin E, 235 mg/day) or placebo. Vastus lateralis biopsies were taken to measure (i) activation of genes for reactive oxygen/nitrogen species (ROS) sensors and inflammatory mediators with quantitative RT PCR and (ii) fibre type-specific proteome adaptations using mass spectrometry-based proteomics. Vitamin treatment decreased the upregulation of genes for ROS sensors and inflammatory regulators during the first SIT session. The three weeks of SIT caused generally larger proteome adaptations in type 2 than in type 1 fibres, and this included larger increases in abundance of proteins involved in mitochondrial energy production. Vitamin treatment blunted the SIT-induced proteome adaptations, whereas it did not affiect the training-induced improvement in maximal cycling performance. In conclusion, (i) the large type 2 fibre recruitment and resulting proteome adaptations are instrumental to the effiectiveness of SIT, and (ii) antioxidant supplementation counteracts positive muscular adaptations to SIT, which would blunt any improvement in submaximal endurance performance, whereas it does not affiect the improvement in maximal cycling performance, where O2 delivery to muscle would be limiting.
Synthetic FLS2 receptor oligomer boosts plant innate immunity
Authors: Ma Zhiming , Xie Yi , Chng Choon-Peng , Huang Changjin , Miao Yansong 
Published: January 2025

AbstractCell surface receptors’ gradual assembly and oligomerization are vital for controlling receptor activation and turnover. However, the spatiotemporal mechanisms of how surface receptor interactions achieve high efficiency and sustain plant immune signaling remain unclear. Here, we synthetically engineered theArabidopsispattern recognition receptor FLS2 to control its oligomerization precisely. We investigated the dynamic FLS2 nanoscale assemblies at the single-molecule level and their corresponding rewired immune signaling. Engineered FLS2 exhibits enhanced defense mechanisms in an oligomerization status-dependent manner. FLS2 dimerization significantly enhances immune responses, while the over-assembled tetrameric version impairs receptor endocytosis, disrupting its timely turnover and weakening sustained immune signaling. Our results reveal precise control of immune receptor assemblies for initial activation and long-lasting immune signaling, offering insights for engineering plant defense receptors.
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE
Authors: Arend Lis , Adamowicz Klaudia , Schmidt Johannes R. , Burankova Yuliya , Zolotareva Olga , Tsoy Olga , Pauling Josch K. , Kalkhof Stefan , Baumbach Jan , List Markus , Laske Tanja 
Published: January 2025

AbstractDespite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from non-biological factors remain a significant challenge in data analysis. In addition, the wide range of available normalization methods renders the choice of a suitable normalization method challenging. We systematically evaluated 17 normalization and two batch effect correction methods, originally developed for pre-processing DNA microarray data but widely applied in proteomics, on six publicly available spike-in and three label-free and tandem mass tag datasets. Opposed to state-of-the-art normalization practice, we found that a reduction in intragroup variation is not directly related to the effectiveness of the normalization methods. Furthermore, our results demonstrated that the methods RobNorm and Normics, specifically developed for proteomics data, in line with LoessF performed consistently well across the spike-in datasets, while EigenMS exhibited a high false positive rate. Finally, based on experimental data, we show that normalization substantially impacts downstream analyses, and the impact is highly dataset-specific, emphasizing the importance of use-case-specific evaluations for novel proteomics datasets. For this, we developed the PROteomics Normalization Evaluator (PRONE), a unifying R package enabling comparative evaluation of normalization methods, including their impact on downstream analyses, while offering considerable flexibility, acknowledging the lack of universally accepted standards. PRONE is available on Bioconductor with a web application accessible athttps://exbio.wzw.tum.de/prone/.
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach
Authors: Dvir Yoav , Snir Sagi 
Published: January 2025

AbstractThe advent of the genomic era has produced an incredible wealth and resolution of molecular data, posing an unprecedented challenge for molecular systematics, necessitating novel techniques and paradigms. Consequently, whole genome approaches were developed to extract the evolutionary signal by taking advantage of a larger amount of data. In parallel and in light of the understanding that in prokaryotes, genome dynamics (GD) events, primarily gene gain and loss, provide a significantly richer signal than point mutations in ubiquitous housekeeping genes, GD-based approaches were suggested. However, proper modeling of these data and the processes generating them has lagged in their pace of accumulation, both because of a lack of deep understanding and because of technical difficulties. Among the central hurdles of accurate modeling of real data is the relaxation of rate constancy, particularly the untying of gain and loss rates. This relaxation violates key assumptions such as constant genome sizes, gene set, and model reversibility and has vast implications for implementation. This work presents a generic stochastic model, the two-ratio process (TRP), which encompasses and deals with these complications. As a special case, it contains the Poissonian process with different gene gain and loss rates as a form of the Birth-Death process with varying population sizes. The lack of reversibility invalidates traditional phylogenetic approaches, yielding a novel two-stage phylogenetic approach in which accurate, bidirectional parameters are first inferred for triplets and later combined by a special cherry-picking method to a complete tree. We show by algebraic techniques that this method is theoretically statistically consistent. The method implemented by the software TDDR (Triplets Directed Distances Reconstruction) was applied to synthetic data, showing an advantage over other approaches handling similar data but without the same model assumption. We also applied it to the Alignable Tight Genomic Clusters (ATGC) Database, which showed a high adequacy to the observed data. The TDDR code is available on GitHub:https://github.com/YoavDvir/TDDR.
Biocompatible sulfonium-based covalent probes for endogenous tubulin fluorescence nanoscopy in live and fixed cells
Authors: Auvray Marie , Koenen Tanja , Dybkov Olexandr , Urlaub Henning , Lukinavičius Gražvydas 
Published: January 2025

AbstractFluorescent probes enable the visualization of dynamic cellular processes with high precision, particularly when coupled with super-resolution imaging techniques that surpass the diffraction limit. Traditional methods include fluorescent protein fusion (e.g., GFP) or organic fluorophores linked to ligands targeting the protein of interest. However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine—as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C9-CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. This labeling technique is compatible with STED nanoscopy in both live and fixed cells, offering a powerful high-resolution imaging tool.
Passive symplastic phloem loading in the duckweedSpirodela polyrhiza
Authors: Li Jiazhou , Liesche Johannes 
Published: January 2025

AbstractThe lemnoidae, commonly called duckweeds, are a group of small, rapidly growing aquatic plants that play an important role in pond ecosystems and are used in biotechnological and remediation applications. While small, duckweeds feature phloem tissue in fronds and roots. To gain insight on duckweed phloem function, we investigated how sugar is loaded into the phloem sieve elements in the giant duckweedSpirodela polyrhiza. Genomes ofS. polyrhizaand three other duckweeds do not feature genes for the sucrose transporters typically associated with active apoplastic phloem loading. Neither did a sucrose transporter inhibitor affect sucrose concentration in phloem exudate. Active symplastic phloem loading was excluded based on the conventional plasmodesmata configuration and absence of oligosaccharides inS. polyrhizaphloem. Instead, uniform plasmodesmata density along the phloem loading pathway indicated a passive symplastic phloem loading type. When plasmodesmata permeability was artificially reduced by hormone treatment, the sucrose concentration in the phloem exudate was reduced, highlighting the potential role of plasmodesmata regulation in setting carbon export rates in species with passive phloem loading. Our results identifyS. polyrhizaas the first monocot species with passive phloem loading. Moreover, they indicate opportunities for optimization of duckweed growth.
Neur-Ally: A deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders
Authors: Prakash Anil , Banerjee Moinak 
Published: January 2025

ABSTRACTLarge scale quantitative studies have identified significant genetic associations for various neurological disorders. Expression quantitative trait loci [eQTL] studies have shown the effect of single nucleotide polymorphisms [SNPs] on the differential expression of genes in brain tissues. However, a large majority of the associations are contributed by SNPs in the noncoding regions which can have significant regulatory function but are often ignored. Besides mutations that are in high linkage disequilibrium [LD] with actual regulatory SNPs will also show significant associations. Therefore, it is important to differentiate a regulatory non-coding SNPs with a non-regulatory one. To resolve this, we developed a deep-learning model named Neur-Ally, which was trained on epigenomic datasets from nervous tissue and cell line samples. The model predicts differential occurrence of regulatory features like chromatin accessibility, histone modifications and transcription-factor [TF] binding on genomic regions using DNA sequence as input. The model was used to predict the regulatory effect of neurological condition specific non-coding SNPs using in-silico mutagenesis. The effect of associated SNPs reported in Genome-wide association studies [GWAS] of neurological condition, Brain eQTLs, Autism Spectrum Disorder [ASD] and reported probable regulatory SNPs in neurological conditions were predicted by Neur-Ally.
Legacy effects of European colonialism on hotspots of biocultural diversity threat
Authors: Lenzner Bernd , Baumann Andreas , Norder Sietze , Essl Franz , Fellner Hannes A. 
Published: January 2025

AbstractPatterns of biological diversity have been shaped by cultural practices in the past, while in turn, cultures and languages have evolved in close interaction with local species and ecosystems. However, in the Anthropocene, humans are putting increasingly more and diverse pressures on ecosystems and cultures resulting in accelerating threat levels on both. Understanding where biological and linguistic diversity (a common measure of cultural diversity) is threatened globally, and which drivers shape their distribution is crucial for pinpointing hotspots and prioritizing efforts to counter these threats. We find that the spatial patterns of the erosion of biological and cultural diversity are weakly congruent on a global scale and that they are driven by differential sets of mechanisms. However, our results also indicate that particularly large-scale historic socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity. The duration of European colonialism (i.e., the time a specific region was occupied by Europeans powers) significantly increases contemporary observed threat levels of biological and linguistic diversity.Significance StatementBiological and cultural diversity are closely intertwined. However, in an increasingly changing world where anthropogenic drivers put increasing pressures on ecosystems and cultures, both are threatened. Understanding how these threats to both, biological and linguistic diversity, are organized in space and where their individual and combined threat hotspots are is crucial for prioritization efforts to safeguard both. We also show what drivers affect their threat level globally and pinpoint that particularly large-scale socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity.
Molecular Basis of PAC1R Allosteric Modulation with Lipids in Membranes
Authors: Hamilton Nicholas B , Yang Bo , Xiang Chijian , Li Tongtong , Schneebeli Severin T. , Li Jianing 
Published: January 2025

AbstractThe pituitary adenylate cyclase-activating polypeptide receptor I (PAC1R) represents a highly sought-after therapeutic target for chronic pain, migraine, and post-traumatic stress. As a class B G protein-coupled receptor (GPCR), the PAC1R is highly expressed throughout the neuronal and central nervous system membranes, with the receptor subject to hormone activation and subsequent signal transduction. Despite its desirable indication, small molecule agonists for PAC1R have been notoriously difficult to develop due to competition with PACAP. For this reason, allosteric activation of the receptor has emerged as a promising pathway. To probe potential allosteric sites, herein, we present a study of the receptor in biomimetic concentrations of lipid membranes. Our results reveal that cholesterol recognizes two canonical and two non-canonical binding sites at PAC1R, which may influence critical residues in the transmembrane domain and PAC1R activation. Also, our simulations suggest the glycolipid GM3 interacts with PAC1R in both the extracellular and transmembrane domains. These lipid binding hotspots may hold high potential for advancing our understanding of class B GPCR signaling and the discovery of new molecules targeting PAC1R.Statement of SignificanceThe PAC1R is a highly sought after therapeutic target in the GPCR family. Understanding its natural process signaling is highly interesting in identifying new modes of control and is currently not well established. This work uses coarse-grained molecular dynamics simulations to examine diverse PAC1R models’ interactions with their endogenous lipid bilayer in compositions that match the regions in the brain where the receptor is expressed. Two lipids, cholesterol and GM3, have been previously identified in similar receptors as allosteric modulators and were specifically examined in this study. This work also showcases multiple new lipid binding sites at transmembrane and extracellular sites highly implicated in PAC1R signaling.
Arousal State Control of Physiological Human Brain Pulsations
Authors: Järvelä Matti , Kananen Janne , Helakari Heta , Korhonen Vesa , Huotari Niko , Raitamaa Lauri , Tuunanen Johanna , Kallio Mika , Piispala Johanna , Ansakorpi Hanna , Kiviniemi Vesa 
Published: January 2025

AbstractSleep promotes cerebrospinal fluid (CSF) to interstitial fluid (ISF) exchange in brain facilitated by brain pulsations. Especially brain vasomotion and arterial pulsations modulated by noradrenaline drive the intracranial fluid dynamics. Narcolepsy type 1 (NT1) entails lessened hypocretinergic output to wake-promoting systems including the noradrenergic locus coeruleus. As arousal state and noradrenergic signaling affect CSF-ISF clearance, we chose patients with NT1 as a human hypocretin-targeted model of sleep-related pathology bridging the gap between healthy awake and sleep with respect to CSF flow pulsations. We also investigated the sensitivity of MREG to detect flow with a phantom model and sought to replicate earlier pulsation findings in sleep.In this case-control study, we used fast fMRI to map brain pulsations in groups of healthy sleeping controls (n=13), healthy awake controls (n=79) and awake NT1 (n=21) patients. We measured the very low frequency (0.008-0.1) and cardiorespiratory frequencies and calculated in each frequency band the coefficient of variation, spectral power, and full band spectral entropy to obtain brain pulsation maps.We uncovered a brain pulsation profile from healthy waking to sleep to a sleep-related pathology NT1 prominently affected in the vascular-related vasomotor and brain arterial pulsations. Our results established how drivers of brain hydrodynamics are affected by a specific loss of key neurotransmitter governing arousal compared to healthy sleep. We also showed with a phantom model that MREG is sensitive to flow-related signal changes and solidified evidence of brain pulsations in the healthy states of sleep and wakefulness.Significance statementThis study establishes how a specific depletion of arousal state controlling neurotransmitter hypocretin-1 affects brain fluid dynamics by comparing patients with narcolepsy type 1 (NT1) to healthy wake and sleeping controls. We used fast fMRI to reveal that reduced hypocretinergic activity and following postulated inconsistent noradrenergic signaling in NT1 leads to high vasomotor and low brain arterial pulsations compared to healthy wakefulness while healthy sleep produces brain arterial and respiratory pulsations that dominate over those observed in NT1. The water flow biometrics we verified in this study with a phantom model indicate that deficient hypocretin-noradrenaline axis in humans leads to opposing changes in vasomotor and arterial induced brain pulsation that may propagate to altered glymphatic solute transportation.