bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read nanopore shotgun eDNA sequencing for river biodiversity, pollution and environmental health monitoring
Authors: Nousias Orestis , Duffy Fiona G. , Duffy Isabelle J. , Whilde Jenny , Duffy David J. 
Published: November 2024

AbstractAs global temperatures rise, species populations and biodiversity decline, and infectious diseases emerge all at unprecedented rates, it is more vital than ever to accurately understand the current state of natural habitats. While traditional methods including direct sampling and observation have their merits, newer technologies offer additional sampling capabilities.Here, we assess the feasibility of a single assay: shotgun long-read sequencing, to monitor species eDNA from across the tree of life, from viruses to complex multicellular organisms, across a river system (mountain tributary to sea). We conducted eDNA sampling and shotgun long-read sampling from water taken from the Avoca River watercourse, Co. Wicklow, Ireland, from a mountain tributary through to the sea, and comparative nearby beach sand sampling. We report that shotgun long-read sequencing and metagenomic analysis have utility for the detection and quantification of organismal DNA present in eDNA samples, from across the tree of life, from microbes (including DNA viruses) to mammals. With this single assay we were able to simultaneously quantify differences in eDNA abundance for a broad range of biodiversity and pathogens across sites and sample types. This included human, wildlife, plant and microbial pathogens and parasites with health, agricultural and economic importance. Additionally, the generated eDNA genomic data enabled population genetic applications even from natural complex community settings, as demonstrated here for blue mussels (Mytilus edulis). The results demonstrate that Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution and environmental health monitoring.This method is more cost-effective and requires less laboratory preparation time or molecular expertise (barcode/primer design) than alternative biodiversity eDNA approaches (e.g. metabarcoding or qPCR). Shotgun analysis approaches will also benefit from the continual expansion of reference genome databases, for environmental, evolutionary and medical reasons, among others. Computation, cloud and artificial intelligence (AI) tools (such as the cloud-based analyses utilized here) can analyze shotgun sequencing eDNA data in a matter of hours and can be used by conservation practitioners, environmentalists and public health personnel without the need for coding or in-depth bioinformatics skills. The proven citizen/community scientist applicability and ease of eDNA sampling may further revolutionize and democratize biodiversity research, conservation surveillance, and environmental health monitoring. Long-read shotgun sequencing of eDNA offers the means to assess whole ecosystems, and the ecological, trophic, and host-pathogen interactions occurring within them.
CELF2 promotes tau exon 10 inclusion via hinge domain-mediated nuclear condensation
Authors: Li Xin , Syed Ishana , Zhang Zhao , Adhikari Rashmi , Tang Dan , Ko SuHyuk , Liu Zhijie , Chen Lizhen 
Published: November 2024

SUMMARYAlternative splicing is a fundamental process that contributes to the functional diversity and complexity of proteins. The regulation of each alternative splicing event involves the coordinated action of multiple RNA-binding proteins, creating a diverse array of alternatively spliced products. Dysregulation of alternative splicing is associated with various diseases, including neurodegeneration. Here we demonstrate that CELF2, a splicing regulator and a GWAS-identified risk factor for Alzheimer’s disease, binds to mRNAs associated with neurodegenerative diseases, with a specific interaction observed in the intron adjacent to exon 10 on Tau mRNA. Loss of CELF2 in the mouse brain results in a decreased inclusion of Tau exon 10, leading to a reduced 4R:3R ratio. Further exploration shows that the hinge domain of CELF2 possesses an intrinsically disordered region (IDR), which mediates CELF2 condensation and function. The functionality of IDR in regulating CELF2 function is underscored by its substitutability with IDRs from FUS and TAF15. Using TurboID we identified proteins that interact with CELF2 through its IDR. We revealed that CELF2 co-condensate with NOVA2 and SFPQ, which coordinate with CELF2 to regulate the alternative splicing of Tau exon 10. A negatively charged residue within the IDR (D388), which is conserved among CELF proteins, is critical for CELF2 condensate formation, interactions with NOVA2 and SFPQ, and function in regulating tau exon 10 splicing. Our data allow us to propose that CELF2 regulates Tau alternative splicing by forming condensates through its IDR with other splicing factors, and that the composition of the proteins within the condensates determines the outcomes of alternative splicing events.
SloR-SRE binding to theS. mutans mntHpromoter is cooperative
Authors: Ziogas Myrto , Drummond India , Todorovic Igor , Kraczkowsky Katie , Zhang Hua , Wu Hui , Spatafora Grace 
Published: November 2024

ABSTRACTStreptococcus mutansis a commensal member of the plaque microbiome. It is especially prevalent when dietary sugars are available forS. mutansfermentation, generating acid byproducts that lower plaque pH and foster tooth decay.S. mutanscan survive in the transient conditions of the mouth, in part because it can regulate the uptake of manganese and iron during periods of feast when metal ions are available, and famine when they are limiting.S. mutansdepends on a 25kDa metalloregulatory protein, called SloR, to modulate uptake of these cations across the bacterial cell surface. When bound to manganese, SloR, binds to palindromic recognition elements in the promoter of thesloABCgenes that encode the major manganese transporter inS. mutans. Reports in the literature describ MntH, an ancillary manganese transporter inS. mutans, that is also subject to SloR control. In the present study, we performed expression profiling experiments that reveal coordinate regulation of thesloABCandmntHgenes at the level of transcription. In addition, we describe a role for themntHgene product that is redundant with that of thesloABC-encoded metal ion uptake machinery. The results of DNA binding studies support direct SloR binding to themntHpromoter region which, like that at thesloABCpromoter, harbors three palindromic recognition elements to which SloR binds cooperatively to repress downstream transcription. These findings expand our understanding of the SloR metalloregulome and elucidate SloR-DNA binding that is essential forS. mutansmetal ion homeostasis and fitness in the oral cavity.
Membrane mimetic thermal proteome profiling (MM-TPP) towards mapping membrane protein-ligand dynamics
Authors: Jandu Rupinder Singh , Al-Seragi Mohammed , Aoki Hiroyuki , Babu Mohan , van Hoa Franck Duong 
Published: November 2024

AbstractIntegral membrane proteins (IMPs) remain the principal target of small-molecule therapeutics, and yet modalities towards probing on and off-target hits against this protein class in a robust, unbiased, and detergent-free manner remain starkly underdeveloped. Previously, we introduced the Peptidisc membrane mimetic (MM) for the water-soluble stabilization of theEscherichia colimembrane proteome and interactome (Carlson et al., 2019). Herein, we implement the Peptidisc into thermal proteome profiling (TPP), enabling for the first time a broad-scale level characterization of membrane protein-ligand interactions while completely circumventing structural perturbations invoked by detergents. Using a library prepared from the whole mouse liver, we determine the influence of ATP and orthovanadate on the thermal stability of IMPs, including pharmaceutically relevant ATP-binding cassette ABC transporters and G-protein coupled receptors. MM-TPP also detects thermal stability changes driven by ATP by-products, where non-canonical ATP binders can be validated with next-generation computational tools. MM-TPP thus offers a robust platform for identifying on- and off-target ligand effects, providing insights into the druggable membrane proteome and its stability as a consequence of changing and often dynamic small molecules.
Methuselah Proteins in Longevity: Unraveling Their Impact Through Mathematical Genomics
Authors: Hassan Sk. Sarif , Nawn Debaleena , Ghosh Ankita , Sil Moumita , Goswami Arunava , Basu Pallab , Lundstrom Kenneth , Uversky Vladimir N. 
Published: November 2024

AbstractThis study provides a quantitative and comprehensive analysis of 18 Methuselah (mth) protein variants from fruit flies, focusing on their evolutionary relationships, structural features, and functional roles in aging and longevity. Phylogenetic analysis identified two major clades of mth proteins, with the first clade indicating conserved functions across Drosophila species and the second clade reflecting gene duplication and diversification. The study found five distinct functional subclasses of mth proteins through amino acid frequency and poly-string analyses, linked to their structural diversity and role in longevity. Structural topology and post-translational modifications reveal similarities with G-protein-coupled receptors (GPCRs), suggesting that mth proteins are crucial for signal transduction and cellular health. Variability in propeptide cleavage sites and intrinsic protein disorder further highlight adaptive roles in signaling. The findings underscore the importance of a quantitative and comprehensive approach to studying Methuselah genes, offering insights into their functional versatility and evolutionary dynamics. This enhanced quantitative understanding contributes to advancing research on aging and longevity.
Platelet Membrane-Coated SPION for Targeted Paclitaxel Delivery and Magnetic Hyperthermia in Cancer Therapy
Authors: Tavakoli Mohamadreza , Maghsoudian Samane , Rezaei-Aderiani Amir , Hajiramezanali Maliheh , Amani Mahdiyar , Sharifikolouei Elham , Ghahremani Mohammad Hossein , Raoufi Mohammad , Motasadizadeh Hamidreza , Dinarvand Rassoul 
Published: November 2024

AbstractDue to the limited therapeutic efficacy and side effects associated with conventional chemotherapy, researchers have turned their attention to developing targeted drug delivery systems using advanced nanotechnology. Coating nanoparticles (NPs) with cell membranes is a promising strategy because it extends their circulation times and allows them to selectively adhere to damaged vessel sites through the platelet membrane surface, thereby enhancing tumor uptake. Herein, we have developed a biomimetic drug delivery system consisting of superparamagnetic iron oxide nanoparticles (SPIONs) coated by platelet membranes (PM) for carrying Paclitaxel (PTX) to exploit the synergism effect of chemotherapy and magnetic hyperthermia. Controlled-release PTX nanoparticles exhibited consistent behavior over time, indicating no significant difference in release between SPION/PTX and SPION/PTX/PM at pH 7.4. However, at pH 5.5, improved release was observed, specifically a 1.4-fold increase for SPION/PTX/PM. The confocal and flow cytometry results show an enhancement in the cellular uptake of SPION/PTX/PM nanoparticles, with an average fluorescence intensity of 142 ±12.5. MTT results indicated that SPION/PTX/PM demonstrates superior cytotoxic effects compared to SPION/PTX and PTX alone, showing an IC50 value of 5 μg/mL after 48 h of treatment. Furthermore, the IC50 decreased to 1 μg/mL when an alternating magnetic field was applied. Hence, the in vivo results and histopathological staining showed that the SPION/PTX/PM-AFM treatment group exhibited the highest rate of tumor growth inhibition, reaching nearly 92.14 %. These findings highlight the potential of using platelet membrane-coated nanoparticles for targeted delivery, combining magnetic hyperthermia and chemotherapy to minimize chemotherapy’s undesirable effects while maximizing therapeutic outcomes.
Augmenting Transcriptome Annotations through the Lens of Splicing Evolution
Authors: Zang Xiaofei Carl , Chen Ke , Khan Irtesam Mahmud , Shao Mingfu 
Published: November 2024

AbstractAlternative splicing (AS) is a ubiquitous mechanism in eukaryotes. It is estimated that 90% of human genes are alternatively spliced. Despite enormous efforts, transcriptome annotations remain, nevertheless, incomplete. Conventional means of annotation were largely driven by experimental data such as RNA-seq and protein sequences, while little insight was shed on understanding transcriptomes and alternative splicings from the perspective of evolution. This study addresses this critical gap by presenting TENNIS (Transcript EvolutioN for New Isoform Splicing), an evolution-based model to predict unannotated isoforms and refine existing annotations without requiring additional data. The model of TENNIS is based on two minimal premises–AS isoforms evolve sequentially from existing isoforms, and each evolutionary step involves a single AS event. We formulate the identification of missing transcripts as an optimization problem and parsimoniously find the minimal number of novel transcripts. Our analysis showed approximately 80% of multi-transcript groups from six transcriptome annotations satisfy our evolutionary model. At a high confidence level, 40% of isoforms predicted by TENNIS were validated by deep long-read RNA-seq. In a simulated incomplete annotation scenario, TENNIS dramatically outperforms two randomized baseline approaches by a 2.25-3 fold-change in precision or a 3.5-3.9 fold-change in recall, after controlling the same level of recall or precision of the baseline methods. These results demonstrate that TENNIS effectively identifies missing transcripts by complying with minimal propositions, offering a powerful approach for transcriptome augmentations through the lens of alternative splicing evolutions. TENNIS is freely available athttps://github.com/Shao-Group/tennis.
Microtubule dynamics are defined by conformations and stability of clustered protofilaments
Authors: Kalutskii Maksim , Grubmüller Helmut , Volkov Vladimir A , Igaev Maxim 
Published: November 2024

AbstractMicrotubules are dynamic cytoskeletal polymers that add and lose tubulin dimers at their ends. Microtubule growth, shortening and transitions between them are linked to GTP hydrolysis. Recent evidence suggests that flexible tubulin protofilaments at microtubule ends adopt a variety of shapes, complicating structural analysis using conventional techniques. Therefore, the link between GTP hydrolysis, protofilament structure and microtubule polymerization state is poorly understood. Here, we investigate the conformational dynamics of microtubule ends using coarse-grained modeling supported by atomistic simulations and cryo-electron tomography. We show that individual bent protofilaments organize in clusters, transient precursors to a straight microtubule lattice, with GTP-bound ends showing elevated and more persistent cluster formation. Differences in the mechanical properties of GTP- and GDP-protofilaments result in differences in intra-cluster tension, determining both clustering propensity and protofilament length. We propose that conformational selection at microtubule ends favors long-lived clusters of short GTP-protofilaments that are more prone to form a straight microtubule lattice and accommodate new tubulin dimers. Conversely, microtubule ends trapped in states with unevenly long and stiff GDP-protofilaments are more prone to shortening. We conclude that protofilament clustering is the key phenomenon that links the hydrolysis state of single tubulins to the polymerization state of the entire microtubule.
Moisture and competition constrain ephemeral resource quality for burying beetle reproduction
Authors: Hayes Tracie E. , Lassérès Léo , Yang Louie H. 
Published: November 2024

AbstractShifts in abiotic factors such as temperature and moisture can change the availability of resources, especially under climate change. Both abiotic and biotic drivers can have profound, rapid effects on species distribution, survival, and reproduction. Little is known about how abiotic factors affect the availability of ephemeral resources. Burying beetles (Nicrophorusspp.) are specialist users of ephemeral resources, as their reproduction requires locating, defending, and burying a small carcass. Environmental moisture, such as coastal fog, could change how quickly carcasses dry out. We tested the role of carcass moisture and interspecific competition with a generalist scavenger,Heterosilphaspp., on reproduction by placing pairs ofNicrophorus guttulain field chambers with fresh and experimentally dehydrated mouse carcasses. Pairs that were given fresh mouse carcasses were more likely to carry out reproductive behaviors and produce viable offspring than pairs that were given a partially dehydrated mouse. For those pairs that reproduced, competition limited the number of offspring. These results indicate that shifts in abiotic factors under climate change, along with biotic factors like competition, can reduce the availability of ephemeral resource patches for consumers.
The maize recombination landscape evolved during domestication
Authors: Epstein Ruth , Wheeler JJ , Hubisz Melissa , Sun Qi , Bukowski Robert , Zhai Jingjing , Lai Wei-Yun , Buckler Edward , Pawlowski Wojtek P. 
Published: November 2024

AbstractMeiotic recombination is an important evolutionary process because it can increase the amount of genetic variation within populations through the breakage of unfavorable linkages and creation of novel allelic combinations. Despite the plethora of knowledge about population-level benefits of recombination and numerous theoretical studies examining how recombination rates can evolve over time, there is a lack of empirical evidence for any hypotheses that have been put forward. To alleviate this gap in knowledge, we characterized the evolution of the recombination landscape inZea maysssp.mays(maize) during its domestication fromZea maysssp.parviglumis(teosinte), explored hypotheses that permitted the evolution of the maize recombination landscape and tied these alterations to changes in the genetic basis of recombination. Using experimental populations and the population genomics approach of ancestral recombination graph (ARG) inference, our data demonstrated that maize had a 12% increase in its genome-wide recombination rate during domestication. Although the maize and teosinte recombination landscapes are highly correlated, r = 0.85 at 1Mb resolution, maize has evolved to have higher recombining regions in interstitial chromosome regions, compared to teosinte which only harbors high recombining regions sub-telomerically. Our data show that the re-patterning of COs towards interstitial chromosome regions came from reduced CO interference levels within maize. Supporting the idea that CO interference is reduced within maize, we found evidence for selection acting on trans-acting recombination-modifiers that participate in the class I CO pathway or CO interference directly. Lastly, we showed that the re-patterning of COs was beneficial to maize evolution because regions that significantly increased in recombination were targeted to gene-rich regions harboring domestication related loci. Because we found regions with significant increases in recombination had a lower deleterious mutation load, compared to regions with decreases in recombination, we concluded that the domestication-related variation in these regions, in which selection acted upon during domestication, was shielded from the Hill-Robertson effect. In conclusion, the re-patterning of CO events during domestication allowed maize to adapt and evolve at a faster rate than previously understood.
Acidic Conditions Promote Clustering of Cancer Cell Derived Extracellular Vesicles and Enhance their Fusion with Synthetic Liposomes
Authors: Fisher William S. , Douglas Jessica , Roshan Sherwin , Perez Ramon , Wei Sophia , Roberts Logan , Ewert Kai K. , Safinya Cyrus R. 
Published: November 2024

ABSTRACTExtracellular vesicles (EVs) are endogenous vesicles secreted by cells. Exosomes, a subset of EVs ranging from 30 to 150 nanometers in diameter, contain cytosolic proteins, gene-silencing miRNA, and gene-encoding mRNA and have roles in intercellular communication. Exosomes show promise as cancer chemotherapeutic drug delivery vehicles given their low immunogenicity and cell-specific delivery of luminal contents to the cytosol of target cells. However, loading exosomes with cancer chemotherapeutic drugs is inefficient, which limits their therapeutic application. To overcome this barrier, methods have been developed which allow fusion of EVs with synthetic liposomes preloaded with therapeutic drug. While these methods show more efficient fusion than passive incubation of EVs with liposomes, they risk either damage to the membrane proteins of the EVs or contamination of the final EV-liposome hybrid with residual depletant molecules, which can cause side effects or hinder content delivery. Here, we present a new, weakly perturbative method which uses acidic conditions (pH 5) to significantly enhance the fusion of EVs and synthetic, neutral liposomes (NLs) compared to passive incubation in pH 7.4 at 37 °C. An adapted Forster resonance energy transfer (FRET) based lipid mixing assay confirms that fusion is enhanced with this method. This significant finding implies that lipid-only synthetic liposomes are able to fuse with EVs, creating EV-liposome hybrids under relevant temperature and pH conditions, with no other non-lipidic component, such as fusogenic amphipathic peptides, added to the synthetic liposomes. Remarkably, differential interference contrast (DIC) and fluorescence microscopy show that this enhancement of fusion corresponds with the onset of clustering of mixtures of EVs and NLs, or EVs alone, in acidicbut not neutralpH conditions. The findings support a hypothesis that content release from EVs in early to late endocytic environment may be a combination of protein-protein clustering interactions and a lipidic component. Further, this study provides a novel method for enhanced fusion of EVs and liposomes which is expected to preserve EV membrane proteins and functionality towards the development of therapeutic hybrid drug delivery vehicles in nanomedicine applications.