bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolomic profiles of stony coral species from the Dry Tortugas National Park display inter- and intraspecies variation
Authors: Deutsch Jessica M. , Demko Alyssa M. , Jaiyesimi Olakunle A. , Foster Gabriel , Kindler Adelaide , Pitts Kelly A. , Vekich Tessa , Williams Gareth , Walker Brian K. , Paul Valerie J. , Garg Neha 
Published: October 2024

AbstractCoral reefs are experiencing unprecedented loss in coral cover due to increased incidence of disease and bleaching events. Thus, understanding mechanisms of disease susceptibility and resilience, which vary by species, is important. In this regard, untargeted metabolomics serves as an important hypothesis-building tool enabling delineation of molecular factors underlying disease susceptibility or resilience. In this study, we characterize metabolomes of four species of visually healthy stony corals, includingMeandrina meandrites,Orbicella faveolata,Colpophyllia natans, andMontastraea cavernosa, collected at least a year before stony coral tissue loss disease reached the Dry Tortugas, Florida and demonstrate that both symbiont and host-derived biochemical pathways vary by species. Metabolomes ofMeandrina meandritesdisplayed minimal intraspecies variability and highest biological activity against coral pathogens when compared to other species in this study. Application of advanced metabolite annotation methods enabled delineation of several pathways underlying interspecies variability. Specifically, endosymbiont-derived vitamin E family compounds, betaine lipids, and host-derived acylcarnitines were among the top predictors of interspecies variability. Since several metabolite features that contributed to inter- and intraspecies variation are synthesized by the endosymbiotic Symbiodiniaceae, which could be a major source of these compounds in corals, our data will guide further investigations into these Symbiodiniaceae-derived pathways.Importance.Previous research profiling gene expression, proteins, and metabolites produced during thermal stress has reported the importance of endosymbiont-derived pathways in coral bleaching resistance. However, our understanding of interspecies variation in these pathways among healthy corals and their role in diseases is limited. We surveyed the metabolomes of four species of healthy corals with differing susceptibilities to the devastating stony coral tissue loss disease and applied advanced annotation approaches in untargeted metabolomics to determine the interspecies variation in host and endosymbiont-derived pathways. Using this approach, we propose the survey of immune markers such as vitamin E family compounds, acylcarnitines, and other metabolites to infer their role in resilience to coral diseases. As time-resolved multi-omics datasets are generated for disease-impacted corals, our approach and findings will be valuable in providing insight into the mechanisms of disease resistance.
Genome of the enigmatic watering-pot shell reveals adaptations of a living suction anchor
Authors: Sigwart Julia D , Wong Nur Leena W.S. , González Vanessa Liz , Machado Fabrizio Marcondes , Greve Carola , Schell Tilman , Chen Zeyuan 
Published: October 2024

AbstractThe watering pot shells have been rightly called “the weirdest bivalves” for their highly modified body plan and fused tubular shell that resemble the spout of a watering can. This adventitious tube has defied rational explanation as an adaptive pathway and yet arose twice convergently. We present the first genome for the clade Anomalodesmata: an annotated chromosome-scale genome ofVerpa penis(Linnaeus, 1758). The first watering pot shell ever described ranges across southeast Asia but is nonetheless extremely rare and has never previously been sequenced. The assembly length of 507 Mb, with a contig N50 of 5.33 Mb, has 96.5% of sequences anchored onto 19 pseudochromosomes. Contrary to expectations from such a highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral condition of heterodont bivalves (1N=19). A new hypothesis based on analysis of the living animals and literature explains the adaptive significance of this body form: it is structurally optimised for vertical stability in soft sediments, with parallels to engineering principles of a suction anchor. Our study offers new insights to a long-standing mystery in molluscan body forms, and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.
Evolutionary conserved sap peptides derived from xylem-specific peptide precursors in woody angiosperms
Authors: Chen Chang-Hung , Liou Pin-Chien , Lin Chih-Ching , Kuo Shang-Che , Wu Chia-Chen , Lin Ying-Chung Jimmy , Chen Ying-Lan 
Published: October 2024

AbstractPeptides act as long-distance mobile signals, transported through vascular sap to coordinate complex developmental processes. Since the tissue-specificity of peptide precursor gene expression is critical in determining peptide signaling function, we integrated vascular sap peptidomes with tissue-level transcriptomes to investigate the roles of sap peptides in two economically important woody plants,Populus trichocarpaandEucalyptus grandis. Xylem exhibited the highest ratio of tissue-specific sap peptide precursor genes. Most of the sap peptides derived from xylem-specific precursor genes ofP. trichocarpaandE. grandiswere highly conserved throughout woody species selected from different clades in angiosperms, including magnoliids, rosids and asterids in eudicots. To further explore the conservation of these peptides, we examined the sap peptidome ofCinnamomum kanehirae(camphor tree), from the ancient clade with three xylem cell types. Approximately 90% of the peptides from xylem-specific precursors that were conserved betweenP. trichocarpaandE. grandis, were also conserved in the vascular sap ofC. kanehirae, demonstrating a remarkably high conservation of these peptides across woody angiosperms. Most of the sap peptides conserved in these three woody species are also highly conserved across land plants, suggesting that these peptides may contribute to plant terrestrialization. Within the sap peptides from xylem- specific precursor genes, a total of 10 peptides were identical across all three woody plants. This substantial enrichment of xylem-specific precursor-derived peptides, along with their high conservation, suggests that these long-distance mobile peptides play a crucial role in secondary xylem development.One sentence summaryIntegration of sap peptidomic and tissue-level transcriptomic data revealed highly conserved long-distance mobile peptides derived from xylem- specific precursors across woody angiosperms.
Odorant receptors tuned to isothiocyanates inDrosophila melanogasterand their evolutionary expansion in herbivorous relatives
Authors: Matsunaga Teruyuki , Reisenman Carolina E. , Goldman-Huertas Benjamin , Rajshekar Srivarsha , Suzuki Hiromu C. , Tadres David , Wong Joshua , Louis Matthieu , Ramírez Santiago R. , Whiteman Noah K. 
Published: October 2024

ABSTRACTPlants release complex volatile compounds to attract mutualists, deter herbivores, and deceive pollinators. Here, we used herbivorous specialist flies that feed on mustard plants (Scaptomyzaspp.) and microbe-feeding species (Drosophila melanogasterandScaptomyzaspp.) to investigate how plant-derived electrophilic toxins such as isothiocyanates (ITCs) affect insects, and how flies detect these compounds through olfaction. In survival assays,D. melanogasterexposed to volatile allyl isothiocyanate (AITC), a toxin derived from many Brassicales plants, were acutely intoxicated, demonstrating the high toxicity of this volatile compound to non-specialized insects. Through single sensillum recordings (SSR) from olfactory organs and behavioral assays, we found that the Odorant receptor 42a (Or42a) is necessary for AITC detection and behavioral aversion. Comparative transcriptome and RNA FISH studies across the drosophilid genusScaptomyzarevealed lineage-specific triplication ofOr42ain the Brassicales specialists and a doubling ofOr42a-positive-olfactory sensory neurons. Heterologous expression experiments showed that Or42a paralogs in Brassicales-specialists exhibited broadened sensitivity to ITCs in a paralog-specific manner. Finally, AlphaFold2 modeling followed by site-directed mutagenesis and SSR identified two critical amino acid substitutions that conferredOr42aheighten sensitivity to Brassicales-derived ITCs. Our findings suggest that ITCs, which are toxic to most insects, can be detected and avoided by non-specialists likeD. melanogasterthrough olfaction. In Brassicales specialists, these same Ors experienced gene duplication events that resulted in an expanded sensitivity to ITC compounds. Thus, the insect’s olfactory system can rapidly adapt to toxic ecological niches provided by chemically-defended host plants through co-option of chemosensory capabilities already present in their ancestors.
A neonicotinoid pesticide causes tissue-specific gene expression changes in bumble bees
Authors: Witwicka Alicja , López-Osorio Federico , Chaudhry-Phipps Hannah , Wurm Yannick 
Published: October 2024

AbstractPesticides often harm beneficial insect pollinators, impairing their ability to navigate the environment, learn, fight off disease, and reproduce. Understanding the mechanisms behind these disorders is essential for improving pesticide risk assessments. To test whether pesticide exposure induces similar or distinct transcriptional responses across tissues, we administered field-realistic dose of the common neonicotinoid clothianidin toBombus terrestrisbumble bees. We then measured gene expression in brains, hind femurs, and Malpighian tubules. Our analyses revealed that 82% of gene expression differences were tissue-specific. Although genes associated with energy metabolism were consistently down-regulated across all tissues, pesticide exposure primarily affected core tissue functions, namely genes linked to ion transport in the brain, muscle function in the hind femur, and detoxification in Malpighian tubules. Furthermore, while the brain holds the highest abundance of pesticide target receptors, other tissues showed more substantial differences in gene expression magnitude. These findings reveal that pesticide exposure causes complex, tissue-specific effects rather than a uniform body-wide response. Our study provides a mechanistic basis for the severe effects of pesticide exposure on bees and shows how transcriptomics can help pinpoint the most affected areas and processes across the body. Accordingly focusing toxicological assays could significantly improve the precision of pesticide safety evaluations.
Raw materials and manufacturing environment as determinants of miso microbial community
Authors: Ito Kohei , Yamaguchi Marin 
Published: October 2024

AbstractMiso is a Japanese traditional fermented food with soybeans, salt and kōji, and has gained attention among people for its sophisticated flavor and preservability. Koshu miso is a unique miso made by mixing two types of koji (rice and barley), and is produced primarily in Yamanashi Prefecture, Japan. We characterized the microbiota of miso products from Gomi-shoyu (Yamanashi, Japan) at three distinct fermentation stages: initial (day one), intermediate (four months), and advanced (ten months). All samples, except the ten-month miso, were fermented in wooden barrels. We collected samples from the manufacturing facility, extracted DNA, and performed high-throughput 16S rRNA sequencing to generate amplicon sequence variants (ASVs). Our analysis revealed that the genusStaphylococcusdominated across all miso samples, withMacrococcusandEnterococcusalso showing significant presence, particularly in the four-month miso. Notably,Staphylococcussequences in the miso matched those found in rice and barley koji, indicating the influence of raw ingredients on the initial microbial community. Additionally, the wooden barrels exhibited a microbial profile similar to the miso, suggesting their role in maintaining consistent fermentation conditions. These findings underscore the critical importance of both raw ingredients and manufacturing equipment in shaping the microbial composition and evolution of miso throughout the fermentation process.
A Review and Evaluation of Species Richness Estimation
Authors: Schmitz Johanna Elena , Rahmann Sven 
Published: October 2024

AbstractMotivationThe statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology and performance is currently lacking.ResultsWe comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant elements. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simpler methods, like the Chao 1 and Chiu estimators, yield accurate predictions for many of the tested species compositions, but tend to underestimate the true richness for heterogeneous populations and small (containing 1% to 5% of the population) samples. When the population size is known, upsampling estimators such as PreSeq and RichnEst often yield more accurate results.Availability and implementationSource code for data simulation and richness estimation is available athttps://gitlab.com/rahmannlab/speciesrichness.
Non-invasive brain-machine interface control with artificial intelligence copilots
Authors: Lee Johannes Y. , Lee Sangjoon , Mishra Abhishek , Yan Xu , McMahan Brandon , Gaisford Brent , Kobashigawa Charles , Qu Mike , Xie Chang , Kao Jonathan C. 
Published: October 2024

SummaryMotor brain-machine interfaces (BMIs) decode neural signals to help people with paralysis move and communicate. Even with important advances in the last two decades, BMIs face key obstacles to clinical viability. Invasive BMIs achieve proficient cursor and robotic arm control but require neurosurgery, posing significant risk to patients. Non-invasive BMIs do not have neurosurgical risk, but achieve lower performance, sometimes being prohibitively frustrating to use and preventing widespread adoption. We take a step toward breaking this performance-risk tradeoff by building performant non-invasive BMIs. The critical limitation that bounds decoder performance in non-invasive BMIs is their poor neural signal-to-noise ratio. To overcome this, we contribute (1) a novel EEG decoding approach and (2) artificial intelligence (AI) copilots that infer task goals and aid action completion. We demonstrate that with this “AI-BMI,” in tandem with a new adaptive decoding approach using a convolutional neural network (CNN) and ReFIT-like Kalman filter (KF), healthy users and a paralyzed participant can autonomously and proficiently control computer cursors and robotic arms. Using an AI copilot improves goal acquisition speed by up to 4.3×in the standard center-out 8 cursor control task and enables users to control a robotic arm to perform the sequential pick-and-place task, moving 4 randomly placed blocks to 4 randomly chosen locations. As AI copilots improve, this approach may result in clinically viable non-invasive AI-BMIs.
Identification of miR136, miR155, and miR183 in vascular calcification in human peripheral arteries
Authors: Corvec Tom Le , Burgaud Mathilde , Steenman Marja , Tesfaye Robel A , Goueffic Yann , Maurel-Desanlis Blandine , Quillard Thibaut 
Published: October 2024

AbstractObjectiveVascular calcification (VC) is an independent risk factor for all-cause and cardiovascular mortality. This process contributes to atherosclerotic plaque disruption and thrombosis when close to the lumen, arterial stiffness, and limits endovascular treatment success. Vascular smooth muscle cells (VSMC) in the arterial wall play a major role in VC as they can acquire mineralizing properties when exposed to osteogenic conditions. Despite its clinical impact, there are still no dedicated therapeutic strategies targeting VC.DesignTo address this question, we used human calcified and none-calcified atherosclerotic arteries (ECLAGEN Biocollection) to screen and identify microRNA (miRs) associated with vascular calcification.MethodsWe combined non-biased miRNomic (microfluidic arrays) and transcriptomic analysis to select miR candidates and their putative target genes, with expression associated with vascular calcification and ossification. We further validated miR functional regulation and function on cell mineralization using primary human vascular SMC.ResultsOur study identified 12 miRs associated with vascular calcification in carotid and femoral arteries. Among those, we showed that miR136, miR155, and miR183 expression were regulated during VSMC mineralization and overexpression of these miRs was sufficient to promote smooth muscle cell mineralization. Cross-analysis of this miRNomic and a transcriptomic analysis led to the identification of CD73 and Smad3 pathways as putative target genes responsible for mediating miR155 pro-mineralizing function.ConclusionThese results highlight the potential benefit of miR155 inhibition in limiting VC development in peripheral atherosclerotic arteries.What this paper addsVascular calcification (VC) is an independent risk factor for all-cause and cardiovascular mortality. No pharmacological treatment is currently available. Our work using human healthy and atherosclerotic peripheral arteries allowed us to non-biasedly identify miR136, miR155, and miR183 as putative players in VC, as they associate with calcification in human atherosclerotic lesions, and are sufficient to induce vascular cell mineralizationin vitro. Among those, miR155 appeared the most important driver of osteogenesisin vitro, making it a candidate for targeting VC in patients.
An ancient competition for the conserved branchpoint sequence influences physiological and evolutionary outcomes in splicing
Authors: Pereira de Castro Karen Larissa , Abril Jose M. , Liao Kuo-Chieh , Hao Haiping , Donohue John Paul , Russell William K. , Fagg W. Samuel 
Published: October 2024

SummaryRecognition of the intron branchpoint during spliceosome assembly is a multistep process that defines both mRNA structure and amount. A branchpoint sequence motif UACUAAC is variably conserved in eukaryotic genomes, but in some organisms more than one protein can recognize it. Here we show that SF1 and Quaking (QKI) compete for a subset of intron branchpoints with the sequence ACUAA. SF1 activates exon inclusion through this sequence, but QKI represses the inclusion of alternatively spliced exons with this intron branchpoint sequence. Using mutant reporters derived from a natural intron with two branchpoint-like sequences, we find that when either branchpoint sequence is mutated, the other is used as a branchpoint, but when both are present, neither is used due to high affinity binding and strong splicing repression by QKI. QKI occupancy at the dual branchpoint site directly prevents SF1 binding and subsequent recruitment of spliceosome-associated factors. Finally, the ectopic expression of QKI in budding yeast (which lacksQKI) is lethal, due at least in part to widespread splicing repression. In conclusion, QKI can function as a splicing repressor by directly competing with SF1/BBP for a subset of branchpoint sequences that closely mirror its high affinity binding site. This suggests thatQKIand degenerate branchpoint sequences may have co-evolved as a means through which specific gene expression patterns could be maintained in QKI-expressing or non-expressing cells in metazoans, plants, and animals.
BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data
Authors: Minch Benjamin , Moniruzzaman Mohammad 
Published: October 2024

AbstractViruses in the kingdomBamfordvirae, specifically giant viruses (NCLDVs) in the phylumNucleocytoviricotaand smaller members in thePreplasmiviricotaphylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom such as giant viruses, polinton-like viruses, and virophages have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets. Here, we present BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, andPreplasmiviricotagenome identification and annotation. BEREN’s performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs andPreplasmiviricotagenomes. Applied to a real-world dataset from the Baltic Sea, BEREN identified diverseBamfordviraemembers, giving insight into viral interactions and metabolic functions in this region. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis.
Template-Independent Enzymatic RNA Synthesis
Authors: Karalkar Nilesh B , Kent Tatiana , Tredinnick Taylor , Betancurt-Anzola Leonardo , Delarue Marc , Pomerantz Richard , Benner Steven A 
Published: October 2024

AbstractA route to prepare ribonucleoside triphosphates featuring a 3’-aminoxy (3’-O-NH2) removable blocking group is reported here. We then show that versions of two DNA polymerases, human DNA polymerase theta (Polθ) and mimiviral PrimPol, accept these triphosphates as substrates to add single nucleotides to an RNA primer under engineered conditions. Cleaving the O-N bond in the 3’-O-NH2group within the extended primer regenerates the 3’-OH group, facilitating subsequent polymerase cycles that add a second, selected, nucleotide. These enzymes and triphosphates together enable template-independent enzymatic RNA synthesis (TIERS) exploiting a cyclic reversible termination framework. The study shows that this process is ready for instrument adaptation by using it to add three ribonucleotides in three cycles using an engineered Polθ. This work creates a new way to synthesize RNA with a de novo defined sequence, without requiring the protecting groups, hazardous solvents, and sensitive reagents that bedevil phosphoramidite-based RNA synthesis.
Aβ*56 is present in brain extracts enriched for extracellular proteins
Authors: Liu Peng , Lapcinski Ian P. , Ashe Karen H. 
Published: October 2024

AbstractAmyloid-β (Aβ) oligomers are believed to be important in the pathogenesis of Alzheimer’s disease (AD). Aβ*56 is an Aβ oligomer that has been reported in several lines of transgenic mice modeling AD, including Tg2576, hAPP-J20, 3xTgAD, 5xFAD, and APPTTA. In Tg2576 mice, Aβ*56 appears several months before neuritic plaques and impairs memory when injected into the brains of healthy rodents. Aβ*56 has several distinctive biochemical features: 1) it is soluble in aqueous buffers, 2) it is stable in the ionic detergent sodium dodecyl sulfate (SDS), 3) it has an apparent mass of 56 kDa whether measured by denaturing SDS polyacrylamide gel electrophoresis or non-denaturing size-exclusion chromatography, 4) it binds to A11 conformational antibodies that recognize non-fibrillar oligomeric assemblies, and 5) it contains canonical Aβ(1-40) and/or Aβ(1-42). Here, we show its presence in Tg2576 brain extracts enriched for extracellular proteins and conclude that Aβ*56 is present in the extracellular space.