bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepBIO is an automated and interpretable deep-learning platform for biological sequence prediction, functional annotation, and visualization analysis
Authors: Wang Ruheng , Jiang Yi , Jin Junru , Yin Chenglin , Yu Haoqing , Wang Fengsheng , Feng Jiuxin , Su Ran , Nakai Kenta , Zou Quan , Wei Leyi 
Published: October 2022

AbstractHere, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop-shop web service that enables researchers to develop new deep-learning architectures to answer any biological question. Specifically, given any biological sequence data, DeepBIO supports a total of 42 state-of-the-art deep-learning algorithms for model training, comparison, optimization, and evaluation in a fully automated pipeline. DeepBIO provides a comprehensive result visualization analysis for predictive models covering several aspects, such as model interpretability, feature analysis, functional sequential region discovery,etc. Additionally, DeepBIO supports 9 base-level functional annotation tasks using deep-learning architectures, with comprehensive interpretations and graphical visualizations to validate the reliability of annotated sites. Empowered by high-performance computers, DeepBIO allows ultra-fast prediction with up to million-scale sequence data in a few hours, demonstrating its usability in real application scenarios. Case study results show that DeepBIO provides an accurate, robust, and interpretable prediction, demonstrating the power of deep learning in biological sequence functional analysis. Overall, we expect DeepBIO to ensure the reproducibility of deep-learning biological sequence analysis, lessen the programming and hardware burden for biologists, and provide meaningful functional insights at both sequence-level and base-level from biological sequences alone. DeepBIO is publicly available athttp://inner.wei-group.net/DeepBIO.
A high quality chromosome-level genome assembly for the golden mussel (Limnoperna fortunei)
Authors: R. N. Ferreira João Gabriel , Americo Juliana A. , do Amaral Danielle L. A. S. , Sendim Fábio , da Cunha Yasmin R. ,   The Darwin Tree of Life Project Consortium, Uliano-Silva Marcela , Rebelo Mauro de F. 
Published: October 2022

AbstractThe golden mussel (Limnoperna fortunei) is a highly adaptive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. In this Data Note, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using Hi-C, PacBio HiFi and 10X sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. Approximately 47% of the genome was annotated as repetitive sequences. A total of 34 862 protein-coding genes were predicted, of which 84.7% were functionally annotated. This new high quality genome is expected to support both basic and applied research on this invasive species.Species taxonomyEukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Spiralia; Lophotrochozoa; Mollusca; Bivalvia; Autobranchia; Pteriomorphia; Mytilida; Mytiloidea; Mytilidae; Arcuatulinae; Limnoperna; Limnoperna fortunei (Dunker, 1857) (NCBI Taxonomy ID: 356393)
Brain-wide associations between white matter and age highlight the role of fornix microstructure in brain ageing
Authors: Korbmacher Max , de Lange Ann Marie , van der Meer Dennis , Beck Dani , Eikefjord Eli , Lundervold Arvid , Andreassen Ole A. , Westlye Lars T. , Maximov Ivan I. 
Published: October 2022

AbstractUnveiling the details of white matter (WM) maturation throughout ageing is a fundamental question for understanding the ageing brain. In an extensive comparison of brain age predictions and age- associations of WM features from different diffusion approaches, we analysed UK Biobank diffusion Magnetic Resonance Imaging (dMRI) data across midlife and older age (N= 35,749, 44.6 to 82.8 years of age). Conventional and advanced dMRI approaches were consistent in predicting brain age. WM-age associations indicate a steady microstructure degeneration with increasing age from midlife to older ages. Brain age was estimated best when combining diffusion approaches, showing different aspects of WM contributing to brain age. Fornix was found as the central region for brain age predictions across diffusion approaches in complement to forceps minor as another important region. These regions exhibited a general pattern of positive associations with age for intra axonal water fractions, axial, radial diffusivities and negative relationships with age for mean diffusivities, fractional anisotropy, kurtosis. We encourage the application of multiple dMRI approaches for detailed insights into WM, and the further investigation of fornix and forceps as potential biomarkers of brain age and ageing.
ROCA: An Ontology to Describe and analyse Tool Use and Tool Making
Authors: Mercuriali Pierre R. , Corbato Carlos Hernandez , Langejans Geeske H.J. 
Published: October 2022

AbstractTo contribute to current discussions on the complexity of extinct and modern non-human and human primate tasks, we explore if ontologies are helpful as a means of representing tool tasks. We thus hope to help illuminate how primates approach tool tasks internally, such as breaking open a nutshell between a wooden anvil and a stone hammer to access its nutritious contents or fishing for termites with a leaf midrib. Ontologies are widely used in domains such as linguistics, medicine, archaeology, and cultural heritage, to help experts organize, reason on, and discover new knowledge in their field. We build a novel ontology, ROCA (from ‘roca’ - - rock, in Spanish) with which we can describe instances of tool use in a formal and uniform manner, including well-known primate ethograms and chaînes opératoires. We will see that representing tool use and tool making with an ontology provides auniform, unified, acentric, dynamic, and human-readable way to handle knowledge obtained from literature and to perform knowledge discovery. We build a representative corpus of 75 articles and books on primate and hominin tool use and tool making. We then extract and give semantic structure such as taxonomical relationships to relevant vocabulary, both manually and automatically, using NLP text mining techniques. We then show how the ontology can be used to discover new knowledge related to tool use and tool making.
βIII-Tubulin is a Brake on Extrinsic Cell-Death in Pancreatic Cancer
Authors: Kokkinos John , Sharbeen George , Ignacio Rosa Mistica C. , Pandzic Elvis , Youkhana Janet , Boyer Cyrille , Haghighi Koroush S. , Gunawarman Matthew , Goldstein David , Gebski Val , Pajic Marina , Pitiyarachchi Omali , Davis Meagan E. , Schulstad Grace , Arkell Oliver S.M. , Kopecky Chantal , Gonzales-Aloy Estrella , Erkan Mert , Morton Jennifer P. , Kavallaris Maria , Gunning Peter W. , Hardeman Edna C. , Johns Amber , Gill Anthony J. , Whan Renee M. , Mawson Amanda ,   Australian Pancreatic Cancer Genome Initiative, McCarroll Joshua A. , Phillips Phoebe A. 
Published: October 2022

AbstractThe microtubule protein, βIII-tubulin, has been implicated as a prognostic, pro-survival, and chemoresistance factor in some of the most lethal malignancies including pancreatic ductal adenocarcinoma (PDAC). However, precise survival mechanisms controlled by βIII-tubulin in cancer cells are unknown. Here, we report an unexpected role of βIII-tubulin as a brake on extrinsic caspase 8-dependent apoptosis in PDAC. We show that βIII-tubulin knockdown frees death-receptor DR5 to increase its membrane diffusion, clustering, and activation of cell-death. We demonstrate that βIII-ubulin silencing increases sensitivity of PDAC cells to chemotherapeutic and microenvironment-derived extrinsic cell-death signals including TRAIL, TNFα, and FasL. Finally, nanoparticle delivery of βIII-tubulin siRNA to mouse orthotopic PDAC tumours in vivo and human patient-derived PDAC tumour explants ex vivo increases extrinsic apoptosis and reduces tumour progression. Thus, silencing of βIII-tubulin represents an innovative strategy to unleash a suicide signal in PDAC cells and render them sensitive to microenvironment and chemotherapy-derived death signals.
Consistent, linear phenological shifts across a century of observations in South Korea
Authors: Pearse William D. , Stemkovski Michael , Lee Benjamin R. , Primack Richard B. , Lee Sangdon 
Published: October 2022

AbstractThe Korea Meteorological Agency (KMA) has monitored flowering dates over the past 100 years for seven economically important woody plant species. This unique dataset is perfect for understanding whether historical patterns of phenological plasticity are breaking down in the face of recent and rapid climate change. Here we show that a scientist armed only 50 years into this study would have been able to predict the phenological shifts of the last 50 years with a high degree of accuracy. This is despite record-breaking warm temperatures and unprecedented early flowering, suggesting consistency in phenological shifts over time.
Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes
Authors: Saadat Nima P. , van Aalst Marvin , Brand Alejandro , Ebenhöh Oliver , Tissier Alain , Matuszyńska Anna B. 
Published: October 2022

AbstractSeveral commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes, giving the prospect of using them as metabolic cell factories. Due to extremely high metabolic fluxes through glandular trichomes, previous research focused on how such flows are achieved. The question regarding their bioenergetics became even more interesting with the discovery of photosynthetic activity in some glandular trichomes. Despite recent advances, how primary metabolism contributes to the high metabolic fluxes in glandular trichomes is still not fully elucidated. Using computational methods and available multi-omics data, we first developed a quantitative framework to investigate the possible role of photosynthetic energy supply in terpenoid production and next tested experimentally the simulation-driven hypothesis. With this work, we provide the first reconstruction of specialised metabolism in Type-VI photosynthetic glandular trichomes ofSolanum lycopersicum. Our model predicted that increasing light intensities results in a shift of carbon partitioning from catabolic to anabolic reactions driven by the energy availability of the cell. Moreover, we show the benefit of shifting between isoprenoid pathways under different light regimes, leading to a production of different classes of terpenes. Our computational predictions were confirmedin vivo, demonstrating a significant increase in production of monoterpenoids while the sesquiterpenes remained unchanged under higher light intensities. The outcomes of this research provide quantitative measures to assess the beneficial role of chloroplast in glandular trichomes for enhanced production of secondary metabolites and can guide the design of new experiments that aim at modulating terpenoid production.GRAPHICAL ABSTRACTPlease check the journal’s author guidelines for whether a graphical abstract, key points, new findings, or other items are required for display in the Table of Contents.
Capsid structure of a metazoan fungal dsRNA megabirnavirus reveals its uniquely acquired structures
Authors: Wang Han , Salaipeth Lakha , Miyazaki Naoyuki , Suzuki Nobuhiro , Okamoto Kenta 
Published: October 2022

ABSTRACTRosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia. necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Contrary to the other structurally associated viral capsid proteins, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission, genome packaging, and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.Author summaryA fungal plant soil-borne pathogen, Rosellinia necatrix, which can cause devastating disease white root rot in many highly valued fruit trees, is difficult to be controlled with conventional approaches such as fungicide applications. Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a dsRNA virus isolated from the R. necatrix field strain, W779, and this virus can be a viro-control candidate to confer hypovirulence in its host R. necatrix. To make use of RnMBV1 in the white root rot disease control, more molecular and structural investigations will offer us more insights. Here, we have performed cryo-electron microscopy (cryo-EM) single-particle analysis, to obtain the first atomic models of RnMBV1 particles. Based on the atomic structures, we found unique both surface and interior features. In addition, we found a previously unexpected protein on the viral surface. These aforementioned structural features might play important roles in the viral life cycles, and will enable us to apply this fungal virus as a viro-control approach.
Quantitative proteomics identifies tumour matrisome signatures in patients with non-small cell lung cancer
Authors: Titmarsh Helen F. , Kriegsheim Alex von , Wills Jimi C. , O’Connor Richard A. , Dhaliwal Kevin , Frame Margaret C. , Pattle Samuel B. , Dorward David A. , Byron Adam , Akram Ahsan R. 
Published: October 2022

The composition and remodelling of the extracellular matrix (ECM) are important factors in the development and progression of cancers, and the ECM is implicated in promoting tumour growth and restricting anti-tumour therapies through multiple mechanisms. The characterisation of differences in ECM composition between normal and diseased tissues may aid in identifying novel diagnostic markers, prognostic indicators and therapeutic targets for drug development. Using tissue from non-small cell lung cancer (NSCLC) patients undergoing curative intent surgery, we characterised quantitative tumour-specific ECM proteome signatures by mass spectrometry, identifying 161 matrisome proteins differentially regulated between tumour tissue and nearby non-malignant lung tissue. We defined a collagen hydroxylation functional protein network that is enriched in the lung tumour microenvironment. We validated two novel putative extracellular markers of NSCLC, the collagen cross-linking enzyme peroxidasin and a disintegrin and metalloproteinase with thrombospondin motifs 16 (ADAMTS16), for discrimination of malignant and non-malignant lung tissue. These proteins were up-regulated in lung tumour samples, and high PXDN and ADAMTS16 gene expression was associated with shorter survival of lung adenocarcinoma and squamous cell carcinoma patients, respectively. These data reveal tumour matrisome signatures in human NSCLC.Abstract Figure
Optimal feature selection and software tool development for bacteriocin prediction
Authors: Akhter Suraiya , Miller John 
Published: October 2022

AbstractAntibiotic resistance is a major public health concern around the globe. As a result, researchers always look for new compounds to develop new antibiotic drugs for combating antibiotic-resistant bacteria. Bacteriocin becomes a promising antimicrobial agent to fight against antibiotic resistance, due to its narrow killing spectrum. Sequence matching methods are widely used to identify bacteriocins by comparing them with the known bacteriocin sequences; however, these methods often fail to detect new bacteriocin sequences due to sequences’ high diversity. The ability to use a machine learning approach can help find new highly dissimilar bacteriocins for developing highly effective antibiotic drugs. The aim of this work is to identify optimal sets of features and develop a machine learning-based software tool for predicting bacteriocin protein sequences with high accuracy. We extracted potential features from known bacteriocin and non-bacteriocin sequences by considering the physicochemical and structural properties of the protein sequences. Then we reduced the feature set using statistical justifications and recursive feature elimination technique. Finally, we built support vector machine (SVM) and random forest (RF) models using the selected features and our models can achieve accuracy up to 95.54%. We compared the performance of our method with a popular sequence matching-based approach and a deep learning-based method. We also developed a software tool called Bacteriocin Prediction (BacPred) that implements the prediction model using the optimal set of features obtained from this study. The software package and its user manual are available at https://github.com/suraiya14/ML_bacteriocins/BacPred.
Asymmetric distribution of centromere proteins between germline stem and daughter cells maintains a balanced niche in Drosophila males
Authors: Kochendoerfer Antje M , Dunleavy Elaine M 
Published: October 2022

AbstractIn the germline, stem cells undergo asymmetric cell division (ACD) to give rise to one new stem cell as well as one daughter cell that differentiates and eventually gives rise to the gamete (egg or sperm). The silent sister hypothesis proposes the selective inheritance of one set of sister chromatids carrying specific epigenetic marks to explain how genetically identical stem and daughter cells can adopt different fates. It also proposes that centromeres of sister chromatids might differ epigenetically. In Drosophila germline stem cells (GSCs), the centromeric histone CENP-A - CID in flies - is asymmetrically distributed between sister chromatids such that chromosomes that end up in the GSC harbour more CID at centromeres. In this system, a model of ‘mitotic drive’ has been proposed. According to this model, stronger and earlier centromere and kinetochore interactions with microtubules bias sister chromatid segregation during ACD. Here we show that in Drosophila males, CID, CENP-C and CAL1 are asymmetrically distributed between newly divided GSCs and daughter cells that have entered S-phase of the next cell cycle. We find that overexpression of CID, overexpression of CID together with CAL1 or CENP-C depletion disrupts CID asymmetry, with an increased pool of GSCs relative to daughter cells detectable in the niche. This result suggests a shift toward GSC self-renewal rather than differentiation, which is important to maintain tissue homeostasis. Over-expression of CAL1 does not disrupt asymmetry, nor does it affect the GSC and daughter cell balance, but instead drives germ cell proliferation in the niche. Our results in male GSCs are closely aligned with previous observations in female GSCs, indicating that despite differences in signaling, organisation and niche composition, centromere asymmetry and its effects on GSC maintenance are conserved between the sexes.
Fluctuations in chromatin state at regulatory loci occur spontaneously under relaxed selection and are associated with epigenetically inherited variation in C. elegans gene expression
Authors: Wilson Rachel , Bourgeois Maxime Le , Perez Marcos , Sarkies Peter 
Published: October 2022

AbstractSome epigenetic information can be transmitted between generations without changes in the underlying DNA sequence. Changes in epigenetic regulation, termed epimutations, can occur spontaneously and be propagated in populations in a manner reminiscent of DNA mutations. Epimutations mediated by small non-coding RNAs occur in C. elegans and persist for around 3-5 generations on average. Here, we explored whether chromatin states also undergo spontaneous change and whether this could be a potential alternative mechanism for transgenerational epigenetic inheritance. We compared the chromatin and gene expression profiles at matched time points from three independent lineages of C. elegans propagated at minimal population size. Spontaneous changes in chromatin occurred in around 1% of regulatory regions each generation. Some were heritable epimutations and were significantly enriched for heritable changes in expression of nearby protein-coding genes. Most chromatin-mediated epimutations were short-lived but a subset had longer duration. Genes subject to long-lived epimutations were enriched for multiple components of xenobiotic response pathways. This points to a possible role for epimutations in adaptation to environmental stressors.
Rapid evolutionary diversification of theflamencolocus across simulans cladeDrosophilaspecies
Authors: Signor Sarah , Vedanayagam Jeffrey , Kim Bernard Y. , Wierzbicki Filip , Kofler Robert , Lai Eric C. 
Published: October 2022

AbstractEffective suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. InD. melanogaster,flamencois a master suppressor of TEs, preventing their movement from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, that is metabolized into Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity.flamencois thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find thatflamencohas undergone radical transformations in sequence content and even copy number acrosssimulansclade Drosophilid species.D. simulans flamencohas duplicated and diverged, and neither copy exhibits synteny withD. melanogasterbeyond the core promoter. Moreover,flamencoorganization is highly variable acrossD. simulansindividuals. Next, we find thatD. simulansandD. mauritiana flamencodisplay signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual stranded clusters. Overall, the physical and functional diversity offlamencoorthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.