bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virulence patterns of oat crown rust in Australia - season 2022
Authors: Henningsen Eva C. , Lewis David , Nguyen Duong T. , Sperschneider Jana , Kianian Shahryar F. , Stone Eric , Dodds Peter N. , Figueroa Melania 
Published: September 2023

AbstractPuccinia coronataf. sp.avenae(Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48Pcaisolates derived from different locations in Australia was characterised using a collection of oat lines often utilised in rust surveys in the USA and Australia. This analysis indicates thatPcapopulations in Eastern Australia are broadly virulent, in contrast to the population in Western Australia (WA). Several oat lines/Pcgenes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the USA oat differential set that display disease resistance toPcain WA, some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the USA. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes forPcain Australia. Nevertheless, thePcapopulation in the USA is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection withPcasupports hypotheses of allelism or redundancy amongPcgenes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.
Weakly supervised identification and generation of adaptive immune receptor sequences associated with immune disease status
Authors: Slabodkin Andrei , Sollid Ludvig M. , Sandve Geir Kjetil , Robert Philippe A. , Greiff Victor 
Published: September 2023

AbstractAdaptive immune receptor (AIR) repertoires carry immune signals as sequence motif imprints of past and present encounters with antigen (immune status). Machine learning (ML)-based identification and generation of antigen-specific immune receptors is potentially immense value for public health. The ideal training data for such ML tasks would be AIR datasets, where each sequence is labeled with its cognate antigen. However, given current technological constraints, sequence-labeled datasets are scarce, contrasted by an abundance of repertoire-labeled ones – AIR repertoire datasets where only the repertoire dataset, but not the individual AIRs, are labeled. Therefore, an unmet need exists for an ML approach that enables predictive identification and generation of disease-specific novel AIR sequences using exclusively repertoire-level immune status information. To address this need, we developed AIRRTM, an end-to-end generative model using an encoder-decoder architecture and Topic Modeling (TM) that requires exclusively repertoire-labeled AIR sequencing data as input. We validated AIRRTM’s capacity to identify and generate novel disease-associated receptors on several ground truth synthetic datasets of increasingly complex immune signals and experimental data. AIRRTM broadens the discovery space for immunotherapeutics by enabling the exploitation of large-scale and broadly available immune repertoire data previously deemed largely unsuitable for this task.
DNMT3L interacts with Piwi and modulates the expression of piRNAs
Authors: Rajeev Ramisetti , Mishra Rakesh , Khosla Sanjeev 
Published: September 2023

AbstractThe epigenetic modulator, DNMT3L, has been shown to be involved in nuclear reprogramming. Previous work from our laboratory had shown the accumulation and inheritance of epimutations across multiple generations when DNMT3L was ectopically expressed in transgenic DNMT3L Drosophila. Here, we show interaction of DNMT3L with Piwi, a member of a family of proteins known to perform their function through their association with piRNAs. Importantly, DNMT3L expression caused a significant alteration in the piRNA profile across multiple generations in transgenic Drosophila. As piRNAs are known to be passed on from one generation to another, we believe that the DNMT3L through its interaction with Piwi act to modify the inherited pool of piRNAs, which in turn allows accumulation of aberrant epigenetic modifications in subsequent generation. Furthermore, we show the interaction of DNMT3L with Histone H1, a non-core histone involved in higher order chromatin organisation. In light of these observations, it is proposed that in addition to its role in modulating core histone modifications, DNMT3L allows for inheritance of non-genetic information through its collaboration with Piwi, piRNAs and histone H1.
Long-read genome assembly of the Japanese parasitic waspCopidosoma floridanum(Hymenoptera: Encyrtidae)
Authors: Toga Kouhei , Sakamoto Takuma , Kanda Miyuki , Tamura Keita , Okuhara Keisuke , Tabunoki Hiroko , Bono Hidemasa 
Published: September 2023

AbstractCopidosoma floridanumis a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth.C. floridanumhas a unique development mode called polyembryony, in which thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae, and their developmental patterns differ between the US and JapaneseC. floridanumstrains. Genome sequencing can accelerate our understanding of the molecular bases underlying polyembryony, including the production of soldier castes. However, only the genome sequence of the US strain has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. Among these, 149 transcripts were not identified in the US strain gene model. Differences in the amino acid sequence of thevasagene were observed between the US and Japanese strains. The genome assemblies constructed in this study will facilitate our understanding of intraspecific variation in the developmental patterns ofC. floridanum.
Src/Fas2-dependent Ephrin phosphorylation initiates Eph/Ephrin reverse signaling through Rac1 to shape columnar units in the fly brain
Authors: Wang Miaoxing , Han Xujun , Lee Yunfei , Takayama Rie , Sato Makoto 
Published: September 2023

AbstractColumns are the morphological and functional units containing multiple neurons in the brain. The molecular mechanisms of column formation are largely unknown. Ephrin/Eph signaling mediates a variety of developmental processes. Ephrin acts as a ligand for Eph to regulate forward signaling, while Eph acts as a ligand for Ephrin to regulate reverse signaling. However, whether and how the uni- or bi-directional Ephrin/Eph signaling is involved in column formation remains elusive. In this study, we show that Ephrin and Eph regulate the morphology and location of columnar neurons through bi-directional repulsive signaling. Furthermore, Eph ligand triggers cytoplasmic tyrosine phosphorylation of Ephrin under the control of Src kinases and Fasciclin II (Fas2), forming Ephrin/Src/Fas2 complex to promote reverse signaling through a downstream regulator, Rac1. This study presents for the first time a unified picture of the molecular interactions in the defined context of column formation using the fly brain as a model.
Activation of a cortical neurogenesis transcriptional program during NEUROD1-induced astrocyte-to-neuron conversion
Authors: Li Wen , Su Dan , Li Xining , Lu Kang , Huang Qingpei , Zheng Jiajun , Luo Xiaopeng , Chen Gong , Fan Xiaoying 
Published: September 2023

AbstractNEUROD1-induced astrocyte-to-neuron (AtN) conversion has garnered significant attention as a potential therapeutic intervention to neurological disorders. To gain insight into the molecular regulations underlying this neuronal reprogramming process, we applied single-cell multiomics analyses onin vitroND1-induced AtN conversion to systematically investigate how ND1 changed the fate of astrocytes at transcriptomic and epigenetic levels. Our findings reveal that the initial immature astrocytes go through an intermediate state where both astrocytic and neuronal genes are activated at early stage of AtN conversion. ND1 directly reshapes the chromatin accessibility landscape of astrocytes to that of neurons, promoting expression of endogenousNeurod1 and otherneurogenic genes such asHes6, Insm1etc. Interestingly, cell proliferation status is highly correlated with conversion rate, and inhibition of cell division significantly reduces the conversion ratio. Moreover, in comparison with another AtN reprogramming transcription factor, ASCL1, external ND1 can activate endogenousNeurod1and directly promote neuronal gene transcription; whereas external ASCL1 hardly activates endogenousAscl1,leading to slower and inefficient conversion. Together, our studies demonstrate thatin vitroAtN conversion mimics neurogenic transcriptional program in embryonic neurogenesis.
Ascites in malignant ovarian cancer confer ovarian cancer cells chemoresistance to platinum. Combination treatment with crizotinib and 2-hydroxyestradiol restores platinum sensitivity
Authors: Carmi Yifat Koren , Agbarya Abed , Khamaisi Hazem , Farah Raymond , Shechtman Yelena , Korobochka Roman , Gopas Jacob , Mahajna Jamal 
Published: September 2023

AbstractOvarian cancer (OC), the second most common form of gynecologic malignancy, has a poor prognosis and is often discovered in the late stages. Platinum-based chemotherapy is the first line of therapy. Nevertheless, treatment OC has proven challenging due to toxicity and the development of acquired resistance to therapy. Tumor microenvironment (TME) has been associated with platinum chemoresistance.Malignant ascites has been used as OC tumor microenvironment and its ability to induce platinum chemoresistance has been investigated.Our results suggest that exposure to OC ascites induces platinum chemoresistance in 11 of 13 cases (85%) on OC cells. In contrast, 75% of cirrhotic ascites (3 of 4) failed to confer platinum chemoresistance to OC cells. Cytokine array analysis revealed that IL -6 and to a lesser extent HGF were enriched in OC ascites, whereas IL -22 was enriched in cirrhotic ascites. Pharmaceutical inhibitors targeting the IL -6/ JAK pathway were mildly effective in overcoming platinum chemoresistance induced by malignant ascites. In contrast, crizotinib, an HGF/c-MET inhibitor, and 2-hydroxyestradiol (2HE2) were effective in restoring platinum chemosensitivity to OC.Our results demonstrate the importance of OC ascites in supporting platinum chemoresistance and the potential of combination therapy to restore chemosensitivity of OC cells.
Responses of root-associated fungal communities of mature beech and spruce during five years of experimental drought
Authors: Weikl Fabian C. , Grams Thorsten E. E. , Pritsch Karin 
Published: September 2023

SummaryDrought affects the fine-root systems of European beech (Fagus sylvaticaL.) and Norway spruce (Picea abies[L.] KARST) in different ways, but little is known about how this impacts their fine-root-associated fungal communities.In a five-year throughfall exclusion experiment (KROOF) in a mature stand, we investigated whether recurrent drought periods progressively alter fine-root associated fungal communities, fine-root vitality, and ectomycorrhizal functionality in relation to the tree root zone (pure beech, pure spruce, or their mixture) and abiotic soil parameters.We found that the influence of recurrent droughts on root fungal communities peaked in the third year of the experiment and affected fungal functional groups in different ways. The root zone was the predominant factor in structuring all functional groups of root-associated fungi, while we did not find a prominent effect of root mixture. The importance of other factors (year of sampling, soil depth) varied among fungal functional groups.Our results indicate a robust biotrophic root-fungal system relying mainly on surviving root tips, complemented by a fluctuating saprotrophic fungal assembly.
In silico optimization of DNA codons in genes encoded by various strains of Ebola Virus
Authors: Mathuria Anshu , Ahmed Mehak , Mani Indra 
Published: September 2023

AbstractEbola hemorrhagic fever (HF) is a severe and often lethal disease that occurs in primates, including humans. It was first identified in 1976 during two outbreaks of fatal haemorrhagic fever in Central Africa. Due to its high fatality rate and lack of a widespread cure, Ebola HF poses a considerable challenge in treatment, making Ebola virus disease (EVD) one of the deadliest zoonotic diseases. The viral genome is ∼19kb long, linear, non-segmented, and negative single-stranded (-SS) RNA. The genome of the Ebola virus (EBOV) comprises seven genes, namely NP, GP, L, and VP (VP30, VP24, VP40, VP35), which encode nucleoprotein, glycoprotein, RNA polymerase, and viral proteins. By optimizing the DNA sequence through codon adaptation, we observed significant enhancements in the codon adaptation index (CAI) and the GC content compared to the wild-type strain. These findings demonstrate that optimized genes hold the potential for improved expression in the host organism without the production of truncated proteins. Further, these optimized genes can facilitate proper protein folding and function. In conclusion, these results have implications for vaccine production, as higher codon optimization enhances the expression of the genes, making them appropriate amounts for vaccine development.
Conditioned Protein Structure Prediction
Authors: Xie Tengyu , Song Zilin , Huang Jing 
Published: September 2023

AbstractDeep learning based protein structure prediction has facilitated major breakthroughs in biological sciences. However, current methods struggle with alternative conformation prediction and offer limited integration of expert knowledge on protein dynamics. We introduce AFEXplorer, a generic approach that tailors AlphaFold predictions to user-defined constraints in coarse coordinate spaces by optimizing embedding features. Its effectiveness in generating functional protein conformations in accordance with predefined conditions were demonstrated through comprehensive examples. AFEXplorer serves as a versatile platform for conditioned protein structure prediction, bridging the gap between automated models and domain-specific insights.
Spatial-Live: A lightweight and versatile tool for single cell spatial-omics data visualization
Authors: Ye Zhenqing , Lai Zhao , Zheng Siyuan , Chen Yidong 
Published: September 2023

AbstractSingle cell spatial-omics data visualization plays a pivotal role in unraveling the intricate spatial organization and heterogeneity of cellular systems. Although various software tools and packages have been developed for this purpose, challenges persist in terms of user-friendly accessibility, data integration, and interactivity. In this study, we introduce Spatial-Live, alightweight andversatile viewer tool designed for flexible single-cell spatial-omics data visualization. Spatial-Live overcomes the fundamental limitations of two-dimensional (2D) orthographic modes by employing a layer-stacking strategy, enabling efficient rendering of diverse data types with interactive features, and enhancing visualization with richer information in a unified three-dimensional (3D) space.
Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions
Authors: Piombo Edoardo , Vetukuri Ramesh Raju , Jensen Dan Funck , Karlsson Magnus , Dubey Mukesh 
Published: September 2023

AbstractThe intricate molecular interplay between beneficial fungi and plants is vital to plant growth promotion and induced defense response. This study explored the role of DCL-mediated RNA silencing in the interaction between the biocontrol fungusClonostachys roseaand wheat roots. We investigated the impact of DCL (Dicer-like) gene deletions inC. roseaon its root colonization ability. Our results revealed that the deletion ofdcl2significantly enhancedC. roseabiomass on wheat roots, indicating a pivotal role of DCL2 in root colonization. Transcriptome sequencing ofC. roseaand wheat during their interactions unveiled extensive gene expression changes. In wheat, genes related to stress responses were upregulated duringC. roseainteractions, while genes associated with plant cell wall modification and metabolic processes were downregulated, suggesting complex regulatory responses and a trade-off between defense mechanisms and growth promotion. Deletion ofC. rosea dcl1anddcl2altered the transcriptomic responses of wheat roots during interactions. Wheat genes associated with stress responses were downregulated during interactions with DCL deletion strains. In contrast, genes involved in metabolic processes and growth were upregulated, emphasizing the cross-kingdom regulatory role ofC. roseasmall RNAs (sRNAs). We identified 18 wheat miRNAs responsive toC. roseainteractions. Furthermore, we identified 24 endogenous and six cross-kingdom potential gene targets for seven and five differentially expressed miRNAs, supported by their inverse gene expression pattern. InC. rosea, we found a large transcriptional reprogramming of genes during interaction with wheat roots. The upregulated genes were associated with carbohydrate and polysaccharide catabolic processes, membrane transporters and effectors. Conversely, downregulated genes were mainly associated with transition metal ion transport and homeostasis processes. The deletion ofdcl1anddcl2had significant effects on gene expression. A higher number of genes upregulated in WT during the interaction were restored in DCL deletion mutants, suggesting DCL-mediated gene expression regulation. Furthermore, we identified 21 differentially expressed micro-RNA-like RNAs (milRNAs) inC. rosea; nine were DCL-dependent. They had putative gene targets inC. rosea, including transcription factors, effectors, transporters, and enzymes involved in specialized metabolite production. Cross-kingdom RNA silencing was also observed, with seven DCL-dependentC. roseamilRNAs potentially targeting 29 genes in wheat. These findings provide valuable insights into the molecular mechanisms underlying the beneficial interaction between fungi and plant roots. In addition, the study shed light on the role of sRNA-mediated gene regulation in theC. rosea-wheat interaction, with potential implications for sustainable agriculture and biocontrol strategies.
Eye-specific detection and a multi-eye integration model of biological motion perception
Authors: De Agrò Massimo , Rößler Daniela C. , Shamble Paul S. 
Published: September 2023

AbstractThe term biological motion refers to the peculiar kinematics of living organisms. Their interconnected joints move at a fixed distance from each other, a pattern that is common among all locomotive, rigid animals. Across the animal kingdom, many species have developed specialized circuitry to visually recognize biologically moving stimuli and discriminate them from other patterns. Recently, this skill has also been observed in the distributed visual system of jumping spiders. These eight-eyed animals use three of their eye pairs to perceive motion. Then, the gaze of the remaining pair is shifted towards the detected object for further inspection. When presented with a biologically moving stimulus and a random one, jumping spiders turn to face the latter, demonstrating discrimination. In the current paper, we systematically tested the ability of jumping spiders to discriminate biological from random displays using every single eye-pair, by blocking the others with paint. The animals were able to discriminate the stimuli only when the anterior-lateral eyes were unblocked, performing at chance level with the other pairs. Crucially, the spiders preferred the biological stimulus, not the random one. To explain this preference reversal we hypothesized a model, describing how the anterior-lateral eyes’ specialization in detecting biological motion feeds into a multi-eye integration system, generating more complex behavior from the combination of the simple, single-eye responses. We propose that this in-built modularity may be a solution to the limited resources of these invertebrates’ brains, constituting a novel approach to visual processing.
Context and Attention Shape Electrophysiological Correlates of Speech-to-Language Transformation
Authors: Anderson Andrew J. , Davis Christopher , Lalor Edmund C. 
Published: September 2023

AbstractTo transform speech into words, the human brain must accommodate variability across utterances in intonation, speech rate, volume, accents and so on. A promising approach to explaining this process has been to model electroencephalogram (EEG) recordings of brain responses to speech. Contemporary models typically invoke speech categories (e.g. phonemes) as an intermediary representational stage between sounds and words. However, such categorical models are typically hand-crafted and therefore incomplete because they cannot speak to the neural computations that putatively underpin categorization. By providing end-to-end accounts of speech-to-language transformation, new deep-learning systems could enable more complete brain models. We here model EEG recordings of audiobook comprehension with the deep-learning system Whisper. We find that (1) Whisper provides an accurate, self-contained EEG model of speech-to-language transformation; (2) EEG modeling is more accurate when including prior speech context, which pure categorical models do not support; (3) EEG signatures of speech-to-language transformation depend on listener-attention.