bluuebunny/crossref_metadata_2025_split huggingface dataset:
First record ofVenturia canescensGRAVENHORST, 1829 (Hymenoptera: Ichneumonidae: Campopleginae) from Tunisia
Authors: Zeiri Asma 
Published: July 2024

AbstractBackgroundVenturia canescensGravenhorst 1829 (Hymenoptera: Ichneumonidae: Campopleginae), a solitary koinobiont endoparasitoid, lives on larvae of various Lepidopteran hosts belonging to the families of Pyralidae, Noctuidae, Tortricidae, Gelechiidae, Tineidae and Yponomeutidae of Lepidoptera (typically Pyralidae). It was frequently reported on the carob mothEctomyeloisceratoniae (Zeller) (Lepidoptera: Pyralidae). TheE. ceratoniaeis an insect pest that causes damage to various crops and fruit trees throughout the world. It was recorded on dates(Phoenix dactylifera), pomegranates (Punica granatum), almonds (Prunus dulcis) and pistachio nut (Pistacia vera), affecting the fruit quality. In Tunisia, this pest was recorded on pomegranate by many authors.ResultsThe parasitoidV. canescens, is accidently recorded from Tunisia within the collection of parasitoids of the almond bark beetleScolytus amygdali(Coleoptera: Curculionidae: Scolytinae) in the orchard of the Professional Training Center of Agriculture, Jammel, Monastir, Tunisia (35°37′60′′ N:10°46′0′′E) rich of fruit trees. The identification ofV. canescenswas carried out using key for females of the genus Venturia to Western Palaearctic species and the specimen is reported as a first record in Tunisia. No male was collected, the host is unknown.ConclusionsThis species is widely distributed in the Palaearctic region. As far as we know this is a first record for the country.
Single cell autofluorescence imaging reveals immediate metabolic shifts of neutrophils with activation across biological systems
Authors: Datta Rupsa , Miskolci Veronika , Gallego-López Gina M. , Britt Emily , Gillette Amani , Kralovec Aleksandr , Giese Morgan A. , Qian Tongcheng , Votava James , Fan Jing , Huttenlocher Anna , Skala Melissa 
Published: July 2024

AbstractNeutrophils, the most abundant leukocytes in human peripheral circulation, are crucial for the innate immune response. They are typically quiescent but rapidly activate in response to infection and inflammation, performing diverse functions such as oxidative burst, phagocytosis, and NETosis, which require significant metabolic adaptation. Deeper insights into such metabolic changes will help identify regulation of neutrophil functions in health and diseases. Due to their short lifespan and associated technical challenges, the metabolic processes of neutrophils are not completely understood. This study uses optical metabolic imaging (OMI), which entails optical redox ratio and fluorescence lifetime imaging microscopy of intrinsic metabolic coenzymes NAD(P)H and FAD to assess the metabolic state of single neutrophils. Primary human neutrophils were imagedin vitrounder a variety of activation conditions and metabolic pathway inhibitors, while metabolic and functional changes were confirmed with mass spectrometry, oxidative burst, and NETosis measurements. Our findings show that neutrophils undergo rapid metabolic remodeling to a reduced redox state indicated by changes in NAD(P)H lifetime and optical redox ratio, with a shift to an oxidized redox state during activation. Additionally, single cell OMI analysis reveals a heterogeneous metabolic response across neutrophils and human donors to live pathogen infection (Pseudomonas aeruginosaandToxoplasma gondii). Finally, consistent OMI changes with activation were confirmed betweenin vitrohuman andin vivozebrafish larvae neutrophils. This study demonstrates the potential of OMI as a versatile tool for studying neutrophil metabolism and underscores its use across different biological systems, offering insights into neutrophil metabolic activity and function at a single cell level.
The prion-like protein Doppel: A soluble biomarker steering ovarian cancer’s peritoneal to circulatory dissemination
Authors: Azam Zulfikar , Zhang Xiaojun , Wahab Riajul , Hasan Md Mahedi , Kang Bowon , Hassan Md Mynul , Karim Mazharul , Choi Jeong Uk , Rana Muhit , Zhang Jiya-Ying , Roy Sourav , Byun Youngro , Kim In-San , Song Jae Yun , Alam Farzana , Toy Eugene P. , Reddy Sireesha Y. , Al-Hilal Taslim A. 
Published: July 2024

AbstractDetecting ovarian cancer (OC) early using existing biomarkers, e.g., cancer antigen 125 (CA125), is challenging due to its ubiquitous expression in many tissues. Doppel, a prion-like protein, expresses in male reproductive organ but absent in female reproductive systems and healthy tissues, but plays an important role in neoangiogenesis. Here, we have shown two platforms, soluble Doppel in sera/ascites and Doppel expressed circulating tumor cells (Dpl+CTC) in the whole blood, to detect subsets of epithelial OC (EOC). Increased level of Doppel in the sera of OC patients, in three different cohorts, confirm Doppel as OC specific biomarker. Serum Doppel level distinguishes EOC subtypes and early stages HGSOCs from non-cancerous conditions with high sensitivity and specificity. Stratifying the EOCs based on Doppel level, we categorized them into Doppel-high (Dplhi) and Doppel-low (Dpllow) groups. Using ascites-derived organoids and single cell sequencing of whole ascites of Dplhiand Dpllowpatients, we identify that Doppel induces epithelial-mesenchymal transition (EMT) and creates an immunosuppressive microenvironment, respectively. Doppel levels in the sera/ascites correlate with the changes ofDpl+CTC number in whole blood, highlighting the association of Doppel-induced EMT with CTC dissemination in circulation. Thus, Doppel-based detection of EOC subtypes could be a promising platform as clinical biomarker and link Doppel-axis with OC dissemination.
User-friendly exploration of epigenomic data in single cells using sincei
Authors: Bhardwaj Vivek , Mourragui Soufiane 
Published: July 2024

AbstractEmerging single-cell sequencing protocols allow researchers to study multiple layers of epigenetic regulation while resolving tissue heterogeneity. However, despite the rising popularity of such single-cell epigenomics assays, the lack of easy-to-use computational tools that allow flexible quality control and data exploration hinders their broad adoption. We introduce the Single-Cell Informatics (sincei) toolkit. sincei provides an easy-to-use, command-line interface for the exploration of data from a wide range of single-cell (epi)genomics protocols directly from aligned reads stored in .bam files. sincei can be installed via bioconda and the documentation is available athttps://sincei.readthedocs.io.
Deep learning-based detector of invasive alien frogs,Polypedates leucomystax and Rhinella marina, on an island at invasion front
Authors: Kimura Kaede , Fukuyama Ibuki , Fukuyama Kinji 
Published: July 2024

AbstractThis study aimed to develop and evaluate a deep learning-based detector for Southeast Asian treefrog (Polypedates leucomystax) and cane toad (Rhinella marina) on Iriomote Island, a Natural World Heritage Site located 30 km from established populations of these alien species on the nearby Ishigaki Island. Although a deep learning model typically requires local training data to be most accurate, the alien frogs have been eradicated from Iriomote Island, making such data unavailable. To address the data gap, we first trained the BirdNET model with acoustic data collected on Ishigaki Island, where these species were common, as well as native frog calls from Iriomote Island. Next, we evaluated model performance using (1) wild sounds on Ishigaki Island, and (2) sounds obtained by playing back the calls of the alien species on Iriomote Island. Model precision and recall for wild sounds were both 0.987 forP. leucomystaxand 1 forR. marina. For playback sounds, model recall values decreased (0.629 forP. leucomystaxand 0.906 forR. marina), while precisions remained nearly identical (1 for bothP. leucomystaxandR. marina). Despite the lower recall particularly forP. leucomystax, playback survey dates were mostly identifiable from the high number of detections. These results suggest that data from Ishigaki Island enabled training a model with adequate, though not complete, generalization across invasion front.
Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model
Authors: Clerkin Ariana Brenner , Pagane Nicole , West Devany W. , Spakowitz Andrew J. , Risca Viviana I. 
Published: July 2024

ABSTRACTThe three-dimensional structure of chromatin has emerged as an important feature of eukaryotic gene regulation. Recent technological advances in DNA sequencing-based assays have revealed locus- and chromatin state-specific structural patterns at the length scale of a few nucleosomes (∼1 kb). However, interpreting these data sets remains challenging. Radiation-induced correlated cleavage of chromatin (RICC-seq) is one such chromatin structure assay that maps DNA-DNA-contacts at base pair resolution by sequencing single-stranded DNA fragments released from irradiated cells. Here, we develop a flexible modeling and simulation framework to enable the interpretation of RICC-seq data in terms of oligonucleosome structure ensembles. Nucleosomes are modeled as rigid bodies with excluded volume and adjustable DNA wrapping, connected by linker DNA modeled as a worm-like chain. We validate the model’s parameters against cryo-electron microscopy and sedimentation data. Our results show that RICC-seq is sensitive to nucleosome spacing, nucleosomal DNA wrapping, and the strength of inter-nucleosome interactions. We show that nucleosome repeat lengths consistent with orthogonal assays can be extracted from experimental RICC-seq data using a 1D convolutional neural net trained on RICC-seq signal predicted from simulated ensembles. We thus provide a suite of analysis tools that add quantitative structural interpretability to RICC-seq experiments.
In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins
Authors: Shinichi Kawaguchi , Xin Xu , Takashi Soga , Kenta Yamaguchi , Ryuuya Kawasaki , Ryota Shimouchi , Susumu Date , Toshie Kai 
Published: July 2024

AbstractProtein-protein interactions are the fundamental features for understanding the molecular functions and regulations of proteins. Despite extensive databases, many interactions remain uncharacterized due to the intensive labor required for experimental validation. In this study, we utilized the AlphaFold2 program to predict interactions among proteins localized in the nuage, a germline-specific non-membrane organelle critical for piRNA biogenesis and RNA regulation. We screened 20 types of nuage proteins for 1:1 interactions and predicted dimer structures. Among those, five pairs represented novel interaction candidates. Three pairs, including Spn-E_Squ, were validated through co-immunoprecipitation in cultured cells and confirmed the interactions. Disruption of the salt bridges at the Spn-E_Squ interface verified their functional importance, underscoring the predictive model’s accuracy. Our analysis was extended to include interactions between three representative nuage components, Vas, Squ, and Tej, and approximately 430 oogenesis-related proteins. Following this extended analysis, co-immunoprecipitation in S2 cells verified interactions for three pairs: Mei-W68_Squ, CSN3_Squ, and Pka-C1_Tej. Furthermore, the majority ofDrosophilaproteins, ∼12,000, were screened for the interaction with Piwi protein, a central player in the piRNA pathway. Approximately 1.5% of the pairs, totaling 164 pairs, with a score above 0.6, were identified as potential binding partners. This in silico approach not only efficiently identifies potential interaction partners but also significantly reduces the gap by facilitating the integration of bioinformatics and experimental biology.
TNF Superfamily Member 14 Drives Post-Influenza Depletion of Alveolar Macrophages Enabling Secondary Pneumococcal Pneumonia
Authors: Malainou Christina , Peteranderl Christin , Ferrero Maximiliano Ruben , Vazquez-Armendariz Ana Ivonne , Alexopoulos Ioannis , Better Julian , Estiri Mohammad , Schultheis Hendrik , Hoppe Judith , del Rio Maria-Luisa , Rodriguez-Barbosa Jose Ignacio , Pfeffer Klaus , Günther Stefan , Looso Mario , Gruber Achim D. , Vadász István , Matt Ulrich , Herold Susanne 
Published: July 2024

AbstractSecondary bacterial infection, often caused byStreptococcus pneumoniae(Spn), is one of the most frequent and severe complications of influenza A virus (IAV)-induced pneumonia. Phenotyping of the pulmonary innate immune landscape after IAV infection revealed a significant depletion of the tissue-resident alveolar macrophage (TR-AM) population at day 7, which was associated with increased susceptibility to Spn outgrowth. To elucidate the molecular mechanisms underlying TR-AM depletion, and to define putative targets for treatment, we combined single-cell transcriptomics and cell-specific PCR profiling in an unbiased manner, usingin vivomodels of IAV infection and IAV/Spn co-infection. The TNF superfamily 14 (TNFSF14) ligand-receptor axis was revealed as the driving force behind post-influenza TR-AM death during the early infection phase, enabling the transition to pneumococcal pneumonia, while intrapulmonary transfer of genetically modified TR-AMs and antibody-mediated neutralization of specific pathway components alleviated disease severity. With a mainly neutrophilic expression and a high abundance in the bronchoalveolar fluid (BALF) of patients with severe virus-induced ARDS, TNFSF14 emerged as a novel determinant of virus-driven lung injury. Targeting the TNFSF14-mediated intercellular communication network in the virus-infected lung can, therefore, improve host defense, minimizing the risk of subsequent bacterial pneumonia, and ameliorating disease outcome.
Multi-Modal CLIP-Informed Protein Editing
Authors: Yin Mingze , Zhou Hanjing , Zhu Yiheng , Lin Miao , Wu Yixuan , Wu Jialu , Xu Hongxia , Hsieh Chang-Yu , Hou Tingjun , Chen Jintai , Wu Jian 
Published: July 2024

AbstractProteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.
Dopamine reveals adaptive learning of actions representation
Authors: Come Maxime , Gulmez Aylin , Keshishian Loussineh , Jehl Joachim , Bousseyrol Elise , Didienne Steve , Vicq Eleonore , Le Borgne Tinaïg , Mourot Alexandre , Faure Philippe 
Published: July 2024

AbstractEfficient decision-making requires two key processes: learning values from actions and identifying a set of relevant actions to learn from in a given context. While dopamine (DA) is a well-known substrate for signaling reward prediction errors (RPEs) from selected actions to adjust behavior, the process of establishing and switching between action representations is still poorly understood. To address this gap, we used fiber photometry and computational modelling in a three-armed bandit task where mice learned to seek rewards delivered through three successive rule sets, displaying distinct strategies in each rule. We show that DA dynamically reflected RPEs computed from different task features, revealing context- specific internal representations. Our findings demonstrate that mice not only learned and updated action values but also action representations, adapting the features from which they learn across rules for flexible adjustment of their decision strategy.
Encoding of antennal position and velocity by the Johnston’s organ in hawkmoths
Authors: Mukunda Chinmayee L , Sane Sanjay P 
Published: July 2024

ABSTRACTInsect antennae function as versatile, multimodal sensory probes in diverse behavioural contexts. In addition to their primary role as olfactory organs, they serve essential mechanosensory functions across insects, including auditory perception, vestibular feedback, airflow detection, gravity sensing, and tactile sensation. These diverse functions are facilitated by the mechanosensory Johnston’s organ (JO), located at the joint between the second antennal segment, known as the pedicel, and the flagellum. The pedicel-flagellum joint lacks muscles which means that the Johnston’s organs can perceive only passive deflections of the flagellum. Earlier work which characterized the sensitivity and short response time of the sensory units of JO in hawkmoths, showed that their sensitivity to a broad frequency range is range-fractionated. This vastly expands the functional repertoire of the JO. However, it is not clear what components of antennal kinematics are encoded by the JO. Here, we conducted experiments to test the hypothesis that JO neurons encode the position and velocity of angular movements of the flagellum. We recorded intracellularly from the axons of primary sensory neurons of JO while stimulating it with ramp-and-hold stimuli in which antennal position or antennal angular velocity was maintained at various constant values. Our study shows that JO neurons encode angular velocity and position of the antenna in their response. We also characterized the neural adaptation of the responses to angular velocities and positions. A majority of neurons were sensitive to a movement in the ventrad direction, in the direction of gravity. The adaptation and the directional response properties give rise to a nonlinear hysteresis-like response. Together, these findings highlight the neurophysiological basis underlying the functional versatility of the JO.
Saturation transposon mutagenesis enables genome-wide identification of genes required for growth and fluconazole resistance in the human fungal pathogenCryptococcus neoformans
Authors: Billmyre R. Blake , Craig Caroline J. , Lyon Joshua , Reichardt Claire , Eickbush Michael T. , Zanders Sarah E. 
Published: July 2024

AbstractFungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system inCryptococcus neoformansthat enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify theCryptococcus neoformansgenome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studiedRIM101pathway in fluconazole susceptibility. We also show that 5’ insertions of transposons can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5’ insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies ofC. neoformans, particularly in examining the consequences of genotypic diversity.
Genetic diversity and evolution of rice centromeres
Authors: Xie Lingjuan , Huang Yujie , Huang Wei , Shang Lianguang , Sun Yanqing , Chen Quanyu , Bi Shuangtian , Suo Mingyu , Zhang Shiyu , Yang Chentao , Zheng Xiaoming , Jin Weiwei , Qian Qian , Fan Longjiang , Wu Dongya 
Published: July 2024

AbstractUnderstanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes fromOryzaAA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Throughde novoannotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats (sati). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model forArabidopsiscentromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.