bluuebunny/crossref_metadata_2025_split huggingface dataset:
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Authors: Ji Yongxin , Shang Jiayu , Guan Jiaojiao , Zou Wei , Liao Herui , Tang Xubo , Sun Yanni 
Published: July 2024

AbstractPlasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO) vocabulary is a fundamental step in various tasks, including plasmid mobility classification. However, GO prediction for plasmid-encoded proteins faces two major challenges: the high diversity of functions and the limited availability of high-quality GO annotations. Thus, we introduce PlasGO, a tool that leverages a hierarchical architecture to predict GO terms for plasmid proteins. PlasGO utilizes a powerful protein language model to learn the local context within protein sentences and a BERT model to capture the global context within plasmid sentences. Additionally, PlasGO allows users to control the precision by incorporating a self-attention confidence weighting mechanism. We rigorously evaluated PlasGO and benchmarked it against six state-of-the-art tools in a series of experiments. The experimental results collectively demonstrate that PlasGO has achieved commendable performance. PlasGO significantly expanded the annotations of the plasmid-encoded protein database by assigning high-confidence GO terms to over 95% of previously unannotated proteins, showcasing impressive precision of 0.8229, 0.7941, and 0.8870 for the three GO categories, respectively, as measured on the novel protein test set.
Bayesian phylodynamics of early vertebrate development in BEAST 2
Authors: Zwaans Antoine , Seidel Sophie , Manceau Marc , Stadler Tanja 
Published: July 2024

AbstractAnalysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. CRISPR-based dynamic lineage tracing relies on recent advances in genome editing and sequencing technologies to generate inheritable, evolving genetic barcode sequences which enable reconstruction of such cell lineage trees, also referred to as phylogenetic trees. Recent work generated custom computational strategies to produce robust tree estimates from such data. We further capitalise on these advancements and introduce GABI (GESTALT Analysis using Bayesian Inference), which extends the analysis of GESTALT (Genome Editing of Synthetic Target Arrays for Lineage Tracing) data to a fully integrated Bayesian phylogenetic inference frame-work in the software BEAST 2. This implementation allows to represent the uncertainty in reconstructed tree reconstruction and enables their scaling in absolute time. Furthermore, based on such time-scaled lineage trees, the underlying processes of growth, differentiation and apoptosis are quantified through so-called phylodynamic inference, typically relying on a birthdeath or coalescent model. After validating the implementation, we demonstrate that the methodology results in robust estimates of lineage trees and growth dynamics characteristics of early zebrafishDanio reriodevelopment. GABI’s codebase is publicly available athttps://github.com/azwaans/GABI.
Cellular and molecular events organizing the assembly of tertiary lymphoid structures in glioblastoma
Authors: Vaccaro Alessandra , Yang Fan , van de Walle Tiarne , Franke Saskia , Lugano Roberta , Dénes Anna , Magoulopoulou Anastasia , Cid-Fariña Inés , Smits Anja , Uhrbom Lene , Libard Sylwia , Latini Francesco , Essand Magnus , Nilsson Mats , He Liqun , Olsson Bontell Thomas , Jakola Asgeir S , Ramachandran Mohanraj , Dimberg Anna 
Published: July 2024

AbstractTertiary lymphoid structures (TLS) are ectopic lymphoid aggregates associated with improved prognosis in numerous tumors. To date, their prognostic value in central nervous system cancers and the events underlying their formation remain unclear. Here, we find that TLS correlate with improved survival in glioblastoma patients. Furthermore, combining spatial transcriptomics of human tissues with longitudinal studies in murine glioma, we establish that the assembly of T cell-rich clusters is a prerequisite for the development of canonical TLS, and show that CD4 T cells play a central role in this process. Indeed, we provide evidence that IL7R+CCR7+Th1 lymphocytes with lymphoid tissue-inducing potential are recruited to TLS nucleation sites, where they can initiate TLS assembly by expressing lymphotoxin β. Our work defines TLS as a potential prognostic factor in glioblastoma and identifies cellular and molecular mechanisms of TLS formation. These findings have broader implications for the development of TLS-inducing therapies for cancer.Graphical abstract
The Impact of TLR9 Expression Loss on Breast Cancer Tumor Cells
Authors: Sible Emily , Weitsman Gregory , Amoyal Salome , Roblot Guillaume , Marotel Marie , Pescarmona Rémi , Bendriss-Vermare Nathalie , Gillet Cheryl , Ceesay Amie , Michallet Marie Cecile , Caux Christophe , Cosset Francois-Loic , Al Alem Umaima , Ng Tony , Hasan Uzma Ayesha 
Published: July 2024

AbstractToll-like receptor 9 (TLR9), primarily expressed in human dendritic and B cells, recognizes double-stranded DNA motifs from pathogens, initiating an inflammatory response. Recent studies have revealed TLR9’s involvement beyond its conventional role in immune response, notably during the tumorigenesis of various cancers such as head and neck, cervical, and ovarian cancers. Here we show by immunohistochemistry analysis demonstrated significantly lower TLR9 levels in breast cancer tumors compared to normal breast tissue epithelium. Similarly, TLR9 downregulation was also observed in several transformed breast cancer cell lines versus untransformed breast epithelial cell lines. Furthermore, overexpression of TLR9 led to reduced proliferation potential of breast cancer cell associated with activation of senescence as was evident by upregulation of proinflammatory cytokine IL-6, chemokines IL-8 and CXCL1; and growth factor GM-CSF. These findings support TLR9’s regulatory role in mitigating breast cancer and highlight its critical connection between the inflammatory response and tumor immunity.
Fully-Automated Multicolour Structured Illumination Module for Super-resolution Microscopy
Authors: Wang Haoran , Brown Peter T. , Ullom Jessica , Shepherd Douglas P. , Heintzmann Rainer , Diederich Benedict 
Published: July 2024

AbstractIn the rapidly advancing field of biological imaging, there is a great need for high-resolution imaging techniques that are both cost-effective and accessible, for example to better observe and understand dynamics in intracellular processes. Structured illumination microscopy (SIM) is the method of choice to achieve high axial and lateral resolution in living samples due to its optical sectioning and minimal phototoxicity. However, the high cost and complexity of conventional SIM systems limit their wide application. In our work, we present an open-source, fully-automated, two-color structured illumination module that is compatible with commercially available microscope stands. The compact design, consisting of low-cost single-mode fiber-coupled lasers and a digital micromirror device (DMD), is integrated into the open-source acquisition and control software (ImSwitch) in order to realize real-time super-resolution imaging. This developed system achieves up to a 1.55-fold improvement in lateral resolution compared to conventional wide-field microscopy. To rationally design this module, we developed a model to ensure optimal DMD diffraction per-formance using tilt and roll pixels, thus covering a wide range of low-cost video projectors for use in coherent SIM setups. Our goal is to democratize SIM-based super-resolution microscopy by providing both comprehensive open-source documentation and a modular software framework that works with various hardware components (e.g. cameras, stages) and reconstruction algorithms. In this way, we try to upgrade as many devices as possible to the super-resolution realm.
Repeat-rich regions cause false positive detection of NUMTs: a case study in amphibians using an improved cane toad reference genome
Authors: Cheung K , Rollins LA , Hammond JM , Barton K , Ferguson JM , Eyck HJF , Shine R , Edwards RJ 
Published: July 2024

AbstractMitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMT) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false positive detection of NUMTs is common when handling repeat-rich sequences, whilst fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10x linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n=5,310), indicating the gene-containing regions were well assembled. We used three complementary methods (NUMTFinder,dinumtandPALMER) to study the NUMT landscape of the cane toad genome. All three methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.SignificanceThis study uses an updated cane toad nuclear genome assembly and multiple NUMT detection methods to confirm a lack of NUMTs that might confound the use of mtDNA as a population genetic marker in the cane toad. We provide an exemplar study for NUMT detection accounting for genome assembly quality and composition, and highlight the risks of using BLASTN-based approaches in highly repetitive nuclear genomes.
Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis
Authors: Arunachalam Easun , Keber Felix C. , Law Richard C. , Kumar Chirag K. , Shen Yihui , Park Junyoung O. , Wühr Martin , Needleman Daniel J. 
Published: July 2024

AbstractA long-standing observation is that in fast-growing cells, respiration rate declines with increasing growth rate and is compensated by an increase in fermentation, despite respiration being more efficient than fermentation. This apparent preference for fermentation even in the presence of oxygen is known as aerobic glycolysis, and occurs in bacteria, yeast, and cancer cells. Considerable work has focused on understanding the potential benefits that might justify this seemingly wasteful metabolic strategy, but its mechanistic basis remains unclear. Here we show that aerobic glycolysis results from the saturation of mitochondrial respiration and the decoupling of mitochondrial biogenesis from the production of other cellular components. Respiration rate is insensitive to acute perturbations of cellular energetic demands or nutrient supplies, and is explained simply by the amount of mitochondria per cell. Mitochondria accumulate at a nearly constant rate across different growth conditions, resulting in mitochondrial amount being largely determined by cell division time. In contrast, glucose uptake rate is not saturated, and is accurately predicted by the abundances and affinities of glucose transporters. Combining these models of glucose uptake and respiration provides a quantitative, mechanistic explanation for aerobic glycolysis. The robustness of specific respiration rate and mitochondrial biogenesis, paired with the flexibility of other bioenergetic and biosynthetic fluxes, may play a broad role in shaping eukaryotic cell metabolism.
Discovery of the missing cytochrome P450 monooxygenase cyclases that conclude glyceollin biosynthesis in soybean
Authors: Khatri Praveen , Kuflu Kuflom , McDowell Tim , Lin Jie , Kovinich Nikola , Dhaubhadel Sangeeta 
Published: July 2024

AbstractGlyceollins are isoflavonoid-derived metabolites produced by soybean that hold great promise in improving human and animal health due to their antimicrobial, and other medicinal properties. They play important roles in agriculture by defending soybean against one of its most destructive pathogens,Phytophthora sojae. Longstanding research efforts have focused on improving accessibility to glyceollins, yet chemical synthesis remains uneconomical. The fact that some of the key genes involved in the final step of glyceollin biosynthesis have not been identified, engineering the accumulation of these important compounds in microbes is not yet possible. Although the activity of a P450 cyclase was inferred to catalyze the final committed step in glyceollin biosynthesis forty years ago, the enzyme in question has never been conclusively identified. This study reports, for the first time, the identification of three cytochrome P450 monooxygenase cyclases that catalyze the final steps of glyceollin biosynthesis. UtilizingP. sojae-soybean transcriptome data, along with genome mining tools and co-expression network analysis, we have identified 16 candidate glyceollin synthases (GmGS). Heterologous expression of these candidate genes in yeast, coupled within vitroenzyme assays, enabled us to discover three enzymes capable of producing two glyceollin isomers. GmGS11A and GmGS11B catalyzed the conversion of glyceollidin to glyceollin I, whereas GmGS13A converted glyceocarpin to glyceollin III. The functionality of these candidates was further confirmedin plantathrough gene silencing and overexpression in soybean hairy roots. This groundbreaking study not only contributes to the understanding of glyceollin biosynthesis, but also demonstrates a new synthetic biology strategy that could potentially be scaled up to produce valuable molecules for crop and disease management.
Migration of Kupffer’s vesicle derived cells is essential for tail morphogenesis in zebrafish embryos
Authors: Hoeksma Jelmer , Hertog Jeroen den 
Published: July 2024

AbstractA phenotypic screen of fungal filtrates on developing zebrafish embryos identified metabolites from the fungusCeratocystis populicolato induce ectopic tail formation, including a split notochord and a duplicated caudal fin. Chemical analyses led to the identification of monoterpene alcohols, in particular geraniol, as active compounds inducing ectopic tail formation during a specific 4 h time window during tail bud stage. Embryos from Tüpfel long fin zebrafish (TL) were more susceptible to ectopic tail formation by geraniol than embryos from Wild Indian Karyotpe (WIK) zebrafish, indicating zebrafish strain specificity. RNA sequencing on tail buds of 15-somite stage embryos revealed downregulation of essential genes of the retinoic acid signaling pathway and differential expression ofcyp26a1andfgf8aand downstreamhox-genes was validated. Time-lapse imaging revealed that Kupffer’s vesicle derived cells failed to migrate shorty after Kupffer’s vesicle collapse upon geraniol treatment and these cells failed to merge with progenitors from the tail bud. Instead, these cells contributed to an ectopic tail, expressing markers for presomitic mesoderm, somite and notochord tissue. Taken together, our data suggests that Kupffer’s vesicle cells harbor tail progenitor capacity, and proper migration of these cells is essential for normal tail morphogenesis.Summary StatementInhibition of Kupffer’s vesicle derived cell migration affected tail morphogenesis and resulted in ectopic tail formation in zebrafish embryos.
Integrated Analysis of Single-Cell and Bulk RNA-Seq Data reveals that Ferroptosis-Related Genes Mediated the Tumor Microenvironment predicts Prognosis, and guides Drug Selection in Triple-Negative Breast Cancer
Authors: Gong Xuantong , Gu Lishuang , Yang Di , He Yu , Li Qian , Qin Hao , Wang Yong 
Published: July 2024

AbstractBackgroundTriple-negative breast cancer (TNBC) is aggressive, lacking methods to predict recurrence and drug sensitivity. Ferroptotic heterogeneity varies in TNBC subtypes. However, the tumor microenvironment (TME) mediated by ferroptosis genes is unclear. Our study aims to integrate single-cell and bulk RNA sequencing (RNA-seq) data to reveal the ferroptosis-mediated TME in TNBC, predicting prognosis and guiding treatment.MethodsThe single-cell and bulk RNA-seq data of TNBC were sourced from the Gene Expression Omnibus (GEO) database. Using these data, a machine learning algorithm was employed to integrate and analyze the characteristics of the TME mediated by ferroptosis-related genes in TNBC. Prediction models for TNBC survival prognosis and drug treatment response were established and then validated in an independent set.ResultsAt the individual cell level, T cells were categorized into three distinct subpopulations, and local macrophages into two subpopulations. The infiltration degree of these different cell subpopulations was closely associated with prognosis and treatment outcomes. Based on this, the risk score model we developed effectively predicted recurrence-free survival in TNBC patients, with independently validated pooled predicted 3-, 4-, and 5-year Area Under the Curves (AUCs) of 0.65, 0.67, and 0.71, respectively. Additionally, we found that patients in the high-risk group may be more responsive to 27 drugs.ConclusionsWe have uncovered the tumor immune cell clusters in TNBC mediated by ferroptosis. A risk score model was constructed to identify high-risk TNBC patients, which can assist physicians in disease monitoring and precision therapy. The genes identified hold significant potential as therapeutic targets for TNBC patients.FundingThis project is funded by the National Natural Science Foundation of China (81974268, 82472000, 82304151), the Talent Incentive Program of Cancer Hospital Chinese, Academy of Medical Sciences (801032247), the Cooperation Fund of CHCAMS (CFA202202023), and the open project of Beijing Key Laboratory of Tumor Invasion and Metastasis Mechanism, Capital Medical University(2023ZLKF03).Impact StatementIntegrating single-cell and bulk RNA-seq data elucidates the role of ferroptosis in TNBC, offering a prognostic model and personalized therapeutic insights.
A novel HER2 protein identification methodology in breast cancer cells using Raman spectroscopy and Raman imaging: an analytical validation study
Authors: Abramczyk H. , Surmacki J. , Kopeć M. 
Published: July 2024

AbstractBackgroundConventional assays such as immunohistochemistry (IHC) andin situhybridization (ISH) used in clinical procedures for quantification of the human epidermal growth factor receptor-2 (HER2) status in breast cancer have many limitations. Our results suggest that a new Raman method may improve specificity that will result in better patients selection for HER2 targeted therapy. In the current study, we have used HER2 expression in a broad range of breast cancer phenotypes to explore the potential utility of a novel immunodetection technique, using Raman spectroscopy and Raman imaging combined with artificial intelligence models.MethodsThe expression of HER2 protein in different cancer subtypes was evaluated using Raman methodology to test correlations with currently used quantitative protein analysis for a broad range of cancer subtypes based on the expression levels of estrogen and progesterone receptors (ER and PR), HER2, cytokeratins and claudins. In the current study, five breast cancer cell lines: MCF-10A, MCF-7, MDA-MB-231, HTB-30 (SK-BR-3) and AU-565 were tested.ResultsThe correlations between Raman method and conventional HER2 testing methodologies (IHC and ISH) have been tested. Raman measurements showed a strong linear correlation (p= 0.05, R2=0,9816) with IHC analysis in the studied breast cell lines: MCF-10A, MCF-7, MDA-MB- 231, HTB-30 (SK-BR-3) and AU-565 representing normal, non-tumorigenic epithelial cells, triple-positive breast carcinoma and triple-negative breast cancer cell lines.ConclusionsAnalytic testing of Raman spectroscopy and Raman imaging demonstrated that this method may offer advantages over currently used diagnostic methodologies. The broad range of HER2 expression on the surface of human breast normal and cancer cells from triple negative to triple positive cell lines were studied. Our data demonstrate that Raman based methods for HER2 quantitation of HER2 may offer significant progress in patient selection for HER2 targeted therapy over conventional HER2 identification. Further studies of HER2 determination by Raman methods within vivocells andex vivotissue are warranted.
Coordination of protein synthesis and decay in mammalian cells
Authors: Sun Michael Shoujie , Martin Benjamin , Dembska Joanna , Deluz Cédric , Suter David M. 
Published: July 2024

AbstractProtein synthesis and decay rates must be tightly coordinated to ensure proteome homeostasis. How this coordination is established is unknown. Here we use quantitative live cell imaging combined with computational inference to determine how changes in global protein synthesis rates alter protein decay rates. We identified two modes of adaptation hinging on differential responses of the cell cycle to changes in protein synthesis rates. A passive adaptation of protein degradation and dilution rates operates in cells tightly coupling proliferation rate to protein synthesis rates, allowing to partially buffer changes in proteome concentrations with increased loss of short-lived proteins. In contrast, the proliferation rate of mouse embryonic stem cells (mESCs) is hyposensitive to moderate changes in protein synthesis. mESCs uncouple protein degradation and dilution rates and robustly maintain their protein levels. Our work illuminates the complex interplay between protein synthesis, degradation, and cell division to regulate proteome homeostasis.
Integrating tDNA Epigenomics and Expression with Codon Usage Unravel an Intricate Connection with Protein Expression Dynamics inTrypanosoma cruzi
Authors: Silva Herbert G. S. , Kimura Satoshi , Lima Pedro L. C. , Pires David S. , Waldor Matthew K. , da Cunha Julia P. C. 
Published: July 2024

AbstractCodon usage bias impacts protein expression across all kingdoms of life, including trypanosomatids. These protozoa, such as theTrypanosoma cruzi, primarily regulate their protein-coding genes through posttranscriptional mechanisms. Here, we integrated analyses of codon usage with multiple high-throughput sequencing data to investigate whether codon usage bias is present into surface virulence factors (disruptive compartment), conserved housekeeping proteins (core compartment), and proteins involved in the developmental stages ofT. cruzi. For the first time in trypanosomatids, tRNA sequencing was employed to reveal coadaptation between codon usage and anticodon availability. Despite notable differences in the proteomes of infective and non-infective forms, they exhibited similar pools of tRNAs and similar codon usage preferences. We observed that open chromatin levels of tRNA genes correlate with tRNA expression in non-infective forms, but not in infective forms, suggesting chromatin states do not control the tRNA pool in the latter. Our analysis also revealed a relationship between anticodon:codon pairing modes and protein abundance. Highly expressed mRNAs favored Watson– Crick base pairing, whereas less expressed mRNAs displayed more wobble base pairing. Overall, our findings suggest that protein expression inT. cruziis influenced by a combination of codon usage bias, tRNA abundance, and anticodon:codon pairing modes.Graphical abstract