bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arbuscular mycorrhizal fungal diversity and association networks in African tropical rainforest trees
Authors: Olanipon Damilola , Boeraeve Margaux , Jacquemyn Hans 
Published: February 2024

AbstractTropical rainforests represent one of the most diverse and productive ecosystems on Earth. High productivity is sustained by efficient and rapid cycling of nutrients through decomposing organic matter, which is for a large part made possible by symbiotic associations between plants and mycorrhizal fungi. In this association, an individual plant typically associates simultaneously with multiple fungi and the fungus associates with multiple plants, creating complex networks between fungi and plants. However, there are still very few studies that have investigated mycorrhizal fungal composition and diversity in tropical rainforest trees, particularly in Africa, and assessed the structure of the network of associations between fungi and rainforest trees. In this study, we collected root and rhizosphere soil samples from Ise Forest Reserve (Southwest Nigeria), and employed a metabarcoding approach to identify the dominant arbuscular mycorrhizal (AM) fungal taxa associating with ten co-occurring tree species and to assess variation in AM communities. Network analysis was used to elucidate the architecture of the network of associations between fungi and tree species. A total of 194 AM fungal Operational Taxonomic Units (OTUs) belonging to six families were identified, with 68% of all OTUs belonging to Glomeraceae. While AM fungal diversity did not differ between tree species, AM fungal community composition did. Network analyses showed that the network of associations was not significantly nested and showed a relatively low level of specialization (H2= 0.43) and modularity (M= 0.44). We conclude that, although there were some differences in AM fungal community composition, the studied tree species associate with a large number of AM fungi. Similarly, most AM fungi had a large host breadth and connected most tree species to each other, thereby potentially working as interaction network hubs.Graphical Abstract
Differential mitochondrial bioenergetics and cellular resilience in astrocytes, hepatocytes, and fibroblasts from aging baboons
Authors: Adekunbi Daniel A. , Huber Hillary F. , Li Cun , Nathanielsz Peter W. , Cox Laura A. , Salmon Adam B. 
Published: February 2024

AbstractBiological resilience, broadly defined as ability to recover from acute challenge and return to homeostasis, is of growing importance to the biology of aging. At the cellular level, there is variability across tissue types in resilience and these differences likely to contribute to tissue aging rate disparities. However, there are challenges in addressing these cell-type differences at regional, tissue and subject level. To address this question, we established primary cells from aged male and female baboons between 13.3-17.8 years spanning across different tissues, tissue regions, and cell types including: (1) fibroblasts from skin and from heart separated into left ventricle (LV), right ventricle (RV), left atrium (LA) and right atrium (RA), (2) astrocytes from the prefrontal cortex and hippocampus and (3) hepatocytes. Primary cells were characterized by their cell surface markers and their cellular respiration assessed with Seahorse XFe96. Cellular resilience was assessed by modifying a live-cell imaging approach we previously reported that monitors proliferation of dividing cells following response and recovery to oxidative (50µM-H2O2), metabolic (1mM-glucose) and proteostasis (0.1µM-thapsigargin) stress. We noted significant differences even among similar cell types that are dependent on tissue source and the diversity in cellular response is stressor specific. For example, astrocytes were more energetic and exhibited greater resilience to oxidative stress (OS) than both fibroblasts and hepatocytes. RV and RA fibroblasts were less resilient to OS compared with LV and LA respectively. Skin fibroblasts were less impacted by proteostasis stress compared to astrocytes and cardiac fibroblasts. Future studies will test the functional relationship of these outcomes to age and developmental status of donors as potential predictive markers.
Peptide-stimulation of autologous T cells reverts immune checkpoint inhibitor resistance of hypermutated colorectal cancer cells
Authors: Schwarz Sandra , Zhaoran Su , Krohn Mathias , Löffler Markus W. , Schlosser Andreas , Linnebacher Michael 
Published: February 2024

AbstractTwo hypermutated colon cancer cases with patient-derived cell lines, peripheral and tumor-infiltrating T cells available were selected for detailed investigation of immunological response.T cells co-cultured with autologous tumor cells showed only low levels of pro-inflammatory cytokines and failed at tumor recognition. Similarly, treatment of co-cultures with immune checkpoint inhibitors (ICI) did not boost antitumor immune responses. Since proteinase inhibitor 9 (PI-9) was detected in tumor cells, a specific inhibitor (PI-9i) was used in addition to ICI in T cell cytotoxicity testing. However, only pre-stimulation with tumor-specific peptides (cryptic and neoantigenic) significantly increased recognition and elimination of tumor cells by T cells independently of ICI or PI-9i.We showed, that ICI resistant tumor cells can be targeted by tumor-primed T cells and also demonstrated the superiority of tumor-naïve peripheral blood T cells compared to highly exhausted tumor-infiltrating T cells. Future precision immunotherapeutic approaches should include multimodal strategies to successfully induce durable anti-tumor immune responses.
DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos
Authors: Fanourgakis Grigorios , Gaspa-Toneu Laura , Komarov Pavel A. , Ozonov Evgeniy A. , Smallwood Sebastien A. , Peters Antoine H.F.M. 
Published: February 2024

ABSTRACTDNA methylation (DNAme) serves a stable gene regulatory function in somatic cells (1). In the germ line and during early embryogenesis, however, DNAme undergoes global erasure and re-establishment to support germ cell and embryonic development (2). Whilede novoDNAme acquisition during male germ cell development is essential for setting genomic DNA methylation imprints, other intergenerational roles for paternal DNAme in defining embryonic chromatin after fertilization are unknown. To approach this question, we reduced levels of DNAme in developing male germ cells through conditional gene deletion of thede novoDNA methyltransferases DNMT3A and DNMT3B in undifferentiated spermatogonia. We observed that DNMT3A serves a DNAme maintenance function in undifferentiated spermatogonia while DNMT3B catalyzesde novoDNAme during spermatogonial differentiation. Mutant male germ cells nevertheless completed their differentiation to sperm. Failingde novoDNAme inDnmt3a/Dnmt3bdouble deficient spermatogonia is associated with increased nucleosome occupancy in mature sperm, preferentially at sites with higher CpG content, supporting the model that DNAme modulates nucleosome retention in sperm (3). To assess the impact of altered sperm chromatin in the formation of embryonic chromatin, we measured H3K4me3 occupancy at paternal and maternal alleles in 2-cell embryos using a newly developed transposon-based tagging assay for modified chromatin. Our data show that reduced DNAme in sperm renders paternal alleles permissive for H3K4me3 establishment in early embryos, independently of possible paternal inheritance of sperm born H3K4me3. Together, this study provides first evidence that paternally inherited DNAme directs chromatin formation during early embryonic development.
Identification of B cell subsets based on antigen receptor sequences using deep learning
Authors: Lee Hyunho , Shin Kyoungseob , Lee Yongju , Lee Soobin , Lee Seungyoun , Lee Eunjae , Kim Seung Woo , Shin Ha Young , Kim Jong Hoon , Chung Junho , Kwon Sunghoon 
Published: February 2024

AbstractB cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
The full length BEND2 protein is dispensable for spermatogenesis but required for setting the ovarian reserve in mice
Authors: Huang Yan , Bucevic Nina , Coves Carmen , Felipe-Medina Natalia , Marcet-Ortega Marina , Nikou Nikoleta , Madrid-Sandín Cristina , López-Panadés Maria , Buza Carolina , Miralles Neus Ferrer , Iborra Antoni , Pujol Anna , Pendás Alberto M. , Roig Ignasi 
Published: February 2024

AbstractInfertility affects up to 12% of couples globally, with genetic factors contributing to nearly half of the cases. Advances in genomic technologies have led to the discovery of genes likeBend2, which plays a crucial role in gametogenesis. In the testis,Bend2expresses two protein isoforms: full-length and a smaller one. Ablation of both proteins results in an arrested spermatogenesis. Because theBend2locus is on the X chromosome, and theBend2−/ymutants are sterile, BEND2’s role in oogenesis remained elusive.In this study, we employed a novelBend2mutation that blocks the expression of the full-length BEND2 protein but allows the expression of the smaller BEND2 isoform. Interestingly, this mutation does not confer male sterility and mildly affects spermatogenesis. Thus, it allowed us to study the role of BEND2 in oogenesis. Our findings demonstrate that full-length BEND2 is dispensable for male fertility, and its ablation leads to a reduced establishment of the ovarian reserve. These results reveal a critical role for full-length BEND2 in oogenesis and provide insights into the mechanisms underlying the establishment of the ovarian reserve. Furthermore, these findings hold relevance for the diagnostic landscape of human infertility.
Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues
Authors: Bai Zhiliang , Zhang Dingyao , Gao Yan , Tao Bo , Bao Shuozhen , Enninful Archibald , Zhang Daiwei , Su Graham , Tian Xiaolong , Zhang Ningning , Xiao Yang , Liu Yang , Gerstein Mark , Li Mingyao , Xing Yi , Lu Jun , Xu Mina L. , Fan Rong 
Published: February 2024

AbstractSpatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combiningin situpolyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.
Reducing Cathodic Drift during Isoelectric Focusing using Microscale Immobilized pH Gradient Gels
Authors: Lomeli Gabriela , Herr Amy E. 
Published: February 2024

ABSTRACTMicrofluidic analytical tools play an important role in miniaturizing proteomic assays for improved detection sensitivity, throughput, and automation. Microfluidic isoelectric focusing (IEF) can resolve proteoforms in lysate from low-to-single cell numbers. However, IEF assays often use carrier ampholytes (CAs) to establish a pH gradient for protein separation, presenting limitations like pH instability in the form of cathodic drift (migration of focused proteins toward the cathode). Immobilized pH gradient (IPG) gels reduce cathodic drift by covalently immobilizing the pH buffering components to a matrix. To our knowledge, efforts to implement IPG gels at the microscale have been limited to glass microdevices. To adapt IEF using IPGs to widely used microfluidic device materials, we introduce a polydimethylsiloxane (PDMS)-based microfluidic device and compare the microscale pH gradient stability of IEF established with IPGs, CAs, and a hybrid formulation of IPG gels and CAs (mixed-bed IEF). The PDMS-based IPG microfluidic device (μIPG) resolved analytes differing by 0.1 isoelectric point within a 3.5-mm separation lane over a 20-min focusing duration. During the 20-min duration, we observed markedly different cathodic drift velocities among the three formulations: 60.1 µm/min in CA-IEF, 2.5 µm/min in IPG-IEF (∼24-fold reduction versus CA-IEF), and 1.4 µm/min in mixed-bed IEF (∼43-fold reduction versus CA-IEF). Lastly, mixed-bed IEF in a PDMS device resolved green fluorescent protein (GFP) proteoforms from GFP-expressing human breast cancer cell lysate, thus establishing stability in lysate from complex biospecimens. µIPG is a promising and stable technique for studying proteoforms from small volumes.
T-cells specific for KSHV and HIV migrate to Kaposi sarcoma tumors and persist over time
Authors: Ravishankar Shashidhar , Towlerton Andrea M.H. , Tiamiyu Iyabode L. , Mooka Peter , Nankoma Janet , Kafeero James , Mubiru Dennis , Sekitene Semei , Aicher Lauri D. , Miller Chris P. , Coffey David G. , Okoche Lazarus , Atwinirembabazi Prisca , Okonye Joseph , White Jessica , Koelle David M. , Jing Lichen , Phipps Warren T. , Warren Edus H. 
Published: February 2024

AbstractKaposi sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi sarcoma (KS), which causes significant morbidity and mortality worldwide, particularly in people living with HIV (PLWH) and in sub-Saharan Africa where KSHV seroprevalence is high. Postulating that T-cells specific for KSHV and HIV would be attracted to KS tumors, we performed transcriptional profiling and T-cell receptor (TCR) repertoire analysis of tumor biopsies from 144 Ugandan adults with KS, 106 of whom were also living with HIV. We show that CD8+T-cells and M2-polarized macrophages are the most common immune cells in KS tumors. The TCR repertoire of T-cells associated with KS tumors is shared across spatially and temporally distinct tumors from the same individual. Clusters of T-cells with predicted shared specificity for uncharacterized antigens, potentially encoded by KSHV or HIV, comprise ∼25% of the T-cells in KS tumors. Single-cell RNA-sequencing of blood from a subset of 9 adults captured 4,283 unique αβ TCRs carried in 14,698 putative KSHV- or HIV-specific T-cells, which carried an antigen-experienced effector phenotype. T-cells engineered to express a representative sample of these TCRs showed high-avidity recognition of KSHV- or HIV-encoded antigens. These results suggest that a polyspecific, high-avidity KSHV- and HIV-specific T-cell response, potentially inhibited by M2 macrophages, migrates to and localizes with KS tumors. Further analysis of KSHV- and HIV-specific T-cells in KS tumors will provide insight into the pathogenesis of KS and could guide the development of specific immune therapy based on adoptive transfer or vaccination.Author SummaryIn this work, we set out to examine Kaposi Sarcoma (KS) tumor tissue, as well as peripheral blood cells from individuals with KS, both living with and without HIV. Our goal was to identify T-cells that specifically recognize antigens encoded by Kaposi sarcoma-associated herpesvirus (KSHV) or HIV. By analyzing the T-cell repertoire in KS tumor biopsies from people in Uganda with different types of KS, we uncovered clusters of T-cells with previously unknown ability to recognize these viruses. Through single-cell sequencing of peripheral blood cells, we also observed that many of these T-cells had cell-killing properties. Notably, they often coexisted with a subset of macrophages with immunosuppressive properties, which we suspect may be suppressing the function of virus-targeting T-cells. Our findings suggest that additional studies of these virus-targeting T-cells and their interaction with immunosuppressive macrophages could significantly advance the development of effective therapeutics against KS.
Invariant set theory for predicting failure of antibiotic cycling
Authors: Anderson Alejandro , Kinahan Matthew W. , Gonzalez Alejandro H. , Udekwu Klas , Hernandez-Vargas Esteban A. 
Published: February 2024

AbstractThe limited availability of antibiotics and the need for prompt decision-making present significant challenges for healthcare practitioners. When faced with this situation, practitioners must prioritize their approach based on several key factors. By leveraging the emergent understanding of collateral sensitivity among antibiotic-exposed pathogens, we demonstrate the utility of control invariant sets to predict treatment failure when antibiotic cycling is applied as a therapeutic strategy aiming to eradicate or prevent emergence of multi-drug resistant pathogens. Our results here pave the way for point-of-care diagnostic technologies to identify infections and select appropriate treatments quickly, reducing unnecessary antibiotic use.
Far-red and sensitive sensor for monitoring real time H2O2dynamics with subcellular resolution and in multi-parametric imaging applications
Authors: Lee Justin Daho , Nguyen Amanda , Jin Zheyu Ruby , Moghadasi Aida , Gibbs Chelsea E. , Wait Sarah J. , Evitts Kira M. , Asencio Anthony , Bremner Samantha B , Zuniga Shani , Chavan Vedant , Williams Andy , Smith Netta , Regnier Michael , Young Jessica E. , Mack David , Nance Elizabeth , Boyle Patrick M. , Berndt Andre 
Published: February 2024

AbstractH2O2is a key oxidant in mammalian biology and a pleiotropic signaling molecule at the physiological level, and its excessive accumulation in conjunction with decreased cellular reduction capacity is often found to be a common pathological marker. Here, we present a red fluorescent Genetically Encoded H2O2Indicator (GEHI) allowing versatile optogenetic dissection of redox biology. Our new GEHI, oROS-HT, is a chemigenetic sensor utilizing a HaloTag and Janelia Fluor (JF) rhodamine dye as fluorescent reporters. We developed oROS-HT through a structure-guided approach aided by classic protein structures and recent protein structure prediction tools. Optimized with JF635, oROS-HT is a sensor with 635 nm excitation and 650 nm emission peaks, allowing it to retain its brightness while monitoring intracellular H2O2dynamics. Furthermore, it enables multi-color imaging in combination with blue-green fluorescent sensors for orthogonal analytes and low auto-fluorescence interference in biological tissues. Other advantages of oROS-HT over alternative GEHIs are its fast kinetics, oxygen-independent maturation, low pH sensitivity, lack of photo-artifact, and lack of intracellular aggregation. Here, we demonstrated efficient subcellular targeting and how oROS-HT can map inter and intracellular H2O2diffusion at subcellular resolution. Lastly, we used oROS-HT with the green fluorescent calcium indicator Fluo-4 to investigate the transient effect of the anti-inflammatory agent auranofin on cellular redox physiology and calcium levels via multi-parametric, dual-color imaging.
Expression of elastin, FBXW2, fibrillin-1, and α-smooth muscle actin in damaged blood vessels of bovine legs
Authors: Akiyama Mari 
Published: February 2024

AbstractElastic fibers present within the internal and external elastic laminae play a vital role in maintaining the health of blood vessels. The impairment of smooth muscle cell function results in the development of vascular diseases. In this study, blood vessels from bovine legs were carefully examined in culture dishes for 5 weeks. Examination of elastin, F-box and WD-40 domain-containing protein 2 (FBXW2), and fibrillin-1 in serial sections revealed that elastin and FBXW2 were present in the internal and external elastic laminae, whereas fibrillin-1 was present outside of them. After 5 weeks, elastin and FBXW2 maintained the shape of the elastic lamina, whereas the fibrillin-1-rich layer spread and migrated from the elastic lamina. When the blood vessel lumen was blocked by tissue rich in fibrillin-1, α-smooth muscle actin (SMA) expression weakened. Although elastin and fibrillin-1 are components of elastic fibers, this study revealed that fibrillin-1 has a role different from that of elastin. This in vitro model is useful for identifying the mechanisms underlying vascular degradation.