bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiologic media renders human iPSC-derived macrophages permissive forM. tuberculosisby rewiring organelle function and metabolism
Authors: Bussi Claudio , Lai Rachel , Athanasiade Natalia , Gutierrez Maximiliano G. 
Published: March 2024

SummaryIn vitrostudies are crucial for our understanding of the human macrophage immune functions. However, traditionalin vitroculture media poorly reflect the metabolic composition of blood, potentially affecting the outcomes of these studies. Here, we analysed the impact of a physiological medium on human induced pluripotent stem cell (iPSC)-derived macrophages (iPSDM) function. Macrophages cultured in a human plasma-like medium (HPLM) were more permissive toMycobacterium tuberculosis(Mtb) replication and showed decreased lipid metabolism with increased metabolic polarisation. Functionally, we discovered that HPLM-differentiated macrophages showed different metabolic organelle content and activity. Specifically, HPLM-differentiated macrophages displayed reduced lipid droplet and peroxisome content, increased lysosomal proteolytic activity, and increased mitochondrial activity and dynamics. Inhibiting or inducing lipid droplet formation revealed that lipid droplet content is a key factor influencing macrophage permissiveness to Mtb. These findings underscore the importance of using physiologically relevant mediain vitrofor accurately studying human macrophage function.
Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions
Authors: Torro Rémy , Díaz-Bello Beatriz , Arawi Dalia El , Dervanova Ksenija , Ammer Lorna , Dupuy Florian , Chames Patrick , Sengupta Kheya , Limozin Laurent 
Published: March 2024

AbstractA current challenge in bioimaging for immunology and immunotherapy research lies in analyzing multimodal and multidimensional data that capture dynamic interactions between diverse cell populations. Here, we introduce Celldetective, an open-source Python-based software designed for high-performance, end-to-end analysis of image-basedin vitroimmune and immunotherapy assays. Purpose-built for multicondition, 2D multichannel time-lapse microscopy of mixed cell populations, Celldetective is optimized for the needs of immunology assays. The software seamlessly integrates AI-based segmentation, Bayesian tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualization, annotation, and training capabilities. We demonstrate its utility with original data on immune effector cell interactions with an activating surface, mediated by bispecific antibodies, and further showcase its potential for analyzing extensive sets of pairwise interactions in antibody-dependent cell cytotoxicity events.
CD39 is expressed on functional effector and tissue resident memory CD8+ T cells
Authors: Isaacs Jordan F. , Degefu Hanna N. , Chen Tiffany , Kleist Sierra A. , Musial Shawn C. , Ford Myles A. , Searles Tyler G. , Lin Chun-Chieh , Skorput Alexander G. J. , Shirai Keisuke , Turk Mary Jo , Zanazzi George J. , Rosato Pamela C. 
Published: March 2024

AbstractThe ecto-ATPase CD39 is expressed on exhausted CD8+ T cells in chronic viral infection and has been proposed as a marker of tumor-specific CD8+ T cells in cancer, but the role of CD39 in an effector and memory T cell response has not been clearly defined. We report that CD39 is expressed on antigen-specific CD8+ short-lived effector cells (SLECs), while it’s co-ecto-enzyme, CD73, is found on memory precursor effector cells (MPEC)in vivo. Inhibition of CD39 enzymatic activity duringin vitroT cell priming enhances MPEC differentiationin vivoafter transfer and infection. The enriched MPEC phenotype is associated with enhanced tissue resident memory (TRM) establishment in the brain and salivary gland following an acute intranasal viral infection, suggesting that CD39 ATPase activity plays a role in memory CD8+ T cell differentiation. We also show that CD39 is expressed on human and murine TRMacross several non-lymphoid tissues and melanoma, while CD73 is expressed on both circulating and resident memory subsets in mice. In contrast to exhausted CD39+ T cells in chronic infection, CD39+ TRMare fully functional when stimulatedex vivowith cognate antigen. This work further expands the identity of CD39 beyond a T cell exhaustion marker.
CLigopt: Controllable Ligand Design Through Target-Specific Optimisation
Authors: Li Yutong , Costa Avelar Pedro Henrique da , Chen Xinyue , Zhang Li , Wu Min , Tsoka Sophia 
Published: March 2024

ABSTRACTMotivationKey challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that compromise property controls across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimisation approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design.ResultsWe propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a Variational AutoEncoder-based model which utilises co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesisability prediction tasks are conducted to prioritise generated molecules to derive potential lead compounds.Availability and ImplementationThe source code is available viahttps://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.
HIV integrase compacts viral DNA into biphasic condensates
Authors: Kolbeck Pauline J. , de Jager Marjolein , Gallano Margherita , Brouns Tine , Bekaert Ben , Frederickx Wout , Konrad Sebastian F. , Van Belle Siska , Christ Frauke , De Feyter Steven , Debyser Zeger , Filion Laura , Lipfert Jan , Vanderlinden Willem 
Published: March 2024

AbstractThe human immunodeficiency virus (HIV) infects non-dividing cells and its genome must be compacted to enter the cell nucleus. Here, we show that the viral enzyme integrase (IN) compacts HIV DNA mimeticsin vitro. Under physiological conditions, IN-compacted genomes are consistent in size with those found for pre-integration complexes in infected cells. Compaction occurs in two stages: first IN tetramers bridge DNA strands and assemble into “rosette” structures that consist of a nucleo-protein core and extruding bare DNA. In a second stage, the extruding DNA loops condense onto the rosette core to form a disordered and viscoelastic outer layer. Notably, the core complex is susceptible towards IN inhibitors, whereas the diffuse outer layer is not. Together, our data suggest that IN has a structural role in viral DNA compaction and raise the possibility to develop inhibitors that target IN-DNA interactions in disordered condensates.TeaserSingle-molecule studies demonstrate the mechanism, dynamics, and drug-susceptibility of viral genome compaction by HIV integrase.
Heterotypic Seeding Generates Mixed Amyloid Polymorphs
Authors: Banerjee S. , Baghel D. , Edmonds H. O. , Ghosh Ayanjeet 
Published: March 2024

AbstractAggregation of the amyloid β (Aβ) peptide into fibrils represents one of the major biochemical pathways underlying the development of Alzheimer’s disease (AD). Extensive studies have been carried out to understand the role of fibrillar seeds on the overall kinetics of amyloid aggregation. However, the precise effect of seeds that are structurally or sequentially different from Aβ on the structure of the resulting amyloid aggregates is yet to be fully understood. In this work, we use nanoscale infrared spectroscopy to probe the spectral facets of individual aggregates formed by aggregating Aβ42 with antiparallel fibrillar seeds of Aβ (16-22) and E22Q Aβ (1-40) Dutch mutant and demonstrate that Aβ can form heterotypic or mixed polymorphs that deviate significantly from its expected parallel cross β structure. We further show that formation of heterotypic aggregates is not limited to coaggregation of Aβ and its isomers, and that the former can form heterotypic fibrils with alpha synuclein and brain protein lysates. These findings highlight the complexity of Aβ aggregation in AD and underscore the need to explore how Aβ interacts with other brain components, which is crucial for developing better therapeutic strategies for AD.
Cholinergic Transmission in an Inducible Transgenic Mouse Model of Paroxysmal Dystonia
Authors: Scarduzio Mariangela , Jaunarajs Karen L Eskow , Standaert David G 
Published: March 2024

AbstractAltered interaction between striatonigral dopaminergic (DA) inputs and local acetylcholine (ACh) in striatum has long been hypothesized to play a central role in dystonia pathophysiology. Indeed, previous research across various genetic mouse models of human isolated dystonia has identified as a shared endophenotype with paradoxical excitation of striatal cholinergic interneurons (ChIs) activity in response to activation of dopamine D2 receptor (D2R). These mouse models lack a dystonic motor phenotype, which leaves a critical gap in comprehending the role of ACh transmission in the manifestation of dystonia. To tackle this question, we used a combination ofex vivoslice physiology andin vivomonitoring of striatal ACh dynamics in the inducible, phenotypically penetrant, transgenic mouse model of paroxysmal non-kinesigenic dyskinesia (PNKD). We found that, similarly to other genetic models, the PNKD mouse displays D2R-induced paradoxical excitation of ChI firing inex vivostriatal brain slices.In vivo, caffeine triggers dystonic symptoms while reversing the D2R-mediated excitation of ChIs and desynchronizing the striatal cholinergic network. In WT littermate controls, caffeine stimulates spontaneous locomotion through a similar but reversed mechanism involving an excitatory switch of the D2R control of ChI activity, associated with enhanced cholinergic network synchronization. Together these observations suggest that D2Rs may play an important role in synchronizing the ChI network during heightened movement states. The “paradoxical excitation” described in dystonia models could represent a compensatory or protective mechanism that prevents manifestation of movement abnormalities and allows for phenotypic dystonia when lost.
Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer’s Disease
Authors: Adeoye Temitope , Shah Syed I , Ullah Ghanim 
Published: March 2024

AbstractAlzheimer’s disease (AD) manifests as a complex systems pathology with intricate interplay among various genes and biological processes. Traditional differential gene expression (DEG) analysis, while commonly employed to characterize AD-driven perturbations, does not sufficiently capture the full spectrum of underlying biological processes. Utilizing single-nucleus RNA-sequencing data from postmortem brain samples across key regions—middle temporal gyrus, superior frontal gyrus, and entorhinal cortex—we provide a comprehensive systematic analysis of disrupted processes in AD. We go beyond the DEG-centric analysis by integrating pathway activity analysis with weighted gene co-expression patterns to comprehensively map gene interconnectivity, identifying region- and cell-type specific drivers of biological processes associated with AD. Our analysis reveals profound modular heterogeneity in neurons and glia as well as extensive AD-related functional disruptions. Co-expression networks highlighted the extended involvement of astrocytes and microglia in biological processes beyond neuroinflammation, such as calcium homeostasis, glutamate regulation, lipid metabolism, vesicle-mediated transport, and TOR signaling. We find limited representation of DEGs within dysregulated pathways across neurons and glial cells, indicating that differential gene expression alone may not adequately represent the disease complexity. Further dissection of inferred gene modules revealed distinct dynamics of hub DEGs in neurons versus glia, highlighting the differential impact of DEGs on neurons compared to glial cells in driving modular dysregulations underlying perturbed biological processes. Interestingly, we note an overall downregulation of both astrocyte and microglia modules in AD across all brain regions, suggesting a prevailing trend of functional repression in glial cells across these regions. Notable genes, including those of the CALM and HSP90 family genes emerged as hub genes across neuronal modules in all brain regions, indicating conserved roles as drivers of synaptic dysfunction in AD. Our findings demonstrate the importance of an integrated, systems oriented approach combining pathway and network analysis for a comprehensive understanding of the cell-type-specific roles of genes in AD-related biological processes.
Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids
Authors: Karakulak Tülay , Zajac Natalia , Bolck Hella Anna , Bratus-Neuenschwander Anna , Zhang Qin , Qi Weihong , Basu Debleena , Oltra Tamara Carrasco , Rehrauer Hubert , von Mering Christian , Moch Holger , Kahraman Abdullah 
Published: March 2024

AbstractSplicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternative splice isoforms. This complex phenomenon can be revealed by an in-depth understanding of cellular heterogeneity at the single-cell level. Recent advances in single-cell long- read sequencing technologies enable comprehensive transcriptome sequencing at the single-cell level. In this study, we have generated single-cell long-read sequencing of Patient-Derived Organoid (PDO) cells of clear-cell Renal Cell Carcinoma (ccRCC), an aggressive and lethal form of cancer that arises in kidney tubules. We have used the Multiplexed Arrays Sequencing (MAS-ISO-Seq) protocol of PacBio to sequence full-length transcripts exceptionally deep across 2,599 single cells to obtain the most comprehensive view of the alternative landscape of ccRCC to date. On average, we uncovered 86,182 transcripts across PDOs, of which 31,531 (36.6%) were previously uncharacterized. In contrast to known transcripts, many of these novel isoforms appear to exhibit cell-specific expression. Nonetheless, >50% of these novel transcripts were predicted to possess a complete protein-coding open reading frame. This finding suggests a biological role for these transcripts within kidney cells. Moreover, an analysis of the most dominant transcript switching events between ccRCC and non-ccRCC cells revealed that many switching events were cell and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC.Overall, our research elucidates the intricate transcriptomic architecture of ccRCC, potentially exposing the mechanisms underlying its aggressive phenotype and resistance to conventional cancer therapies.
Hairpin-RNA Spray Confers Resistance to Mungbean Yellow Mosaic India Virus in Mungbean
Authors: Dhobale Kiran Vilas , Sahoo Lingaraj 
Published: March 2024

ABSTRACTThe prevalence of Begomovirus diseases poses a significant threat to legume crops, necessitating the exploration of innovative control measures. This investigation explores the utilization of dsRNA molecules to initiate RNA interference (RNAi) targeting begomovirus, particularly focusing onMungbean yellow mosaic India virus(MYMIV) and its potential threat to mungbean crops. Given the lack of genetic resistance in commercially available mungbean varieties, the study endeavors to employ RNAi as a strategic method for the effective control of MYMIV. The approach involves the preparation of vectors for the transient expression of three dsRNA targeting multiple overlapping ORFs of MYMIV DNA A through agroinoculation, and the selection of a highly efficient construct for dsRNA expression in bacteria, enabling topical application to mungbean plants in growth chamber experiments. Agroinoculation assays demonstrate effective resistance against MYMIV, as confirmed by reduced symptom severity, limited virus accumulation, and the presence of viral mRNAs. The stability of the prepared dsRNA against nucleases is confirmed, showcasing its ability to enter plant cells, move to non treated trifoliate leaves, and form siRNA when sprayed onto mungbean leaves, as validated by qRT-PCR and northern blotting. Varied combinations of the timing of dsRNA spray and virus infection reveal differential resistance against the virus. Notably, spraying two days before or on the same day as virus exposure emerges as the most suitable time to achieve optimal resistance against virus infection. In light of these findings, the topical application of dsRNAs stands out as a promising and effective strategy for MYMIV control in mungbean crops.
Ca2+-independent ZmCPK2 is inhibited by Ca2+-dependent ZmCPK17 during drought response in maize
Authors: Hu Xiaoying , Cheng Jinkui , Lu Minmin , Fang Tingitng , Zhu Yujuan , Li Zhen , Wang Xiqing , Wang Yu , Guo Yan , Yang Shuhua , Gong Zhizhong 
Published: March 2024

ABSTRACTCalcium oscillations are induced by different stresses. Calcium-dependent protein kinases (CDPKs/CPKs) are one major group of the plant calcium decoders that are involved in various processes including drought response. Some CPKs are calcium-independent. Here, we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize pool. We found that ZmCPK2 does not bind calcium, and its activity is modulated likely in an oscillation manner during short time ABA treatment. Interestingly, ZmCPK2 interacts with and is inhibited by calcium-dependent ZmCPK17, a positive regulator of drought resistance, which is activated by ABA. ZmCPK17 activity exhibits opposite patterns relative to ZmCPK2 under ABA treatment, and could prevent the nuclear localization of ZmCPK2 when co-expressed. ZmCPK2 interacts with and phosphorylates ZmYAB15, a negative transcriptional factor for drought resistance. Our results suggest that drought stress-induced Ca2+can be decoded by corresponding CPK17 likely in an oscillation manner, thereby promoting plant adaptation to water deficit.
Atypical retinal function in a mouse model of Fragile X syndrome
Authors: Vlasits Anna L. , Syeda Maria , Wickman Annelise , Guzman Pedro , Schmidt Tiffany M. 
Published: March 2024

SummaryAltered function of peripheral sensory neurons is an emerging mechanism for symptoms of autism spectrum disorders. Visual sensitivities are common in autism, but whether differences in the retina might underlie these sensitivities is not well-understood. We explored retinal function in the Fmr1 knockout model of Fragile X syndrome, focusing on a specific type of retinal neuron, the “sustained On alpha” retinal ganglion cell. We found that these cells exhibit changes in dendritic structure and dampened responses to light in the Fmr1 knockout. We show that decreased light sensitivity is due to increased inhibitory input and reduced E-I balance. The change in E-I balance supports maintenance of circuit excitability similar to what has been observed in cortex. These results show that loss of Fmr1 in the mouse retina affects sensory function of one retinal neuron type. Our findings suggest that the retina may be relevant for understanding visual function in Fragile X syndrome.
Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription
Authors: Chang Yi-Che , Quinodoz Sofia A. , Brangwynne Clifford P. 
Published: March 2024

AbstractChromatin structure and dynamics are crucial for eukaryotic nuclear functions. Hi-C and related genomic assays have revealed chromatin conformations, such as A/B compartments, in fixed cells, but the dynamic motion of such structures is not well understood. Moreover, elucidating the relationship between the motion of chromatin and transcriptional activity is hampered by a lack of tools for specifically measuring the mobility of active euchromatin. Here, we introduce a CRISPR-based strategy for live imaging of the gene-rich A compartment by labeling Alu elements — a retrotransposon family enriched within the transcriptionally active A compartment. Surprisingly, within euchromatin, microscopy analysis reveals that Alu-rich regions do not correlate with lower local H2B density, and form irregular foci of a few hundred nanometers in diameter, underscoring the heterogeneity of euchromatin organization. Alu-rich (gene-rich) chromatin is also more mobile than Alu-poor (gene-poor) chromatin, and transcription inhibition by actinomycin D results in decreased chromatin mobility of Alu-rich regions. These observations highlight the complexity of chromatin organization and dynamics and connect them to transcriptional activity on a genome-wide scale.
Social state gates vision using three circuit mechanisms inDrosophila
Authors: Schretter Catherine E. , Sten Tom Hindmarsh , Klapoetke Nathan , Shao Mei , Nern Aljoscha , Dreher Marisa , Bushey Daniel , Robie Alice A. , Taylor Adam L. , Branson Kristin M. , Otopalik Adriane , Ruta Vanessa , Rubin Gerald M. 
Published: March 2024

AbstractAnimals are often bombarded with visual information and must prioritize specific visual features based on their current needs. The neuronal circuits that detect and relay visual features have been well-studied. Yet, much less is known about how an animal adjusts its visual attention as its goals or environmental conditions change. During social behaviors, flies need to focus on nearby flies. Here, we study how the flow of visual information is altered when femaleDrosophilaenter an aggressive state. From the connectome, we identified three state-dependent circuit motifs poised to selectively amplify the response of an aggressive female to fly-sized visual objects: convergence of excitatory inputs from neurons conveying select visual features and internal state; dendritic disinhibition of select visual feature detectors; and a switch that toggles between two visual feature detectors. Using cell-type-specific genetic tools, together with behavioral and neurophysiological analyses, we show that each of these circuit motifs function during female aggression. We reveal that features of this same switch operate in males during courtship pursuit, suggesting that disparate social behaviors may share circuit mechanisms. Our work provides a compelling example of using the connectome to infer circuit mechanisms that underlie dynamic processing of sensory signals.