bluuebunny/crossref_metadata_2025 huggingface dataset:
Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer
Authors: Li Shan , Song Kai , Sun Huiyun , Tao Yong , Huang Arthur , Bhatia Vipul , Hanratty Brian , Patel Radhika A. , Long Henry W. , Morrissey Colm , Haffner Michael C. , Nelson Peter S. , Graeber Thomas G. , Lee John K.
Published: February 2025

Neuroendocrine prostate cancer (NEPC) arises primarily through neuroendocrine transdifferentiation (NEtD) as an adaptive mechanism of therapeutic resistance. Models to define the functional effects of putative drivers of this process on androgen receptor (AR) signaling and NE cancer lineage programs are lacking. We adapted a genetically defined strategy from the field of cellular reprogramming to directly convert AR-active prostate cancer (ARPC) to AR-independent NEPC using candidate factors. We delineated critical roles of the pioneer factors ASCL1 and NeuroD1 in NEtD and uncovered their abilities to silence AR expression and signaling by remodeling chromatin at the somatically acquired AR enhancer and global AR binding sites with enhancer activity. We also elucidated the dynamic temporal changes in the transcriptomic and epigenomic landscapes of cells undergoing acute lineage conversion from ARPC to NEPC which should inform future therapeutic development. Further, we distinguished the activities of ASCL1 and NeuroD1 from the inactivation of RE-1 silencing transcription factor (REST), a master suppressor of a major neuronal gene program, in establishing a NEPC lineage state and in modulating the expression of genes associated with major histocompatibility complex class I (MHC I) antigen processing and presentation. These findings provide important, clinically relevant insights into the biological processes driving NEtD of prostate cancer.
Reinforced molecular dynamics: Physics-infused generative machine learning model explores CRBN activation process
Authors: Kolossváry István , Coffey Rory
Published: February 2025

We propose a simple and practical machine learning-based desktop solution for modeling biologically relevant protein motions. We termed our technology reinforced molecular dynamics (rMD) combining MD trajectory data and free-energy (FE) map data to train a dual-loss function autoencoder network that can explore conformational space more efficiently than the underlying MD simulation. The key insight of rMD is that it effectively replaces the latent space with an FE map, thus infusing the autoencoder network with a physical context. The FE map is computed from an MD simulation over a low-dimensional collective variable space that captures some biological function. One can directly use then the FE map for example, to generate more protein structures in poorly sampled regions, follow paths on the FE map to explore conformational transitions, etc. The rMD technology is entirely self-contained, does not rely on any pre-trained model, and can be run on a single GPU desktop computer. We present our rMD computations in a key area of molecular-glue degraders aimed at a deeper understanding of the structural transition from open to closed conformations of CRBN.
Tuning of Task-Relevant Stiffness in Multiple Directions
Authors: Zhang Chenguang , Tessari Federico , Hermus James , Akolkar Himanshu , Hogan Neville , Schwartz Andrew B.
Published: February 2025

The dynamics of any mechanical system can be described in terms of forces and motions. The interaction of these terms is often captured in the metric of mechanical impedance – a generalization of stiffness – used to describe how a mechanical system resists the application of force. The ability to adaptively change impedance is advantageous when encountering variable environmental conditions. Changing impedance in robotic systems is limited, whereas humans can rapidly and elegantly adapt the impedance of their limbs, especially during initial contact with objects. This is especially true for movements of our arms and hands. Multiple studies have examined the arm’s response to perturbation with the idea of impedance as areactivecomponent. In this study, we investigate the ability of humans topredictivelyset their arm impedance in a contact breaking task to perform fast movements to target positions in different directions. Our findings show that subjects (n=20) predictively co-activate antagonist muscles to primarily adjust one component of the arm’s impedance – stiffness – to match different task constraints before the movement begins irrespective of movement direction. Interestingly, the subjects’ performance was limited by the task-dependent stiffness rather than the required force and they tended to generate minimal stiffness to perform the task. With this robust strategy, task success is optimized at the expense of energy efficiency. This type of control is essential for the uniquely human ability to interact with objects.
Predicting animal movement with deepSSF: a deep learning step selection framework
Authors: Forrest Scott W. , Pagendam Dan , Hassan Conor , Drovandi Christopher , Potts Jonathan R. , Bode Michael , Hoskins Andrew J.
Published: February 2025

Predictions of animal movement are vital for understanding and managing wild populations. However, the fine-scale, complex decision-making of animals can pose challenges for the accurate prediction of trajectories. Step selection functions (SSFs), a common tool for inferring relationships between animal movement and the environment, are also increasingly used to simulate animal trajectories for prediction. Although admitting a lot of flexibility, the SSF framework is limited to its reliance on pre-defined functional forms for fitting to data, and SSFs that involve complex functional forms to model detailed processes can be prohibitively difficult to fit and interpret.

Here, we presentdeepSSF, an approach to fit and predict animal movement data using deep learning. Whilst not specific to any particular model, we denote thedeepSSFapproach as building and training a neural network architecture that receives multiple environmental layers and scalar values as inputs, and outputs a single layer representing the next-step probability. To demonstrate adeepSSFmodel, we build a model inPyTorchthat has distinct but interacting habitat selection and movement subnetworks, which allows for explicit representation of both processes and interpretable intermediate outputs. We apply our model to GPS data of introduced water buffalo (Bubalus bubalis) in the tropical savannas of Northern Australia.

OurdeepSSFmodel was able to learn features that are present in the habitat covariate layers, such as linear features (rivers, forest edges), and the composition of certain habitat areas, without having to specify them pre-emptively within the SSF framework. It was also able to capture the complex interactions between the habitat covariates as well as temporal dynamics across time of day and year.

We expect that thedeepSSFapproach will generate accurate and informative animal movement trajectories, which can be used for deepening our understanding of animal-environment systems and for the practical management of species. Considering the wide range of deep learning tools, thedeepSSFapproach could be extended to represent memory and social dynamic processes, with the potential for integrating non-spatial data sources such as accelerometers and physiological sensors.
Single Cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway
Authors: Juric Ivan , Fink Emily E. , Qiu Hong , Desprez Pierre-Emmanuel , Ravi Arvind , Holton Mark , Makarov Vladimir , Almassi Nima , Min Booki , Getz Gad , Chan Timothy A. , Alban Tyler , Ting Angela H. , Lee Byron H.
Published: February 2025

Non-muscle invasive bladder cancer (NMIBC) represents 70–80% patients with newly diagnosed bladder cancer, and Bacillus Calmette-Guérin (BCG) remains a cornerstone treatment for intermediate-and high-risk NMIBC to prevent disease recurrence and progression. However, many patients experience recurrence after induction BCG, posing significant challenges in the management of the disease. We conducted single cell RNA sequencing on freshly collected NMIBC samples, distinguishing between those naïve to BCG treatment and those that recurred post-BCG treatment. We observed a clear activation of inflammatory pathways across cell types during recurrence, but these were not associated with canonical immune checkpoint or T cell exhaustion phenotypes. Analysis of cell-to-cell communication revealed enhanced interactions between T cells and urothelial cells in BCG-recurrence, predominantly modulated by CD6 and ALCAM. Furthermore, we found CD6hiT cells to be immunosuppressed and enriched in recurrent samples, suggesting a potential role for CD6 as an immune evasion signal in NMIBC.

SIGNIFICANCE

These findings uncover a novel mechanism responsible for bladder cancer recurrence after BCG treatment. Enhanced T cell-urothelial cell communication in recurrent tumors mediated by CD6 and ALCAM leads to an immunosuppressed state. Thus, CD6 may have potential as a therapeutic target to augment BCG response in non-muscle invasive bladder cancer.
TET3 protects the Dlk1-Dio3 Imprinted Locus from DNA hypomethylation during adult NSC Reprogramming
Authors: Lázaro-Carot Laura , Jiménez-Villalba Esteban , Planells Jordi , Lozano-Ureña Anna , Díaz-Moncho Jennifer , Montalbán-Loro Raquel , Lleches-Padilla Adela , Kirstein Martina , Ito Mitsuteru , Radford Elizabeth J. , Ferrón Sacri R.
Published: February 2025

Genomic imprinting is an epigenetic mechanism that drives monoallelic gene expression depending on parental origin. Loss of imprinting (LOI) is associated with human imprinting disorders, fetal development, and cancer progression. Imprinted genes, organized in clusters, are regulated by methylation at imprint control regions (ICRs), differentially methylated regions (DMRs) between parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool for studying pluripotency and holds promise for patient-specific therapies. Discerning whether genomic imprinting changes during reprogramming represent epigenetic abnormalities or essential adaptations linked to pluripotency is crucial. Here, we perform RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from neural stem cells (NSCs). Our findings reveal that ICRs undergo DNA hypomethylation, confirming widespread LOI in pluripotent cells. However, the IG-DMR within the Dlk1-Dio3 imprinted cluster resists hypomethylation, a hallmark of successful pluripotency acquisition. We also identify a non-canonical role of TET3 in IG-DMR methylation protection through transcriptional regulation ofOct4andTrim28. These findings highlight genomic imprinting as a key mechanism of gene dosage control in pluripotency acquisition and maintenance.
Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation
Authors: Palma C.S.D. , Haller D.J. , Tabor J.J. , Igoshin O.A.
Published: February 2025

Under starvation conditions,B. subtilissurvives by differentiating into one of two cell types: biofilm matrix-producing cells or sporulating cells. These two cell-differentiation pathways are activated by the same phosphorylated transcription factor - Spo0A~P. Despite sharing the activation mechanism, these cell fates are mutually exclusive at the single-cell level. This decision has been shown to be controlled by the effects of growth rate on gene dosage and protein dilution in the biofilm matrix production network. In this work, we explore an alternative mechanism of growth rate-mediated control of this cell fate decision. Namely, using deterministic and stochastic modeling, we investigate how the growth-rate-dependent pulsing dynamics of Spo0A~P affect biofilm matrix deactivation and activation. Specifically, we show that the Spo0A~P pulsing frequency tunes the biofilm matrix deactivation probability without affecting the probability of biofilm matrix activation. Interestingly, we found that DNA replication is the cell cycle stage that most substantially contributes to the deactivation of biofilm matrix production. Finally, we report that the deactivation of biofilm matrix production is not primarily regulated by the effects of growth rate on gene dosage and protein dilution. Instead, it is driven by changes in the pulsing period of Spo0A~P. In summary, our findings elucidate the mechanism governing biofilm deactivation during the late stages of starvation, thereby advancing our understanding of how bacterial networks interpret dynamic transcriptional regulatory signals to control stress-response pathways.

Author Summary

Bacteria have evolved various adaptation mechanisms to survive under challenging environmental conditions. For instance, under mild starvation,B. subtilisbacteria form biofilms — communities of cells encapsulated in a protective extracellular matrix. On the other hand, these bacteria differentiate into highly resistant spores under severe starvation. Interestingly, sporulating cells are often found within biofilm communities, but they do not contribute to biofilm matrix production. This is thought to be an energy-conservation strategy, as biofilm formation is an energy-intensive process and is therefore halted before sporulation begins. Though previous work has focused on the mechanisms driving biofilm disassembly, few studies have explored the regulatory processes thatB. subtilisemploys to halt matrix production prior to starting sporulation. In this study, we use mathematical models to demonstrate that the temporal dynamics of the biofilm master regulator Spo0A~P control the deactivation of matrix production. Understanding the regulation of biofilm, a common lifestyle in bacteria, can lead to the development of synthetic strategies to either enhance or disrupt biofilm formation, with potential applications in medicine and industry.
Combined Transplantation of Mesenchymal Progenitor and Neural Stem Cells to repair cervical spinal cord injury
Authors: White Seok Voon , Ma Yee Hang Ethan , Plant Christine D , Harvey Alan R , Plant Giles W
Published: February 2025

Mesenchymal progenitor cells (MPC) are effective in reducing tissue loss, preserving white matter and improving forelimb function after spinal cord injury (SCI) (White et al., 2016). We proposed that by preconditioning the mouse by intravenous delivery (IV) of MPCs for 24 hours following SCI that this would provide a more favorable tissue milieu for NSC intraspinal bridging transplantation at day 3 and day 7. In com-bination these transplants will provide better anatomical and functional outcomes. The intravenous MSCs would provide cell protection and reduce inflammation. NSCs would provide a tissue bridge for axonal regeneration and myelination and reconnect long tract spinal pathways. Results showed that initial protection of the injury site by IV MPCs transplantation resulted in no increased survival of the NSCs transplanted at Day 7. However, integration of transplanted NSCs was increased at the Day 3 time point indicating MPCs influence very early immune signaling. We show in this study that MPC transplantation resulted in a co-operative NSC cell survival improvement at Day 3 post SCI. In addition to increased NSC survival at day 3 there was an increase in NSC derived mature oligodendrocytes at this early time point. In vitro analysis confirmed MPC driven oligodendrocyte differentiation which was statistically increased when compared to control NSC only cultures. These observations provide important information about the combination, delivery, and timing of two cellular therapies in treating SCI. This study provides important new data on understanding the MPC inflammatory signaling within the host tissue and time points for cellular transplantation survival and oligodendroglia differentiation. These results demonstrate that MPC transplantation can alter the therapeutic window for intraspinal transplantation by controlling both the circulating inflammatory response and local tissue milieu.
The 5-HT1F Receptor Agonist Lasmiditan improves Cognition and Ameliorates Associated Cortico-Hippocampal Pathology in Aging Parkinsonian Mice
Authors: Ishii Atsushi , Meredith Jasmine R , Corenblum Mandi J , Bernard Kelsey , Wene Paige V , Menakuru Nainika , Santiago Paul V , Schnellmann Rick G , Madhavan Lalitha
Published: February 2025

While the etiopathology of Parkinson’s disease (PD) is complex, mitochondrial dysfunction is established to have a central role. Thus, mitochondria have emerged as targets of therapeutic interventions aiming to slow or modify PD progression. We have previously identified serotonergic 5-HT1F receptors as novel mediators of mitochondrial biogenesis (MB) - the process of producing new mitochondria. Given this, here, we assessed the therapeutic potential of the FDA-approved 5-HT1F receptor agonist, lasmiditan, in a chronic progressive PD model (Thy1-aSyn ‘line 61’ mice). It was observed that systemic lasmiditan exhibited robust brain penetration and reversed cognitive deficits in young (4-5.5 months old) Thy1-aSyn mice (1mg/kg, every other day). Anxiety-like behavior was also improved while motor function remained unaffected. These behavioral changes were associated with enhanced MB and mitochondrial function, paired with reduced alpha-synuclein aggregation particularly in cortico-hippocampal regions. Furthermore, in older (10-11.5 months old) mice, although the effects were milder, daily lasmiditan administration increased MB and bettered cognitive abilities. In essence, these findings indicate that repurposing lasmiditan could be a potent strategy to address PD-related cognitive decline.
Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions
Authors: Delafrouz Pourya , Farooq Hammad , Du Lin , Ma Ao , Liang Jie
Published: February 2025

The interactions between chromatin and lamin proteins localized on the nuclear envelope play a crucial role in the three-dimensional (3D) organization of the genome. This study investigates the influence of lamin associated domains (LADs) on genome organization at the chromosome level using 3D polymer models of mouse embryonic fibroblasts (MEFs) and embryonic stem cells (mESCs). By integrating genome-wide LAD maps from DamID assays, we simulated chromatin conformations with and without LAD attachment to the nuclear envelope. Our results show that incorporating LAD-lamin interactions yields a radial chromatin distribution consistent with experimental observations. Moreover, LAD-lamin interactions induce significant super long-range chromatin contacts across distant genomic regions. These findings suggest two distinct mechanisms driving induction of chromatin interactions by LAD-lamin attachment.
Phenethylaminylation: PreliminaryIn VitroEvidence for the Covalent Transamidation of Psychedelic Phenethylamines to Glial Proteins using 3,5-Dimethoxy-4-(2-Propynyloxy)-Phenethylamine as a Model Compound
Authors: Rangan Rajiv S. , Petty R. Max , Acharya Suchismita , Emmitte Kyle A. , do Valle Rafael S. , Lam Chandra , Essajee Salman I. , Mayhew William , Young Olivia , Brooks Calvin D. , Forster Michael J. , Tovar-Vidales Tara , Clark Abbot F.
Published: February 2025

Psychedelics are well known for their ability to produce profoundly altered states of consciousness. But, more importantly, the effects of psychedelics can influence neurobehavioral changes that last well after these acute subjective effects end. This phenomenon is currently being leveraged in the development of psychedelic-assisted psychotherapies for the treatment of multiple neuropsychiatric disorders. The cellular and molecular mechanisms by which single doses of psychedelics are able to mediate long-term cognitive changes are an active area of research. We hypothesize that psychedelics contribute to long term changes in cellular state by covalently modifying proteins. This post-translational modification by psychedelics is possible through the transglutaminase-mediated transamidation of their amine termini to glutamine carboxamide residues. Here, we synthesize and utilize a propargylated analogue of mescaline – the classic serotonergic psychedelic phenethylamine found in cacti species – to identify putative protein targets of psychedelic modifications through the use of click-chemistry in a primary human astrocyte cell culture model. Our preliminary findings indicate that a diverse array of glial proteins may be substrates for transglutaminase 2-mediated monoaminylation by our model phenethylamine (“phenethylaminylation”). Based on these points, we speculatively highlight new directions for the study of this putative noncanonical psychedelic activity.
Kingdom-Wide CRISPR Guide Design with ALLEGRO
Authors: Mohseni Amirsadra , Nia Reyhane Ghorbani , Tafrishi Aida , Liu Xin-Zhan , Stajich Jason E. , Wheeldon Ian , Lonardi Stefano
Published: February 2025

Designing CRISPR single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we present ALLEGRO, a combinatorial optimization algorithm able to design minimal, yet highly effective sgRNA libraries targeting thousands of species. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting several genes of interest for over 2,000 species across the fungal kingdom. We experimentally validated the sgRNAs designed by ALLEGRO inKluyveromyces marxianus, Komagataella phaffii, andYarrowia lipolytica. In addition, we adopted a generalized Cas9-Ribonucleoprotein delivery system coupled with protoplast transformation to extend ALLEGRO’s sgRNA libraries to other untested fungal genomes, such asRhodotorula araucariae. Our experimental results, along with cross-validation, show that ALLEGRO enables efficient CRISPR genome editing, supporting the development of universal sgRNA libraries applicable to entire taxonomic groups.
Bioinformatics analysis of next generation sequencing data reveals novel biomarkers and signaling pathways associated with recurrent implantation failure
Authors: Vastrad Basavaraj , Vastrad Chanabasayya
Published: February 2025

Recurrent implantation failure (RIF) is a cases in which women have had three fruitless in vitro fertilization (IVF) bid with positive quality embryos. The RIF originates from uterine endometrium microbiota has been implicated in reproductive failure, and poor prognosis and lacks effective treatment. Efforts have been made to elucidate the molecular pathogenesis of RIF. To identify key genes and signaling pathways in RIF, the next genetation sequencing data GSE243550 was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between RIF and normal controls samples were identified using t-tests in the limma R bioconductor package. Using the DEGs, we further performed a series of gene ontology (GO) and REACTOME pathway enrichment analyses. Protein-protein interaction network was derived using the IMex interactome database and visualized using Cytoscape software. The most significant modules from the PPI network were selected for GO and pathway enrichment analysis. A miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed depending on key hub genes and visualized using Cytoscape software. A receiver operating characteristic curve (ROC) analysis was plotted to diagnose RIF. In total, 958 DEGs were identified, of which 479 were up regulated genes and 479 were down regulated genes. GO and REACTOME pathway enrichment analysis results revealed that the upregulated genes were mainly enriched in multicellular organismal process, membrane, small molecule binding and extracellular matrix organization, whereas downregulated genes were mainly enriched in organonitrogen compound metabolic process, intracellular anatomical structure, catalytic activity and translation. Through analyzing the PPI network, we screened hub genes APP, HSP90AA1, CAND1, CUL1, HSP90AB1, SIRT7, SRC, CDKN1A, ISG15 and RPS16 by the Cytoscape software. The regulatory network analysis revealed that microRNAs (miRNAs) include hsa-miR-574-3p and hsa-mir-208a-3p, and transcription factors (TFs) include SREBF1 and RELA might be involved in the development of RIF. Receiver operating characteristic curve analysis demonstrated that the hub genes screened for RIF were of good diagnostic significance. Overall, these results thus highlight a range of novel signaling pathways and genes that are linked to the incidence and progression of RIF, providing a list of important diagnostic and prognostic molecular markers that have the potential to aid in the clinical diagnosis and treatment of RIF.
Database Chemistry for Genomics-Based Safety and Quality Evaluation of Biologics
Authors: Ogata Norichika , Matsuda Tomoko , Hosaka Aoi , Shina Akihisa , Hashiba Noriko , Uchida Kazuhisa , Kawabe Yoshinori , Kamihira Masamichi , Yamaoka Takanori , Kurita Hiromu , Yamano-Adachi Noriko , Omasa Takeshi
Published: February 2025

Genomics-based safety and quality evaluation studies are advancing the bioindustry by enhancing various aspects, including viral safety, host cell protein (HCP) control, product heterogeneity control, cellular heterogeneity control, and process reproducibility. High-throughput instruments and genome-scale databases are essential in genomics, with the reference genome sequence being the most critical database. The completeness and accuracy of these genome sequences depend on DNA quality, sequencing instruments, read coverage, and assembly strategies. Significant efforts are being made to perfect genome assembly and continuously improve it. However, the quantitative impact of reference genome sequence accuracy on the safety of biologics is not yet fully understood. In this study, we compared and benchmarked six Chinese hamster genomes, including four newly sequenced genomes derived from Chinese hamster cell lines, from an industrial perspective. We also developed database assembly techniques to enhance the safety of biologics. We recommend using two or more independent reference genomes for viral safety studies. For HCP control, we suggest using protein sequences in which trypsin degradation peptides that overlap with high-risk proteins should be masked and unified. Additionally, we can predict microenvironments using single-cell transcriptome data. In bioengineering processes, any nucleotide samples have potential commercial benefits.
Near 100% efficient homology-dependent genome engineering in the human fungal pathogenCryptococcus neoformans
Authors: Nalley Matthew J. , Banerjee Sanjita , Huang Manning Y. , Madhani Hiten D.
Published: February 2025

We recently described CRISPR/Cas9-based short homology-dependent genome engineering in the human fungal pathogenCryptococcus neoformans, a haploid budding yeast that is the most common cause of fungal meningitis and an emerging model organism. This was achieved by electroporation of strains stably expressing a codon-optimized Cas9 with two separate DNA molecules, one encoding a selectable marker flanked by short homology arms and a second encoding a sgRNA under the control of the U6 snRNA promoter. However, the efficiency of desired homology-dependent repair relative to undesired non-homologous end-joining (NHEJ) events can be low and variable. Here, we describe methods and strains enabling extremely efficient (∼99%) homology-dependent genome editing inC. neoformans. This high-efficiency method requires two manipulations. First, we placed the sgRNA-expressing segment into the marker-containing DNA flanked by targeting homology; thus, only a single DNA molecule is introduced into cells. Second, we used a strain mutant for the non-homologous end-joining factor Ku80 (encoded byYKU80). We also report the engineering of ayku80::amdSmutant strain harboring an insertion mutation that can be removed scarlessly via recombination between direct repeats. This enables the functional restoration ofYKU80after homology- dependent genome editing via selection against theamdSmarker using fluoroacetamide. This approach minimizes documented drawbacks of using Ku-defective strains in downstream experiments. Finally, we describe a plasmid series that enables rapid cloning of sgRNA-marker constructs for genomic manipulation ofC. neoformans, including gene deletion and C-terminal tagging. These methods, strains, and plasmids accelerate the genomic manipulation ofC. neoformans.
The Role of Microglia and Complement C5/C5a in the Pathogenesis of Rhegmatogenous Retinal Detachment with Choroidal Detachment
Authors: Xu Huiyan , Wang Qiuhong , Chen Xuan , Huang Qingyu , Xu Shasha , Wu Zhifeng
Published: February 2025

Background

Rhegmatogenous retinal detachment with choroidal detachment (RRDCD) is an uncommon and sight-threatening disorder marked by fast development and significant inflammation. This study aimed to identify cellular and molecular signatures distinguishing RRDCD from typical rhegmatogenous retinal detachment (RRD) and to investigate the roles of microglia and the complement C5/C5a pathway in disease pathogenesis.

Methods

Single-cell RNA sequencing (scRNA-seq) was employed to analyze vitreous samples from patients with RRD and RRDCD, indicating its involvement in blood-retina barrier impairment.

Results

Our findings revealed a distinct cellular landscape in RRDCD, characterized by enhanced connectivity between microglia and dendritic cells, alongside a significant upregulation of the complement C5-C5AR1 interaction. In vitro experiments indicated that treatment with complement C5 promoted microglial proliferation and activation, induced apoptosis in RF/6A endothelial cells, and disrupted tight junctions in ARPE-19 epithelial cells, suggesting a role in blood-retina barrier dysfunction.

Conclusion

The findings substantiate the inflammatory hypothesis regarding the pathogenesis of RRDCD, emphasizing the critical functions of microglia and the complement C5/C5a pathway in intensifying retinal inflammation and undermining vascular integrity.
Age- and Virus-Specific Signatures ofIn VitroReconstituted Human Airway Epithelia in the Presence and Absence of Respiratory Viral Infections
Authors: Bellon Mathilde , Alvarez Catia , Buendia Gustavo Ruiz , Sattonnet-Roche Pascale , Dbeissi Damien , Sarmiento Yoann , Kaiser Laurent , Didierlaurent Arnaud , Eckerle Isabella , Essaidi-Laziosi Manel
Published: February 2025

While Influenza Virus and Respiratory Syncytial Virus (RSV) are considered as a significant health burden in children, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes milder diseases in this age group compared to adults. To investigate the involvement of the upper respiratory tract human airway epithelium (HAE) in this pattern, we established an in-house model of reconstituted HAE cultured in air-liquid interface from nasal swabs of children and adults and characterised it before and afterex vivorespiratory viral infections using focused and unbiased approaches. Fully differentiated paediatric HAE exhibited an increasing induction level of genes related to mucociliary clearance, while higher expression of innate immune pathways was found in the ones from adults. While similar viral replication kinetics in both age groups were shown for SARS-CoV-2, Influenza A Virus (IAV), RSV and Rhinovirus (RV) infection, transcriptomic analysis showed stronger and earlier induction of IFN-related pathways in SARS-CoV-2-infected HAE from children compared to IAV, RSV and RV. IAV and RSV had the weakest innate immune response increase in HAE from children versus adults. RV infection showed an intermediate pattern, resembling SARS-CoV-2 more than RSV or IAV. Our work demonstrates a distinct sensing of SARS-CoV-2 compared to other respiratory virusesex vivo, which may contribute to the milder course of disease in SARS-CoV-2 infected children and argues for a role of early virus-HAE interaction in shaping viral pathogenesis. Furthermore, we show that innate immune responses towards respiratory viruses are virus-specific and differ between age groups. Hence, findings on SARS-CoV-2 cannot be extrapolated to other respiratory viruses.
Adaptive time course of the skeletal muscle proteome during programmed resistance training in rats
Authors: Stead Connor A , Hesketh Stuart J , Thomas Aaron C.Q , Viggars Mark R , Sutherland Hazel , Jarvis Jonathan C , Burniston Jatin G
Published: February 2025

Resistance training (RT) promotes muscle protein accretion and myofiber hypertrophy, driven by dynamic processes of protein synthesis and degradation. While molecular studies have focused on acute signalling or long-term hypertrophy and strength gains, a critical gap remains in understanding the intermediate processes of muscle adaptation. Acute signalling does not always correlate directly with long-term outcomes, highlighting the need for a time-course analysis of protein abundance and turnover rates. To address this, we utilised deuterium oxide labelling and peptide mass spectrometry to quantify absolute protein content and synthesis rates in skeletal muscle. A daily programmed resistance training regimen was applied to the rat tibialis anterior (TA) via electrical stimulation of the left hind limb for 10, 20, and 30 days (5 sets of 10 repetitions daily). Muscle samples from stimulated (Stim) and contralateral control (Ctrl) limbs were analysed, quantifying 658 protein abundances and 215 protein synthesis rates. Unsupervised temporal clustering of protein responses revealed distinct phases of muscle adaptation, with early (0-10 days) and mid (10-20 days) responses driven by differential protein accretion rates in ribosomal and mitochondrial networks, respectively. These findings suggest that subsets of proteins exhibit distinct adaptation timelines due to variations in translation and/or degradation rates. A deeper understanding of these temporal shifts could improve strategies for optimising muscle growth and functional adaptation to resistance training.
Long-term offspring loss in lactating rats: Neurobiological and emotional consequences in a novel animal model
Authors: Demarchi Luisa , Sanson Alice , Boos Anna-Lena , Bosch Oliver J.
Published: February 2025

The maternal bond is a vital social connection that supports the survival and well-being of both the caregiver and offspring. Disruption of this bond, particularly following offspring loss, can result in profound trauma with long-lasting consequences. While considerable research has focused on the impact of maternal separation on offspring development, the biological effects of offspring loss on the mother remain largely unexplored. In this study, we examined the long-term effects of offspring loss on neuroplasticity, the oxytocin (OXT) and corticotropin-releasing factor (CRF) systems, and stress-coping behaviors in Sprague-Dawley rat mothers. We compared mothers that experienced one day of motherhood followed by 19 days of offspring loss, mothers that were with their pups throughout the 20 days, and naive virgin rats.

Our results reveal that mothers who lost their pups expressed increased oxytocin receptor binding and decreased dendritic spine density in limbic brain regions, with no changes in estrogen receptor α or calbindin cells. Additionally, separated mothers showed increased passive stress-coping behaviors in the forced swim test and elevated plasma corticosterone levels. Remarkably, the passive stress-coping behavior was rescued by central CRF receptor blockade but not by oxytocin treatment, suggesting that the CRF system plays a key role in the grieving process following offspring loss, and highlights the suitability of the rat model for studying maternal grief. This research provides insights into the complex neurobiology of grief, and suggests potential directions for future studies.
Candida albicansgenome adaptation in azole resistant isolates from autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) patients
Authors: Alwathiqi Faten , Gago Sara , Novak-Frazer Lily , Richardson Riina , Bowyer Paul
Published: February 2025

Chronic mucocutaneous candidosis due toCandida albicansis frequent in patients with autoimmune polyendocrinopathy candidosis ectodermal dystrophy (APECED). These patients require lifelong antifungal treatment with azoles which might result in the emergence of azole-resistantC. albicansisolates. However, the molecular mechanisms that allowC. albicansto cause disease and adapt to antifungal treatment in these patients in vastly unknown. Here we comparatively analysed the genome sequences and antifungal susceptibility profile of 14C. albicansisolates from the oral cavities of five APECED patients. 14/13C. albicansisolates showed reduced-susceptibly or resistance to fluconazole. Phylogenetic analyses demonstrated that all APECED isolates from individual patients arose from patient-specific lineages. Single nucleotide variants in genes related to homologous DNA repair mechanisms such as meiosis were associated with APECED (p <0.0001). Altogether our data demonstrates that antifungal adaptation ofC. albicansin APECED patients might be associated with polymorphisms in proteins responsible for maintaining DNA repair mechanisms.

Importance

Chronic mucocutaneous canididosis (CMC) caused byCandida albicansis common in patients with primary immunodeficiencies such as autoimmune polyendocrinopathy candidosis ectodermal dystrophy (APECED). These patients receive to long-term antifungal therapy thus promoting the emergence of antifungal resistance. Our knowledge about the mechanisms facilitating CMC in patients with APECED is very limited. Here we demonstrated that mostC. albicansisolates from patients with CMC are resistant to azoles and that polymorphisms in genes responsible for maintaining DNA repair mechanisms might facilitate infection.
Long-term innovative potential of genetic research and its suppression
Authors: Chae Junghun , Kim WooJoong , Jung Woochul , Jeong Dawoon , Lim Roktaek , Chamlagain Manoj , Jung Giju , Jang Juneil , Lee Jae Won , Kang Nam Kyu , Baek Kwangryul , Shin Jonghyeok , Lee Ye-Gi , Koh Hyun Gi , Kim Chanwoo , Yook Sangdo , Cheung Allen Ka Loon , Jin Yong-Su , Youn Hyejin , Kim Pan-Jun , Ghim Cheol-Min
Published: February 2025

Current technological revolutions, involving artificial intelligence, mRNA vaccines, and quantum computing, are largely driven by industry. Despite the existing perception that commercial motives promote cutting-edge innovation, concerns may arise about their risk of limiting scientific exploration from diverse perspectives, which nurtures long-term innovative potential. Here, we investigate the interplay between scientific exploration and industrial influence by analyzing about 20 million papers and US, Chinese, and European patents in genetic research, a domain of far-reaching societal importance. We observe that research on new genes has declined since the early 2000s, but the exploration of novel gene combinations still underpins biotechnology innovation. Fields of highly practical or commercial focus are less likely to adopt the innovative approaches, exhibiting lower research vitality. Additionally, continuous scientific research creates exploratory opportunities for innovation, while industry’s R&D efforts are typically short-lived. Alarmingly, up to 42.2–74.4% of these exploratory opportunities could be lost if scientific research is restrained by industry interests, highlighting the cost of over-reliance on commercially-driven research. Given the industry’s dominance in recent technologies, our work calls for a balanced approach with long-term scientific exploration to preserve innovation vitality, unlock the full potential of genetic research and biotechnology, and address complex global challenges.
The ParB-CTP Cycle Activates Phase Separation in Bacterial DNA Segregation
Authors: Delimi Linda , Revoil Perrine , Rech Jérôme , Bouet Jean-Yves , Walter Jean-Charles
Published: February 2025

Cell function relies on liquid-like organelles formed through phase transitions, yet the mechanisms ensuring their specificity and rapid assembly remain poorly understood. In bacterial chromosome segregation via the ParABS system, hundreds of ParB proteins are recruited around the centromere-likeparSsequence forming the partition complex. Recent studies have shown that ParB binds CTP and undergoes cycles of binding and unbinding nearparS, however, this accounts for the recruitment of only a small fraction of ParB molecules, leaving its role unclear. Separately, a lattice gas model with fixed interaction energy has been proposed to describe ParB phase separation, but it fails to explain key experimental observations, including the absence of droplets in ParB variants. We reconcile these two perspectives by proposing that the ParB-CTP cycle acts as a molecular switch that enhances ParB-ParB interactions, triggering phase transition from vapor to liquid-like condensates. Our hypothesis is supported by numerical simulations of droplet formation and experiments showing that ParB variants disrupting the CTP cycle fail to undergo phase separation. These findings establish a mechanistic framework for ParB-CTP-mediated phase transitions and may have broader implications for understanding the spatial control of intracellular condensate formation.
Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data
Authors: Liu Hongyi , Ma Zhuo , Lih T. Mamie , Chen Lijun , Hu Yingwei , Wang Yuefan , Sun Zhenyu , Huang Yuanyu , Xu Yuanwei , Zhang Hui
Published: February 2025

In this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average. We adopted a comprehensive approach to select representative samples with different mutation sites, considering histopathological, immune, methylation, and non-negative matrix factorization (NMF)-based subtypes, along with clinical characteristics (gender, grade, and stage) to capture the complexity and diversity of ccRCC tumors. We used machine learning identified 55 protein signatures that distinguish RCC tumors from NATs. Furthermore, 39 protein signatures that differentiate different RCC tumor subtypes were also identified. Our findings offer an extensive perspective of the proteomic landscape in RCC, illuminating specific proteins that serve to distinguish RCC tumors from NATs and among various RCC tumor subtypes.
THE CORRELATION BETWEEN REDOX ACTIVITY AND ANTIMICROBIAL PROPERTIES OF PYOCYANIN FROMPseudomonas aeruginosa
Authors: Saini Mansi , Das Subrata K , Dharmesh  , Dutt Gaurav , Singh Kishlay Kant , Prakash Divya
Published: February 2025

Pseudomonas aeruginosa, a metabolically versatile gram-negative bacterium, has garnered attention for its ability to thrive in diverse environments and its capacity to produce pyocyanin, a secondary metabolite with multifunctional properties. Pyocyanin, a redox-active phenazine compound, plays a critical role in mediating the ecological competitiveness ofP. aeruginosathrough its antimicrobial, biofilm-modulating, and reactive oxygen species (ROS)-generating activities. Beyond its contributions to bacterial virulence, pyocyanin demonstrates significant potential in various industrial and biomedical applications due to its redox properties and ability to function under diverse environmental conditions. This study investigates the electrochemical behaviour and pH-dependent antimicrobial activity of pyocyanin to evaluate its applicability in environmental and medical fields. Soil-derivedP. aeruginosaisolates were cultured for pyocyanin (PYO) production, and the pigment was characterized using UV-visible spectroscopy to get its spectral integrity. Electrochemical analysis through cyclic voltammetry revealed enhanced redox activity in acidic environments and stable functionality in alkaline conditions. Antimicrobial assays demonstrated that pyocyanin exhibited optimal activity at neutral to slightly alkaline pH, effectively inhibiting bacterial and fungal growth, while extreme acidic conditions reduced its efficacy.

The findings highlight pyocyanin’s versatility as both a redox mediator and an antimicrobial agent. In medical contexts, its pH-sensitive activity aligns well with physiological conditions, offering promise for combating multidrug-resistant pathogens. Future optimization of pyocyanin biosynthesis, particularly through cost-effective and scalable methods, could unlock its full potential in biotechnological and therapeutic innovations.
Deep-learning-based interpolation of longitudinal microbiome data powers biologically informative discovery
Authors: Qu Yixiang , Lyu Ruiqi , Wang Duan , Dai Yifan , Turcan Alistair , Yu Shilin , Xie Jialiu , Roach Jeffrey , Butler Catherine , Yap Pew-Thian , Zhu Hongtu , Dashper Stuart , Ribeiro Apoena Aguiar , Li Didong , Divaris Kimon , Wu Di
Published: February 2025

The human microbiome is a foundational and dynamic foundation for several health-related functions and disease processes. Advances in microbiome sequencing have enabled the characterization of microbial communities in several niches. Longitudinal microbiome studies further strive to discover clinically informative microbial community trajectories. However, these data are fraught with dropout events, high noise, and irregular sampling that limit and prevent the use of many available longitudinal analysis tools. To address these challenges, we introduce Bidirectional GRU-ODE-Bayes (BGOB), a deep learning framework developed for longitudinal microbiome interpolation. BGOB combines bidirectional information flow and ODE-based continuous modeling to jointly interpolate and smoothen trends across individual participants, providing uniform, denoised time intervals across patients. BGOB enables vastly improved performance in differential abundance testing and time-to-event analysis, and makes possible longitudinal analyses requiring uniformity, such as lead-lag detection and temporal clustering. After interpolation, previously low-powered datasets are able to broadly recapitulate known microbiology and elucidate interacting microbial communities. We highlight several associations between microbial taxa and disease, including novel species associated with Early Childhood Caries and disruption of key healthy gut microbiota in Inflammatory Bowel Disease. The BGOB package is publicly available athttps://github.com/Rachel-Lyu/BGOB_n_test.
Macromolecular crystallography at SPring-8 and SACLA
Authors: Yamamoto Masaki , Kumasaka Takashi
Published: February 2025

Since the groundbreaking determination of the first protein crystal structure by J. C. Kendrew in 1959, macromolecular crystallography (MX) has remained at the forefront of structural biology, driven by continuous technological advancements. The advent of synchrotron radiation in the 1990s revolutionized the field, enhancing data quality, introducing novel phasing methods, and broadening the scope of target samples to include membrane proteins and supramolecular complexes. In 1997, Japan inaugurated SPring-8, one of the world's largest third-generation synchrotron radiation facilities. With its high-brilliance radiation from insertion devices, SPring-8 has dramatically increased the capability of MX. This paper describes MX's evolution, current developments, and prospects at SPring-8 and SACLA.