bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of drug induced nuclear CTSL (nCTSL) in DNA damage response in cancer- therapeutic implications
Authors: Thirsangu Prabhu , Jin Ling , Ray Upasana , Zhao Anya , Wu Xinyan , Hou Xiaonan , VanBlaricom Jamison L , Aalam Syed Mohamed Musheer , Oberg Ann , Kannan Nagarajan , Weroha John , Chien Jeremy , Kaufmann Scott H , Bakkum-Gamez Jamie N , Shridhar Viji
Published: January 2025

In our efforts to enhance sensitivity to PARP inhibitors, we identified clofarabine (CLF) as a potential therapy for drug-resistant ovarian cancer and nuclear trafficking of Cathepsin L (CTSL) as a treatment- responsive biomarker. Using PARP inhibitor-sensitive and -resistant OC cell lines, ex vivo cultures of patient-derived ovarian ascites (OVA), primary ovarian tumors, and xenografts (PDX), we found that CLF monotherapy induces nuclear CTSL (nCTSL) in CLF-responsive cells (CLF-r) and sensitizes them to PARP inhibitors olaparib and rucaparib. In CLF non-responsive cells (CLF-nr), a combination of CLF with olaparib is necessary for nCTSL trafficking and synergy. CLF+olaparib synergy was observed in 47% of CLF-r and 24% of CLF-nr OVA samples. Drug-induced nCTSL is crucial for DNA damage response, including cell cycle arrest and apoptosis. Knockdown of CTSL in both CLF-r and CLF-nr cells conferred resistance to the CLF+olaparib combination, emphasizing nCTSL’s role in the DNA damage response pathway (DDR). Mechanistically, CLF facilitates CTSL nuclear import via KPNB1 in CLF-r cells. In CLF-nr cells, both olaparib and CLF are needed to facilitate CTSL nuclear import. Additionally, CLF downregulates the nuclear export protein CRM1 (XPO1) in both cohorts. Interestingly, CLF does not downregulate CRM1 in a subset of OVAs (29%), and they were classified as CLF-resistant (CLF- Res). In these samples, inhibiting CRM1 with KPT8602 restored synergy between CLF and PARP inhibitors. In vivo, CLF-r and CLF-nr PDX models exhibited enhanced DDR, reduced tumor burden, and prolonged survival with the CLF+olaparib combination. These findings suggest the CLF+olaparib combination is a promising therapeutic strategy for drug-resistant OC by inducing DDR through CTSL nuclear localization.
Image-based 3D active sample stabilization on the nanometer scale for optical microscopy
Authors: Vorlaufer Jakob , Semenov Nikolai , Kreuzinger Caroline , Javoor Manjunath G. , Zens Bettina , Agudelo Nathalie , Tavakoli Mojtaba R. , Suplata Marek , Jahr Wiebke , Lyudchik Julia , Wartak Andreas , Schur Florian KM , Danzl Johann G.
Published: January 2025

Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. While drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nm stability in three dimensions. However, these high-performance implementations significantly added to the complexity of the hardware and/or sample preparation. Here, we present a scheme for active drift correction that delivers the nm-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement. Using a refined algorithm that does not depend on sparse peaks typically provided by fiducial markers added to the sample, we stabilized our sample position to ~1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a standard widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases.
Open-Source 3DActive Sample Stabilization for Fluorescence Microscopy
Authors: Patil Sanket , Vicidomini Giuseppe , Slenders Eli
Published: January 2025

Super-resolution microscopy has enabled imaging at nanometer-scale resolution. However, achieving this level of detail without introducing artifacts that could mislead data interpretation requires maintaining sample stability throughout the entire imaging acquisition. This process can range from a few seconds to several hours, particularly when combining live-cell imaging with super-resolution techniques. Here, we present a 3Dactive sample stabilization system based on real-time tracking of fiducial markers. To ensure broad accessibility, the system is designed using readily available off-the-shelf optical and photonic components. Additionally, the accompanying software is open-source and written in Python, facilitating adoption and customization by the community. We achieve a standard deviation of the sample movement within 1 nm in both the lateral and axial direction for a duration in the range of hours. Our approach allows easy integration into existing microscopes, not only making prolonged super-resolution microscopy more accessible but also allowing confocal and widefield live-cell imaging experiments spanning hours or even days.
Inhibition of Glutamine Metabolism Suppresses Tumor Progression through Remodeling of the Macrophage Immune Microenvironment
Authors: Li Tianhe , Akhtarkhavari Sepehr , Chang Tu-Yung , Shen Yao-An , Yang JinMing , Slusher Barbara , Shih Ie-Ming , Gaillard Stephanie , Wang Tian-Li
Published: January 2025

Background

Targeting glutamine metabolism has emerged as a promising strategy in cancer therapy. However, several barriers, such asin vivoanti-tumor efficacy, drug toxicity, and safety, remain to be overcome to achieve clinical utility. Prior preclinicalin vivostudies had generated encouraging data showing promises of cancer metabolism targeting drugs, although most were performed on immune-deficient murine models. It is being recognized that aside from tumor cells, normal cells such as immune cells in the tumor microenvironment may also utilize glutamine for maintaining physiological functions. To provide an in-depth view of glutamine antagonist (GLNi) treatment on the tumor immune microenvironment, the current study made several unique approaches.

Method

First, to evaluate GLNi treatment modality that potentially involves immune cells, the study was performed on immunocompetent murine models of gynecological cancers. Second, to enhance safety and reduce potential off-target effects, we developed a GLNi prodrug, JHU083, which is bio-activated restrictively in cancer tissues. Third, to unbiasedly decode the response of single cells in the tumor microenvironment to GLNi treatment, single-cell RNA sequencing (scRNA-seq) was performed on cells prepared from tumors of the JHU083 or vehicle control-treated mice.

Results

In both immunocompetent murine tumor models, we observed a significant anti-tumor efficacy, resulting in reduced tumor burden and impeded tumor progression. Similarly, in both tumor models, scRNA-seq revealed significantly impeded immunosuppressive M2-like macrophages by JHU083, while the treatment spared pro-inflammatory M1-like tumor macrophages. In many tumor microenvironment (TME) cells, JHU083 downregulated genes regulated by Myc and hypoxia. M2 macrophages’ greater sensitivity to glutamine antagonism when compared to M1 macrophages or monocytes was further validated onex vivocultures of bone marrow-derived macrophages.

Conclusion

Our findings support a converged mechanism of glutamine metabolism antagonists. JHU083 exerted its anti-tumor efficacy through not only direct targeting of glutamine-addicted cancer cells but also by suppressing glutamine-dependent M2 macrophages, leading to a shift in the M1/M2 macrophage landscape in favor of an immune-stimulatory microenvironment.
The “value perspectives of nature” scale: A validated scale to measure plural value perspectives of future nature from a transformative angle
Authors: Buijs Arjen E. , Dressel Sabrina , Jacobsen Jette B. , de Kruiff Tim M. , Uribe Laura Quintero , Smith Angus M. , Gamborg Christian
Published: January 2025

Just sustainability transformation is a process of change that has a dual commitment to human well-being and environmental sustainability. Inclusive transformation critically depends on recognition of the plural values of nature in society. Lack of value alignment can lead to profound disagreements with those in society not sharing the same views on nature.

To explore plural value perspectives, we introduce the Value Perspectives of Nature (VPN) scale. This scale builds on existing value literature and measurement scales as well as on transformative approaches, most notable the Nature Futures Framework.

Using a seven-step process that includes qualitative expert evaluations, cognitive interviews, and three rounds of quantitative pre-testing and validation, the scale is developed, refined, and validated across five European countries (representative sample; N=1000).

The final VPN scale consists of 11 items, measuring instrumental value perspectives (material and nonmaterial contributions to people), relational value perspectives (place attachment and identity; Fulfilment and well-being; Spirituality; and Kinship) and intrinsic value perspectives (nature as an end in itself and acknowledgement of the rights of nature). The final validation study shows moderate to high internal consistency, reliability, and predictive validity of the scale across all countries.

While existing scales often focus on single values, the VPN is the first cross-culturally validated scale that integrates intrinsic, instrumental, and relational value perspectives into one composite scale with a focus on changes for the future. Based on the development and analysis of the VPN, we discuss several theoretical and conceptual issues in relation to relational values.

Policy implications: The VPN scale can be used in survey research to understand attitudes towards nature restoration measures. This may facilitate dialogue on effective and just transformative change in nature, through sensitising to the plural values of diverse communities. It may also be used to monitor the diversity of value perspectives over time and between communities and stakeholders. Understanding such changes in mind-sets and taking into account concerns from critical groups in society will help navigate towards positive nature futures supported by the general public.
A new map of South Manchurian mixed forests facilitates the estimation of their area for conservation purposes
Authors: Dzizyurova Violetta , Dudov Sergey , Petrenko Tatyana , Krestov Pavel , Grishchenko Mikhail , Korznikov Kirill
Published: January 2025

Questions

South Manchurian mixed forests (SMMFs) are among the most species-rich forest ecosystems in the world’s temperate zone. These forests are experiencing significant degradation and have largely been replaced by secondary forests or agricultural lands and anthropogenic non-forest vegetation. A precise quantitative assessment of the remaining forest area is crucial due to their high conservation value. This study aims to assess the current area of these forests and evaluate changes over a historical period.

Location

Korean Peninsula, northeastern China, and southern Primorsky Krai in Russia.

Methods

We used the original SMMFs distribution dataset, including vegetation relevés, literature on the distribution of these forests, and regional small-scale maps, to create a training set for classifying satellite data. We used Landsat Analysis Ready Data (1997–2001 and 2017–2021) as the basis for mapping. Mapping accuracy and area were estimated using a random stratified sampling, and forest changes were evaluated. Original relevés and literature sources were used to verify SMMFs distribution.

Results

The total area of SMMFs was estimated at 2,791.5±1,496.2 km², with significant uncertainty due to limited data from North Korea. Our results indicate that 45% of SMMFs are located in North Korea, 32% in Russia, 20% in China, and 3% in South Korea. Although historical declines in SMMF area have been documented, no significant changes were detected over the past 20 years. In 2021, SMMFs are highly fragmented ecosystems, primarily associated with protected areas.

Conclusions

We developed a high-accuracy (0.97±0.03) map of mixed forests using remote sensing techniques. This map facilitates the identification of valuable temperate forest regions and enhances understanding of current forest distribution. Our map is essential for planning restoration and conservation efforts for these critical ecosystems.
A novel murine tail model for radiation-induced skin injury following localized irradiation at varying doses
Authors: Wang Guojian , Zhao Na , Long Shuang , Gao Jining , Zhou Qing , Ran Xinze , Wang Junping , Wang Tao
Published: January 2025

Background

Radiation therapy is one cornerstone of oncologic treatment. Radiation-induced skin injury (RISI) is a dose-limiting complication of radiotherapy. RISI is also common in victims of accidental exposure, which often aggravates the patient’s condition and becomes a difficult medical issue. However, the damage mechanisms of RISI remain unclear, and the prevention and treatment measures are limited. An appropriate animal model holds great significance for addressing these issues.

Methods

C57BL/6 mice were employed to establish RISI model by irradiating 2 cm section of the mouse tail with 20Gy, 30Gy, and 40Gy of single irradiation. Skin injuries were scored with a modified semi-quantitative scale. H&E staining, IHC for dopachrome tautomerase (DTC) and Masson staining were used for histopathological evaluations of RISI.

Results

We innovatively established animal models of RISI through tail irradiation. The model mice showed typical symptoms of dry desquamation, moist desquamation, ulcers and necrosis in the irradiated area, which were highly similar to the clinical manifestations. Concurrently, we discovered that in the later stage of this model, the interstitial tissue at irradiated site presented a fibrotic phenotype with good dose dependence. It should be noted that tail irradiation causes dynamic changes in skin melanin, with early excessive deposition and late loss, which renders the observation of radiation-induced skin erythema difficult. For this reason, we specifically revised the scoring criteria for RISI.

Conclusion

In conclusion, this study established an easily operable and highly reproducible tail irradiation model, providing a novel platform for in-depth research on the mechanisms and translational applications of RISI.
Physiologically Relevant Coculture Model for Oral Microbial-Host Interactions
Authors: Pang Zeyang , Cady Nicole , Cen Lujia , Schmidt Thomas M. , He Xuesong , Li Jiahe
Published: January 2025

Understanding microbial-host interactions in the oral cavity is essential for elucidating oral disease pathogenesis and its systemic implications.In vitrobacteria-host cell coculture models have enabled fundamental studies to characterize bacterial infection and host responses in a reductionist yet reproducible manner. However, existingin vitrococulture models fail to replicate the physiological oxygen gradients critical for studying these interactions. Here, we present an asymmetric gas coculture system that simulates the oral microenvironment by maintaining distinct normoxic and anaerobic conditions for gingival epithelial cells and anaerobic bacteria, respectively. UsingFusobacterium nucleatum, a key oral pathobiont, we demonstrate that the system preserves bacterial viability and supports the integrity of telomerase-immortalized gingival keratinocytes. Compared to conventional models, this system enhanced bacterial invasion, elevated intracellular bacterial loads, and elicited more robust host pro-inflammatory responses, including increased secretion of CXCL10, IL-6, and IL-8. Additionally, the model enabled precise evaluation of antibiotic efficacy against intracellular pathogens. These results underscore the utility of this coculture platform for studying oral microbial pathogenesis and screening therapeutics, offering a physiologically relevant approach to advance oral and systemic health research.

TOC
Coexistence of Virome-Encoded Human Probiotic Genes and Pathogenic Genes in Global Habitats
Authors: Qian Min , Zhu Dong , Yao Ke-yu , Liu Shu-yue , Li Meng-ke , Ye Mao , Zhu Yong-guan
Published: January 2025

Some probiotic genes for humans obtained through horizontal gene transfer (HGT) have been screened in viral genomes, yet the occurrence mode, geographic distribution, and functional characteristics of these genes in viruses and the coexistence between pathogenic virulence genes and probiotic genes in the viral genome, remain insufficiently understood and verified. In this study, using IMG/VR v4 database, 4,556 viruses carrying probiotic gene segments have been discovered in eight habitat types (humans, animals, freshwater, marine, other water bodies, soil, and plants), 13 regions of 76 countries around the world. Among them, the 478 viruses carrying probiotic genes that distributed in humans account for the highest proportion among the viruses with predictable hosts. In viruses carrying probiotic genes,BCO1,bioB,COQ2,GPX1,GSTs,GSTT1,GULO,andmenAare not only probiotic genes encoded by viruses, but also auxiliary metabolic genes. Four virulence genes harmful to humans in viral sequences carrying probiotic genes with transcription and expression potential, have been found, indicating that virulence genes encoded by viruses can coexist with probiotic genes. Further metagenome sequencing revealed the consistency between the probiotic gene asd in the bacillus prophage and the corresponding phage auxiliary metabolic genes. This study integrates probiotic gene databases into viral genomics, revealing the compatibility between viral probiotic and virulence genes, and offering new insights for viral applications.

IMPORTANCE

Probiotic genes acquired by humans through horizontal gene transfer (HGT) have been identified within viral genomes. However, their occurrence, distribution, and functions, along with the coexistence of pathogenic and probiotic genes in viruses, remain poorly understood. This study advocates for the utilization of probiotic gene databases in viral genomes and innovatively elucidates the phenomenon of compatibility between viral probiotic genes and virulence genes, offering fresh perspectives on the diverse applications of viruses. By promoting the application of these databases, the study reveals the compatibility between probiotic and pathogenic genes in viruses, providing novel and insightful implications for the various utilizations of viruses.
Impacts of Habitat Transformation on Amphibian and Reptile Communities in a Heterogeneous Andean Landscape
Authors: Falcón-Espitia Nelson , Ríos-Orjuela Juan Camilo , Perez-Rojas Sebastian , Plazas-Cardona Dennys , Arias-Escobar Alejandra
Published: January 2025

The Andean region of Colombia is recognized for its exceptional biodiversity and high levels of endemism, particularly among amphibians and reptiles. However, this region faces significant challenges due to habitat loss and fragmentation driven by agricultural activities, urbanization, and livestock farming. This study evaluates the effects of habitat alterations on herpetofaunal communities within the Sumapaz province, focusing on three habitat types: secondary Andean forests, coffee plantations, and open areas associated with low-intensity livestock farming. We also compiled a comprehensive inventory of 85 species based on fieldwork conducted (2021-2022) and biodiversity databases, recognizing 35 amphibians and 50 reptiles for the region. We found that forests support the highest richness and diversity of species, while open areas exhibited greater reptile abundance. Crops showed lower biodiversity but demonstrated potential as secondary habitats for certain species. These findings highlight the importance of preserving forested areas and designing mixed-use landscapes to promote biodiversity and maintain ecological functions. This study provides a baseline for future conservation strategies in the Sumapaz region.
Single-Photon Single-Particle Tracking
Authors: Xu Lance W.Q. , Ronceray Nathan , Mitsioni Marianna Fanouria , Radenovic Aleksandra , Pressé Steve
Published: January 2025

Multiple biological “particles”, from biomolecules to viral capsids, diffuse with rates exceeding 1µm2/s, introducing blurring so significant when imaged with traditional integrative detectors such as sCMOSs and EMCCDs that one particle may appear as many. While single-photon detector arrays hold promise to strongly mitigate blurring artefacts by allowing for tenfold temporal resolution improvement, tracking from arrays with binary 1-bit output (photon detected or not) falls outside the existing tracking paradigm. For instance, the core of existing tracking algorithms relies on intensity-based information per pixel to achieve single-particle localization. Yet this is not possible with a 1-bit output. Here, we circumvent the localization paradigm and directly analyze single-photon detector array output to leverage the temporal resolution afforded by short single-photon detector array exposures. To achieve this, we propose a computationally feasible strategy to propose particle numbers and associated trajectories consistent with the entire 1-bit per pixel image stack. Our method, single-photon single-particle tracking (SP2T), deals with both hot and cold pixels to which single-photon detector array data interpretation is highly sensitive. We consider multiple examples, including controlled experiments with fluorescent beads following pre-programmed trajectories, where ground truth is partially available, and the diffusion of aerolysin monomers on supported lipid bilayers. These results showcase SP2T as a powerful tool capable of tenfold temporal resolution improvement for advancing the resolution of dynamical events from single-photon detector array architectures.
Exploring vitamin D and its analogues as a possible therapeutic intervention in targeting inflammatory mediators in neurodegenerative disorders like Parkinson’s disease
Authors: Pal Randrita , Das Nilansu , Basu Barnali Ray
Published: January 2025

Parkinson’s disease characterized by dopaminergic neuronal death has been linked with neuroinflammatory processes which involve self-perpetuating detrimental events leading to prolonged neurodegeneration. Vitamin D has been found to possess neuroprotective and immuno-modulatory effects which might justify elevated inflammation and hypovitaminosis D in PD patients. So, we aimed to find the possible interactions of Vitamin-D and its analogues with inflammatory mediators prevalent in PD to get more insight into Vitamin-D’s role in neuroinflammation by assessing specific interactions between Vitamin-D and its marketed analogues with different inflammatory mediators. Moreover, revealing a possible drug repurposing with Vitamin-D analogues against neuroinflammation and other inflammatory conditions.

Molecular docking was conducted with 10 inflammatory markers (p38 MAPK, NF-κB, iNOS, nNOS, COX-2, TNFα, IL6, TNFα, IL1β, CRP) with bio-active form of Vitamin-D (calcitriol) and its analogues. Among the studied ligands, calcitriol, calcipotriol, seocalcitol, paricalcitol and falecalcitriol were found to be potential inhibitors of different inflammatory agents. Specific standard drugs or experimental inhibitors were used to compared the binding affinity between protein and ligand. BBB permeability of the tested ligands also checked as well as neurotoxicity. Most of the ligands were found to be BBB permeable possibly interacting with inflammatory mediators within the brain and were also found to be non-neurotoxic.

This study sheds light on VD and its analogues being possible candidates against various inflammatory markers. The findings could further be used as stepping stone for new study on repurposing of these analogues in neuroinflammation and other inflammatory disease conditions.
Improving SBRT by re-wiring immunosuppressive neutrophils in murine pancreatic ductal adenocarcinoma
Authors: Murphy Joseph D. , Hannon Gary , Mills Bradley N. , Hughson Angela L. , Uccello Taylor P. , Gavras Nicholas W. , Ye Jian , Belt Brian A. , Lesch Maggie L. , Eckl Sarah L. , Lord Edith M. , Kim Minsoo , Qiu Haoming , Linehan David C. , Gerber Scott A.
Published: January 2025

Radiation is used to treat pancreatic ductal adenocarcinoma (PDAC) in the locally-advanced setting. Stereotactic body radiation therapy (SBRT), in particular, has shown improved outcomes against conventional RT in a number of clinical trials. One key cell type involved in the response to RT are neutrophils. These innate immune cells are the first responders to tissue damage and infiltrate irradiated tumors in high numbers to rectify injury. Neutrophils typically possess an immunosuppressive, wound healing phenotype in this scenario, which allows the tumor to recover and actively suppress immunological efforts to eradicate the disease. Here, we aimed to elucidate the role of neutrophils in a murine model of PDAC treated with SBRT. Mice harboring PDAC tumors were treated with targeted SBRT and neutrophils were determined to be significantly increased in the tissue when compared to unirradiated controls. Additionally, phenotypic analysis determined that these cells were largely immunosuppressive and depletion studies confirmed they played a key role in acquired radioresistance in our model. In order to establish whether these infiltrating cells could be re-wired to contribute to anti-tumor immunity, we utilized a novel combination therapy consisting of SBRT and microspheres containing recombinant IL-12 to attempt to repolarize these cells. Transcriptomic analysis confirmed intratumoral neutrophils underwent considerable changes indicative of an immunostimulatory, anti-tumor phenotype following treatment. Moreover, depleting these cells resulted in a loss of treatment efficacy, suggesting that neutrophil re-wiring was vital for the therapeutic outcome. This study highlights neutrophils as key players in SBRT and IL-12 treatment and confirms they can act as a double-edged sword depending on the treatment employed.
How does urbanization shape shell phenotype, behaviour and parasite prevalence in the snailCornu aspersum?
Authors: Dahirel Maxime , de Tombeur Youna , Gérard Claudia , Ansart Armelle
Published: January 2025

Urbanization is a complex and multivariate environmental change inducing major disturbances, e.g. habitat fragmentation/loss, changes in local climate, soil imperviousness, pollution… As slow-moving, ectothermic and humidity-sensitive animals, land snails have to cope with urbanization-induced changes, likely to influence their behaviour, life traits and host-parasite interactions. In this context, we studied how, in the brown garden snailCornu aspersum, shell phenotype (shell size and colour/reflectance), behaviour (food intake, mobility) and metazoan parasite prevalence respond to urbanization. We found that snails from more urbanized sites closer to the urban centre were smaller, whereas urbanization had no detectable effect on shell reflectance, parasite prevalence or behaviour. Larger snails and snails with paler shells were more likely to be infected by trematode metacercariae and sexually-transmitted nematodes (Nemhelix bakeri), respectively. Snails harbouring trematode sporocysts ate typically less, while those infected byN. bakerimoved more slowly. We discuss the decrease of snail size along the urbanization gradient in relation with the Urban Heat Island effect and the potential decrease of resource quality and availability in urban sites. The absence of detectable effects of urbanization on shell reflectance, mobility and prevalence may be due to scale mismatches between how urbanization is measured and how snails experience microhabitats. We propose further experimental and field studies to decipher interactions between urbanization effects, shell phenotype, life-history traits and parasitism.
Langerhans Cells Drive Tfh and B Cell Responses Independent of Canonical Cytokine Signals
Authors: Bouteau Aurélie , Qin Zhen , Zurawski Sandra , Zurawski Gerard , Igyártó Botond Z.
Published: January 2025

Dendritic cells (DCs) are key regulators of adaptive immunity, guiding T helper (Th) cell differentiation through antigen presentation, co-stimulation, and cytokine production. However, in steady-state conditions, certain DC subsets, such as Langerhans cells (LCs), induce T follicular helper (Tfh) cells and B cell responses without inflammatory stimuli. Using multiple mouse models andin vitrosystems, we investigated the mechanisms underlying steady-state LC-induced adaptive immune responses. We found that LCs drive germinal center Tfh and B cell differentiation and antibody production independently of interleukin-6 (IL-6), type-I interferons, and ICOS ligand (ICOS-L) signaling, which are critical in inflammatory settings. Instead, these responses relied on CD80/CD86-mediated co-stimulation. Our findings challenge the conventional three-signal paradigm by demonstrating that cytokine signaling is dispensable for LC-mediated Tfh and B cell responses in steady-state. These insights provide a framework for understanding homeostatic immunity and the immune system’s role in maintaining tolerance or developing autoimmunity under non-inflammatory conditions.

SUMMARY STATEMENT

Langerhans cells (LCs) drive germinal center Tfh and B cell responses in steady-state conditions independently of IL-6, type-I interferons, and ICOS ligand, challenging the established cytokine-centric model of T cell differentiation.
MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony
Authors: Eluru Gangadhar , De Gieter Steven , Schenck Stephan , Stroobants Annelore , Shrestha Binesh , Erbel Paul , Brunner Janine D. , Efremov Rouslan G.
Published: January 2025

Single particle cryo-EM enables reconstructing near-atomic or even atomic resolution 3D maps of proteins by visualizing thousands to a few million purified protein particles embedded in nanometer- thick vitreous ice. This corresponds to picograms of purified protein, which can potentially be isolated from a few thousand cells. Hence, cryo-EM holds the potential of one of the most sensitive analytical methods that deliver a high-resolution protein structure as a readout. In practice, more than a million times more starting biological material is required to prepare cryo-EM grids. To close the gap, we developed a micro isolation (MISO) method that combines microfluidics-based protein purification with cryo-EM grid preparation. We validated the method on soluble bacterial and eukaryotic membrane proteins. We showed that MISO enables protein structure determination starting from below one microgram of a target protein and going from cells to cryo-EM grids within a few hours. This scales down the purification by a factor of a few hundred to a few thousand and opens possibilities for the structural characterization of hitherto inaccessible proteins.
CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field
Authors: Qu Huaizhi , Wang Xiao , Zhang Yuanyuan , Wang Sheng , Noble William Stafford , Chen Tianlong
Published: January 2025

Cryogenic electron microscopy (cryo-EM) has become a widely used technique for determining the 3D structures of proteins. However, cryo-EM datasets often exhibit heterogeneity, with protein particle images from multiple conformations or compositional states. Here we proposeCryoNeRF, a novel neural radiance fields (NeRF)-based cryo-EM reconstruction framework operating directly in Euclidean 3D space. CryoNeRF introduces a multi-resolution hash encoding and heterogeneity-aware cryo-EM encoder to model cryo-EM heterogenity. Extensive experiments demonstrate the stability and superior performance of CryoNeRF in both homogeneous and heterogeneous settings. On homogeneous datasets, CryoNeRF achieves 15.8% improvement over previous state-of-the-art methods. On both simulated and experimental heterogeneous datasets, CryoNeRF demonstrates exceptional capability in handling both conformational and compositional variations, which is consistent with previous experimental discoveries. Notably, CryoNeRF successfully distinguishes assembly states that even only account for 2% particles of the dataset in cases of compositional heterogeneity.
Antibiotic ResistantE. Coliare Common in Waller Creek, an Urban Waterway Chronically Contaminated with Fecal Bacteria
Authors: Olivera Perez Lena L. , Reichler Stuart
Published: January 2025

The emergence of antibiotic-resistant bacteria has created a significant threat to global health. Some strains ofEscherichia coli(E. coli), a common bacteria with both commensal and pathogenic strains, can be resistant to common antibiotics. This study investigates the prevalence ofE. coliresistance to ampicillin, erythromycin, and ciprofloxacin in Waller Creek, an urban waterway in Austin, Texas with chronically high levels of fecal bacteria. Approximately 134 samples were collected from three different sites along Waller Creek and spiked with varying antibiotic concentrations.E. coliresistance to ampicillin and erythromycin was found to be up to 26.92% and 48.37% respectively, while resistance to ciprofloxacin was much lower ranging between 0%-2%. The highest levels of resistance were associated with dense urbanization, high levels of homelessness, and after heavy precipitation. These findings indicate the need for regular monitoring of antibiotic concentrations and antibiotic resistant fecal bacteria within urban waterways. This data is needed to identify potential human health risks and understand key factors that contribute to the quantity of antibiotic-resistant pathogens.
TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging
Authors: Hospelhorn Blythe G. , Kesler Benjamin K. , Jashnsaz Hossein , Neuert Gregor
Published: January 2025

Characterizing the movement of biomolecules in single cells quantitatively is essential to understanding fundamental biological mechanisms. RNA fluorescent in situ hybridization (RNA-FISH) is a technique for visualizing RNA in fixed cells using fluorescent probes. Automated processing of the resulting images is essential for large datasets. Here we demonstrate that our RNA-FISH image processing tool, TrueSpot, is useful for automatically detecting the locations of RNA at single molecule resolution. TrueSpot also performs well on images with immunofluorescent (IF) and GFP tagged clustered protein targets. Additionally, we show that our 3D spot detection approach substantially outperforms current 2D spot detection algorithms.
Polysialylation is a general feature of immune activation
Authors: Makhsous Sogand , Hunter Carmanah , van Eeden Charmaine , Osman Mohammed , Willis Lisa
Published: January 2025

Sialic acids are critical regulators of immune responses and the sialic acid-Siglec axis has receive much attention recently for it role as a new immune checkpoint. While α2,3- and α2,6-linked sialosides have been well studied, much less is known about the α2,8-linked polysialic acid (polySia), especially in the adaptive immune system. We demonstrate here that polySia is actually found in all major classes of circulating immune cells, including B and T cells, where it is strongly associated with prior antigen exposure. Cell surface expression of polySia could be observed within 24 h of activation of naïve T cells but did not correlate with expression of the immune-specific polysialyltransferase ST8Sia4. Finally, we assessed the effects of smoking on polySia levels, and noted substantial increased levels of polySia, particularly on effector T cells and preferentially in males.

Significance Statement

The immune system is central to human health and holds the key to treating many chronic diseases. We show for the first time that the immunomodulatory glycan polysialic acid is widespread in the human immune system and associated with immune cell activation. Moreover, sex-dependent increases in polysialic acid could be observed on key populations of immune effector cells in smokers. This study offers insight into how glycans might contribute to sex differences in development and progression of chronic diseases.
Light-induced conformational switching and magnetic sensitivity of Drosophila cryptochrome
Authors: Chandler Shane A. , Gehrckens Angela S. , Shah Laila M. N. , Buckton Katherine E. , Cao Guodong , Sen Navoneel , Zollitsch Tilo , Rodriguez Ryan , Solov’yov Ilia A. , Schleicher Erik , Weber Stefan , Hore Peter J. , Timmel Christiane R. , Mackenzie Stuart R. , Benesch Justin L.P.
Published: January 2025

Cryptochromes are flavoproteins with a number of established and proposed biological functions based on their sensitivity to light. Amongst the latter is the possibility that cryptochromes mediate the geomagnetic compass sense used by migratory birds as a navigational cue. This hypothesis rests on a magnetically sensitive photochemical reaction of the flavin chromophore in which a series of electron transfers within the protein scaffold ultimately generates a signal propagated within the central nervous system of the animal. Although there is a good understanding of the photochemistry and the electron transfer pathway, the protein-mediated mechanisms of signal transduction are still unclear. Here we have examined the response ofDrosophila melanogastercryptochrome –DmCRY, an archetypal cryptochrome – to photochemical activation by means of molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and cavity ring-down spectroscopy. We were able to measure the dynamics ofDmCRY at near-residue level resolution, revealing a reversible, long-lived, blue-light induced conformational change in the C-terminal tail of the protein. This putative signalling state was validated using different illumination conditions, and by examiningDmCRY variants in which the electron transfer chain was disrupted by point mutation. Our results show how the photochemical behaviour of the flavin chromophore generates a state ofDmCRY that may act as a key primer for modulating downstream interactions.
CellUntangler: separating distinct biological signals in single-cell data with deep generative models
Authors: Chen Sarah , Regev Aviv , Condon Anne , Ding Jiarui
Published: January 2025

Single-cell RNA-seq data have provided new insights into intracellular and intercellular processes. Because multiple processes are active in each cell simultaneously, such as its cell type program, differentiation, the cell cycle, and environmental responses, their respective signals can confound one another, requiring methods that can separate and filter different complex biological signals. Each such signal is based on different gene activities and can define different relationships between cells. However, existing methods often focus on a single process or rely on overly restrictive assumptions, thus removing, rather than disentangling biological signals. Here, we develop CellUntangler, a deep generative model that embeds cells into a flexible latent space composed of multiple subspaces, each designed with an appropriate geometry to capture a distinct signal. We apply CellUntangler to datasets containing only cycling cells and both cycling and non-cycling cells, generating embeddings in which the cell cycle signal is disentangled from non-cell cycle specific signals, such as cell type or differentiation trajectory. We demonstrate CellUntangler’s extensibility by using it to capture and separate spatial from non-spatial signals. With CellUntangler, we can obtain latent embeddings that capture various biological signals and perform enhancement or filtering at the gene expression level for downstream analyses.
A systematic screen for genetic factors underpinning transposon defense systems across the fungal kingdom
Authors: Badet Thomas , Croll Daniel
Published: January 2025

Fungal genome sizes exhibit more than a 100-fold variation, largely driven by the expansion of repetitive sequences such as transposable elements (TEs). Genomic defenses have evolved to counteract TE proliferation through silencing mechanisms operating at the epigenetic or transcript level. In fungi, repeat-induced point mutation (RIP) targets TEs by recognizing repetitive sequences and inducing mutagenesis. However, the prevalence of RIP across the fungal kingdom and the fidelity of the canonical C-to-T mutation signatures remain unclear. In this study, we address these gaps by tracking shifts in genome architecture across the fungal kingdom. We show that the loss of RIP components is associated with an 80% (∼30 Mb) increase in genome size in ascomycetes (class of Leotiomycetes). To track the impact of genome defenses, we designed a quantitative screen for RIP-like mutation signatures. The phylum of ascomycetes was unique in showing enrichment in mutation signatures in non-coding and repetitive sequences, consistent with a phylogenetically restricted occurrence of RIP-like genome defense systems. Then, we gene functions associated in a phylogenetic context with RIP-like mutation signatures. We identified a zinc-finger protein as the strongest candidate underpinning a novel mechanism of genome defenses. Our findings reveal the multifaceted drivers of genome defense systems and their close ties to genome size evolution in fungi, highlighting how proximate molecular mechanisms can shape genome evolution on deep phylogenetic scales.
The antiviral activity of licensed therapeutics against Mpox clade Ib,in vitro; alternative options for the treatment of Mpox
Authors: Horton Amanda , Berryman Helen , Surani Yasmin M. , Bewley Kevin , Wand Matthew E. , Sutton J. Mark , Tree Julia A.
Published: January 2025

Clade Ib mpox is a newly emerged strain of the mpox virus (MPXV). The antiviral efficacy of 12 different therapeutic drugs was evaluated,in vitrousing a live-virus, foci reduction assay, against MPXV clade Ib. We report that antiviral activity is retained against clade Ib with inhibitory concentrations (required to reduce the viral foci count by 50% (IC50)) of 0.025 ± 0.018 and 43.8 ± 15.2 μM for tecovirimat and cidofovir, respectively. These values are not significantly different from those observed for clade IIb, when measured in the same foci reduction assay (IC50values of 0.010 ± 0.02 and 15.7 ± 14.3 μM for tecovirimat and cidofovir, respectively). Activity was also demonstrated for other antivirals, with the IC50of the active metabolites of molnupiravir (EIDD-1931; 4.47 ± 1.72 μM) and remdesivir (GS-441524; 11.8 ± 6.43 μM) and with other licensed antivirals such as ribavirin (34.4 ± 10.3 μM) and baloxavir marboxil (22.6 ± 10.5 μM). In contrast, no inhibitory activity was observed with acyclovir, L-valacyclovir hydrochloride or favipiravir (IC50>100 μM). Interestingly, the anti-parasitic drugs nitazoxanide, mefloquine hydrochloride and chloroquine diphosphate, showed inhibitory activity against the clade Ib virus, with IC50values of 14.5 ± 3.41, 5.37 ± 1.37 and 24.7 ± 2.38 μM, respectively. This study shows that several therapeutics, including several licensed antivirals, may offer alternative treatment options for mpox clade Ib.
miR-379-3p counteracts cancer cachexia through regulation of pyrimidinergic receptor, mitochondrial stress and interferon response
Authors: Borja-Gonzalez Maria , González-Ojeda Raúl , Sannicandro Anthony J , Su Chao , McCarthy Elan C , Sanz-Nogués Clara , Dwyer Roisin M , McDonagh Brian , Goljanek-Whysall Katarzyna
Published: January 2025

Cancer cachexia is a highly prevalent wasting syndrome in cancer patients. Inflammation is hallmarks of symptomatic cachexia, however early stages of cachexia are not well understood, including differences between biological sexes. In a mouse model of early cachexia, muscle from males showed strong mitochondrial defects, whereas females were characterized by inflammatory and stress response. We demonstrate a novel link between the increase in purinergic receptor P26Y, and dysregulated Ca2+homeostasis, mitochondrial dysfunction and damage, and inflammation during early stages of cancer cachexia. Low levels of miR-379-3p were associated with poor survival of patients with lung cancer. Restoring miR-379-3p levels in mice prevented loss of muscle mass and function. miR-379-3p targeted P2r6y and restored mitochondrial content and function, inhibited type II interferon response, and regulated the expression of Ca2+-related and apoptotic markers. This supports miR-379-3p as a hub regulating multiple processes underlying cachexia and represent a therapeutic target for cancer patients.
Estimating the effects of exercise-based cardiac rehabilitation on health-related quality of life in patients with myocardial infarction in Sweden: A registry-based study using non-experimental methods
Authors: Stanke Anja N. , Leósdóttir Margrét , Bäck Maria , Ekman Björn
Published: January 2025

Participation in exercise-based cardiac rehabilitation (EBCR) improves long-term prognosis for patients following myocardial infarction (MI). Evaluating the effects of EBCR is challenging due to the voluntary nature of participation in the program. Using register data on 18,978 patients hospitalized for MI in 2011 to 2013 in Sweden, a non-experimental study design is employed to evaluate the effects of EBCR on the health-related quality of life (HRQoL). Conditional independence from non-random treatment assignment is considered through set of potential-outcome (PO) models to estimate the average treatment effect (ATE) and the ATE on the treated (ATET) of EBCR on HRQoL using the EQ-5D-3L instrument. Changes in the EuroQoL Visual Analogue Scale (EQ-VAS; range 0 to 100) and the EQ5D-Index (range -0.594 to 1) between 6-10 weeks and one-year post-MI are compared between two groups of participants in EBCR (complete participants [≥3 months] and non-complete participants [<3 months]) and non-participants (control group). In total, 43% of patients participated in EBCR to some extent (12% complete, 31% non-complete). Participants showed greater improvement on the EQ-VAS scale compared with non-participants. Patients who completed an EBCR program had a larger improvement (ATE of between 1.851-1.917 points; p < 0.001) compared with participants who did not complete the full program (0.974-1.017 points; p < 0.01). Full participation in the program increased the EQ5D-Index of between 0.014 and 0.017 points (p < 0.05), while no statistically significant effect was observed among non-completers. The effect of EBCR on HRQoL was more pronounced among younger patients and those reporting dyspnea and angina than older and non-symptomatic patients. Participating in EBCR may improve the health-related quality of life of patients post-MI. The clinical relevance of the observed impact of EBCR on HRQoL warrants further investigation. The effects of EBCR participation can be readily estimated using broadly applicable non-experimental approaches and commonly available register data.