bluuebunny/crossref_metadata_2025 huggingface dataset:
Circulating Exosomal PCNA: A Biomarker for Early and Pan-Cancer Detection
Authors: Shi Weibing , Sun Xiaojie , Zhou Haishen , Da Hongting , Li Hong , Cai Chunlin
Published: February 2025

Detecting multiple cancers with a single, non-invasive liquid biopsy test remains a challenge, as no universally shared cancer biomarker with clinical significance has been identified in bodily fluids. In this study, we identified proliferating cell nuclear antigen (PCNA), a well-established pathological cancer biomarker in tissue biopsies, as being secreted into peripheral bodily fluids within exosomes. Our research demonstrated that cultured cancer cells continuously release large quantities of exosomal PCNA into their surrounding media. Furthermore, we confirmed its presence in human serum. Most importantly, cancer patients exhibited significantly higher levels of exosomal PCNA in their sera compared to healthy individuals. To assess its diagnostic potential, we evaluated the sensitivity and specificity of exosomal PCNA in a cohort of cancer patients and healthy controls. Receiver operating characteristic (ROC) analysis revealed a sensitivity of 77.2% and a specificity of 94.4%. These findings establish exosomal PCNA in peripheral bodily fluids as a promising universal biomarker for the early detection, diagnosis, and monitoring of multiple cancers through liquid biopsy.
Export dynamics of protists across the southern subtropical frontal zone reveal taxon-specific patterns
Authors: Ong Denise Rui Ying , Gutiérrez-Rodríguez Andrés , Bilewitch Jaret , Nodder Scott , Stukel Michael R. , Décima Moira , Lopes dos Santos Adriana
Published: February 2025

Gravitational particle sinking is the main mechanism for carbon export in the biological carbon pump. However, the export dynamics of the particle-associated protist community are not fully understood. We used 18S rRNA gene metabarcoding to characterise the exported protist community within sinking particles and bathypelagic surficial sediments in oligotrophic subtropical and high-nutrient, low-chlorophyll subantarctic waters. Sinking particles were collected with formalin-fixed and preservative-free particle interceptor traps (fixed and live traps, respectively) to identify the community involved in particle export (fixed) and protist loss from remineralisation (live). We paired this with community analysis of the upper and lower water column (mixed layer and below mixed layer to mesopelagic, respectively) to compare the relative sources of exported protists. Amplicon sequences variants (ASVs) from upper water column samples accounted for 2 to 4-fold higher proportion of reads and ASV rich-ness compared to lower water column samples in fixed trap and sediment samples, suggesting low influence of the suspended protist community from the lower water column on export. We further traced the export patterns of upper water column protist taxa by analysing the change in taxa relative abundance across the mixed layer to mesopelagic depths. Export patterns differed between taxa, which is similarly suggested by taxa-specific loss of ASV richness between fixed and live traps, but remained the same across biogeochemically-contrasting water masses. This could imply that the drivers for protist loss during export are related to characteristics consistent across environmental conditions, such as specific microbial interactions or inherent cell properties.
Target cell adhesion limits macrophage phagocytosis and promotes trogocytosis
Authors: Rollins Kirstin , Fiaz Sareen , Morrissey Meghan
Published: February 2025

Macrophage phagocytosis is an essential immune response that eliminates pathogens, antibody-opsonized cancer cells and debris. Macrophages can also trogocytose, or nibble, targets. Trogocytosis and phagocytosis are often activated by the same signal, including IgG antibodies. What makes a macrophage trogocytose instead of phagocytose is not clear. Using both CD47 antibodies and a Her2 Chimeric Antigen Receptor (CAR) to induce phagocytosis, we found that macrophages preferentially trogocytose adherent target cells instead of phagocytose in both 2D cell monolayers and 3D cancer spheroid models. Disrupting target cell integrin using an RGD peptide or through CRISPR-Cas9 knockout of the αV integrin subunit in target cells increased macrophage phagocytosis. Conversely, increasing cell adhesion by ectopically expressing E-Cadherin in Raji B cell targets reduced phagocytosis. Finally, we examined phagocytosis of mitotic cells, a naturally occurring example of cells with reduced adhesion. Arresting target cells in mitosis significantly increased phagocytosis. Together, our data show that target cell adhesion limits phagocytosis and promotes trogocytosis.
Super-resolution compatible DNA labeling technique reveals chromatin mobility and organization changes during differentiation
Authors: Pabba Maruthi K. , Kuba Miroslav , Kraus Tomáš , Celikay Kerem , Meyer Janis , Pradhan Sunik Kumar , Maiser Andreas , Harz Hartmann , Leonhardt Heinrich , Rohr Karl , Hocek Michal , Cardoso M. Cristina
Published: February 2025

Chromatin dynamics play a crucial role in cellular differentiation, yet tools for studying global chromatin mobility in living cells remain limited. Here, we developed a novel probe for the metabolic labeling of chromatin and tracking its mobility during neural differentiation. The labeling system utilizes a newly developed silicon rhodamine-conjugated deoxycytidine triphosphate (dCSiRTP). We show that this dCTP is efficiently delivered into living human induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) via a synthetic transporter (SNTT1). Using correlative confocal microscopy and stimulated emission depletion (STED) super-resolution microscopy, we quantified the sizes of labeled chromatin domains. Time lapse super-resolution microscopy combined with single particle tracking revealed that chromatin mobility decreases during the transition from iPSCs (pluripotent state) to NSCs and neurons (differentiated state). This reduction in mobility correlates with the differentiation state, suggesting a role for chromatin dynamics in cellular plasticity. Concomitant mechanistic insights obtained from MNase digestion assays, chromatin compaction and histone modification analyses revealed a decrease in chromatin accessibility during neuronal differentiation, indicating that chromatin adopts a more constrained and compacted structure. These findings provide new insights into chromatin regulation during neurogenesis.
AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications
Authors: Galindo Gabriel , Maejima Daiki , DeRoo Jacob , Burlingham Scott R. , Fixen Gretchen , Morisaki Tatsuya , Febvre Hallie P. , Hasbrook Ryan , Zhao Ning , Ghosh Soham , Mayton E. Handly , Snow Christopher D. , Geiss Brian J. , Ohkawa Yasuyuki , Sato Yuko , Kimura Hiroshi , Stasevich Timothy J.
Published: February 2025

Intrabodies are engineered antibodies that function inside living cells, enabling therapeutic, diagnostic, and imaging applications. While powerful, their development has been hindered by challenges associated with their folding, solubility, and stability in the reduced intracellular environment. Here, we present an AI-driven pipeline integrating AlphaFold2, ProteinMPNN, and live-cell screening to optimize antibody framework regions while preserving epitope-binding complementarity-determining regions. Using this approach, we successfully converted 19 out of 26 antibody sequences into functional single-chain variable fragment (scFv) intrabodies, including a panel targeting diverse histone modifications for real-time imaging of chromatin dynamics and gene regulation. Notably, 18 of these 19 sequences had failed to convert using the standard approach, demonstrating the unique effectiveness of our method. As antibody sequence databases expand, our method will accelerate intrabody design, making their development easier, more cost-effective, and broadly accessible for biological research.
Trymethylamine-N-oxide, a gut-derived metabolite, induces myofibroblastic activation of valvular interstitial cells through endoplasmic reticulum stress
Authors: Sudi Samanvitha , Suresh Sai Drishya , Kolli Tanmayee , Porras Ana Maria
Published: February 2025

Calcific aortic valve disease currently lacks effective treatments beyond surgical valve replacement, due to an incomplete understanding of its pathogenesis. Emerging evidence suggests that the gut microbiome influences cardiovascular health through the production of metabolites derived from dietary components. Among them, trimethylamine-N-oxide (TMAO) has been identified as a potential causal factor for several cardiovascular conditions. However, its role in the development of aortic valve disease remains poorly understood. This study sought to investigate the impact of TMAO on valvular interstitial cells (VICs), the most abundant cell type in the aortic valve. Here, we demonstrate that TMAO activates VICs towards a myofibroblastic profibrotic phenotype. Using anin vitroprotocol to generate quiescent VICs, we found that TMAO induces the upregulation of myofibroblastic markers in a sex-independent manner. These quiescent VICs were more sensitive to TMAO than conventionally cultured VICs. Treatment with TMAO also elevated extracellular matrix production and oxidative stress, phenotypic hallmarks of an activated profibrotic state. Finally, inhibition of the endoplasmic reticulum stress kinase prior to TMAO treatment blocked all effects of this metabolite. These findings suggest that TMAO contributes to the early stages of valve disease by promoting VIC activation through endoplasmic reticulum stress mechanisms. Understanding the role of TMAO and other gut-derived metabolites in the pathogenesis of valve disease could inform the development of novel preventive or therapeutic strategies to modify or delay disease progression. Furthermore, these insights underscore the importance of host-microbiome interactions and highlight the potential for targeted dietary interventions to mitigate cardiovascular disease risk.
A Retrospective Efficacy and Safety Study of Pembrolizumab/ Cetuximab Neoadjuvant Therapy in Locally Advanced Hypopharyngeal Cancer
Authors: Yao Guangnan , Wu Xiaobo , Lin Hanqing , Chen Zhihong , Lin Chang , Lin Gongbiao
Published: February 2025

Background

The primary objective of this study was to retrospectively assess the efficacy and safety profiles of two neoadjuvant regimens combining either pembrolizumab or cetuximab with paclitaxel and cisplatin in patients with locally advanced hypopharyngeal cancer (LAHPC).

Methods

LAHPC patients who received surgical resection at our hospital between August 2022 and February 2024 were enrolled in the study. All patients received neoadjuvant treatment before surgery and postoperative adjuvant therapy. They were categorized into two groups based on the neoadjuvant regimen: the paclitaxel + cisplatin + pembrolizumab (TP + PEMBRO) group and the paclitaxel + cisplatin + cetuximab (TP + CETUX) group. We evaluated various parameters including treatment response rate, adverse effects, surgical modalities, and survival outcomes for both groups.

Results

A total of 32 LAHPC patients were enrolled into the study, with 16 patients in each group. The TP + PEMBRO group demonstrated a significantly superior objective response rate (ORR) of neoadjuvant treatment compared to the TP + CETUX group (87.5% vs 68.75%, P < 0.05). In terms of surgical procedures, the TP + PEMBRO group exhibited a higher proportion of minimally invasive surgeries (87.5% vs 56.25%, P < 0.05), and both the tracheotomy rate and indwelling gastric tube rate were relatively lower in this group. Regarding patient prognosis, the 1-year overall survival (OS) rate in the TP + PEMBRO group was 100%, and the 1-year relapse-free survival (RFS) rate was 92.31%. In contrast, the TP + CETUX group had a 1-year OS rate of 93.75% and a 1-year RFS rate of 81.25%. There was no significant disparity in adverse events between the two groups, and no grade 3 - 4 severe adverse events occurred.

Conclusion

The neoadjuvant TP regimen integrating pembrolizumab or cetuximab was associated with higher transoral surgery (TOS) rates and laryngeal preservation rates. Notably, the TP + PEMBRO regimen outperformed the TP + CETUX regimen in terms of treatment response rate and the proportion of minimally invasive surgeries, suggesting a novel and efficacious neoadjuvant treatment for LAHPC.
Novel Genetic Variants Associated with Gout Identified Through a Genome-Wide Study in the UK Biobank (N = 150,542)
Authors: Tao Yiwen , Cai Tengda , Pan Qi , Yang Luning , Lin Sen , Haque Mainul , Dottorini Tania , Abhishek Abhishek , Meng Weihua
Published: February 2025

Gout is a prevalent and painful form of inflammatory arthritis associated with hyperuricemia, which leads to monosodium urate crystal deposition in joints and surrounding tissues, triggering acute inflammatory responses. This disease is also closely linked to serious comorbidities, including cardiovascular diseases, chronic kidney diseases, diabetes, and increased mortality risk, significantly impacting global health. In this study, we conducted a comprehensive genome-wide association study (GWAS) based on the UK Biobank pain questionnaire 2019, comprising 10,474 gout cases and 140,068 controls, identifying 13 loci associated with gout, including four novel loci. These findings were further explored in the FinnGen cohort, with 12 loci being replicated significantly. Sex-stratified analyses revealed notable differences, with 16 loci identified in males and two loci identified in females, reflecting both shared and sex-specific genetic influences on gout susceptibility. In addition, genetic correlation analyses demonstrated strong associations between gout and traits related to urate levels, specific medication use, and metabolic functions. Transcriptome-wide association studies highlighted several genes, such asSLC16A9andASAH2B, which showed significant expression patterns across various tissues, implicating metabolic and immune pathways in gout. Phenome-wide association studies of significant SNPs revealed links to metabolic, immunological, and skeletal traits, underscoring the multi-faceted nature of gout. These results contribute valuable insights into the genetic architecture and biological mechanisms underlying gout, suggesting potential avenues for tailored interventions.
Neighborhood Socioeconomic Status and Cardiometabolic Outcomes in Urban Jamaica: Exploring Novel Measures
Authors: Dyer Harika P. , Ferguson Trevor S. , Mckenzie Joette , Coleman Novie Younger- , Tulloch-Reid Marshall , Blake Alphanso L , Bennett Nadia R. , McFarlane Shelly , Wilks Rainford J. , Gary-Webb Tiffany L.
Published: February 2025

Introduction

Cardiometabolic outcomes burden Afro-Caribbean populations disproportionately and their relationship with neighborhood socioeconomic status (SES) is unclear. This study explores neighborhood SES and cardiometabolic outcomes in urban Jamaica.

Methods

We analyzed data from 833 participants (women=557, men=276) to examine associations between neighborhood SES, determined by median property sales price, and measured diabetes, hypertension, high cholesterol, and obesity outcomes. We adjusted for covariates using survey-weighted Poisson regression models.

Results

High neighborhood SES was associated with increased prevalence of hypertension (PR=1.33, p=0.044) and high cholesterol (PR=2.46, p<0.001) in fully adjusted models compared with low neighborhood SES. We observed increased obesity for the middle (PR=1.46, p<0.001) and high (PR=1.60, p<0.001) SES tiers and several sex-specific relationships. High neighborhood SES was associated with more obesity among women (P=1.32, p=0.015) and high total cholesterol among men (PR=4.70, p=0.005). Mid SES was associated with increased hypertension among men (PR=2.02, p=0.024).

Conclusion

Associations between neighborhood SES and cardiometabolic outcomes in urban Jamaica appear to be nonlinear and influenced by a combination of sex, individual risk factors, and neighborhood characteristics. These findings challenge some conventional assumptions about the protective effects of higher SES on health and underscore the need for a robust understanding of the complex interplay individual and neighborhood determinants in similar contexts worldwide.
Calpain-mediated sodium channel fragments in the monocentric SpasT-SCI-T trial: Biomarkers for central nervous system injuries and spasticity prediction
Authors: Baucher Guillaume , Liabeuf Sylvie , Brocard Cécile , Ponz Aurélie , Baumstarck Karine , Troude Lucas , Leone Marc , Roche Pierre-Hugues , Brocard Frédéric
Published: February 2025

Spinal cord injury and traumatic brain injury are major causes of long-term disability and are often complicated by spasticity, a motor disorder characterized by increased muscle tone and exaggerated reflexes that significantly impair quality of life. Current diagnostic methods lack the sensitivity needed to accurately predict the severity of injury or the onset and progression of spasticity. Trauma-induced calcium dysregulation activates calpains, a family of proteases that cleave sodium channels, disrupting their inactivation and increasing persistent sodium currents. This cascade drives the overexcitability of motoneurons, contributing to the development of spasticity. Consequently, sodium channel fragments have emerged as promising biomarkers that link injury mechanisms to clinical outcomes. The present SpasT-SCI-T clinical trial protocol aims to evaluate sodium channel fragments as blood biomarkers for assessing the severity of spinal cord and traumatic brain injuries, as well as their potential to predict clinical outcomes, including the development of spasticity. This prospective, multicenter, case-control and cohort study involves 40 participants: 20 individuals with spinal cord injury, 10 individuals with traumatic brain injury, and 10 healthy controls. Blood samples are collected within six hours of injury and at follow-up points over six months. Clinical outcomes, including spasticity (assessed using the Modified Ashworth Scale), neurological recovery (measured by the American Spinal Injury Association Impairment Scale and Glasgow Coma Scale), and quality of life (evaluated using the Short Form-36 Health Survey), are analyzed in correlation with biomarker levels. We anticipate that calpain-mediated sodium channel fragments will transform the management of central nervous system injuries by enabling early diagnosis, improving prognostic accuracy, and guiding personalized therapeutic strategies. The clinical trial is registered on ClinicalTrials.gov (NCT06532760, January 10, 2024), with Assistance Publique–Hôpitaux de Marseille as the sponsor.
Human amyotrophic lateral sclerosis/motor neuron disease: The disease-associated microglial pathway is upregulated and APOE ε2 is protective
Authors: Ashford Bridget A , Simpson Julie E , Dawson Charlotte , Boche Delphine , Cooper-Knock Johnathan , Heath Paul R , Fillingham Daniel , Appleby-Mallinder Charlie , Wei Wenbin , Dunning Mark , Highley J Robin
Published: February 2025

A key role for inflammation in amyotrophic lateral sclerosis/motor neuron disease (ALS/MND) has been identified. It is vital to assess which central nervous system structures are most affected and which inflammatory processes are responsible in humans. The inflammatory transcriptome was characterized in the cervical spinal cord and motor cortex in post mortem frozen and formalin-fixed paraffin embedded specimens from human sporadic ALS/MND and control cases using the nCounter® Neuroinflammation Panel. Archival data were re-analysed and compared with the nCounter data. Immunohistochemistry was used to examine the inflammatory response in the spinal cord, motor cortex, and regions across the brain and validate changes found at during transcriptomic analyses. In the spinal cord, marked inflammation was observed while less inflammation was detected in the motor cortex. Examination of differentially expressed genes in the spinal cord highlightedTREM2,TYROBP,APOE, andCD163as well as phagocytic pathways. In sporadic ALS/MND spinal cord, significant microglial reactivity, and involvement of TREM2, ApoE (encoded byAPOE) and TYROBP was confirmed, suggesting the involvement of the disease-associated microglial (DAM) phenotype. The corticospinal tracts showed greater inflammation than the ventral horns. The precentral gyrus of ALS/MND again showed less immune reactivity to disease when compared to controls. Finally, in the largest cohort assessed to date, we demonstrate an association between theAPOEhaplotype and ALS/MND risk, age of onset and survival. We confirm associations betweenAPOEε4 and a more aggressive disease; and between ε2 and a less severe disease phenotype. We conclude that while there is widespread inflammation in the CNS in sporadic ALS/MND, this is more marked in the spinal cord, especially the corticospinal tract. The specific markers stress the DAM phenotype as having a key role together with a possible influx of somatic macrophages. In addition, APOE function and genotype may be relevant in ALS/MND.
Exploring bed sensor sleep technology: insights from an interdisciplinary team in a geriatric assessment inpatient setting
Authors: Zhao Yong , Acosta Cromwell G. , Ye Yayan , Wong Karen Lok Yi , Lawrence Joanna , Towell Michelle , D’Oyley Heather , Mackay-Dunn Marion , Chow Bryan , Hung Lillian
Published: February 2025

Sleep quality is a critical component of health and recovery for hospitalized older adults, yet current monitoring practices often lack the precision and detail required for effective intervention. This qualitative study aimed to evaluate the feasibility and acceptance of implementing the Sleepsense bed sensor for sleep monitoring in a geriatric inpatient hospital setting. This qualitative study involved interviews with 22 patients and focus groups with 33 interdisciplinary staff members. Data were analyzed using an interpretive description approach, guided by the technology acceptance model and unified theory of acceptance and use of technology, to explore the feasibility and acceptance of Sleepsense bed sensors in a geriatric inpatient setting. Key findings from thematic analysis emerged in three main themes representing the feasibility and acceptance of Sleepsense bed sensors among hospitalized older adults: user acceptance, integration with somnolog into clinical practice, and implementation barriers and practical challenges. Staff reported high acceptance of Sleepsense technology due to its nonintrusiveness and ability to reduce disruptive nighttime checks. However, challenges such as the need for consent, data interpretation and occasional inaccuracies were also identified. Integrating Sleepsense with existing care practices was recommended to enhance patient care while maintaining staff confidence. These findings underscore the potential of advanced sleep monitoring technologies in subacute care settings and highlight the importance of addressing implementation barriers for effective adoption.
The physio-affective symptoms of Long COVID are strongly predicted by the severity of the acute infectious phase, and lowered antioxidants, nitric oxide, and alanine transaminase levels.
Authors: Maes Michael , Tunvirachaisakul Chavit , Semeao Laura de Oliveira , Michelin Ana Paula , Matsumoto Andressa K. , Brinholi Francis F. , Barbosa Decio S. , Zhang Yingqian , Sodsai Pimpayao , Hirankarn Nattiya , Almulla Abbas F.
Published: February 2025

Aims: This study investigated a) whether the affective, chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME), respiratory, and neurological Long COVID (LC) symptom domains are intercorrelated manifestations of an underlying construct, namely the LC phenome; and b) the predictive effects of clinical symptoms and biomarkers of the COVID-19 infectious phase on LC. Methods: This cohort study included 71 LC patients who had suffered from COVID-19 six months prior. The patients complied with the LC disease criteria set forth by the World Health Organization (WHO). We used the WHO symptom list to score the LC symptoms and assessed SARS-CoV-2 positivity using real-time reverse transcription-polymerase chain reaction (RT-PCR), white blood cell counts, anion gap, alanine transaminase (ALT) levels, paraoxonase 1 (PON1) activity and genotypes, total radical trapping potential of plasma (TRAP), and nitric oxide metabolites (NOx). Results: All four clinical LC subdomains are significantly intercorrelated, allowing for the extraction of a single latent construct encompassing affective, CFS/ME, respiratory, and neurological symptoms, labeled the physio-affective phenome of LC. The latter was strongly predicted by dyspnea and productive sputum, RT-PCR SARS-CoV-2 cycle threshold values, lower anion gap, and increased neutrophil percentage during the infectious phase. Other predictive biomarkers were lower ALT, TRAP, and NOx levels, and the PON1 QR192 over dominant gene model (protective). Conclusions: LC may be a clinically homogeneous disease characterized by highly intercorrelated affective, CFS, neurological, and respiratory subdomains. The physio-affective phenome and its domains are strongly predicted by biomarkers of acute infection and associated inflammation and oxidative stress.
Dynamic dysregulation of Tenascin-X/Tenascin-C balance controlled by Transforming Growth Factor-β leads to tumor cell proliferation during pancreatic carcinogenesis
Authors: Liot Sophie , Schmitter Céline , Mercier-Gouy Perrine , Kholti Naïma El , Balas Jonathan , Prigent Laura , Aubert Alexandre , Lethias Claire , Chitty Jessica L. , Koch Manuel , Fenouil Tanguy , Cox Thomas R. , Hennino Ana , Hervieu Valérie , Ricard-Blum Sylvie , Valcourt Ulrich , Lambert Elise
Published: February 2025

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers due to late diagnosis and poor therapeutic efficiency. Throughout PDAC progression, a dense extracellular matrix (ECM) is deposited around neoplastic cells and accompanies tumor development and aggressiveness. This significant stroma, both in terms of quantity and through its impact on tumor cells, is now considered as a target for innovative therapies to improve patient survival. Among ECM proteins, Tenascins (TNs) are a family of four glycoproteins (TNC, TNW, TNR and TNX) sharing a common modular structure, but exhibiting different expression patterns and functions depending on the physiological and physio-pathological contexts. In PDAC, TNC is up-regulated and is considered as a pro-tumorigenic actor, whereas TNX’s role remains to be elucidated. Herein, we demonstrated that unlike TNC, TNX is drastically decreased in PDAC, and that this loss is correlated with reduced patient survival. Dysregulation of the TNX/TNC balance is attributable to Transforming Growth Factor-beta (TGF-β) upregulation during pancreatic carcinogenesis. Interestingly, we found that TNX is first highly deposited in low grade lesions before being clearly decreased in later stages suggesting an elaborate stromal remodelling during PDAC development. Finally, low TNX and high TNC deposition around precursor lesions are correlated with increased preneoplastic cell proliferation. Altogether, our results (i) demonstrate the importance of Tenascin ratios during pancreatic carcinogenesis, (ii) suggest an anti-proliferative role for TNX unlike its pro-tumoral counterpart, TNC and (iii) underscore TNX and TNC as valuable targets for the development of new drugs for pancreatic cancer and/or solid tumor treatment.

Statement of significance

The tumor microenvironment plays a prominent but contradictory role in pancreatic cancer. Our study highlights the role of a TGF-β-controlled TNX/TNC balance and designates TNX as an inhibitor of tumor cell proliferation.
Robustness of high-throughput prediction of leaf ecophysiological traits using near infra-red spectroscopy and poro-fluorometry
Authors: Coindre Eva , Boulord Romain , Chir Laurine , Freitas Virgilio , Ryckewaert Maxime , Laisné Thomas , Bouckenooghe Virginie , Lis Maëlle , Cabrera-Bosquet Llorenç , Doligez Agnès , Simonneau Thierry , Pallas Benoît , Coupel-Ledru Aude , Segura Vincent
Published: February 2025

Background

Water resource is a major limiting factor impacted by climate change that threatens crop production and quality. Understanding the ecophysiological mechanisms involved in the response to water deficit is crucial to select new varieties more drought tolerant. A major bottleneck hampering such advances is the lack of methods for measuring ecophysiological traits on large populations of individuals. We investigated the relevance of spectroscopy and poro-fluorometry with related high-throughput measurement devices to predict leaf morphological and ecophysiological traits using partial least square regression (PLSR) models. This work relies on a grapevine diversity panel grown in pots under contrasted conditions, outdoors under well watered conditions and in a greenhouse with three different soil water treatments. We took advantage of these experimental designs to specifically assess the robustness of predictive models.

Results

Some complementarity between measuring devices were found, with spectrometers being able to predict leaf mass per area, water content and water quantity (R²>0.58), while the poro-fluorometer could predict net CO2assimilation (R²>0.72), regardless of the water treatment. The prediction of leaf mass per area appeared to be quite robust between outdoors and greenhouse experiments. The prediction of water use efficiency was highly dependent on the water treatment, with much better predictions under moderate (R²>0.73) than severe water deficit. We then used the high-throughput devices alone to measure the whole grapevine panel, by applying calibration models to predict ecophysiological traits and estimated their broad sense heritability. Leaf mass per area was also directly determined on the entire diversity panel and its heritability was similar whether calculated on observed or predicted values. The highest computed heritabilities for these traits reached values close to 0.5.

Conclusions

This study showed that spectrometers and poro-fluorometer could be reliable nondestructive tools for the high-throughput phenotyping of ecophysiological traits on thousands of plants, paving the way for studying the genetic determinism of such traits.
Polarity reversal of stable microtubules during neuronal development
Authors: Iwanski Malina K. , Serweta Albert K. , Verwei H. Noor , Donders Bronte C. , Kapitein Lukas C.
Published: February 2025

Neurons critically depend on long-distance transport orchestrated by motor proteins walking over their highly asymmetric microtubule cytoskeleton. These microtubules are organized uniformly in axons with their plus-end pointing away from the soma. In contrast, in the dendrites of vertebrate neurons, microtubules are of mixed polarity, but organized into bundles of uniform polarity with stable, long-lived microtubules preferentially oriented minus-end-out and dynamic microtubules oriented plus-end-out. This organization is thought to be essential for guiding selective transport into dendrites, yet how this organization is established is unclear. Here we use a combination of single molecule localization microscopy, expansion microscopy, and live-cell imaging to examine how the microtubule cytoskeleton is reorganized during neuronal development of cultured rat hippocampal neurons. We find that, while the youngest neurites contain microtubules of mixed polarity, stable microtubules are initially preferentially oriented plus-end-out. At this stage of development many stable microtubules are connected to the centrioles, providing an explanation for their plus-end out orientation in emerging neurites. In later stages, these microtubules are released from the centrioles and reorient by sliding between or within neurites to become progressively more minus-end-out. Moreover, prior to axon specification, we commonly observed already one or two minor neurites with an almost uniformly plus-end-out microtubule network, indicative of transient polarization. Together, our findings reveal how stable microtubules are reorganized to help establish the stereotypical microtubule networks seen in the axon and dendrites of mature vertebrate neurons.
Pleomorphic effects of three small-molecule inhibitors on transcription elongation byMycobacterium tuberculosisRNA polymerase
Authors: Herrera-Asmat Omar , Tong Alexander B. , Lin Wenxia , Kong Tiantian , Del Valle Juan R , Guerra Daniel G. , Ebright Yon W. , Ebright Richard H. , Bustamante Carlos
Published: February 2025

TheMycobacterium tuberculosisRNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N(α)-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared toEscherichia coliRNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizesE. colipause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.
Diversity, abundance, and biogeography of CO2fixing microorganisms in peatlands
Authors: Le Geay Marie , Mayers Kyle , Sytiuk Anna , Dorrepaal Ellen , Küttim Martin , Lamentowicz Mariusz , Tuittila Eeva-Stiina , Lauga Béatrice , Jassey Vincent E.J.
Published: February 2025

Microbial communities play a crucial role in the carbon (C) dynamic of peatlands— a major terrestrial C reservoir. While heterotrophic microorganisms attracted much attention over the past decades due to their role in peatland greenhouse gases emissions, CO2fixing microorganisms (CFMs) remained particularly overlooked. Here, by leveraging metabarcoding and digital droplet PCR (ddPCR), we provide a comprehensive survey of CFM communities, including oxygenic phototrophs, chemoautotrophs and aerobic anoxygenic phototrophic bacteria (AAnPBs), in different peatland types. We demonstrate that CFMs are very abundant and diverse in peatlands, with on average 1021 CFMs contributing up to 40% of the total bacterial abundance. In particular, we show that oxygenic phototrophs (mostly Cyanophyceae and Palmophylloceae) are the most abundant CFMs, closely followed by chemoautotrophs (Proteobacteria) and AAnPBs (Vulcanimicrobiia). Using a joint-species distribution model, we further find that CFMs aggregate into six major clusters with different niche size. These clusters constitute the core and specific CFM microbiome. The core microbiome, which the occurrence is strongly influenced by temperature and nutrients, directly modulate the diversity and abundance of CFMs. Our findings highlight the importance of CFM diversity and abundance in peatlands, further reveal their complex structuration in link with environmental conditions and suggest that changes in environmental conditions could shift CFMs communities. These results are the foundation to better understand the role of CFMs for the peatland C cycle inputs.
Multi-protein silencing using WRAP-based nanoparticles: a proof of concept
Authors: Konate Karidia , Pezzati Irène , Redjatti Karima , Agnel Estelle , Vivès Eric , Faure Sandrine , de Santa Barbara Pascal , Boisguérin Prisca , Deshayes Sébastien
Published: February 2025

Cancer remains the leading cause of death, with chemotherapy, radiotherapy, and surgical resection being the primary treatment methods. However, chemotherapy’s side effects, surgical limitations, and drug resistance present significant challenges. Small interfering RNA (siRNA) has emerged as a promising tool in cancer therapy due to its ability to silence disease-related genes selectively. Recent advancements in non-viral delivery systems, particularly cell-penetrating peptides (CPPs), have enhanced the efficacy of siRNA delivery. The use of siRNA as a therapeutic tool in cancer treatment has been reported. However, silencing only one target protein has only minor effects on tumor cell proliferation as previously shown for WRAP-based nanoparticles targeting cyclin-dependent kinase 4 (CDK4) in human glioblastoma cells. Here, we designed a more sophisticated approach to enhance therapeutic efficacy, encapsulating multiple siRNAs targeting CDK4, cyclin D1 (CD1), and Mcl-1 proteins. The siRNA cocktail, delivered via WRAP5 nanoparticles, effectively silenced these targets and reduced cell proliferation in human glioblastoma cells. Furthermore, the nanoparticles also demonstrated potential therapeutic impact in gastrointestinal stromal tumors (GIST), a rare cancer characterized by its tendency to resist standard treatments. This study highlights the versatility of WRAP5 nanoparticles as a platform for personalized cancer therapy, suggesting that siRNA delivery systems may be tailored to specific cancer types for more effective treatment strategies.
Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide15N(1H) NMR Relaxation
Authors: Lesovoy Dmitry , Roshchin Konstantin , Sala Benedetta Maria , Sandalova Tatyana , Achour Adnane , Agback Tatiana , Orekhov Vladislav , Agback Peter
Published: February 2025

Conformational heterogeneity is critical for protein function, but the validation of dynamic ensembles remains a challenge. In this study, we introduced an approach that integrates free MD simulations, using an AlphaFold-generated structure as the starting point, with experimental relaxation data to identify biologically relevant conformational ensembles. For the extracellular region ofStreptococcus pneumoniaePsrSp, we found that only certain segments of the MD long trajectory aligned well with experimental data. The defined ensembles revealed two regions with increased flexibility that play important functional roles.
Cryo-correlative light and electron tomography of dopaminergic axonal varicosities reveals non-synaptic modulation of cortico-striatal synapses
Authors: Lapios Paul , Anger Robin , Paget-Blanc Vincent , Marza Esther , Lučić Vladan , Fronzes Rémi , Herzog Etienne , Perrais David
Published: February 2025

Dopamine is an essential brain neuromodulator involved in reward and motor control. Dopaminergic (DA) neurons project to most brain areas, with particularly dense innervation in the striatum. DA varicosities bind to target striatal synapses and form dopamine hub synapses (DHS). However, the basic features of dopamine release sites are still largely unknown. Here we studied the ultrastructure of fluorescent DA and glutamatergic (GLU) synaptosomes isolated from the striatum of adult mice with cryo-correlative light and electron microscopy and cryo-electron tomography. We observed that DA synaptosomes display ∼10 times fewer vesicles than GLU ones. DA vesicles are bigger and less round. Vesicle organization at single nanometer scale indicates that most GLU synaptosomes have tethered and primed vesicles, indicative of a readily releasable pool, while only 39 % of DA synaptosomes have tethered vesicles, which appear not to be primed. In addition, GLU terminals contacted by DA terminals in DHS have more primed vesicles than others. While DA varicosities do not form genuine synapses, their adhesion to cortico-striatal synapses may convey a local regulation of synaptic release properties.
Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline
Authors: Hu Ming , Wan Penglong , Chen Chengjie , Tang Shuyuan , Chen Jiahao , Wang Liang , Chakraborty Mahul , Zhou Yongfeng , Chen Jinfeng , Gaut Brandon S. , Emerson J.J. , Yi Liao
Published: February 2025

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specifi c aligners or optimized for specifi c organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF fi les. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specifi c LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.
Navigational Frames of Reference as Critical Regulators of Hippocampal Interneuron Coding Properties
Authors: Bott Jean-Bastien , Penazzi Lorene , Al-Achkar Salodin , Cho Minyoung , Rivard Bruno , Lafreniere Etienne Gautier , Williams Sylvain
Published: February 2025

Efficient spatial navigation relies on the hippocampus integrating local (proximal) and global (distal) cues, collectively called frames of reference, to guide behavior and support memory. Although these cues control the anchoring of principal cell fields, how these frames tune interneuron functions remains unknown. Traditionally, interneurons such as O-LM and VIP cells have been viewed primarily as speed encoders, although some also encode spatial information or respond to discrete stimuli. Using calcium imaging in freely behaving mice performing a new spatial learning task that differentiates between reference frames, we demonstrate that O-LM cells displayed a striking bimodal activity pattern, altering both their speed and spatial encoding properties. In contrast, VIP interneurons were largely unaffected by changes in the frame of reference, instead correlating with familiarization. Notably, linear decoding using speed scores revealed that only O-LM interneurons provide an accurate readout of the dominant reference frame, enabling prediction of the animal’s navigation strategy. These findings highlight that hippocampal interneurons can flexibly adapt their functions depending on cognitive factors such as the reference frames used to guide behavior.
FG-Nup Sequence Length Polydispersity Enhances Selectivity of NPC Translocation
Authors: Patel Manoj K , Panwar Ajay S
Published: February 2025

The central channel of the nuclear pore complex (NPC) exhibits polydispersity in FG-nucleoporin (FG-Nup) sequence length, with longer FG-Nups on the periphery and shorter FG-Nups in the interior of the pore. The functional role of FG-Nup polydispersity in NPC transport was investigated using a minimal, coarse-grained model and Langevin dynamics simulations. The NPC was modelled as a cylindrical pore lined with a random copolymer brush composed of hydrophobic and hydrophilic segments, mimicking FG-Nups. The total number of hydrophobic segments corresponded to the fraction of FG-repeats,f, in the FG-Nups. The translocation of karyopherin-bound spherical cargo (12 nm spherical tracers) was simulated through two model NPCs; a homogeneous NPC (h-NPC) with uniform FG-Nup lengths and an inhomogeneous NPC (ih-NPC) featuring shorter FG-Nups in the middle and longer FG-Nups at the periphery. Theih-NPC demonstrated enhanced selectivity and significantly higher passage probabilities for karyopherin-bound tracers, with an increase of up to 90% compared toh-NPC. Analysis of binding contacts between tracers and FG-Nup hydrophobic segments revealed that tracer translocation was facilitated by a handover process between successive FG-Nups along the NPC length. The enhanced selectivity of theih-NPC was attributed to an increase in binding contacts of the tracer with the shorter FG-Nups in its middle region. These findings provide a biophysical basis for the evolutionary significance of FG-Nup polydispersity in selective NPC transport.
Experimental insights on the behaviour and development of Near Eastern Fire salamanders (Salamandra infraimmaculata) indicate general strategies to cope with aquatic predators
Authors: Reinhardt Timm , Küpfer Eliane , Segev Ori , Blaustein Leon , Tobias Krause E. , Steinfartz Sebastian
Published: February 2025

Fishes are key predators of amphibian larvae with often devastating consequences for their abundance and survival.In Israel, the Near Eastern Fire salamander (Salamandra infraimmaculata) reaches the southern limit of the geographic distribution of the whole genusand has tocope with xeric terrestrial habitats- and a scarcity of suitable sites for the deposition of larvaewith permanentsprings and streams arebeingrare. One such location is the Tel Dan National Park in the North of Israel, were, surprisingly salamander larvae and fishes coexist successfully in a system of larger and smaller streams. In three experiments we tested different anti-predator behaviour with salamanders from Tel Dan and other locations. We analysedwhether gravid females avoid the presence of fish when depositing their larvae; if the presence of fish impacts larval development and if salamander larvae show active hiding behaviour when confronted with fish cues. While females from Tel Dan showed a bet-hedging strategy in site selection irrespective of fish presence, larval developmental rate was reduced in the presence of fish probably due to a lower feeding activity. Lastly, larvae from different sites displayed hiding behaviour in the presence of fish, irrespective whether they naturally coexist with fish or not. We infer from our results and existing studies thatS. infraimmaculatahas general rather than site-specific adaptations to cope with the presence of fish. We conclude that the general adaptations are essential to sustain this species in a range of extreme habitats at the southern limit of the s distribution.