bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil Carbon Sequestration inNothofagus obliquaForests with Different Canopy Cover Levels under Silvopastoral Management
Authors: Ramos Camila , Zagal Erick , Timmusk Salme , Dube Francis , Paulino Leandro , Ortiz Juan , Intriago Jean , Fuentes Juan Pablo
Published: January 2025

Agroforestry contributes to slowing deforestation, favouring ecosystem regeneration and improving land use sustainability. In this study, we evaluated the effect of agroforestry on the recovery of degraded soils in a native forest and its capacity to capture and stabilize carbon (C) and nitrogen (N) in the soil. We conducted the study in a native forest ofNothofagus obliqua(oak) located in Ranchillo Alto (37°04′52″ S, 71°39′14″ W), in the Ñuble region, Chile. This site includes three silvopastoral systems with different levels of forest degradation: open (Op), semi- open (SOp) and semi-closed (SC), together with a control treatment without silvopastoral treatment (Ctr). The analysis was conducted at four soil depths (0-10, 10-20, 20-30 and 30-60 cm). To evaluate carbon and nitrogen sequestration and fixation in relation to the different forest cover treatments, we performed chemical, physical and biological soil analyses. We also included a physical fractionation by particle size to separate soil organic matter (SOM) into meaningful fractions with different characteristics and dynamics: particulate organic matter (POM) and organic matter associated with the mineral matrix (MAOM). Our results indicated that Op, despite being the most degraded condition, showed the highest values of C, N and non- oxidizable carbon (Cnox). This condition could be associated with the history of potato burning in this sector, which generates stable pyrogenic carbon in the soil. Analyses of C and N, as well as Cnox in the MAOM fraction, and C stock revealed that the three silvopastoral systems showed higher values than the control treatment without silvopastoral treatment. This suggests that the adoption of silvopastoral practices can improve soil quality and contribute to long-term carbon sequestration. These results support the application of sustainable practices to mitigate soil degradation and enhance carbon sequestration in degraded ecosystems.
Assessment of developmental neurotoxicology-associated alterations in neuronal architecture and function usingCaenorhabditis elegans
Authors: Huayta Javier , Seay Sarah , Laster Joseph , Rivera Nelson A. , Joyce Abigail S. , Ferguson P. Lee , Hsu-Kim Heileen , Meyer Joel N.
Published: January 2025

Few of the many chemicals that regulatory agencies are charged with assessing for risk have been carefully tested for developmental neurotoxicity (DNT). To speed up testing efforts, as well as to reduce the use of vertebrate animals, great effort is being devoted to alternate laboratory models for testing DNT. A major mechanism of DNT is altered neuronal architecture resulting from chemical exposure during neurodevelopment.Caenorhabditis elegansis a nematode that has been extensively studied by neurobiologists and developmental biologists, and to a lesser extent by neurotoxicologists. The developmental trajectory of the nervous system inC. elegansis easily visualized, normally entirely invariant, and fully mapped. Therefore, we hypothesized thatC. eleganscould be a powerfulin vivomodel to test chemicals for the potential to alter developmental patterning of neuronal architecture. To test whether this might be true, we developed a novelC. elegansDNT testing paradigm that includes exposure throughout development, examines all major neurotransmitter neuronal types for architectural alterations, and tests behaviors specific to dopaminergic, cholinergic, and glutamatergic functions. We used this paradigm to characterize the effects of early-life exposures to the developmental neurotoxicants lead, cadmium, and benzo(a)pyrene (BaP) on dopaminergic, cholinergic, and glutamatergic architecture. We also assessed whether exposures would alter neuronal specification as assessed by expression of reporter genes diagnostic of specific neurotransmitters. We identified no cases in which the apparent neurotransmitter type of the neurons we examined changed, but many in which neuronal morphology was altered. We also found that neuron-specific behaviors were altered duringC. elegansmid-adulthood for populations with measured morphological neurodegeneration in earlier stages. The functional changes were consistent with the morphological changes we observed in terms of type of neuron affected. We identified changes consistent with those reported in the mammalian DNT literature, strengthening the case forC. elegansas a DNT model, and made novel observations that should be followed up in future studies.
Debiasing Sinkhorn divergence in optimal transport of cellular dynamics
Authors: Cooper Jayshawn , Young Christina , Lee Pilhwa
Published: January 2025

Single-cell RNA-seq analysis characterizes developmental mechanisms of cellular differentiation, lineage determination, and reprogramming with differential conditioning of the microenvironment. In this article, the underlying dynamics are formulated via optimal transport with algorithms that calculate the transition probability of the state of cell dynamics over time. The algorithmic biases of optimal transport (OT) due to entropic regularization are balanced by Sinkhorn divergence, which normally de-biases the regularized transport by centering them. In the case of reprogramming mouse embryonic fibroblasts [1] with dense time points, Sinkhorn divergence is shown to improve the trajectories of targeted cell fates depending on the specific cell types. When the time points are filtered out with sparser 9 and 5 time points, some cell phenotypes show better outcomes from strong entropic regularization. For 9 time points with 2 days interval, Sinkhorn divergence shows a clear advantage with broad bandwith of optimal entropic regularization. For these derived time points, when the cell population is scaled down fromn= 8000ton= 2000, there comes no benefit from Sinkhorn divergence for some specific cell types. In the case of stratifying morphogenesis of the epidermis [2], the sparsity of time points makes it not significant to prescribe Sinkhorn divergence in the accuracy of transporting to the expected cell fates. Overall, whether to prescribe Sinkhorn divergence for the accurate prediction of lineages of single cells depends on temporal sparsity.
Non-canonical activation of PAR1 induces autophagy in mammalian breast cancer cells
Authors: Saha Saibal , Kumar Rishikesh , Sarangi Snehanjan , Tapader Rima , Ray Tanusree , Gope Animesh , Nag Niraj , Pal Ananda , Pal Amit
Published: January 2025

The question of whether autophagy is a boon or a bane for the body does not lend itself to a straightforward answer, as its consequences are intricately tied to the pathophysiological context that triggers its activation. The intricate nature of autophagy’s effects on the body, compounded by its multifaceted regulation through various upstream signaling pathways, warrants a deeper and more nuanced research. This study delves into the regulation of autophagy through the non-canonical activation of protease activated receptor 1 (hereafter, termed as PAR1) by Hemagglutinin protease (hereafter, referred as HAP). In contrast to the canonical activation of PAR1 by thrombin, which promotes cell proliferation via the upregulation of mTOR signaling, HAP-induced, non-canonical activation of PAR1 triggers autophagy by downregulating mTOR activation and modulating subsequent key signaling pathways in mammalian breast cancer cells. This non-canonical activation results in the generation of a new N-terminal sequence of PAR1. Moreover, synthetic peptide designed to replicate this newly generated N-terminal sequence effectively triggers autophagy in mammalian breast cancer cells, thereby establishing that induction of autophagy via non-canonical PAR1 activation is independent of the activating agent of PAR1 itself. The study also explores the implications of peptide-induced autophagy in the context of early-stage, low-grade breast cancer using a BALB/c mouse model, demonstrating substantial inhibition of tumor growth and a delay in carcinogenesis progression. Importantly, the absence of notable PAR1 expression in normal, healthy cells ensures that they remain unaffected by the peptide, positioning it as a promising candidate for targeted therapy in low-grade breast cancer.
Skeletal muscle mitochondria contain nuclear-encoded RNA species prior to and following adaptation to exercise training in rats
Authors: Silver Jessica L. , Lamon Séverine , Loke Stella , Mazzarino Gisella , Croft Larry , Ziemann Mark , Wadley Glenn. D. , Trewin Adam J.
Published: January 2025

Skeletal muscle mitochondria adaptation to exercise training is mediated by molecular factors that are not fully understood. Mitochondria import over 1000 proteins encoded by the nuclear genome, but the RNA population resident within the organelle is generally thought to be exclusively encoded by the mitochondrial genome. However, recentin vitroevidence suggests that specific nuclear-encoded miRNAs and other non-coding RNAs (ncRNAs) can reside within the mitochondrial matrix. Whether these are present in mitochondria of skeletal muscle tissue, and if this affected by endurance training - a potent metabolic stimulus for mitochondrial adaptation - remains unknown. Rats underwent four weeks of moderate intensity treadmill exercise training, then humanely killed and tissues collected for molecular profiling. Mitochondria from gastrocnemius skeletal muscle were isolated by immunoprecipitation, further purified, then the resident RNA was sequenced to assess the mitochondrial transcriptome. Exercise training elicited typical transcriptomic responses and functional adaptations in skeletal muscle, including increased mitochondrial respiratory capacity. We identified 24 nuclear-encoded, coding or non-coding RNAs in purified mitochondria, in addition to 50 nuclear-encoded miRNAs that met a specified abundance threshold. Although none were differentially expressed in the exercise vs control group at FDR<0.05, exploratory analyses suggested that the abundance of 3 miRNAs were altered (p<0.05) in mitochondria isolated from trained compared with sedentary skeletal muscle. We report the presence of a specific population of nuclear-encoded RNAs in the mitochondria isolated from rat skeletal muscle tissue, which could play a role in regulating exercise adaptations and mitochondrial biology.

KEY POINTS

Mitochondria are a central metabolic and signalling hub, particularly in tissues with high energy demand such as skeletal muscle. Their ability to adapt to stimuli such as exercise training is directly related to improved metabolic health. Understanding the factors that regulate these adaptive processes is therefore essential.

Mitochondria contain RNA encoded by their own genome (mtDNA); typically are not thought to contain nuclear-encoded RNA.

Here, we report that mitochondria from rat skeletal muscle do indeed contain a select population of nuclear-encoded protein coding and non-coding RNAs, including 3 microRNAs whose expression tended to be altered by exercise training.

These findings suggest that mitochondria-localised nuclear-encoded RNAs may play a role in mediating beneficial adaptive responses to exercise.
Initiation of primary T cell—B cell interactions and extrafollicular antibody responses in an organized microphysiological model of the human lymph node
Authors: Zatorski Jonathan M. , Raskovic Djuro , Arneja Abhinav , Kiridena Saweetha , Ozulumba Tochukwu , Hammel Jennifer H. , Anbaei Parastoo , Ortiz-Cárdenas Jennifer E. , Braciale Thomas J. , Munson Jennifer M. , Luckey Chance John , Pompano Rebecca R.
Published: January 2025

Antibody production is central to protection against new pathogens and cancers, as well as to certain forms of autoimmunity. Antibodies often originate in the lymph node (LN), specifically at the extrafollicular border of B cell follicles, where T and B lymphocytes physically interact to drive B cell maturation into antibody-secreting plasmablasts. In vitro models of this process are sorely needed to predict aspects of the human immune response. Microphysiological systems (MPSs) offer the opportunity to approximate the lymphoid environment, but so far have focused primarily on memory recall responses to antigens previously encountered by donor cells. To date, no 3D culture system has replicated the engagement between T cells and B cells (T—B interaction) that leads to antibody production when starting with naïve cells. Here, we developed a LN-MPS to model early T—B interactions at the extrafollicular border built from primary, naïve human lymphocytes encapsulated within a collagen-based 3D matrix. Within the MPS, naïve T cells exhibited CCL21-dependent chemotaxis and chemokinesis as predicted. Naïve T and B cells were successfully skewed on chip to an early T follicular helper (pre-Tfh) and activated state, respectively, and co-culture of the latter cells led to CD38+ plasmablast cells and T cell dependent production of IgM. These responses required differentiation of the T cells into pre-Tfhs, physical cell-cell contact, and were sensitive to the ratio at which pre-Tfh and activated B cells were seeded on-chip. Dependence on T cell engagement was greatest at a 1:5 T:B ratio, while cell proliferation and CD38+ signal was greatest at a 1:1 T:B ratio. Furthermore, plasmablast formation was established starting from naïve T and B cells on-chip. We envision that this MPS model of primary lymphocyte physiology will enable new mechanistic analyses of human humoral immunity in vitro.
Stable, Easy-to-Handle, Fully Autologous Electrospun Polymer-Peptide Skin Equivalent for Severe Burn Injuries
Authors: Cohen-Gerassi Dana , BenShoshan Marina , Liiani Adi , Reuveni Tomer , Loboda Offir , Haratz Moti , Haik Josef , Binderman Itzhak , Shacham-Diamand Yosi , Sitt Amit , Segni Ayelet Di , Adler-Abramovich Lihi
Published: January 2025

Severe burn injuries represent a significant clinical challenge due to their complex healing process and the high risk of complications, including infection, scarring, and contracture formation. Current therapeutic approaches for burn wound treatment include autologous donor-site grafting and advanced cell therapy techniques like cultured epidermal autografts (CEA), which successfully facilitate wound closure through re-epithelialization. However, CEAs are limited by fragility, shrinkage, lack of a dermal layer, and risks of contamination. Here, aiming to overcome these limitations, we developed a personalized skin equivalent featuring an engineered scaffold composed of electrospun polycaprolactone (PCL) functionalized with the bioactive peptide fluorenylmethyloxycarbonyl-phenylalanine-arginine-glycine-aspartic acid (Fmoc-FRGD). This scaffold is designed to mimic the natural extracellular matrix (ECM), promoting cellular adhesion, integration, and proliferation while maintaining structural integrity.In-vitroanalysis demonstrated the scaffold’s ability to support multi-layered human skin cell growth, whilein-vivoexperiments confirmed its efficacy in facilitating wound closure and full-thickness skin regeneration in a murine model. This bioengineered skin equivalent is mechanically robust, easy to handle, fully autologous and exhibits no contraction, offering a transformative therapeutic alternative for the treatment of severe burn injuries.
Exploring the visual system of the black Grouse (Lyrurus tetrix): Combining experimental and molecular approaches to inform strategies for reducing collisions
Authors: Potier Simon , Lassance Jean-Marc , Blary Constance , Coulombier Justine , Berthillot Sandrine , Dos Santos Virginie , Andraud Christine , Liénard Marjorie A.
Published: January 2025

Understanding the visual systems of birds can inform conservation efforts and mitigate anthropogenic threats, such as collisions with man-made structures. This study investigates the visual abilities of the black grouse (Lyrurus tetrix), a European mountain bird highly vulnerable to collisions. Using an integrative approach, we assessed key visual components including visual field configuration, spatial resolution, contrast sensitivity, and spectral sensitivity. Behavioral assays revealed that black grouse have an extensive visual field with a wide binocular overlap and minimal blind spots, allowing for efficient predator detection and foraging. However, their spatial resolution and contrast sensitivity are relatively low, consistent with other prey species. Molecular analyses identified four cone opsins (SWS1, SWS2, Rh2, and LW) with spectral sensitivities spanning ultraviolet to long wavelengths (393–546 nm). These findings highlight the black grouse’s ability to detect UV light. Our results emphasize the need for collision mitigation measures tailored to species-specific visual abilities, including diverters designed with enhanced reflectance and increased visibility. This study advances our understanding of avian vision and provides critical insights to guide conservation strategies for reducing bird collisions in alpine habitats.
Characterizing Gene Regulatory Network Ensembles in Kidney Injury and Repair
Authors: Tannenbaum Eitan , Markiewitz Dana , Kalisky Tomer , Kugler Hillel
Published: January 2025

The inference of gene regulatory networks (GRNs) from single-cell RNAseq data allows for mechanistic characterization of the different cell states and their dynamics in complex biological processes. While numerous algorithms have been proposed to infer GRNs from single-cell transcriptomic data, multiple network solutions may explain the same dataset, posing a challenge for biologically meaningful interpretation. Here, we use the Reasoning Engine for Interaction Networks (RE:IN), a computational tool based on formal reasoning, to characterize GRN ensembles in the context of acute kidney injury (AKI). To this end, we applied RE:IN to a single-cell RNAseq dataset from a mouse ischemiareperfusion injury (IRI) model, focusing on distinct proximal tubule cell states related to kidney injury and repair. We first created an Abstract Boolean Net-work (ABN) model for the kidney using RE:IN and synthesized an ensemble of consistent network solutions. Then, we visualized the ensemble in latent space using Principal Components Analysis (PCA) and discovered four distinct GRN families compatible with the input gene expression and regulatory constraints. Finally, we identified two specific network substructures that discern between the four different network families. This study provides a methodology for characterizing and interpreting GRN heterogeneity in complex processes such as tissue development, disease, and repair.
Make it grow,Pseudozyma aphidisextract promotes plant growth
Authors: Fennec Anton , Rotem Neta , Levy Maggie
Published: January 2025

Increasing global population demands higher agricultural yield while avoiding the use of harmful products in agriculture. The use of beneficial micro-organisms is an Eco-friendly approach to reduce the use of fertilizers and plant growth promoting (PGP) products. This study is focused on the fungusPseudozyma aphidis (P. aphidis), a yeast like dimorphic fungus beneficial to plants and related to the phytopathogenic fungusUstilago maydisthat causes corn smut disease. Our lab isolated a uniqueP. aphidisstrain (PA12) that has shown significant plant protection and plant growth activity. We extracted and screened the active PGP fraction from PA12, calibrated treatment dosage and application method. Tomato, corn and melon plants treated with PA12 extract exhibited; increased germination, shoot length, biomass and higher yield. Our results demonstrate the potential ofP. aphidisextract application as an eco-friendly PGP agent that can contribute to reduction of harmful agricultural products usage.
Effects of increasing hydrostatic pressures on marine microbial enzymatic activities
Authors: Balmonte John Paul , Arnosti Carol , Bartlett Douglas H. , Caddell Stephanie , Glud Ronnie N.
Published: January 2025

High hydrostatic pressure is characteristic of the deep ocean and presumed to influence microbial functions and viability. However, marine microbial processes are typically measured only at atmospheric pressure (0.1 MPa), limiting our understanding of pressure effects on the activities of microbes that sink as part of the biological carbon pump as well as those that reside in the deep ocean. To test pressure effects on microbial functions, we measured extracellular enzymatic activities—the first step in organic matter remineralization—of a moderate piezophile (Photobacterium profundum SS9), as well as of microbial communities in waters and sediments from shallow to abyssal (5,500 m) depths and their cell-free enzymes (<0.2 µm). Activities were measured at 0.1-100 MPa to assess the pressure effects across the nearly full range of oceanic depths.P. profundumSS9 enzymes show varying pressure effects, from considerable stimulation at optimal pressure (28 MPa) to near complete inhibition (100 MPa). Pressure effects were measured for diverse protein- and carbohydrate-degrading and phosphorus-acquiring enzymes among pelagic and benthic microbial communities. The most common pressure effect is partial activity reduction, indicating a dampening of the initial step of carbon remineralization at increasing pressures. However, retention of cell-free enzymatic activities at higher pressures was occasionally observed even for enzymes from surface-originating assemblages, indicating functionality down to hadal depths and their potential for piezotolerance. These variable pressure effects must be considered when quantifying degradation rates of sinking and deposited particulate matter at increasing pressures in the deep ocean.
Global extent and change in human modification of terrestrial ecosystems from 1990 to 2022
Authors: Theobald David M. , Oakleaf James R. , Moncrieff Glenn , Voigt Maria , Kiesecker Joe , Kennedy Christina M.
Published: January 2025

Habitat loss and degradation associated with industrial development is the primary threat and dominant driver of biodiversity loss globally. Spatially-explicit datasets that estimate human pressures are essential to understand the extent and rate of anthropogenic impacts on ecosystems and are critical to inform conservation commitments and efforts under the Global Biodiversity Framework. We leveraged the human modification framework to generate comprehensive, consistent, detailed, robust, temporal, and contemporary datasets to map cumulative and individual threats associated with industrial human activities to terrestrial biodiversity and ecosystems from 1990 to 2022. In ∼2022, 43% of terrestrial lands had very low levels of modification, while 27%, 20%, and 10% had low, moderate, and high modification, respectively. Nearly ⅔ of biomes and ½ of ecoregions currently (∼2022) are moderately-modified, and 24% of terrestrial ecosystems (31 M km2) experienced increased modification from 1990 to 2020. About 29% of countries and 31% of ecoregions might also be particularly vulnerable to biodiversity loss given their above-average increased modification and less than 30% protection.
Kinking and buckling instability in growing bacterial chains
Authors: McMahon Sean G. , Neu John C. , Chen Jing
Published: January 2025

Many gram-positive bacteria likeBacillus subtilisandClostridiumspecies, exhibit a growing chain–mediated sliding motility that is driven entirely by the force of cell growth. Particularly, the bacteria maintain cell-cell linkage after cell division and form long chains of many cells. The cells in a chain are continuously pushed outward by the mechanical force of cell growth. As the cell number in a chain grows, the cells toward the tip of the chain accelerate, and can in principle reach very high speeds. Although this seems to suggest a highly efficient motility mechanism, recent modeling work predicted mechanical stress builds up in the growing chain and the resulting chain breakage beyond a critical chain length, which ultimately sets a mechanical limitation in the maximum speed of the chain-mediated sliding. In this work we developed models to show that under different conditions the chain can either form sharp kinks or smooth buckles under the increasing stress. This can explain differential behaviors observed in different bacterial species. Our model further predicted how kinking and buckling affect the susceptibility of the chain to breakage. Our model provides a theoretical framework for predicting the dynamics and efficiency of growing chain–mediated bacterial sliding, and suggest cell properties that can optimize sliding efficiency.
A Lung CT Foundation Model Facilitating Disease Diagnosis and Medical Imaging
Authors: Gao Zebin , Zhang Guoxun , Liang Hengrui , Liu Jiaxin , Ma Liangdi , Wang Tianyun , Guo Yanchen , Chen YuJia , Yan Zeping , Chen Xiangru , Guo Yuchen , He Jianxing , Xu Feng , Wong Tien Yin , Dai Qionghai
Published: January 2025

The concomitant development and evolution of lung computed tomography (CT) and artificial intelligence (AI) has allowed non-invasive lung imaging to be a key part of the clinical care of patients with major diseases, such as lung cancer. However, the paucity of labeled lung CT data has limited the training highly efficacious AI models and thereby has retarded broad-scale adoption and deployment of AI-based lung CT imaging in the real-world clinical setting. In this paper, We introduce LCTfound, a foundational model that encodes images along with correlated clinical information, into a neural network. LCTfound used self-supervised learning pre-trained by diffusion models using a large dataset containing 105,184 lung CT scans (totaling more than 28 million images) from multiple centers. LCTfound was evaluated on 8 categories of lung CT tasks, ranging from scanning-level clinical diagnosis to pixel-level image restoration, including segmentation of mediastinal neoplasm, diagnosis of pulmonary alveolar proteinosis, prognosis of non-small cell lung cancer, prediction of major pathological response to neoadjuvant chemoimmunotherapy, whole lung 3D modeling for surgical navigation, virtual lung computed tomography angiography(CTA), reconstruction of lung CT from sparse views, and enhancement of low-dose CT images. Equipped with the robust few-shot learning capability, LCTfound outperformed the previously state-of-the-art pre-trained models in all the above tasks. LCTfound is a major advancements in self-supervised representation learning on lung CT, laying the groundwork for a foundational model that operates with high efficacy across the spectrum of low-level and high-level clinical tasks and serving a dual purpose in aiding in clinical diagnosis of lung diseases and improving the quality of lung CT imaging.
Predicting Metabolic Dysfunction Associated Steatotic Liver Disease Risk Using Patient-Derived Induced Pluripotent Stem Cells
Authors: Qin Yuanyuan , Chhetri Parth , Theusch Elizabeth , Lim Grace , Teker Sheila , Kuang Yu-Lin , Aziziraftar Shahrbanoo Keshavarz , Mehraban Mohammad Hossein , Munoz-Howell Antonio , Saxena Varun , Le Guillou Dounia , Mattis Aras N. , Maher Jacquelyn J. , Medina Marisa W.
Published: January 2025

Background and Aims

Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) is reversible at early stages, making early identification of high-risk individuals clinically valuable. Previously, we demonstrated that patient-derived induced pluripotent stem cells (iPSCs) harboring MASLD DNA risk variants exhibit greater oleate-induced intracellular lipid accumulation than those without these variants. This study aimed to develop an iPSC-based MASLD risk predictor using functional lipid accumulation assessments.

Methods

We quantified oleate-induced intracellular lipid accumulation in iPSCs derived from three cohorts of diverse ancestry: 1) CIRM cohort (20 biopsy-confirmed MASH cases, 2 biopsy-confirmed MASLD cases, 17 controls), 2) POST cohort (18 MASLD cases, 17 controls), and 3) UCSF cohort (4 biopsy-confirmed MASH cases, 8 controls). Lipid accumulation levels in the CIRM cohort were used to define an iPSC-based MASLD risk score, which was used to predict case/control status in the POST and UCSF cohorts.

Results

In all three cohorts, lipid accumulation was higher in MASLD/MASH cases vs. controls (CIRM cases vs. controls 3.32 ± 0.25 vs. 2.70 ± 0.19 -fold change, p=0.06; POST cases vs. controls 3.63 ± 0.33 vs. 2.70 ± 0.31, p=0.05; and UCSF cases vs. controls 4.39±0.46 vs. 2.03±0.20, p=0.0002). The iPSC-based MASLD risk score achieved a sensitivity of 44% and specificity of 75% in the POST cohort and 75% and 100%, respectively, in the UCSF cohort. Differences in cohort disease severity and cardiometabolic profiles may explain performance variability.

Conclusion

While validation in larger cohorts is needed, these findings suggest that oleate-induced intracellular lipid accumulation in subject-derived iPSCs is predictive of MASH development. Additional cellular phenotypes and donor information should be explored to improve predictive accuracy to inform MASLD surveillance and prevention strategies.
A simple demonstration of a privacy-preserving de-centralised genotype imputation workflow
Authors: Letaillandier Alban , Picard-Druet David , Ludwig Thomas E. , Marenne Gaëlle , Herzig Anthony F.
Published: January 2025

Recently, a number of studies have looked at the problem of privacy and data-sharing restrictions in the context of missing genotype imputation servers. This relates to the most typical imputation pipelines which involve a whole-genome sequenced haplotype reference panel being compared to genotyped study individuals (who have missing data to be imputed). Hence, involving two datasets from separate sources coming together in one informatic environment, where relatively complicated statistical models are applied; specifically, hidden Markov modelling. We give a short review of the current literature in this domain, observing three prevalent strategies: complicated data encryption, technical solutions to secure computation environments, and rearrangements of haplotype data in an effort to provide anonymisation. We embarked on a thought experiment to provide a potential fourth type of solution involving federating the different internal tasks within the statistical methods used for imputation. This idea is relevant considering there is currently motivation for federated analyses platforms in Europe for making combined inference across multiple genomic data resources. This allows for very simple manipulations to protect sensitive individual level data, which enable imputation algorithms to complete on simple plain-text files. We provide here an illustration of how such a federated imputation server could be put in place, along with associated code, including a simple implementation of the Li-Stephens haplotype mosaic model to achieve the imputation of missing genotypes. We name our general framework ANONYMP for anonymised imputation. A demonstration of the concept is given involving simulated data generated with msprime. We show that dividing different parts of the required calculations for statistical imputation between several sites is a valuable new avenue in the field of privacy-preserving imputation server development.
A novel tool for designing targeted gene amplicons and an optimised set of primers for high-throughput sequencing in tuberculosis genomic studies
Authors: Wang Linfeng , Thawong Naphatcha , Thorpe Joseph , Higgins Matthew , Kia Ik Mark Tan , Sawaengdee Waritta , Mahasirimongkol Surakameth , Perdigao Joao , Campino Susana , Clark Taane G. , Phelan Jody E.
Published: January 2025

Amplicon sequencing (Amp-Seq) ofMycobacterium tuberculosisgenes associated with drug resistance and strain typing offers a cost-effective approach for profiling infections and tailoring the clinical management of tuberculosis. However, Amp-Seq assays require continual updates to incorporate new loci and mutations linked to drug resistance. We introduce TOAST (Tuberculosis Optimised Amplicon Sequencing Tool), a customisable software tool that optimises amplicon design across any loci and sequencing platforms (e.g., Illumina, Oxford Nanopore Technology (ONT)), informed by an integrated and expanding database of mutations from >50KM. tuberculosisisolates. TOAST software allows users to define parameters such as melting temperature, amplicon length, and GC content, while accounting for potential primer interactions like homodimer formation and non-specific binding. To demonstrate its robustness, we designed 33 amplicons in a single multiplex group, prioritising coverage of resistance-associated mutations in the form of insertions, deletions and single nucleotide polymorphisms (SNPs) for 13 different drugs. An efficient experimental protocol was established, resulting in a minimum depth coverage exceeding 50-fold for each amplicon region as validated by ONT sequencing of two clinical samples with multi-drug resistance. TOAST software enables the development of Amp-Seq assays for the rapid detection of drug-resistant TB, enhancing treatment strategies, improving outcomes, and curbing resistant infections. The cost-effectiveness and adaptability of Amp-Seq approaches make it crucial for managing TB in resource-limited settings, advancing global control efforts.
ARDUINO-BASED ORGAN PERFUSION SYSTEM
Authors: Domenico Stefano Di
Published: January 2025

Laboratory equipment could be expensive and their cost can be unsustainable for scientists with limited financial resources. In order to overcome these impediments and to improve our experimental studies on liver resection in rats, a multipurpose organ perfusion system was projected and realized using low-cost components.

The device is based on Arduino boards, an easy-to-use and open-source microcontroller, that receives digital and analog inputs, can produce digital outputs and it is programmable in C++. Our perfusion system is composed of: 1) the main control unit that receives pressure data from two independent pressure transducers commonly used in the OR, it receives input from two potentiometers, seven switches, and a push-button; it can display data with an LCD and it can control the speed and the direction of two independent peristaltic-pump, 2) a motor unit composed by peristaltic pumps controlled by two stepper motors, 3) a thermostatic unit that received data from temperature probe and can control up to three heating units.

The pulsating flow generated by the peristaltic pump can be flattened by a dampener unit to simulate the portal flow, and the interposition of a hollow-fiber micro-oxygenator can increase the pO2 of the perfusion fluid in the arterial line.

This cheap system is designed to measure the compliance of regenerating rat liver at increasing and decreasing portal and arterial flow during normothermic ex-vivo perfusion. However the system can be easily rearranged to perform different kinds of organ perfusion: subnormothermic o hypothermic ex-vivo preservation tests can be done by adding a Peltier-based cooling module. Indeed the main control unit can be programmed to control the flow rate based on pressure data to realize peritoneal perfusion or isolated limb perfusion.
Resorbable alginate embolic microsphere for Musculoskeletal embolization applications
Authors: Agarwal Sankalp , Pandey Masum , Duggan Ronan , O’ Brien Con , Lewis Andrew. L. , Duffy Brendan , McCabe Joan , Farrissey Liam
Published: January 2025

Resorbable embolic agents can be used for musculoskeletal (MSK) pain relief applications using a Transarterial Embolisation (TAE) technique. However, inconsistent particle size and shape, degradation rates, and unpredictable resorption and excretion of the breakdown products, limit their widespread clinical adoption. The present study reports self-degradable, rehydratable, freeze-dried, resorbable Ca²⁺-crosslinked alginate microspheres as a novel vascular embolic agent. The alginate lyase enzyme was incorporated into the alginate microspheres to achieve a controlled degradation rate under physiological conditions. Whilst the feasibility of alginate microspheres as embolic agents has been demonstrated, this is the first study where the controlled release is achieved in physiological conditions. To incorporate the alginate lyase enzyme in the alginate matrix, its activity was reversibly inhibited by preparing an alginate lyase-alginate-excipient mixture in a pH 3.6–3.9 buffered solution. An electrostatic encapsulator enabled the scalable preparation of microspheres of size 210 ± 8 µm at room temperature. The results showed that freeze-dried microspheres regained their shape and size within two minutes after reconstitution with saline, along with active alginate lyase. The reperfusion time of alginate microspheres was evaluated using digital subtraction angiography (DSA) and compared with imipenem and celestine (IMP-CS)in a porcine renal arterial embolisation model. It was observed that most of the blood vessels reperfused within 130–210 minutes, and complete vascular blush was recovered within 24 hours. Embolization with resorbable alginate microspheres induced recoverable ischemic necrosis in the targeted renal arteries. This unique feature of resorbable alginate microspheres in inducing ischemic necrosis, potentially in pain-propagating neovessels, makes it an ideal candidate embolic agent for treating MSK-associated pain using the TAE technique.
Paclitaxel causesde novoinduction of invasive breast cancer cells by repolarizing tumor-associated macrophages
Authors: Friedman-DeLuca Madeline , Karagiannis George S. , Duran Camille L. , Shukla Suryansh , Li Jiufeng , Condeelis John S. , Oktay Maja H. , Entenberg David
Published: January 2025

Background

Metastasis is the leading cause of breast cancer (BC) death, and tumor cells must migrate and invade to metastasize. BC cells that express the pro-metastatic actin regulatory protein MenaINV have an enhanced ability to migrate and intravasate within the primary tumor and extravasate at secondary sites. Though chemotherapy improves patient survival, treatment with paclitaxel leads to upregulation of MenaINV and an increase in metastasis in mice. MenaINV expression can be induced in BC cells through cooperative NF-κB/ Notch1 signaling with macrophages, which are often increased in tumors in response to chemotherapy. MenaINV-expressing cells are also resistant to paclitaxel, begging the question of whether paclitaxel increases MenaINV byde novoinduction or by selectively killing non-MenaINV-expressing cells. We hypothesized that paclitaxel causesde novoMenaINV induction by increasing macrophage-tumor cell NF-κB/ Notch1 signaling. Understanding this pro-metastatic effect of chemotherapy is crucial to refining treatment strategies.

Findings

Paclitaxel-treated tumors expressed significantly more MenaINV than vehicle-treated tumors. This effect was dependent upon both macrophages and NF-κB/ Notch signaling. This indicates that chemotherapy increases MenaINV expression by induction. Mechanistically, paclitaxel causes macrophages to take on a pro-inflammatory phenotype and increase NF-κB/ Notch1 signaling with tumor cells.

Conclusion

Paclitaxel causesde novoMenaINV induction. Mechanistically, paclitaxel repolarizes tumor-associated macrophages towards a pro-inflammatory phenotype. These pro-inflammatory macrophages then participate in enhanced NF-κB/ Notch1 signaling with tumor cells, which leads to MenaINV induction in the tumor cells. These results lay the groundwork for novel microenvironment-based therapies to alleviate the pro-metastatic effects of chemotherapy in BC.
Exploring the impact of mitonuclear discordance on disease in Latin American admixed populations
Authors: Ruiz Mauricio , Böhme Daniela , Repetto Gabriela M. , Rebolledo-Jaramillo Boris
Published: January 2025

The coevolution of nuclear and mitochondrial genomes has guaranteed mitochondrial function for millions of years. The introduction of European (EUR) and African (AFR) genomes into the Ameridian continent during the Columbus exchange in Latin America created an opportunity to naturally test different combinations of nuclear and mitochondrial genomes. However, the impact of potential “mitonuclear discordance” (MND, differences in ancestries) has not been evaluated in Latin American admixed individuals (AMR) affected with developmental disorders, even though MND alters mitochondrial function and reduces viability in other organisms. To characterize MND in healthy and affected AMR individuals, we used AMR genotype data from the 1000 Genomes Project (n=385), two cohorts of 22q.11 deletion syndrome patients 22qDS-ARG (n=26) and 22qDS-CHL (n=58), and a cohort of patients with multiple congenital anomalies and/or neurodevelopmental disorders (DECIPHERD, n=172). Based on their importance to mitochondrial function, genes were divided into all mitonuclear genes (n=1035), high-mt (n=167), low-mt (n=793), or OXPHOS (n=169). We calculated local ancestry using FLARE, and estimated MND as the fraction of nuclear mitochondrial genes ancestry not matching the mtDNA ancestry, and ΔMND as (MNDoffspring- MNDmother)/MNDmother. Generally, MND showed population and haplogroup distinctive distributions (ANOVA p<0.05), with haplogroup D showing the lowest MND 0.49±0.17 (mean ± s.d.). MND was significantly lower in 22qDS-ARG patients 0.43±0.24 and DECIPHERD patients 0.56±0.12 compared to healthy individuals 0.60±0.09 (ANOVA p<0.05). OXPHOS and high-mt showed the same trend, but with greater differences between healthy and affected individuals. MND seems to inform population history, and constraint among affected individuals, especially for OXPHOS and high-mt genes.

Author summary

We investigated the role of mitonuclear discordance (MND) in disease among Latin American admixed populations, describing how mismatches between nuclear and mitochondrial ancestries could impact mitochondrial function and disease phenotypes. Utilizing datasets from the 1000 Genomes Project and cohorts with rare genetic disorders, we demonstrated population- and haplogroup-specific patterns of MND, with haplogroup A showing the highest MND values. Affected individuals exhibited significantly lower MND than healthy controls, particularly in genes related to oxidative phosphorylation, suggesting potential links between MND and disease. Intergenerational analyses also revealed constraints on MND, pointing to selective pressures in disease contexts. These findings underscore the importance of mitonuclear interactions in shaping disease phenotypes and highlight the need for further research into their functional and clinical implications, particularly in underrepresented populations.
Wnt/β-catenin signaling promotes posterior axial regeneration in non-regenerative tissue of the annelidCapitella teleta
Authors: Kunselman Lauren F. , Seaver Elaine C.
Published: January 2025

To rescue regeneration, the mechanisms underlying regeneration failure must be identified and overcome. In the annelidCapitella teleta, a transverse cut triggers asymmetric responses across the amputation plane: head fragments regenerate the tail, but tail fragments do not regenerate. We compare regeneration of head fragments (successful regeneration) to that of tail fragments (unsuccessful regeneration) using cell proliferation assays, immunolabeling, andin situhybridization. Surprisingly, following amputation, a dynamic response of the nervous system occurs in the non-regenerating tail fragments ofC. teletathat has not previously been described in annelids. Wnt/β-catenin signaling plays a conserved role in patterning the primary axis of some bilaterians during regeneration, but this role has never been demonstrated in annelids. Wnt/β-catenin pathway components are expressed in the blastema of head fragments but not at the cut site of tail fragments inC. teleta. Experimental activation of Wnt/β-catenin signaling following amputation of tail fragments (24 – 72 hr post amputation) induces expression of stem cell markers, increases cell division at the wound site, and produces differentiated muscle and hindgut. Furthermore, activation of Wnt/β-catenin signaling induces ectopic posterior identity at the amputation site, as it does in other bilaterians. Inhibition of Wnt/β-catenin signaling does not rescue head regeneration. Our results indicate thatC. teletatail fragments have latent regenerative potential that is activated by Wnt/β-catenin signaling. However, the incomplete regenerative response suggests that additional cell signaling pathways are required for this complex process. Comparing tissues with different regenerative abilities elucidates the mechanisms underlying regeneration regulation, thereby enabling the prospect of rescuing or increasing regeneration ability in regeneration-deficient tissues.
Repertoire-level generation of T-cell epitopes with a large-scale generative transformer
Authors: Ma Minuk , Tu Wilson , Vasquez-Rios Carlos , Ding Jiarui
Published: January 2025

Single-cell TCR sequencing enables high-resolution analysis of T Cell Receptor (TCR) diversity and clonality, offering valuable insights into immune responses and disease mechanisms. However, identifying cognate epitopes for individual TCRs requires complex and costly functional assays. We address this challenge with EpitopeGen, a large-scale transformer model based on the GPT-2 architecture that generates potential cognate epitope sequences directly from TCR sequences. To overcome the scarcity of TCR-epitope binding pairs (≈ 100,000), EpitopeGen uses a semi-supervised learning method, termed BINDSEARCH, which searches over 70 billion potential pairs and incorporates high binding affinity predictions as pseudo-labels. To incorporate CD8+T cell biology into the model as an inductive bias, EpitopeGen employs a novel data balancing method, termed Antigen Category Filter, that carefully controls antigen category ratios in its training dataset. EpitopeGen significantly outperforms baseline approaches, generating epitopes with high binding affinity, diversity, naturalness, and biophysical stability. Notably, the epitopes generated by EpitopeGen follow biologically plausible antigen category distributions, a crucial feature not achieved by other models. Using EpitopeGen, we directly identify subsets of clonally expanded tumor-infiltrating lymphocytes that recognize tumor-associated antigens, exhibiting elevated cytotoxicity and reduced exhaustion markers. From COVID-19 patients, EpitopeGen detects T cells that recognize COVID-19 spike proteins and non-structural proteins with distinct transcriptomic characteristics. In conclusion, EpitopeGen represents the first computational method that enables direct inference of antigen recognition profiles of CD8+T cells from plain TCR repertoires.
Zonal endothelial cell heterogeneity underlies murine renal vascular development
Authors: Luo Peter M , Ahuja Neha , Chaney Christopher , Pi Danielle , Cwiek Aleksandra , Markowska Zaneta , Hiremath Chitkale , Marciano Denise , Hirschi Karen K , Iruela-Arispe M Luisa , Carroll Thomas J , Cleaver Ondine
Published: January 2025

The renal vasculature consists of highly specialized blood vessels that carry out distinct physiological functions. Defining their transcriptional signatures and tracing their developmental ontogeny has thus far been challenging due to a lack of regionally specific endothelial biomarkers. Here, we performed single nuclear RNA sequencing (snucRNA-Seq) to interrogate embryonic renal endothelial cells. We identified nine different endothelial cell types, and validated expression of novel candidates using multiplex RNAScope. We interrogate biological characteristics, including cell cycle stage, of developmental blood vessels with a variety ofinvivo tools. Using genetic tools based on expression of tip cell markerEsm1, we performed detailed lineage tracing, demonstrating multi-clonal and multi-directional endothelial contribution to glomerular vasculature. Together, this study provides the first validated, tool-focused developmental atlas of the murine renal vasculature and elucidates several novel cellular mechanisms of nephron vascularization.