bluuebunny/crossref_metadata_2025 huggingface dataset:
Frequency-dependent and capacitive tissue electrical properties in spinal cord stimulation models
Authors: Khadka Niranjan , Wang Boshuo , Bikson Marom
Published: November 2024

Background

Models of spinal cord stimulation (SCS) simulate the electric fields (E-fields) generated in targeted tissues, which in turn can predict physiological and then behavioral outcomes. Notwithstanding increasing sophistication and use in optimizing therapy, SCS models typically calculate E-fields using the quasi-static approximation (QSA). QSA, as implemented in neuromodulation models, neglects the frequency dispersion of tissue conductivity, as well as propagation, capacitive, and inductive effects on the E-field. The reliability of QSA specifically for SCS has not been considered in detail, especially for higher-frequency SCS.

Methods

We implemented a frequency-dependent finite element method (FEM) and solved a high- resolution RADO-SCS model with voltage-controlled (VC) and current-controlled (CC) stimulation to assess the impact of frequency-dependent conductivity (dispersion) and permittivity of spinal tissues on E-fields generated at three different spinal column locations (epidural space, spinal cord, and root) for frequencies spanning from 1 Hz to 10 MHz. Results were compared with predictions of QSA method, with varied conductivity values of purely resistive tissues. We further assessed the impact of frequency-dependent and capacitive tissue properties on spinal heating and distortion of the E-field waveform.

Results

Tissue-specific electric properties around the energized leads and mode of stimulation-control impacted the magnitude of E-fields. In the spinal cord, the VC-SCS E-field generated with the frequency-dependent and capacitive properties was comparable to the QSA with 2X epidural fat conductivity, whereas the CC-SCS generated E-field was minimally impacted by frequency- dependent and capacitive properties up to 10 kHz. Spinal cord heating predicted by frequency- dependent and capacitive tissue properties was comparable to the QSA conditions with VC-SCS, whereas with CC-SCS, there was no impact of the frequency-dependent and capacitive tissue properties in spinal cord heating. E-field waveform distortion in the spinal cord, with CC-SCS at 1 kHz-specific electrical properties, was significant when fat capacitance (permittivity) was increased by 10X, whereas with VC-SCS, there was no effect of tissue capacitance.

Conclusion

Regardless of the mode of SCS, QSA was still valid in predicting SCS-induced E-field and heating at the spinal tissues- acrossαandβdispersion region of spinal tissue’s dielectric spectrum for VC-SCS and up to 10 kHz for CC-SCS.
Novel Immunological Markers of Intestinal Impairment Indicative of HIV-1 Status and/or Subclinical Atherosclerosis
Authors: Moreira Gabriel Etiene , Dias Jonathan , Caballero Ramon Edwin , Salinas Tomas Wiche , Nayrac Manon , Filali-Mouhim Abdelali , Chartrand-Lefebvre Carl , Routy Jean-Pierre , Durand Madeleine , El-Far Mohamed , Tremblay Cécile , Ancuta Petronela
Published: November 2024

Antiretroviral therapy (ART) controls HIV-1 replication in people with HIV-1 (PWH), but immunological restauration at mucosal barrier surfaces is not achieved. This fuels microbial translocation, chronic immune activation, and increased comorbidities, including cardiovascular disease (CVD). Here, we sought to identify novel markers of mucosal barrier impairment in the blood to predict the HIV and/or CVD status. Flow cytometry was used to characterize CD326/EpCAM+intestinal epithelial cells (IEC); CD4+T-cells; CD8+and CD4+intraepithelial lymphocytes (IELs); and subsets of CD4+T-cells expressing Th17 (CCR6) and gut-homing (Itgβ7) markers. To this aim, we collected peripheral blood mononuclear cells (PBMCs) from 42 ART-treated PWH (HIV+) and 40 uninfected participants (HIV-) from the Canadian HIV and Aging Cohort Study (CHACS). Both groups were categorized based on the presence of coronary atherosclerotic plaques measured by CT scan angiography as total plaque volume (TPV, mm3). Our findings associate the HIV-1 status with increased frequencies of circulating CD326+IEC; CD326+CD4+T-cells with activated (CD69+HLA-DR+) and gut-homing (ItgαE+CCR6+CCR9+) phenotypes, CCR6+Itgβ7-CD4+T-cells; and decreased frequencies of CD8+IELs. Logistic regression analyses confirmed the predictive capacity of the above cellular markers regarding HIV status. Spearman correlation revealed a positive correlation between TPV and CCR6+Itgβ7-and CCR6+Itgβ7+CD4+T-cell frequencies.Together, these results highlighted significant immune dysregulation and persistent mucosal barrier alterations despite effective viral suppression by ART and linked the abundance of CCR6+Itgβ7+and CCR6+Itgβ7-CD4+T-cells to increased atherosclerotic plaque burden. Thus, strategies targeting the gut-immune axis restoration may reduce CVD onset and improve long-term health outcomes in PWH.
Predicting missing links in food webs using stacked models and species traits
Authors: Van Kleunen Lucy , Dee Laura E. , Wootton Kate L. , Massol François , Clauset Aaron
Published: November 2024

Networks are a powerful way to represent the complexity of complex ecological systems. However, most ecological networks are incompletely observed, e.g., food webs typically contain only partial lists of species interactions. Computational methods for inferring such missing links from observed networks can facilitate field work and investigations of the ecological processes that shape food webs. Here, we describe a stacked generalization approach to predicting missing links in food webs that can learn to optimally combine both structural and trait-based predictions, while accounting for link direction and ecological assumptions. Tests of this method on synthetic food webs show that it performs very well on networks with strong group structure, strong trait structure, and various combinations thereof. Applied to a global database of 290 food webs, the method often achieves near-perfect performance for missing link prediction, and performs better when it can exploit both species traits and patterns in connectivity. Furthermore, we find that link predictability varies with ecosystem type, correlates with certain network characteristics like size, and is principally driven by a subset of ecologically-interpretable predictors. These results indicate broad applicability of stacked generalization for studying ecological interactions and understanding the processes that drive link formation in food webs.
Repression of the Wnt pathway effector TCF7L2 reverses lethal cachexia in mice with intestinal cancers
Authors: Leong Mei Ling , Ruedl Christiane , Karjalainen Klaus
Published: November 2024

Hyper-activation of the canonical Wnt signaling pathway drives small intestine and colon tumors. As the major Wnt pathway effector in healthy intestines, TCF7L2 is a suspected oncogene in both cancer types. However, this has been challenging to verify becauseTcf7l2knockout is lethal. To circumvent lethality, we generated a novel transgenic mouse that allows dose-dependent, systemic, inducible and reversible repression of endogenousTcf7l2expression. Using this mouse, we demonstrate that TCF7L2 is essential for early adenoma development in the small intestine (ApcMin/+mouse model) but not colon (DSS-treatedApcMin/+mouse model). Once established however, neither small intestine nor colon adenomas require TCF7L2 for maintenance. Despite this,Tcf7l2repression rescues both types of cancer mice from lethal cachexia—a prevalent cancer comorbidity characterized by debilitating weight loss and skeletal muscle atrophy. In colon cancer cachexia, elevated TCF7L2 in the gastrocnemius muscle induces atrophy by activating the transcription of multiple atrophy genes within the ubiquitin-proteasome and autophagy-lysosome systems. Hence, repressingTcf7l2normalizes atrophy gene expression back to non-cachectic expression levels and restores muscle mass. The cachexia recovery mechanism in small intestine cancer remains undefined but is independent of the gastrocnemius. This study shows that systemic and partialTcf7l2repression is both well-tolerated and effective in rescuing moribund cancer mice from cachexia-induced death. Hence this is a promising treatment strategy for cancer patients suffering from cachexia. Additionally, our transgenic mouse is a valuable tool to study muscle atrophy across other conditions including aging, diabetes and neuromuscular disease.
Fluorescence based live cell imaging identifies exon 14 skipped hepatocyte growth factor receptor (MET) degraders
Authors: Mallareddy Jayapal Reddy , Yang Lin , Lin Wan-Hsin , Feathers Ryan , Ayers-Ringler Jennifer , Tolosa Ezequiel , Kizhake Amritha G. , Kizhake Smitha , Kubica Sydney P. , Boghean Lidia , Alvarez Sophie , Naldrett Michael J. , Singh Sarbjit , Rana Sandeep , Zahid Muhammad , Schaefer-Klein Janet , Roden Anja , Kosari Farhad , Anastasiadis Panos Z. , Borad Mitesh , Natarajan Amarnath , Mansfield Aaron S.
Published: November 2024

Despite ongoing efforts to employ structure-based methods to discover targeted protein degraders (TPD), the prevailing strategy continues to be the synthesis of a focused set of heterobifunctional compounds and screen them for target protein degradation. Here we used a fluorescence based live cell imaging screen to identify degraders that target exon 14 skipped hepatocyte growth factor receptor (MET). MET is a known oncogenic driver. MET exon 14 skipping mutations (METex14Δ) are found in lung cancers and result in the loss of a degron that is required for E3-ligase recognition and subsequent ubiquitination, prolonging the half-life and oncogenicity of MET. Since proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules that promote target degradation by the proteosome, we sought to restore degradation of MET lost with METex14Δ using a MET-targeting PROTAC. We generated a library of sixty PROTACs of which 37 used the MET inhibitor capmatinib as the protein of interest targeting ligand. We screened this PROTAC library for targeted degradation of METex14Δ-GFP using live cell imaging. We benchmarked out MET-targeting PROTACs to that of a previously reported MET-targeting PROTAC, SJF8240. Curve fitting live cell imaging data affords determination of time required to degrade 50% of the target protein (DT50), which was used in determining structure activity relationships. A promising candidate, 48-284, identified from the screen, exhibited classic PROTAC characteristics, was > 15-fold more potent than SJF8240, had fewer off targets compared to SJF8240, and degraded MET in multiple cell lines.
Cells transit through a quiescent-like state to convert to neurons at high rates
Authors: Beitz A , Teves JMY , Oakes C , Johnstone C , Wang N , Brickman JM , Galloway KE
Published: November 2024

While transcription factors (TFs) provide essential cues for directing and redirecting cell fate, TFs alone are insufficient to drive cells to adopt alternative fates. Rather, transcription factors rely on receptive cell states to induce novel identities. Cell state emerges from and is shaped by cellular history and the activity of diverse processes. Here, we define the cellular and molecular properties of a highly receptive state amenable to transcription factor-mediated direct conversion from fibroblasts to induced motor neurons. Using a well-defined model of direct conversion to a post-mitotic fate, we identify the highly proliferative, receptive state that transiently emerges during conversion. Through examining chromatin accessibility, histone marks, and nuclear features, we find that cells reprogram from a state characterized by global reductions in nuclear size and transcriptional activity. Supported by globally increased levels of H3K27me3, cells enter a quiescent-like state of reduced RNA metabolism and elevated expression of REST and p27, markers of quiescent neural stem cells. From this transient state, cells convert to neurons at high rates. Inhibition of Ezh2, the catalytic subunit of PRC2 that deposits H3K27me3, abolishes conversion. Our work offers a roadmap to identify global changes in cellular processes that define cells with different conversion potentials that may generalize to other cell-fate transitions.

Highlights

Proliferation drives cells to a compact nuclear state that is receptive to TF-mediated conversion.

Increased receptivity to TFs corresponds to reduced nuclear volumes.

Reprogrammable cells display global, genome-wide increases in H3K27me3.

High levels of H3K27me3 support cells’ transits through a state of altered RNA metabolism.

Inhibition of Ezh2 increases nuclear size, reduces the expression of the quiescence marker p27.

Acute inhibition of Ezh2 abolishes motor neuron conversion.

One Sentence Summary

Cells transit through a quiescent-like state characterized by global reductions in nuclear size and transcriptional activity to convert to neurons at high rates.

Graphical Abstract
On the robustness to gene tree rooting (or lack thereof) of triplet-based species tree estimation methods
Authors: Zaman Tanjeem Azwad , Jahin Rabib , Bayzid Md. Shamsuzzoha
Published: November 2024

Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. This process becomes particularly challenging due to gene tree heterogeneity (discordance), often resulting from Incomplete Lineage Sorting (ILS). Triplet- and quartet-based approaches for species tree estimation have gained substantial attention as they are provably statistically consistent in the presence of ILS. However, unlike quartet-based methods, the limitation of rooted triplet-based methods in handling unrooted gene trees has restricted their adoption in the systematics community. Furthermore, since the induced triplet distribution in a gene tree depends on the placement of the root, the accuracy of triplet-based methods depends on the accuracy of gene tree rooting. Despite progress in developing methods for rooting unrooted gene trees, greatly understudied is the choice of rooting technique and downstream effects on species tree inference under realistic model conditions. This study involves rigorous empirical testing with different gene tree rooting approaches to establish a nuanced understanding of the impact of rooting on species tree accuracy. Moreover, we aim to investigate the conditions under which triplet-based methods provide more accurate species tree estimations than the widely-used quartet-based methods such as ASTRAL.
Oxidative Injury to Lung Mitochondrial DNA is a Key Contributor for the Development of Chemical Lung Injury
Authors: Dubey Shubham , Yu Zhihong , Stephens Emily Morgan , Lazrak Ahmed , Ahmad Israr , Aggarwal Saurabh , Andrabi Shaida , Hossain M. Iqbal , Jilling Tamas , Fernadez Solana R. , Bartels Jennifer L. , Lapi Suzanne E. , Mobley James , Pastukh Viktor M. , Gillespie Mark , Matalon Sadis
Published: November 2024

The mechanisms and extent to which inhalation of oxidant gases damage the mitochondrial genome contributing to the development of acute and chronic lung injury have not been investigated. C57BL/6 mice exposed to chlorine (Cl2) gas and returned to room air, developed progressive loss of lung DNA glycosylase OGG1, significant oxidative injury to mtDNA, decreased intact lung mitochondrial (mt) DNA, generation of inflammatory pathway by DAMPs causing airway and alveolar injury with significant mortality. Global proteomics identified over 1400 lung proteins with alteration of key mitochondrial proteins at 24 h post Cl2exposure. Intranasal instillation of a recombinant protein containing mitochondrial targeted OGG1 (mitoOGG1) post exposure, decreased oxidative injury to mtDNA, lung mitochondrial proteome, severity of the acute and chronic lung injury and increased survival. These data show that injury to the mt-genome is a key contributor to the development of acute and chronic lung injury.
Bacterial lipoate protein ligases rescue lipoylation and respiration deficiency in mammals
Authors: Hu Zhijuan , Yu Junru , Liu Ziwei , Jiang Min , Zeng An-Ping
Published: November 2024

Human lipoylation pathway deficiencies caused by LIPT2/LIAS/LIPT1 gene mutations lead to inherited metabolic disorders characterized by severe defects of mitochondrial energy and amino acids metabolism. Patients with such mutations suffer from hyperlactic acidemia, encephalopathy, hypotonia and early death. So far there is no effective treatment. Here we introduced the bacteria salvage lipoylation pathway, which is absent in eukaryotes, into lipoylation defective human cells and mouse models. BothE. coli-derived LplA andB. subtilis-derived LplJ restored the phenotypes of LIPT2/LIAS/LIPT1 gene knockout cells to those of wildtype cells with lipoic acid supplementation. Biochemical and isotope tracing analysis demonstrated LplA and LplJ function through direct lipoylation of the H protein of glycine cleavage system and the E2 subunits of 2-oxoacid dehydrogenases, thereby reactivating the short-circuited TCA cycle and amino acids metabolism. This strategy is further extended to treat lipoyl precursor supply defects caused by MECR and FDX1 mutations and its efficacy and safety are validated inLipt1-/-andLplAOE/+mouse models. This study provides systematic characterization of lipoylation deficiency and paves the way to gene therapy for treatment of lipoylation-deficient patients.
An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer
Authors: Shimada Kenichi , Michaud Daniel E. , Cui Yvonne Xiaoyong , Zheng Kelly , Goldberg Jonathan , Ju Zhenlin , Schnitt Stuart J. , Pastorello Ricardo , Kania Lukas D. , Hoffer John , Muhlich Jeremy L. , Hyun Nhan , Krueger Robert , Gottlieb Alexander , Nelson Adam , Wanderley Carlos W. , Antonellis Gabriella , McAllister Sandra S. , Tolaney Sara M. , Waks Adrienne G. , Jeselsohn Rinath , Sorger Peter K. , Agudo Judith , Mittendorf Elizabeth A. , Guerriero Jennifer L.
Published: November 2024

T cells are generally sparse in hormone receptor-positive (HR+) breast cancer, potentially due to limited antigen presentation, but the driving mechanisms of low T cell abundance remains unclear. Therefore, we defined and investigated programs (‘gene modules’), related to estrogen receptor signaling (ERS) and immune signaling using bulk and single-cell transcriptome and multiplexed immunofluorescence of breast cancer tissues from multiple clinical sources and human cell lines. The ERS gene module, dominantly expressed in cancer cells, was negatively associated with immune-related gene modules TNFα/NF-κB signaling and type-I interferon (IFN-I) response, which were expressed in distinct stromal and immune cell types, but also, in part, expressed and preserved as a cancer cell-intrinsic mechanisms. Spatial analysis revealed that ERS strongly correlated with reduced T cell infiltration, potentially due to its association with suppression of TNFα/NF-κB-induced angiogenesis and IFN-I-induced HLA expression in macrophages. Preoperative endocrine therapy in ER+/HER2-breast cancer patients produced better responses in ERS-high patients, with TNFα/NF-κB expression associated with reduced ERS. Targeting these pathways may enhance T cell infiltration in HR+ breast cancer patients.

Statement of Significance

This study elucidates the immunosuppressive role of ER signaling in breast cancer, highlighting a complex interplay between cancer, stromal, and immune cells and reveals potential approaches to enhance immunogenicity in HR+ breast cancer. These findings offer crucial insights into immune evasion in breast cancer and identify strategies to enhance T cell abundance.
Comparative transcriptomics ofLathyrus sativusreveals accession-specific resistance responses againstErysiphe pisi
Authors: Marques Rita Maravilha , Fernandes Telma , Barros Pedro M. , Leitão Susana Trindade , Rubiales Diego , Vaz Patto Maria Carlota , Santos Carmen
Published: November 2024

Lathyrus sativus(grass pea) is a valuable crop for sustainable agriculture, offering both dietary benefits and desirable agronomic traits. However, its yield stability is limited by different diseases such as powdery mildew caused byErysiphe pisi. Frequent fungal resistance to pesticides and growing environmental concerns highlight the need for research investment to develop resistant crop varieties. FourL. sativusaccessions, exhibiting varying levels of resistance toE. pisi(resistant, partially resistant, partially susceptible, and susceptible), were analysed using dual RNA-seq to identify key defence mechanisms and effector genes involved in this plant-pathogen interaction. The dual transcriptomic analysis highlighted a host biphasic response, characterised by an initial burst of gene expression, followed by a quiescent phase, and a second wave of intense gene expression at 72 hours after inoculation. CommonL. sativusdefence mechanisms, including antifungal protein expression, cell wall reinforcement, reactive oxygen species-mediated defence were activated by all accessions compared to susceptible accession. Unique responses in the resistant accession integrate early reinforcement of structural barriers with sustained chemical defences and stress responses. Overall, the partially resistant accession exhibited a front-loaded defence response, focused on biotic stimuli and interspecies interactions at early infection stages. In contrast, partial susceptible accessions exhibited a weaker baseline defence system, with a slower and less robust response specifically targeting pathogen infection. We identified potentialE. pisieffectors, including genes involved in cell wall hydrolysis, nutrient acquisition, and virulence, with a higher diversity of effectors identified in the susceptible accession. This study identifies novel targets within the complex defence mechanisms of theLathyrus sativus-Erysiphe pisiinteraction that will support to future breeding programs aimed at enhancing resistance toE. pisiinL. sativusand other related species.
Global picoplankton biogeography revealed by metagenomic and climatic data integration
Authors: Salazar Vinícius W. , Verbruggen Heroen , Marcelino Vanessa Rossetto , Cao Kim-Anh Lê
Published: November 2024

Microbial plankton play fundamental roles in biogeochemical cycles, driving nutrient cycling that influences the global climate and supports life on Earth. Picoplankton are the smallest and most abundant planktonic organisms. The distribution and ecology of these organisms is determined by environmental factors and their biogeography is largely shaped by basin-scale patterns of physicochemical composition of ocean waters. The increased availability of high-throughput sequencing data of microbial communities has enabled the description of how the global oceans are partitioned into distinct microbial biogeographical provinces. However, the key attributes associated with such provinces are still unclear. Here we present a model of picoplankton biogeography based on 1454 metagenomes from multiple sampling consortia, resulting in the largest integrated surface ocean metagenome analysis to date. We identify ten distinct groups based on metagenomic dissimilarity, divided into three categories: polar (Arctic and Antarctic), temperate (coastal temperate, temperate/subtropical transition, oceanic temperate, Mediterranean-like) and tropical (tropical low nutrient, tropical high nutrient, subtropical oceanic gyres). Using machine learning and omics data integration techniques, we predict province areas across the surface oceans and describe their environmental, taxonomical, and functional features. We quantify the relationship between environmental factors and each biogeographical province, identify their main representative taxa and the importance of carbon degradation and antimicrobial resistance pathways in functional community composition, and discuss implications for establishing a model for global picoplankton biogeography.
ON-OFF nanopores for optical control of transmembrane ionic communication
Authors: Wang Xingzao , Kerckhoffs Aidan , Riexinger Jorin , Cornall Matthew , Langton Matthew J. , Bayley Hagan , Qing Yujia
Published: November 2024

[Abstract]

Nanoscale photoswitchable proteins could facilitate precise spatiotemporal control of transmembrane communication and support studies in synthetic biology, neuroscience, and bioelectronics. Through covalent modification of the α-hemolysin protein pore with arylazopyrazole photoswitches, we have produced “photopores” that transition between iontronic resistor and diode modes in response to irradiation at orthogonal wavelengths. In the diode mode, a low-leak OFF-state nanopore exhibits a reversible increase in unitary conductance of more than 20-fold upon irradiation at 365 nm. A rectification ratio of >5 was achieved with photopores in the diode state by either direct or alternating voltage input. Unlike conventional electronic phototransistors with intensity-dependent photoelectric responses, the photopores regulated current output solely based on the wavelength(s) of monochromatic or dual-wavelength irradiation. Dual-wavelength irradiation at various relative intensities allowed graded adjustment of photopore conductance. By using these properties, photonic signals were converted into ionic signals, highlighting the potential applications of photopores as components of smart devices in synthetic biology.
In-silicomodeling and interpretation of RBP binding disentangle m6A-RBP interaction
Authors: Liu Jianche , Zhu Xinlu , Yin Yang , Xu Zhoutong , He Jialin , Xiong Xushen
Published: November 2024

RNA binding protein (RBP) binding andN6-methyladenosine (m6A) are both essential post-transcriptional regulatory layers for RNA fate decisions. However, the intricate mechanism underlying the interaction between m6A and RBP binding remains underexplored. Here, we develop TransRBP, an interpretable deep learning framework, to model the base-resolution binding of RBPs from RNA sequences and to subsequently investigate the interaction between m6A and RBPs. TransRBP achieves a median accuracy of 0.59 across 32 m6A-related RBPs, representing a 28% increase over the state-of-the-art model. Using gradient-based interpretation, we demonstrate that the binding motifs of the m6A-related RBPs strongly enrich for splicing consensus, laying a foundation for studying the RBP-dependent crosstalk between m6A and splicing. Moreover, we develop anin-silicomutagenesis assay to assess the impact of m6A on RBPs, and utilize the self-attention mechanism to elucidate the interplay between RBP binding and m6A. We further uncover 1,806 variant-RBP combinations with thein-silicomutagenesis, revealing variants that strongly alter RBP binding for genetic diseases including Parkinson’s disease, autism, and cardiomyopathy. In particular, we identify m6Acis-acting variants that alter RBP binding in an m6A-proximal manner, including the binding of UPF1 that contributes to Alzheimer’s disease, and the DDX3X binding to cardiomyopathy and muscular dystrophy. Together, TransRBP accurately models the binding of RBP and its interaction with m6A, shedding light on the m6A-RBP dynamics and providing multi-layer mechanistic insights for genetic diseases.
Molecular mechanism of Na+/H+antiporting in NhaA
Authors: Xie Tengyu , He Jiahao , Sun Shuo , Chen Yulei , Huang Jing , Huang Yandong
Published: November 2024

Sodium-proton antiporter NhaA ofEscherichia coliis a paradigm to investigate the mechanistic basis of the fundamental Na+/H+exchange in cells. However, all existing crystal structures of NhaA are inward-facing (IF) and the putative outward-facing (OF) structures are still unsolved by experiment, limiting a complete understanding of the transport cycle where Lys300 plays a key role in both structural stability and transport function. Here, we report a set of regular molecular dynamics (MD) simulations that start from the structure predicted by an artificial intelligence method that generates function-relevant alternative conformations. It is found that NhaA rapidly relaxes into either the IF or OF conformation. Further-more, neutralization of Lys300 allows two sodium ions bound to the reaction cavity, which is associated with enhanced conformational sampling. Based on these observations, we propose a sodium-coupled mechanism of Na+/H+antiporting.
Cacao genome sequence reveals insights into the flavonoid biosynthesis
Authors: Marin Recinos Maria Fernanda , Winnier Sarah , Lagerhausen Kiersten , Ajayi Blessing , Wolff Katharina , Friedhoff Ronja , Dassow Chiara Marie , Choudhary Nancy , Pucker Boas
Published: November 2024

Theobroma cacaois well known for its role in producing cacao. Many different cacao varieties are cultivated in equatorial regions, each distinguished by unique phenotypic traits. An instance of this is the pod color variation, which has been linked to differences in anthocyanin content. Anthocyanins are produced by one branch of the flavonoid biosynthesis. The highly continuous genome sequence and comprehensive gene set generated in this study enabled an investigation of the genetic basis of the flavonoid biosynthesis. Expression differences between paralogs in the proanthocyanidin biosynthesis suggest subfunctionalization. In pod husks, one copy of the leucoanthocyanidin reductase gene (LAR) displayed substantially higher expression than the other copy.
Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival
Authors: Alnahhas Razan N. , Andreani Virgile , Dunlop Mary J.
Published: November 2024

Heteroresistance can allow otherwise drug-susceptible bacteria to survive and resume growth after antibiotic exposure. This temporary form of antibiotic tolerance can be caused by the upregulation of stress response genes or a decrease in cell growth rate. However, it is not clear how expression of multiple genes contributes to the tolerance phenotype. By using fluorescent reporters for stress related genes, we conducted real time measurements of expression prior to, during, and after antibiotic exposure. We first identified relationships between growth rate and reporter levels based on auto and cross correlation analysis, revealing consistent patterns where changes in growth rate were anticorrelated with fluorescence following a delay. We then used pairs of stress gene reporters and time lapse fluorescence microcopy to measure the growth rate and reporter levels in cells that survived or died following antibiotic exposure. Using these data, we asked whether combined information about reporter expression and growth rate could improve our ability to predict whether a cell would survive or die following antibiotic exposure. We developed a Bayesian inference model to predict how the combination of dual reporter expression levels and growth rate impact ciprofloxacin survival inEscherichia coli. We found clear evidence of the impact of growth rate and thegadXpromoter activity on survival. Unexpectedly, our results also revealed examples where additional information from multiple genes decreased prediction accuracy, highlighting an important and underappreciated effect that can occur when integrating data from multiple simultaneous measurements.
Tertiary lymphoid structure as a therapeutic target of Crohn’s disease: modulation by TNFα blockade
Authors: Nagase Yoshihiro , Okano Soh , Furukawa Asuka , Kanazawa Takumi , Yamamoto Kouhei , Yamamoto Kurara , Ohashi Kenichi , Yamana Tetsuo , Nojiri Shuko , Suzuki Yutaka , Kanai Akinori , Yao Takashi , Abe Keiko , Ohteki Toshiaki , Kodama Makoto
Published: November 2024

Inflammatory diseases, such as Crohn’s disease (CD), are primarily treated with therapies aimed at alleviating inflammation. Notably, biological agents like TNFα inhibitors have transformed the management of these conditions. Previous research has indicated that TNFα inhibitors affect the cells in the lamina propria. However, this study demonstrates that infliximab, a type of TNFα inhibitor, reduces the presence of tertiary lymphoid structures (TLS) and alleviates inflammation of CD by targeting follicular dendritic cells and macrophages within these structures. TLS could also be a potential target for various biological agents used to treat inflammatory diseases beyond CD. Furthermore, our study suggests that the status of TLS may serve as a predictor for the response to TNFα inhibitor treatment. Our research could pave the way for new treatment strategies and the advancement of personalized medicine for inflammatory diseases.
Cell-specific oxidative metabolism of the renal cortex
Authors: Feola Kyle , Venable Andrea H. , Broomfield Tatyana , Llamas Claire B. , Mishra Prashant , Huen Sarah C.
Published: November 2024

The metabolic health of the kidney is a primary determinant of the risk of progressive kidney disease. Our understanding of the metabolic processes that fuel kidney functions is limited by the kidney’s structural and functional heterogeneity. As the kidney contains many different cell types, we hypothesize that intra-renal mitochondrial heterogeneity contributes to cell-specific metabolism. To interrogate this, we utilized a recently developed mitochondrial tagging technique to isolate kidney cell-type specific mitochondria. Here, we investigate mitochondrial functional capacities and the metabolomes of the early and late proximal tubule (PT) and the distal convoluted tubule (DCT). The conditional MITO-Tag allele was combined withSlc34a1-CreERT2,Ggt1-Cre, orPvalb-Crealleles to generate mouse models capable of cell-specific isolation of hemagglutinin (HA)-tagged mitochondria from the early PT, late PT, or the DCT, respectively. Functional assays measuring mitochondrial respiratory and fatty acid oxidation (FAO) capacities and metabolomics were performed on anti-HA immunoprecipitated mitochondria from kidneys of ad libitum fed and 24-hour fasted male mice. The renal MITO-Tag models targeting the early PT, late PT, and DCT revealed differential mitochondrial respiratory and FAO capacities which dynamically changed during fasting conditions. Changes with mitochondrial metabolomes induced by fasting suggest that the late PT significantly increases FAO during fasting. The renal MITO-Tag model captured differential mitochondrial metabolism and functional capacities across the early PT, late PT, and DCT at baseline and in response to fasting.

Translational Statement

While the renal cortex is often considered a single metabolic compartment, we discovered significant diversity of mitochondrial metabolomes and functional capacities across the proximal tubule and the distal convoluted tubule. As mitochondrial dysfunction is a major biochemical pathway related to kidney disease progression, understanding the differences in mitochondrial metabolism across distinct kidney cell populations is thus critical in the development of effective and targeted therapeutic therapies for acute and chronic kidney disease.
Combined inhibition of S100A4 and TIGIT suppresses late-stage breast cancer metastasis to the lung by activating T and NK cells
Authors: Leu Jia-Shiun , Deng Hui , Tran Han Nhat , Wei Xiong , Hashiomoto Chihiro , Leonard Fransisca , Wong Thomas , Abdelfattah Nourhan , Benítez Salazar José M , Kang Reece , Maldonado Jose A , Cristobal Carlo D. , Lee Hyun Kyoung , An Zhiqiang , Zhang Ningyan , Yun Kyuson
Published: November 2024

Cancer metastasis is responsible for approximately 90% of cancer-related deaths, but very few treatment options exist currently. While the role of S100A4 in promoting metastasis has been known for decades, this knowledge has not been translated in the clinic. Here, we report that a novel monoclonal antibody against the human S100A4 protein (S1004-11) effectively suppresses breast cancer metastasis in two different mouse models. Importantly, a novel combination of ant-TIGIT and S100A4-11 can suppress lung metastases even in late-stage disease after the lung premetastatic niche (PMN) has already been established similar to a stage when many breast cancer patients are diagnosed. Mechanistically, S1004-11 mAb treatment block the formation of PMN by suppressing neutrophil infiltration and activating natural killer (NK) and T cells in the lung. Single-cell RNA-sequencing and cell:cell communication analyses indicate that TIGIT signaling suppresses NK cells, which is reversed in S100A4-11 treated PMN. In summary, this study provides compelling evidence for a novel mechanism of S100A4 function in PMN formation and the feasibility of using S100A4-11 monoclonal antibody to suppress metastases at different stages of breast cancer progression.
Adipose-derived Mesenchymal Stem Cells and Retinal Pigment Epithelial Cells Interactions in Stress Environment via Tunneling Nanotubes
Authors: Gozel Merve , Senkoylu Karya , Kesim Cem , Hasanreisoglu Murat
Published: November 2024

This study aims to demonstrate the formation of TNTs between AdMSCs and RPE-1 and their alterations in response to experimental stress conditions. Serum starvation was employed as a stress condition to induce TNTs between the AdMSC and RPE-1. The presence of TNTs was demonstrated through immunofluorescence microscopy while scanning electron microscopy was utilized to determine the average thickness. Cell viabilities were assessed after stress by CTG, and H2DCFH-DA probes evaluated the cells’ reactive oxygen species (ROS) levels. Further, JC-1 labeled mitochondrial exchange between cells via TNTs was supported by videos. A transmembrane culture system was employed to inhibit TNT formation. In this study, we investigated the role of TNTs in facilitating intercellular communication and mitochondrial transfer between AdMSCs and RPE-1 under stress. We found that TNT-mediated mitochondrial transfer from AdMSCs to RPE-1 helps to reduce ROS levels and improve cell viability. We demonstrated that direct interaction between AdMSCs and RPE-1 was crucial for stress recovery. Co-culture enhanced viability and sustained retinal epithelial cell function after stress-induced damage. Mechanical inhibition of TNT formation decreased cell viability and increased ROS levels, indicating the importance of TNTs in cellular protection. The findings can provide a new perspective on the therapeutic potential of stem cell-based therapy in protecting RPE against stress-induced damage and promoting tissue regeneration.
The effectiveness of Large Language Models with RAG for auto-annotating phenotype descriptions
Authors: Kainer David
Published: November 2024

Ontologies are highly prevalent in biology and medicine and are always evolving. Annotating biological text, such as observed phenotype descriptions, with ontology terms is a challenging and tedious task. The process of annotation requires a contextual understanding of the input text and of the ontological terms available. While text-mining tools are available to assist they are largely based on directly matching words and phrases and so lack understanding of the meaning of the query item and of the ontology term labels. Large Language Models (LLMs), however, excel at tasks that require semantic understanding of input text and therefore may provide an improvement for the auto-annotation of text with ontological terms. Here we describe a series of workflows incorporating OpenAI GPT’s capabilities to annotateArabidopsis thalianaand forest tree phenotypic observations with ontology terms, aiming for results that resemble manually curated annotations. These workflows make use of an LLM to intelligently parse phenotypes into short concepts, followed by finding appropriate ontology terms via embedding vector similarity or via Retrieval-Augmented Generation (RAG). The RAG model is a state-of-the-art approach that augments conversational prompts to the LLM with context-specific data to empower it beyond its pre-trained parameter space. We show that the RAG produces the most accurate automated annotations that are often highly similar or identical to expert-curated annotations.

Short description

Large Language Models excel at tasks that require semantic understanding of text. Here we use that capability to auto-annotate plant phenotypes with ontological terms and compare to expert annotation.
High-fidelityin vitropackaging of diverse synthetic cargo into encapsulin protein cages
Authors: Szyszka Taylor N. , Siddiquee Rezwan , Loustau Alex , Adamson Lachlan S. R. , Rennie Claire , Huang Tiancheng , Young Reginald , Care Andrew , Lau Yu Heng
Published: November 2024

Cargo-filled protein cages are powerful tools in biotechnology with demonstrated potential as catalytic nanoreactors and vehicles for targeted drug delivery. While endogenous biomolecules can be packaged into protein cages during their expression and self-assembly inside cells, synthetic cargo molecules are typically incompatible with live cells and must be packagedin vitro. Here we report a fusion-basedin vitroassembly method for packaging diverse synthetic cargo into encapsulin protein cages that outperforms standardin celluloassembly, producing cages with superior uniformity and thermal stability. Fluorescent dyes, proteins and cytotoxic drug molecules can all be selectively packaged with high efficiencyviaa peptide-mediated targeting process. The exceptional fidelity and broad compatibility of ourin vitroassembly platform enables generalisable access to cargo-filled protein cages that host novel synthetic functionality for diverse biotechnological applications.
The Virtual Brain links transcranial magnetic stimulation evoked potentials and inhibitory neurotransmitter changes in major depressive disorder
Authors: Hofsähs Timo , Pille Marius , Kern Lucas , Negi Anuja , Meier Jil Mona , Ritter Petra
Published: November 2024

Background

Transcranial magnetic stimulation evoked potentials (TEPs) show promise as a biomarker in major depressive disorder (MDD), but the origin of the increased TEP amplitude in these patients remains unclear. Gamma aminobutyric acid (GABA) may be involved, as TEP peak amplitude is known to increase with GABAergic activity, but paradoxically MDD patients exhibit reduced GABA levels. We employed a computational modeling approach to investigate this contradiction.

Methods

Whole-brain simulations in ‘The Virtual Brain’ (thevirtualbrain.org), employing the Jansen and Rit neural mass model, were optimized to simulate TEPs of healthy individuals (Nsubs=20, 14 females, 24.5±4.9 years). To mimic MDD, a GABAergic deficit was introduced to the simulations by altering one of two selected inhibitory parameters, the inhibitory synaptic time constantbor the number of inhibitory synapsesC4. The TEP amplitude was quantified and compared for all simulations.

Results

Both parameters, the inhibitory synaptic time constant (r=-0.6, p<0.001) and the number of inhibitory synapses (r=-0.79, p<0.001), showed a significant negative linear correlation to the TEP amplitude. Thus, under local parameter changes, we were able to alter the TEP amplitude towards pathological levels, i.e. creating an MDD-like increase of the global mean field amplitude in line with empirical results.

Conclusions

Our model suggests specific GABAergic deficits as the cause of increased TEP amplitude in MDD patients, which may serve as therapeutic targets. This work highlights the potential of whole-brain simulations in the investigation of neuropsychiatric diseases.
Vocal grooming in meerkats: weakly bonded subordinates call more in response to dominants
Authors: Demartsev Vlad , Gall Gabriella , Strandburg-Peshkin Ariana , Manser Marta B
Published: November 2024

Physical grooming is often used to maintain social bonds in animal groups but the time available for grooming each group member may be limited. Vocal exchanges have been proposed to serve as a solution for sustaining social bonds without the need for physical proximity. To explore this possible social function of vocal exchanges, we examined the effect of dominance and dyadic bond strength of the interacting partners on the intensity of vocal interaction in meerkats (Suricata suricatta). Focusing on “sunning calls”, socially facilitated vocalisations produced when meerkats warm themselves in the sun, we conducted experiments, where we played sunning calls to individuals and recorded their responses. Subordinates increased their call rate in response to calls from dominants with whom they had weak associations during sunning periods and to calls from subordinates with whom they had strong associations. These patterns support the notion of meerkat sunning calls having a social regulatory function, potentially as a bonding or appeasing signal. Our results reflect the dichotomy between the subordinate and dominant individuals and underscore the strategic nature of social relationships within a despotic society. Engaging in continuous reciprocal interactions can signify commitment, promoting tolerance and cooperation. Investing in such interaction with influential dominants could lower the chances of aggression and would fit the “vocal grooming” functionality of such call exchanges. Accumulation of evidence of vocal exchanges reflecting social relationships, together with establishing a causal link between them, would demonstrate that remote “vocal grooming” is a fundamental mechanism for maintaining social affinity in nature.
Embryonic Signatures of Intergenerational Inheritance across Paternal Environments and Genetic Backgrounds
Authors: Dura Mathilde , Ranjan Bobby , Paribeni Rossella , Paribeni Violetta , Serrano Joana B. , Villacorta Laura , Benes Vladimir , Boruc Olga , Boskovic Ana , Hackett Jamie A.
Published: November 2024

The paternal preconception environment has been implicated as a modulator of phenotypic traits and disease risk in F1offspring. However, the prevalence and mechanisms of such intergenerational epigenetic inheritance (IEI) in mammals remain poorly defined. Moreover, the interplay between paternal exposure, genetics, and age on emergent offspring features is unexplored. Here, we measure the quantitative impact of three paternal environments on early embryogenesis across genetic backgrounds. Usingin vitrofertilisation (IVF) at scale, we capture batch-robust transcriptomic signatures of IEI with single-blastocyst resolution. Amongst these, paternal gut microbiota dysbiosis is linked with aberrant expression of lineage regulators in blastocysts, particularly affecting extra-embryonic tissues. Conversely, paternal low-protein high-sugar diet associates with subtle preimplantation developmental delay. We further identify gene expression variability as a paternally-induced F1phenotype, and highlight confounding issues for IEI such as batch-effects and under-sampling. Finally, paternal genetic background and age exert a dominant influence over the inherited environmental signature. This study systematically characterises how paternal conditioning programmes subtle but detectable molecular responses in early embryos, and suggests guiding principles to dissect intergenerational phenomenology.
DNA replication timing reveals genome-wide features of transcription and fragility
Authors: Berkemeier Francisco , Cook Peter Richard , Boemo Michael A
Published: November 2024

DNA replication in humans requires precise regulation to ensure accurate genome duplication and maintain genome integrity. A key indicator of this regulation is replication timing, which reflects the interplay between origin firing and fork dynamics. We present a high-resolution (1-kilobase) mathematical model that maps firing rate distributions to replication timing profiles across various cell lines, validated using Repli-seq data. The model effectively captures genome-wide replication patterns while identifying local discrepancies. Notably, regions where the model and data diverge often overlap with fragile sites and large genes, highlighting the influence of genomic architecture on replication dynamics. Conversely, regions of high concordance are associated with open chromatin and active promoters, where elevated firing rates facilitate timely fork progression and reduce replication stress. By establishing these correlations, our model provides a valuable framework for exploring the structural interplay between replication timing, transcription, and chromatin organisation, offering new insights into the mechanisms underlying replication stress and its implications for genome stability and disease.