bluuebunny/crossref_metadata_2025 huggingface dataset:
PP2A catalytic subunit alpha is critically required for CD8+T cell homeostasis and anti-bacterial responses
Authors: Zhou Xian , Li Meilu , Ai Minji , Li Yanfeng , Zhu Xingxing , Hansen Michael J. , Zhong Jun , Johnson Kenneth L. , Zenka Roman , Pandey Akhilesh , Pease Larry R. , Zeng Hu
Published: February 2024

While the functions of tyrosine phosphatases in T cell biology have been extensively studied, our knowledge on the contribution of serine/threonine phosphatases in T cells remains poor. Protein phosphatase 2A (PP2A) is one of the most abundantly expressed serine/threonine phosphatases. It is important in thymocyte development and CD4+T cell differentiation. Utilizing a genetic model in which its catalytic subunit alpha isoform (PP2A Cα) is deleted in T cells, we investigated its contribution to CD8+T cell homeostasis and effector functions. Our results demonstrate that T cell intrinsic PP2A Cα is critically required for CD8+T cell homeostasis in secondary lymphoid organs and intestinal mucosal site. Importantly, PP2A Cα deficient CD8+T cells exhibit reduced proliferation and survival. CD8+T cell anti-bacterial response is strictly dependent on PP2A Cα. Expression of Bcl2 transgene rescues CD8+T cell homeostasis in spleens, but not in intestinal mucosal site, nor does it restore the defective anti-bacterial responses. Finally, proteomics and phosphoproteomics analyses reveal potential targets dependent on PP2A Cα, including mTORC1 and AKT. Thus, PP2A Cα is a key modulator of CD8+T cell homeostasis and effector functions.
Viral delivery of compact CRISPR-Cas12f forin vivogene editing applications
Authors: Sharrar Allison , Meacham Zuriah , Staples-Ager Johanna , de Tacca Luisa Arake , Rabuka David , Collingwood Trevor , Schelle Michael
Published: February 2024

Treating human genetic conditionsin vivorequires efficient delivery of the CRISPR gene editing machinery to the affected cells and organs. The gene editing field has seen clinical advances withex vivotherapies and within vivodelivery to the liver using lipid nanoparticle technology. Adeno-associated virus (AAV) serotypes have been discovered and engineered to deliver genetic material to nearly every organ in the body. However, the large size of most CRISPR-Cas systems limits packaging into the viral genome and reduce drug development flexibility and manufacturing efficiency. Here, we demonstrate efficient CRISPR gene editing using a miniature CRISPR-Cas12f system with expanded genome targeting packaged into AAV particles. We identified efficient guides for four therapeutic gene targets and encoded the guides and the Cas12f nuclease into a single AAV. We then demonstrate editing in multiple cell lines, patient fibroblasts, and primary hepatocytes. We then screened the cells for off-target editing, demonstrating the safety of the therapeutics. These results represent an important step in applyingin vivoCRISPR editing to diverse genetic sequences and organs in the body.
Gentle rhodamines for live-cell fluorescence microscopy
Authors: Liu Tianyan , Kompa Julian , Ling Jing , Lardon Nicolas , Zhang Yuan , Chen Jingting , Reymond Luc , Chen Peng , Tran Mai , Yang Zhongtian , Zhang Haolin , Liu Yitong , Pitsch Stefan , Zou Peng , Wang Lu , Johnsson Kai , Chen Zhixing
Published: February 2024

Rhodamines have been continuously optimized in brightness, biocompatibility, and colors to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity. We identified a general strategy for the generation of Gentle Rhodamines, which preserved their outstanding spectroscopic properties and cell permeability while showing an efficient reduction of singlet-oxygen formation and diminished cellular photodamage. Paradoxically, their photobleaching kinetics do not go hand in hand with reduced phototoxicity. By combining COT-conjugated spirocyclization motifs with targeting moieties, these gentle rhodamines compose a toolkit for time-lapse imaging of mitochondria, DNA, and actin and synergize with covalent and exchangeable HaloTag labeling of cellular proteins with less photodamage than their commonly used precursors. Taken together, the Gentle Rhodamines generally offer alleviated phototoxicity and allow advanced video recording applications, including voltage imaging.
S-nitrosylation of EZH2 at C329 and C700 interplay with PRC2 complex assembly, methyltransferase activity, and EZH2 stability to regulate endothelial functions
Authors: Sakhuja Ashima , Katakia Yash T , Tripathi Shailesh Mani , Bhattacharyya Ritobrata , Thakkar Niyati Pandya , Ramakrishnan S , Chakraborty Srinjoy , Thakar Sumukh , Sundriyal Sandeep , Chowdhury Shibasish , Majumder Syamantak
Published: February 2024

Nitric oxide (NO), a versatile bio-active molecule modulates cellular function through diverse mechanisms including S-nitrosylation of proteins. However, the role of this post-translational modification in regulating epigenetic pathways was very limitedly explored. Herein, we report that NO causes S-nitrosylation of selected cysteine residues of EZH2 in endothelial cells (EC) resulting in SUZ12 dissociation from EZH2 bound PRC2 complex, reduced methyltransferase activity, and diminished nuclear localization eventually hampering its stability. We detected a significant reduction in H3K27me3 upon exposure to NO as contributed by the early dissociation of SUZ12 from the PRC2 complex. Longer exposure to NO donors caused EZH2 cytosolic translocation, its ubiquitination, and further degradation primarily through the autophagosome-lysosome pathway. Throughin silicoS-nitrosylation prediction analysis and site-directed mutagenesis assay, we identified three cysteine residues namely at locations 260, 329, and 700 in EZH2 and further determined that S-nitrosylation of cysteine 329 induced EZH2 instability while S-nitrosylation of cysteine 700 abrogated EZH2’s catalytic activity. A double mutant of EZH2 containing mutations at Cysteine 329 and 700 remained undeterred to NO exposure. Furthermore, reinforcing H3K27me3 in NO exposed EC through the use of an inhibitor of H3K27me3 demethylase, we confirmed a significant contribution of the EZH2-H3K27me3 axis in defining NO-mediated regulation of endothelial gene expression and migration. Molecular dynamics simulation study revealed SUZ12’s inability in efficiently binding to the SAL domain of EZH2 upon S-nitrosylation of C329 and C700. Taken together, our study for the first-time reports that S-nitrosylation dependent regulation of EZH2 and its associated PRC2 complex –influences endothelial homeostasis.
Trackoscope: A Low-Cost, Open, Autonomous Tracking Microscope for Long-Term Observations of Microscale Organisms
Authors: Soneji Priya , Challita Elio J. , Bhamla M. Saad
Published: February 2024

Cells and microorganisms are motile, yet the stationary nature of conventional microscopes impedes comprehensive, long-term behavioral and biomechanical analysis. The limitations are twofold: a narrow focus permits high-resolution imaging but sacrifices the broader context of organism behavior, while a wider focus compromises microscopic detail. This trade-off is especially problematic when investigating rapidly motile ciliates, which often have to be confined to small volumes between coverslips affecting their natural behavior. To address this challenge, we introduceTrackoscope, a 2-axis autonomous tracking microscope designed to follow swimming organisms ranging from 10µmto 2mmacross a 325cm2area (equivalent to an A5 sheet) for extended durations—ranging from hours to days—at high resolution. UtilizingTrackoscope, we captured a diverse array of behaviors, from the air-water swimming locomotion ofAmoebato bacterial hunting dynamics inActinosphaerium, walking gait inTardigrada, and binary fission in motileBlepharisma.Trackoscopeis a cost-effective solution well-suited for diverse settings, from high school labs to resource-constrained research environments. Its capability to capture diverse behaviors in larger, more realistic ecosystems extends our understanding of the physics of living systems. The low-cost, open architecture democratizes scientific discovery, offering a dynamic window into the lives of previously inaccessible small aquatic organisms.
Identification of early-stage liver fibrosis by modifications in the interstitial space diffusive microenvironment using fluorescent single-walled carbon nanotubes
Authors: Lee Antony , Simon Apolline A. , Boyreau Adeline , Allain-Courtois Nathalie , Lambert Benjamin , Pradère Jean-Philippe , Saltel Fredéric , Cognet Laurent
Published: February 2024

During liver fibrosis, recurrent hepatic injuries lead to accumulation of collagen and other extracellular matrix components in the interstitial space, ultimately disrupting liver functions. Early stages of liver fibrosis may be reversible, but opportunities for diagnosis at these stages are currently limited. Here, we show that the alterations of the interstitial space associated with fibrosis can be probed by tracking individual fluorescent single-walled carbon nanotubes (SWCNTs) diffusing in that space. In a mouse model of early liver fibrosis, we find that nanotubes generally explore elongated areas, whose length decrease as the disease progresses even in regions where histopathological examination does not reveal fibrosis yet. Furthermore, this decrease in nanotube mobility is a purely geometrical effect, as the instantaneous nanotube diffusivity stays unmodified. This work establishes the promise of SWCNTs both for the diagnosis of liver fibrosis at an early stage, and for more in-depth studies of the biophysical effects of the disease.
Bayesian Modelling Approaches for Breath-Hold Induced Cerebrovascular Reactivity
Authors: Hayes Genevieve , Bulte Daniel P. , Moia Stefano , Craig Martin , Chappell Michael , Uruñuela Eneko , Sparks Sierra , Caballero-Gaudes César , Pinto Joana
Published: February 2024

Cerebrovascular reactivity (CVR) reflects the ability of blood vessels to dilate and constrict in response to a vasoactive stimulus and is an important indicator of cerebrovascular health. CVR can be mapped non-invasively with functional magnetic resonance imaging (fMRI) based on blood oxygen level-dependent (BOLD) contrast in combination with a breath-hold (BH) task. There are several ways to analyse this type of data and retrieve individual CVR amplitude and timing information. The most common approach involves employing a time-shifted general linear model with the measured end-tidal carbon dioxide signal as a regressor of interest. In this work, we introduce a novel method for CVR mapping based on a variational Bayesian approach. We analysed BOLD fMRI data from six participants that performed a BH task in ten different sessions each, and computed the corresponding CVR amplitude and delay maps for each session/subject. No statistically significant differences were observed between the modelling approaches in the CVR delay and amplitude maps in grey matter. Notably, the largest difference between methods was apparent in the case of low CVR amplitude, attributed to how each method addressed noisy voxels, particularly in white matter and cerebral spinal fluid. Both approaches showed highly reproducible CVR amplitude maps where between-subject variability was significantly larger than between-session variability. Furthermore, our results illustrated that the Bayesian approach is more computationally efficient, and future implementations could incorporate more complex noise models, non-linear fitting, and physiologically meaningful information into the model in the form of priors. This work demonstrates the utility of variational Bayesian modelling for CVR mapping and highlights its potential for characterising BOLD fMRI dynamics in the study of cerebrovascular health and its application to clinical settings.
Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species
Authors: Daigle Austin , Johri Parul
Published: February 2024

The accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill- Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, when inferring the distribution of selection coefficients, there is an overestimation of nearly neutral and strongly deleterious mutations and an underestimation of mildly deleterious mutations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.
CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data
Authors: Simon Franck , Comes Maria Colomba , Tocci Tiziana , Dupuis Louise , Cabeli Vincent , Lagrange Nikita , Mencattini Arianna , Parrini Maria Carla , Martinelli Eugenio , Isambert Hervé
Published: February 2024

Live-cell microscopy routinely provides massive amount of time-lapse images of complex cellular systems under various physiological or therapeutic conditions. However, this wealth of data remains difficult to interpret in terms of causal effects. Here, we describe CausalXtract, a flexible computational pipeline that discovers causal and possibly time-lagged effects from morphodynamic features and cell-cell interactions in live-cell imaging data. CausalXtract methodology combines network-based and information-based frameworks, which is shown to discover causal effects overlooked by classical Granger and Schreiber causality approaches. We showcase the use of CausalXtract to uncover novel causal effects in a tumor-on-chip cellular ecosystem under therapeutically relevant conditions. In particular, we find that cancer associated fibroblasts directly inhibit cancer cell apoptosis, independently from anti-cancer treatment. CausalXtract uncovers also multiple antagonistic effects at different time delays. Hence, CausalXtract provides a unique computational tool to interpret live-cell imaging data for a range of fundamental and translational research applications.
Crypt and Villus Enterochromaffin Cells are Distinct Stress Sensors in the Gut
Authors: Touhara Kouki K. , Rossen Nathan D. , Deng Fei , Chu Tifany , Harrington Andrea M. , Garcia Caraballo Sonia , Brizuela Mariana , O’Donnell Tracey , Cil Onur , Brierley Stuart M. , Li Yulong , Julius David
Published: February 2024

The crypt-villus structure of the small intestine serves as an essential protective barrier, with its integrity monitored by the gut’s sensory system. Enterochromaffin (EC) cells, which are rare sensory epithelial cells that release serotonin (5-HT), surveil the mucosal environment and signal both within and outside the gut. However, it remains unclear whether EC cells in intestinal crypts and villi respond to different stimuli and elicit distinct responses. In this study, we introduce a new reporter mouse model to observe the release and propagation of serotonin in live intestines. Using this system, we show that crypt EC cells exhibit two modes of serotonin release: transient receptor potential A1 (TRPA1)-dependent tonic serotonin release that controls basal ionic secretion, and irritant-evoked serotonin release that activates gut sensory neurons. Furthermore, we find that a thick protective mucus layer prevents TRPA1 receptors on crypt EC cells from responding to luminal irritants such as reactive electrophiles; if this mucus layer is compromised, then crypt EC cells become susceptible to activation by luminal irritants. On the other hand, villus EC cells detect oxidative stress through TRPM2 channels and co-release serotonin and ATP to activate nearby gut sensory fibers. Our work highlights the physiological importance of intestinal architecture and differential TRP channel expression in sensing noxious stimuli that elicit nausea and/or pain sensations in the gut.
Inhibition of ULK1/2 and KRASG12Ccontrols tumor growth in preclinical models of lung cancer
Authors: Ghazi Phaedra C. , O’Toole Kayla T. , Srinivas Boggaram Sanjana , Scherzer Michael T. , Silvis Mark R. , Zhang Yun , Bogdan Madhumita , Smith Bryan D. , Lozano Guillermina , Flynn Daniel L. , Snyder Eric L. , Kinsey Conan G. , McMahon Martin
Published: February 2024

Mutational activation ofKRASoccurs commonly in lung carcinogenesis and, with the recent FDA approval of covalent inhibitors of KRASG12Csuch as sotorasib or adagrasib, KRAS oncoproteins are important pharmacological targets in non-small cell lung cancer (NSCLC). However, not all KRASG12C-driven NSCLCs respond to these inhibitors, and the emergence of drug resistance in those patients that do respond can be rapid and pleiotropic. Hence, based on a backbone of covalent inhibition of KRASG12C, efforts are underway to develop effective combination therapies. Here we report that inhibition of KRASG12Csignaling increases autophagy in KRASG12Cexpressing lung cancer cells. Moreover, the combination of DCC-3116, a selective ULK1/2 inhibitor, plus sotorasib displays cooperative/synergistic suppression of human KRASG12C-driven lung cancer cell proliferationin vitroand superior tumor controlin vivo. Additionally, in genetically engineered mouse models of KRASG12C-driven NSCLC, inhibition of either KRASG12Cor ULK1/2 decreases tumor burden and increases mouse survival. Consequently, these data suggest that ULK1/2-mediated autophagy is a pharmacologically actionable cytoprotective stress response to inhibition of KRASG12Cin lung cancer.
Single-molecule evidence of Entropic Pulling by Hsp70 chaperones
Authors: Rukes Verena , Rebeaud Mathieu E. , Perrin Louis , De Los Rios Paolo , Cao Chan
Published: February 2024

Hsp70 chaperones are central components of the cellular network that ensure the structural quality of proteins. Despite their crucial roles in processes as diverse as the prevention of protein aggregation and protein translocation into organelles, their molecular mechanism of action has remained a hotly debated issue. Due to a lack of suitable methods, no experimental data has directly proven any of the models that have been proposed (Power Stroke, Brownian Ratchet, and Entropic Pulling). Recently, nanopores have emerged as a powerful tool to analyze the function of motor enzymes, as well as protein-protein interactions. Here, we used anin vitrosingle-molecule nanopore to mimicin vivotranslocation of proteins, and to investigate the molecular mechanism of Hsp70. Our experiments demonstrate that Hsp70s forcefully extract polypeptide substrates that are trapped inside the pore. The forces they exert are strong at the molecular level, being equivalent to 46 pN over distances of 1 nm, and depend on the size of Hsp70. These findings provide unambiguous evidence supporting the Entropic Pulling mechanism of action of Hsp70s, thus solving a long-standing debate, and proposing a potentially universal principle governing diverse cellular processes. In addition, these results emphasize the utility of biological nanopores for studying protein function at the single-molecule level.
Scrutinizing science to save lives: uncovering flaws in the data linking L-type calcium channels blockers to CRAC channels and heart failure
Authors: Bird Gary S. , Lin Yu-Ping , Tucker Charles J. , Mueller Geoffrey , Shi Min , Padmanabhan Sandosh , Parekh Anant B.
Published: February 2024

Hypertension is estimated to affect almost 1 billion people globally and significantly increases risk of myocardial infarction, heart failure, stroke, retinopathy and kidney disease. One major front line therapy that has been used for over 50 years involves L-type Ca2+channel blockers (LCCBs). One class of LCCBs is the dihydropyridine family, with amlodipine being widely prescribed regardless of gender, race, ethnicity or age. In 2020, Johnson et al.7reported that all LCCBs significantly increased the risk of heart failure, and attributed this effect to non-canonical activation of store-operated Ca2+entry. A major approach on which they based many of their arguments was to measure cytosolic Ca2+using the fluorescent Ca2+indicator dye fura-2. We recently demonstrated that amlodipine is highly fluorescent within cells and overwhelms the fura-2 signal, precluding the use of the indicator dye with amlodipine24. Our meta-analyses and prospective real world study showed that dihydropyridines were not associated with an increase in heart failure, likely explained by the lack of consideration by Johnson et al.7of well-known confounding factors such as age, race, obesity, prior anti-hypertensive treatment or diabetes24. Trebak and colleagues have responded to our paper with a forthright and unwavering defence of their work27. In this paper, we carry out a forensic dissection of Johnson et al.,7and conduct new experiments that address directly points raised by Trebak et al.27. We show that there are major flaws in the design and interpretation of their key experiments, that fura-2 cannot be used with amlodipine, that there are fundamental mathematical misunderstandings and mistakes throughout their study leading to critical calculations on heart failure that are demonstrably wrong, and several of their own results are inconsistent with their interpretation. We therefore believe the study by Johnson et al.7is flawed at many levels and we stand by our conclusions.
Cross-species prediction of transcription factor binding by adversarial training of a novel nucleotide-level deep neural network
Authors: Zhang Qinhu
Published: February 2024

Cross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In this study, we first propose a novel Nucleotide-Level Deep Neural Network (NLDNN) to predict TF binding within or across species. NLDNN regards the task of TF binding prediction as a nucleotide-level regression task. Beyond predictive performance, we also assess model performance by locating potential TF binding regions, discriminating TF-specific single-nucleotide polymorphisms (SNPs), and identifying causal disease-associated SNPs. Then, we design a dual-path framework for adversarial training of NLDNN to further improve the cross-species prediction performance by pulling the domain space of human and mouse species closer.
Expanding the mutational spectrum ofGCKin Turkish pediatric population
Authors: Topcu Vehap , Buyukyilmaz Gonul , Adiguzel Keziban Toksoy , Boyraz Mehmet
Published: February 2024

Heterozygous loss-of-function variants inGCKcause persistent, mildly elevated plasma glucose beginning at birth. Recently, clinical phenotype created by deleterious variants inGCKis called GCK-MODY, although currently registered as “MODY, type 2” (maturity-onset diabetes of the young type 2, MODY2, MIM # 125851) in OMIM. The hyperglycemia of GCK-MODY is a benign and non-progressive condition, usually suspected upon detection of hyperglycemia in adulthood. Medication is not essential, nevertheless, pregnant females may require special attention. Here, we report recurrent and novelGCKvariants detected in 43 pediatric patients who were investigated for hyperglycemia by the referring pediatric endocrinologist. Electronic medical records (EMR) of the patients were collected and reviewed retrospectively. All patients applied to Ankara City Hospital between April 2019 and June 2022.GCKvariants were screened on NovaSeq 6000 next-generation sequencing platform (Illumina). Variants detected inGCKwere checked with recent literature for a proper pathogenicity classification. In 43 patients, 28 distinctGCKvariants were identified. Of these variants, 25 were classified as likely pathogenic/pathogenic variants (c.1342G>A, c.112C>T, c.1178T>C, c.130G>A, c.565A>G, c.208+3A>T, c.349G>C, c.863+5G>A, c.214G>A, c.1292C>A, c.830_831delTG, c.106C>T, c.572G>A, c.107G>C, c.454T>C, c.793G>A, c.645C>A, c.377T>A, c.667G>A, c.46-1G>A, c.149A>C, c.1079C>G, c.401T>C, c.758T>G, c.467_483+6del; NM_000162.5), while remaining 3 variants (c.950A>C, c.186G>T, c.188G>A; NM_000162.5) were classified as variant of uncertain significance. According to the variant effect, missense variants accounted for the majority (71%; 20/28), followed by splice junction (14%; 4/28), premature termination (7%; 2/28), frameshift (4%; 1/28), and synonymous (4%; 1/28) alterations. There were 3 novel variants: c.830_831del, c.377T>A, c.467_483+6del.
Preeclampsia prediction with maternal and paternal polygenic risk scores: the TMM BirThree Cohort Study
Authors: Ohseto Hisashi , Ishikuro Mami , Obara Taku , Narita Akira , Takahashi Ippei , Shinoda Genki , Noda Aoi , Murakami Keiko , Orui Masatsugu , Iwama Noriyuki , Kikuya Masahiro , Metoki Hirohito , Sugawara Junichi , Tamiya Gen , Kuriyama Shinichi
Published: February 2024

Background

Genomic information from pregnant women and their husbands may provide effective biomarkers for preeclampsia. This study investigated how parental polygenic risk scores (PRSs) for blood pressure (BP) and preeclampsia are associated with preeclampsia onset and evaluated predictive performances of PRSs with clinical predictive variables.

Methods

In the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study, participants were genotyped using either Affymetrix Axiom Japonica Array v2 (further divided into two cohorts—the PRS training cohort and the internal-validation cohort—at a ratio of 1:2) or Japonica Array NEO (external-validation cohort). PRSs were calculated for systolic BP (SBP), diastolic BP (DBP), and preeclampsia. Associations between PRSs and preeclampsia, including preeclampsia superimposed on chronic hypertension, were examined using logistic regression analysis; prediction models were developed using a competing-risks approach with clinical predictive variables and PRSs.

Results

In total, 19,836 participants were included. Hyperparameters for PRS calculation were optimized for 3,384 participants in the training cohort. In internal- and external-validation cohorts, 357 of 6,768 (5.3%) and 269 of 9,684 (2.8%) participants developed preeclampsia, respectively. Preeclampsia onset was significantly associated with maternal PRSs for SBP and DBP in internal- and external-validation cohorts and with paternal PRSs for SBP and DBP only in the external-validation cohort. Maternal PRSs for DBP calculated using “LDpred2” most improved prediction models. Maternal PRSs for DBP provided additional predictive information on clinical predictive variables. Paternal PRSs for DBP improved prediction models in the internal-validation cohort.

Conclusions

Parental PRS, along with clinical predictive variables, is potentially useful for predicting preeclampsia.
Interactions in abnormal synergies between the upper and lower extremities in various phases of stroke: A cohort study
Authors: Kim Dongwon , Ko Sung-Hwa , Han Junhee , Kim Young-Taek , Kim Yun-Hee , Chang Won Hyuk , Shin Yong-Il
Published: February 2024

Objective

The flexion synergy and extension synergy are a representative consequence of a stroke and appear in the upper extremity and lower extremity. Since the ipsilesional corticospinal tract (CST) is the most influential neural pathway for both extremities in motor execution, damage by a stroke to this tract could lead to similar motor pathological features (e.g., abnormal synergies) in both extremities. However less attention has been paid to the inter-limb correlations in the flexion synergy and extension synergy across different recovery phases of a stroke.

Methods

In this study, we used results of the Fugl-Meyer assessment (FMA) to characterize those correlations in a total of 512 participants with hemiparesis post stroke from the acute phase to 1 year. The FMA provides indirect indicators of the degrees of the flexion synergy and extension synergy post stroke.

Results

We found that generally, strong inter-limb correlations (r>0.65 with all p-values<0.0001) between the flexion synergy and extension synergy appeared in the acute-to-subacute phase (<90 days). But correlations of lower-extremity extension synergy with upper-extremity flexion synergy and extension synergy decreased (down to r=0.38) around 360 days after stroke (p<0.05).

Interpretation

These results suggest that the preferential use of alternative neural pathways after damage by a stroke to the CST enhances inter-limb correlations between the flexion synergy and extension, however a recovery of the CST or/and the functional fragmentation (remodeling) of the alternative neural substrates in the chronic phase contribute to diversity in neural pathways in motor execution, eventually leading to reduced inter-limb correlations.
Systems Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis
Authors: Wei Jessica , Moon Jeonghyeon , Yasumizu Yoshiaki , Zhang Le , Radassi Khadir , Buitrago-Pocasangre Nicholas , Deerhake M. Elizabeth , Strauli Nicholas , Chan Alan , Herman Ann , Pedotte Rosetta , Raposo Catarina , Tackenberg Björn , Yim Isaiah , Pappalardo Jenna , Longbrake Erin E. , Sumida Tomokazu S. , Axisa Pierre-Paul , Hafler David A.
Published: February 2024

Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven “in vivo perturbation” modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq). We demonstrate that B cell depletion leads to cell type-specific changes in the abundance and function of CSF macrophages and peripheral blood monocytes. Specifically, a CSF-specific macrophage population with an anti-inflammatory transcriptomic signature and peripheral CD16+monocytes increased in frequency post-B cell depletion. In addition, we observed increases in TNFα messenger RNA and protein in monocytes post-B cell depletion, consistent with the finding that anti-TNFα treatment exacerbates autoimmune activity in MS. In parallel, B cell depletion also induced changes in peripheral CD4+T cell populations, including increases in the frequency of TIGIT+regulatory T cells and marked decreases in the frequency of myelin peptide loaded-tetramer binding CD4+T cells. Collectively, this study provides an exhaustive transcriptomic map of immunological changes, revealing different mechanisms of action contributing to the high efficacy in B cell depletion treatment of MS.
An iPSC-derived bio-inspired scaffold modelling the structure and the effects of extracellular matrix in cardiac fibrosis
Authors: Niro Francesco , Fernandes Soraia , Cassani Marco , Apostolico Monica , La Cruz Jorge Oliver-De , Sousa Daniel Pereira- , Pagliari Stefania , Vinarsky Vladimir , Zdráhal Zbyněk , Potesil David , Pustka Vaclav , Pompilio Giulio , Sommariva Elena , Rovina Davide , Maione Angela Serena , Bersanini Luca , Becker Malin , Rasponi Marco , Forte Giancarlo
Published: February 2024

Cardiac fibrosis occurs following insults to the myocardium and is characterized by the abnormal accumulation of non-compliant extracellular matrix (ECM), which compromises cardiomyocyte contractile activity and eventually leads to heart failure. This phenomenon is driven by the differentiation of cardiac fibroblasts (cFbs) into myofibroblasts and results in changes in ECM biochemical, structural and mechanical properties. The lack of predictivein vitromodels of heart fibrosis has so far hampered the search for innovative treatments. Here, we devised a single-step decellularization protocol to obtain and thoroughly characterize the biochemical and micro-mechanical properties of the ECM secreted by activated cFbs differentiated from human induced pluripotent stem cells (iPSCs). We activated iPSC-derived cFbs to the myofibroblast phenotype by tuning basic fibroblast growth factor (bFGF) and transforming growth factor beta 1 (TGF-β1) signalling and confirmed that activated cells acquired key features of myofibroblast phenotype, like SMAD2/3 nuclear shuttling, the formation of aligned alpha-smooth muscle actin (α−SMA)-rich stress fibres and increased focal adhesions (FAs) assembly. Next, we used Mass Spectrometry, nanoindentation, scanning electron and confocal microscopy to unveil the characteristic composition and the visco-elastic properties of the abundant, collagen-rich ECM deposited by cardiac myofibroblastsin vitro. Finally, we demonstrated that the fibrotic ECM activates mechanosensitive pathways in iPSC-derived cardiomyocytes, impacting on their shape, sarcomere alignment, phenotype, and calcium handling properties. We thus propose human bio-inspired decellularized matrices as animal-free, isogenic cardiomyocyte culture substrates recapitulating key pathophysiological changes occurring at the cellular level during cardiac fibrosis.
Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrentClostridioides difficileinfection
Authors: McMillan Arthur S , Zhang Guozhi , Dougherty Michael K , McGill Sarah K , Gulati Ajay S , Baker Erin S , Theriot Casey M
Published: February 2024

RecurrentC. difficileinfection (rCDI) is an urgent public health threat for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms which mediate a successful FMT are not well understood. Here we use longitudinal stool samples collected from patients undergoing FMT to evaluate changes in the microbiome, metabolome, and lipidome after successful FMTs. We show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae, which encode carnitine metabolism genes, and Lachnospiraceae, which encode bile salt hydrolases andbaiAgenes. LC-IMS-MS revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here we define the structural and functional changes in successful FMTs. This information will help guide targeted Live Biotherapeutic Product development for the treatment of rCDI and other intestinal diseases.
Protein property prediction based on local environment by 3D equivariant convolutional neural networks
Authors: Chen He , Cheng Yifan , Dong Jianqiang , Mao Jie , Wang Xin , Gao Yuan , Li Yuchao , Wang Chengzhi , Wu Qiong
Published: February 2024

Predicting the properties of proteins is an important procedure in protein engineering. It determines the subspace of mutations for protein modifications, which is critical to the success of the project, but heavily relies on the knowledge and experience of scientists. In this study, we propose a novel deep 3D-CNN model, Eq3DCNN, specifically designed for local environment-related tasks in protein engineering. Eq3DCNN uses basic atom descriptors and their coordinates as inputs, utilizing customized data augmentations to enhance its training efficiency. To make the Eq3DCNN extracted features with more generalization capability, we incorporated a rotation equivariant module to get rotation invariant features. Using cross-validations with different data splitting strategies and under the scenarios of zero-shot predictions, we demonstrate that Eq3DCNN outperformed other 3D-CNN models in stability predictions, and also well-preformed on other prediction tasks, such as the binding pocket and the secondary structure predictions. Our results also identified the key factors that contribute to the model’s accuracy and the scope of its applications. These findings may help scientists in designing better mutation experiments and increasing the success rate in protein engineering.
Interpretable Drug Response Prediction through Molecule Structure-aware and Knowledge-Guided Visible Neural Network
Authors: Xie Jiancong , Zhang Zhe , Li Youyou , Rao Jiahua , Yang Yuedong
Published: February 2024

Precise prediction of anti-cancer drug responses has become a crucial obstruction in anti-cancer drug design and clinical applications. In recent years, various deep learning methods have been applied to drug response prediction and become more accurate. However, they are still criticized as being non-transparent. To offer reliable drug response prediction in real-world applications, there is still a pressing demand to develop a model with high predictive performance as well as interpretability. In this study, we propose DrugVNN, an end-to-end interpretable drug response prediction framework, which extracts gene features of cell lines through a knowledge-guided visible neural network (VNN), and learns drug representation through a node-edge communicative message passing network (CMPNN). Additionally, between these two networks, a novel drug-aware gene attention gate is designed to direct the drug representation to VNN to simulate the effects of drugs. By evaluating on the GDSC dataset, DrugVNN achieved state-of-the-art performance. Moreover, DrugVNN can identify active genes and relevant signaling pathways for specific drug-cell line pairs with supporting evidence in the literature, implying the interpretability of our model.
Traditional uses and pharmacological activities ofTetracera alnifolia(Wild) Drake
Authors: Camara A.K. , Baldé E.S. , Diallo M.S.T. , Camara M.K. , Bah T.V. , Condé M. , Soumah A. , Kamano K. , Tietjen I. , Baldé A.M.
Published: February 2024

Ethnopharmacological relevance

Tetracera alnifolia(Wild) Drake, is well used in traditional Guinean medicine for the treatment of infectious skin diseases. The present aim was to contribute to the valorization ofTetracera alnifolialeaves, focused on ethnomedical, biological and phytochemical investigations.

Materials and methods

we conducted an ethnomedical survey across several markets of the city of Conakry to identify 39 healers. Chloroform, methanol, dichloromethane, and aqueous extracts were tested for activities against protozoa, bacteria, fungi, HIV, and SARS-CoV-2.

Results

the traditional healers indicated thatT. alnifoliais used in the treatment of more than 15 pathologies includingFassa(marasmus/malnutrition),Soukhou kouyé(white discharge in women), andTèmou bankhi(sexual weakness in men). Leaves were the most used part. The modes of preparation included decoction and powder. Data from biological activities identicatied good activities of the methanolic extract againstLeishmania infantum(MIC = 8.11 μg / ml) and a moderate activity onTrypanosoma brucei(MIC = 28.15 μg / ml) andStaphylococcus aureus(MIC = 29.91 μg / ml), while dichloromethane extracts acted on live SARS-CoV-2 replication with up to 53.4% inhibition at 50 μg/mL.

Conclusion

these results explain at least in part the traditional use ofT. alnifolia
Modified histone peptides uniquely tune the material properties of HP1α condensates
Authors: Deshpande Priyasha , Prentice Emily , Vidal Ceballos Alfredo , Casaccia Patrizia , Elbaum-Garfinkle Shana
Published: February 2024

Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation of condensed chromatin states. HP1α localization to heterochromatic regions is mediated by its binding to specific repressive marks on the tail of histone H3, such as trimethylated lysine 9 on histone H3 (H3K9me3). However, whether epigenetic marks play an active role in modulating the material properties of HP1α and dictating emergent functions of its condensates, remains only partially understood. Here, we leverage a reductionist system, comprised of modified and unmodified histone H3 peptides, HP1α and DNA to examine the contribution of specific epigenetic marks to phase behavior of HP1α. We show that the presence of histone peptides bearing the repressive H3K9me3 is compatible with HP1α condensates, while peptides containing unmodified residues or bearing the transcriptional activation mark H3K4me3 are incompatible with HP1α phase separation. In addition, inspired by the decreased ratio of nuclear H3K9me3 to HP1α detected in cells exposed to uniaxial strain, using fluorescence microscopy and rheological approaches we demonstrate that H3K9me3 histone peptides modulate the dynamics and network properties of HP1α condensates in a concentration dependent manner. These data suggest that HP1α-DNA condensates are viscoelastic materials, whose properties may provide an explanation for the dynamic behavior of heterochromatin in cells in response to mechanostimulation.

Statement of significance

The organization of genomic information in eukaryotic cells necessitates compartmentalization into functional domains allowing for the expression of cell identity-specific genes, while repressing genes related to alternative fates. Heterochromatin hosts these transcriptionally silent regions of the genome - which ensure the stability of cell identity -and is characterized by repressive histone marks (H3K9m3) and other specialized proteins (HP1a), recently shown to phase separate with DNA. We show that HP1a forms condensates with DNA which persist in the presence of H3K9me3 peptides. The viscoelastic nature of these condensates depend on H3K9me3:HP1 ratios, which are modulated by mechanical strain in cells. Thus, phase separation may explain the dynamic behavior of heterochromatin in cells, in response to mechanostimulation.
Association between mitochondrial DNA copy number and production traits in pigs
Authors: Molinero Eduard , Pena Ramona N. , Estany Joan , Ros-Freixedes Roger
Published: February 2024

Mitochondria are essential organelles in the regulation of cellular energetic metabolism. Mitochondrial DNA copy number (mtDNA_CN) can be used as a proxy for mitochondria number, size, and activity. The aims of our study are to evaluate the effect of mtDNA_CN and mitochondrial haploblocks on production traits in pigs, and to identify the genetic background of this cellular phenotype. We collected performance data of 234 pigs and extracted DNA from skeletal muscle. Whole-genome sequencing data was used to determine mtDNA_CN. We detected positive correlations of muscle mtDNA_CN with backfat thickness at 207 d (+0.14;p-value = 0.07), and negative correlations with carcase loin thickness (–0.14;p-value = 0.03). Pigs with less mtDNA_CN had greater loin thickness (+4.1 mm;p-value = 0.01) and lower backfat thickness (–1.1 mm;p-value = 0.08), which resulted in greater carcase lean percentage (+2.4%;p-value = 0.04) than pigs with high mtDNA_CN. These results support the hypothesis that a reduction of mitochondrial activity is associated with greater feed efficiency. Pork from pigs with less mtDNA_CN may also tend to have lower ultimate pH (correlation: +0.19;p-value < 0.01). We found no association of the most frequent mitochondrial haploblocks with mtDNA_CN or the production traits, but several genomic regions that harbour potential candidate genes with functions related to mitochondrial biogenesis and homeostasis were associated to mtDNA_CN. These regions provide new insights into the genetic background of this cellular phenotype but it is still uncertain if such associations translate into noticeable effects on the production traits.
Atypical landscape of transposable elements in the large genome ofAedes aegypti
Authors: Daron Josquin , Bergman Alexander , Lopez-Maestre Hélène , Lambrechts Louis
Published: February 2024

Transposable elements (TEs) contribute significantly to variation in genome size among eukaryotic species, but the factors influencing TE accumulation and diversification are only partially understood. Most of our current knowledge about TE organization, dynamics and evolution derives from investigations in model organisms with a relatively small genome size such asDrosophila melanogasterorArabidopsis thaliana. Whether the observed patterns hold true in larger genomes remains to be determined. The Diptera order is an ideal taxon to address this question, because it includes a forty-year model of TE biology (D. melanogaster) as well as mosquito species with significantly larger genomes. Here, we use a comparative genomics approach to characterize the genomic forces that have shaped the TE content of theAedes aegyptigenome (1.3 Gb) relative to theAnopheles coluzziigenome (300 Mb) and theD. melanogastergenome (180 Mb). Leveraging a newly developed high-quality TE library forAe. aegypti, our results reveal a contrasted pattern of TE organization inAe. aegypticompared toAn. coluzziiandD. melanogaster. Our analyses suggest that the substantial TE fraction observed in theAe. aegyptigenome reflect both a high rate of TE transposition and a low rate of TE elimination. Together, our results indicate that TE organization and evolutionary dynamics in the large genome ofAe. aegyptiare distinct from those of other dipterans with smaller genomes.
Modelling the spatiotemporal dynamics of multispecies population interactions in the context of climate change
Authors: Christou Katerina , Schmucki Reto , Audusseau Hélène
Published: February 2024

Species interactions are fundamental to the stability and productivity of ecosystems. To improve our capacity to predict and understand how climate change shapes the distribution of species and the dynamics of biotic interactions, we need to develop spatially explicit multi-species models that are built upon species-specific responses to changing conditions.

We developed a two-dimensional diffusion-advection-reaction predator-prey model that integrates species-specific responses to heterogeneous landscapes, affecting species dispersal, reproduction and survival rates. We derived conditions for the stability and feasibility of the coexistence steady-state and observed how temperature variation stabilises or destabilises the system.

We conducted numerical simulations to explore the effect of predicted extreme temperatures on the spatial dynamics of a parasitoid-butterfly system and their interactions. Applied to four different climatic environments, the numerical approximations demonstrate the asymmetric impact of a warming climate on interacting species. The output density distribution maps highlight the capability of our model to produce interpretable multiscale predictions which can be used to identify and evaluate species vulnerability locally and across their range.

By building upon a solid mechanistic understanding of species-specific responses to environmental change, our model can be extended to other species and variables, including environments where the availability of empirical data is limited, and explore the dynamics and distribution of interacting species under different scenarios of environmental change.