bluuebunny/crossref_metadata_2025 huggingface dataset:
Glophyt: a user-friendly, general-purpose program for nonlinear and multidimensional curve fitting via a hybrid stochastic and deterministic approach
Authors: Czaplicki Georges , Mazeres Serge
Published: April 2024

Background

Model validation depends on the agreement between the predicted and experimental data. However, finding solutions to problems, described by equations with many parameters, for which virtually nothing is known, is a difficult task. For example, the extraction of kinetic parameters from complex schemes representing the conversion of a substrate into a product by an enzyme in the presence of an inhibitor is extremely difficult, as even the orders of magnitude of the parameters are not known. This makes curve fitting very difficult in case of multidimensional and nonlinear data. This article presents a graphical user interface-based program employing a hybrid stochastic and deterministic approach, which allows for easy and reliable determination of model parameters.

Results

The program has been extensively used in several laboratories at our institute and has proven to be efficient in determining model parameters in many different fields. Although its origins are related to kinetic studies in enzymology, it has been successfully tested on data from various sources, such as pharmacological studies of ligand−receptor binding, entomological studies of populations, bacterial growth, photosynthesis, toxicology, differential scanning calorimetry, isothermal titration calorimetry and nuclear magnetic resonance spectroscopy.

Conclusions

This program presents an effective solution for researchers facing the problem of extracting model parameters from multidimensional and nonlinear data where even the orders of magnitude of parameters are not known. Its graphical user interface makes it easy to use, does not require any programming skills, and it is cost-free. It is available for Windows and Linux platforms.
Estimating intra-subject and inter-subject oxygen consumption in outdoor human gait using multiple neural network approaches
Authors: Müller Philipp , Pham-Dinh Khoa , Trinh Huy , Rauhameri Anton , Cronin Neil J.
Published: April 2024

Oxygen consumptionis an important parameter for exercise test, such as walking and running, that can be measured using portable spirometers or metabolic analyzers. However, these devices are not feasible for regular use by consumers as they intervene with the user’s physical integrity, and are expensive and difficult to operate. To circumvent these drawbacks, indirect estimation ofusing neural networks combined with motion parameters and heart rate measurements collected with consumer-grade sensors has been shown to yield reasonably accuratefor intra-subject estimation. However, estimatingwith neural networks trained with data from other individuals than the user, known as inter-subject estimation, remains an open problem. In this paper, five types of neural network were tested in various configurations for inter-subjectestimation. To analyse predictive performance, data from 16 participants walking and running at speeds between 1.0 m/s and 3.3 m/s were used. The most promising approach was XceptionNet, which in most configurations even yielded a lower average estimation error than the LSTM neural network from an earlier study for intra-subject estimation. This suggests that XceptionNet could be embedded in portable devices for real-time estimation of oxygen consumption during walking and running.
Productivity and resilience of Chinook salmon compromised by ‘Mixed-Maturation’ fisheries in marine waters
Authors: Gayeski Nick , Swanson Devin , MacDuffee Misty , Rosenberger Andrew
Published: April 2024

Most Chinook salmon (Oncorhynchus tshawytscha) in the northeast Pacific Ocean are harvested in mixed-stock marine fisheries. Here, multiple populations with varying abundance and productivities are encountered. In addition, many of these fisheries generally encounter both mature and immature Chinook. Hence, these fisheries are better described as mixed-stock and “mixed-maturation” (MM) fisheries. Harvest of immature fish can skew the age composition of Chinook populations towards younger, and hence smaller, individuals. Older Chinook are generally larger and contribute disproportionately to the productivity of their populations. We developed an individual-based demographic-genetic model of ocean-type Chinook to evaluate the effects of fisheries that harvest immature Chinook. We then compared those effects to terminal fisheries that harvest only mature fish. Our model provides the ability to assess the benefits of terminal Chinook fisheries to both landed catch and Chinook rebuilding. Recovered populations show a more archetypal age– and sex-structure than contemporary ocean-type Chinook subject to marine mixed-maturation fisheries. In our modeled scenarios of mixed-maturation fisheries, we found that immature Chinook can comprise up to 59% of the total numbers of fish caught, and 47% of the total weight of the catch. If instead, these Chinook were not harvested until they mature and reach terminal fisheries, they would contribute greater biomass to landed catches. These terminal fisheries allow a higher percentage of larger, older Chinook to escape, and would increase the fecundity and productivities of their populations. The benefits of terminal fisheries would accrue to fishers, sustainable wild harvesting, wildlife, and the rebuilding of depleted Chinook runs.
Tumor-expressed SPPL3 supports innate anti-tumor immune responses
Authors: Verkerk Tamara , de Waard Antonius A. , Koomen Sofie J.I. , Sanders Jasper , Jorritsma Tineke , Pappot Anouk T. , Zandhuis Nordin D. , Zhang Tao , Wuhrer Manfred , Stockinger Hannes S.J. , van Gisbergen Klaas P.J.M. , Spaapen Robbert M. , van Ham S. Marieke
Published: April 2024

The development of an effective anti-tumor response relies on the synergistic actions of various immune cells that recognize tumor cells via distinct receptors. Tumors, however, often manipulate receptor-ligand interactions to evade recognition by the immune system. Recently, we highlighted the role of neolacto-series glycosphingolipids (nsGSLs), produced by the enzyme β1,3-N-acetylglucosaminyltransferase 5 (B3GNT5), in tumor immune escape. We previously demonstrated that loss of signal peptidase like 3 (SPPL3), an inhibitor of B3GNT5, results in elevated levels of nsGSLs and impairs CD8 T cell activation. The impact of loss of SPPL3 and an elevated nsGSL profile in tumor cells on innate immune recognition remains to be elucidated. This study investigates the anti-tumor efficacy of neutrophils, NK cells, and γδ T cells on tumor cells lacking SPPL3. Our findings demonstrate that SPPL3-deficient target cells are less susceptible to trogocytosis by neutrophils and killing by NK cells and γδ T cells. Mechanistically, SPPL3 influences trogocytosis and γδ T cell instigated killing through modulation of nsGSL expression while SPPL3-mediated reduced killing by NK cells is nsGSL-independent. The nsGSL-dependent SPPL3 sensitivity depends on the proximity of surface receptor domains to the cell membrane and the affinity of receptor-ligand interactions as shown with various sets of defined antibodies.

Thus, SPPL3 expression by tumor cells alters crosstalk with immune cells through the receptor-ligand interactome thereby driving escape not only from adaptive but also from innate immunity. These data underline the importance of investigating a potential synergism of GSL synthesis inhibitors with current immune cell activating immunotherapies.
Standardizing protein corona characterization in nanomedicine: a multi-center study to enhance reproducibility and data homogeneity
Authors: Ashkarran Ali Akbar , Gharibi Hassan , Modaresi Seyed Majed , Saei Amir Ata , Mahmoudi Morteza
Published: April 2024

Our recent findings reveal substantial variability in the characterization of identical protein corona across different proteomics facilities, demonstrating that protein corona datasets are not easily comparable between independent studies. We have shown that heterogeneity in the final composition of the identical protein corona mainly originates from variations in sample preparation protocols, liquid chromatography mass spectrometry (LC-MS) workflows, and raw data processing. Here, to address this issue, we developed standardized protocols and unified sample preparation workflows, and distributed identical protein corona digests to several proteomics centers that performed better in our previous study. Additionally, we examined the influence of using similar mass spectrometry instruments on data homogeneity. Furthermore, we evaluated whether standardizing database search parameters and data processing workflows could enhance data uniformity. More specifically, our new findings reveal a remarkable, stepwise improvement in protein corona data consistency across various proteomics facilities. Streamlining the whole workflow results in a dramatic increase in protein ID overlaps from 11% for good centers to 40% across core facilities that utilized similar instruments and were subjected to a uniform database search. This comprehensive analysis identifies key factors contributing to data heterogeneity in mass spectrometry-based proteomics of protein corona and plasma-related samples. By streamlining these processes, our findings significantly advance the potential for consistent and reliable nanomedicine-based diagnostics and therapeutics across different studies.
Identifying key regulatory genes in drug resistance acquisition: Modeling pseudotime trajectories of single-cell transcriptome
Authors: Iida Keita , Okada Mariko
Published: April 2024

Single-cell RNA-sequencing (scRNA-seq) technology has provided significant insights into cancer drug resistance at the single-cell level. However, understanding dynamic cell transitions at the molecular systems level remains limited, requiring a systems biology approach. We present an approach that combines mathematical modeling with pseudotime analysis using time-series scRNA-seq data obtained from the breast cancer cell line MCF-7 treated with tamoxifen. Our single-cell analysis identified five distinct subpopulations, including tamoxifen-sensitive and -resistant groups. Using a single-gene mathematical model, we discovered approximately 560–680 genes out of 6,000 exhibiting multistable expression states in each subpopulation, including key estrogen receptor-positive breast cancer cell survival genes, such asRPS6KB1. Bifurcation analysis elucidated their regulatory mechanisms, and we mapped these genes into a molecular network associated with cell survival and metastasis-related pathways. Our modeling approach comprehensively identifies key regulatory genes for drug resistance acquisition, enhancing our understanding of potential drug targets in breast cancer.

Despite recent advancements in experimental technology for genome-wide molecular profiling, our understanding of the dynamic mechanism underlying cancer drug resistance remains limited. In this study, we present an approach that combines mathematical modeling with the pseudotime analysis of single-cell time-series transcriptome data of drug-treated breast cancer cells. Our method identifies approximately 600 genes out of 6,000 exhibiting multistable expression states, includingRPS6KB1, a predictor of poor prognosis, cell survival, and growth in estrogen receptor-positive breast cancers. The bifurcation analysis elucidates the regulatory mechanisms of the key regulatory genes, which can also be mapped into a molecular network based on cell survival and metastasis-related pathways, providing a comprehensive understanding of the interplay between signaling pathways and regulatory genes. Our method serves as a powerful tool for deciphering the complexities of drug resistance mechanisms in human diseases.
Working memory as a representational template for reinforcement learning
Authors: Shibata Kengo , Klar Verena , Fallon Sean J , Husain Masud , Manohar Sanjay G
Published: April 2024

Working memory (WM) and reinforcement learning (RL) both influence decision-making, but how they interact to affect behaviour remains unclear. We assessed whether RL is influenced by the format of visual stimuli in WM, either feature-based or unified, object-based representations. In a pre-registered paradigm, participants learned stimulus-action combinations, mapping four stimuli onto two feature dimensions to one of two actions through probabilistic feedback. In parallel, participants retained the RL stimulus in WM and were asked to recall this stimulus after each trial. Crucially, the format of representation probed in WM was manipulated, with blocks encouraging either separate features or bound objects to be remembered. Incentivising a feature-based WM representation facilitated feature-based learning, shown by an improved choice strategy. This reveals a role of WM in providing sustained internal representations that are harnessed by RL, providing a framework by which these two cognitive processes cooperate.
The adhesion GPCR ADGRV1 controls glutamate homeostasis in hippocampal astrocytes supporting neuron development: first insights into to pathophysiology ofADGRV1-associated epilepsy
Authors: Güler Baran E. , Zorin Mark , Linnert Joshua , Nagel-Wolfrum Kerstin , Wolfrum Uwe
Published: April 2024

ADGRV1 is the largest member of adhesion G protein-coupled receptor (aGPCR) family. In the cell, aGPCRs have dual roles in cell adhesion and signal transduction. Mutations inADGRV1have been linked not only to Usher syndrome (USH), which causes deaf-blindness, but recently also to various forms of epilepsy. While the USH defects are attributed to the loss of fiber links between membranes formed by the extracellular domain of ADGRV1, the pathomechanisms leading to epilepsy remain elusive to date.

Here, we study the specific functions of ADGRV1 in astrocytes where it is highest expressed in the nervous system. Affinity proteomics showed the interaction of ADRGV1 with proteins enriched in astrocytes. Dysregulations of cellular processes important in astrocyte function were indicated by the different transcriptomes of patient-derived cells and Adgrv1-deficent mouse hippocampi compared to appropriate controls. Alteration in morphology and reduced numbers of astrocytes in the hippocampus of Adgrv1-deficent mice. Monitoring the glutamate uptake in colorimetric assay and by live cell imaging of a genetic glutamate reporter consistently showed that glutamate uptake from the extracellular environment is significantly reduced in Adgrv1-deficent astrocytes. Expression analyses of key enzymes of the glutamate-glutamine cycle in astrocytes and the glutamate metabolism indicated imbalanced glutamate homeostasis in Adgrv1-deficient astrocytes. Finally, we provide evidence that the supportive function of astrocytes in neuronal development also relies on ADGRV1 expression in astrocytes. Our data collectively provides first insights into the molecular pathophysiology underlying the development of epilepsy associated with mutations inADGRV1.

Highlights

ADGRV1 deficiency reduces the number of astrocytes in CA1 and changes the morphology of astrocytes in the hippocampus.

ADGRV1 interacts with numerous proteins enriched in astrocytes.

Differential transcriptomes revealed differential expression of genes related to glutamate homeostasis and epilepsy in ADGRV1 deficient models.

ADGRV1 controls glutamate uptake and regulates homeostasis in astrocytes.

ADGRV1 in astrocytes is vital for neuron morphogenesis.

First insights into the molecular pathophysiology underlying the development of epilepsy associated with mutations in ADGRV1.

Graphical Abstract
Cell Painting and chemical structure read-across can complement each other for rat acute oral toxicity prediction in chemical early de-risking
Authors: Camilleri Fabrice , Wenda Joanna M. , Pecoraro-Mercier Claire , Comet Jean-Paul , Rouquié David
Published: April 2024

Early de-risking decisions in the development of new chemical compounds, enable the identification of novel chemical candidates with improved safety profiles. In vivo studies are traditionally conducted in the early assessment of acute oral toxicity of crop protection products to avoid compounds which are considered “very acutely toxic”, with an in vivo Lethal Dose of 50% (LD50) ≤ 60 mg/kg bodyweight. Those studies are lengthy, costly, and raise ethical concerns, catalyzing the use of non-animal alternatives. The objective of our analysis was to assess the predictive efficacy of read-across approaches for acute oral toxicity in rats, comparing the use of chemical structure information, in vitro biological data derived from the Cell Painting profiling assay on U2OS cells or the combination of both. Our findings indicate that the classification of compounds as very acute oral toxic (LD50 ≤ 60 mg/kg) or not is possible using a read-across approach, with chemical structure information, morphological profiles, or a combination of both. When classifying compounds structurally similar to those in the training set, chemical structure was more predictive (balanced accuracy of 0.82). Conversely, when the compounds to be classified were structurally different from those in the training set, the morphological profiles were more predictive (balanced accuracy of 0.72). Combining the two models allowed for the classification of compounds structurally similar to those in the training set, to slightly improve the predictions (balanced accuracy of 0.85).

Abstract Figure

For Table of Contents Only
Sex-Specific Deflection of Age-Related DNA Methylation and Gene Expression in Mouse Heart by Perinatal Toxicant Exposures
Authors: Wang Kai , Sartor Maureen A. , Colacino Justin A. , Dolinoy Dana C. , Svoboda Laurie K.
Published: April 2024

Background

Global and site-specific changes in DNA methylation and gene expression are associated with cardiovascular aging and disease, but how toxicant exposures during early development influence the normal trajectory of these age-related molecular changes, and whether there are sex differences, has not yet been investigated.

Objectives

We used an established mouse model of developmental exposures to investigate the effects of perinatal exposure to either lead (Pb) or diethylhexyl phthalate (DEHP), two ubiquitous environmental contaminants strongly associated with CVD, on age-related cardiac DNA methylation and gene expression.

Methods

Dams were randomly assigned to receive human physiologically relevant levels of Pb (32 ppm in water), DEHP (25 mg/kg chow), or control water and chow. Exposures started two weeks prior to mating and continued until weaning at postnatal day 21 (3 weeks of age). Approximately one male and one female offspring per litter were followed to 3 weeks, 5 months, or 10 months of age, at which time whole hearts were collected (n ≥ 5 per sex per exposure). Enhanced reduced representation bisulfite sequencing (ERRBS) was used to assess the cardiac DNA methylome at 3 weeks and 10 months, and RNA-seq was conducted at all 3 time points. MethylSig and edgeR were used to identify age-related differentially methylated regions (DMRs) and differentially expressed genes (DEGs), respectively, within each sex and exposure group. Cell type deconvolution of bulk RNA-seq data was conducted using the MuSiC algorithm and publicly available single cell RNA-seq data.

Results

Thousands of DMRs and hundreds of DEGs were identified in control, DEHP, and Pb-exposed hearts across time between 3 weeks and 10 months of age. A closer look at the genes and pathways showing differential DNA methylation revealed that the majority were unique to each sex and exposure group. Overall, pathways governing development and differentiation were most frequently altered with age in all conditions. A small number of genes in each group showed significant changes in DNA methylation and gene expression with age, including several that were altered by both toxicants but were unchanged in control. We also observed subtle, but significant changes in the proportion of several cell types due to age, sex, and developmental exposure.

Discussion

Together these data show that perinatal Pb or DEHP exposures deflect normal age-related gene expression, DNA methylation programs, and cellular composition across the life course, long after cessation of exposure, and highlight potential biomarkers of developmental toxicant exposures. Further studies are needed to investigate how these epigenetic and transcriptional changes impact cardiovascular health across the life course.
Caspar specifies primordial germ cell count and identity inDrosophila melanogaster
Authors: Das Subhradip , Hegde Sushmitha , Wagh Neel , Sudhakaran Jyothish , Roy Adheena Elsa , Deshpande Girish , Ratnaparkhi Girish S
Published: April 2024

Repurposing of pleiotropic factors during execution of diverse cellular processes has emerged as a regulatory paradigm. Embryonic development in metazoans is controlled by maternal factors deposited in the egg during oogenesis. Here, we explore maternal role(s) of Caspar (Casp), theDrosophilaorthologue of human Fas-associated factor-1 (FAF1) originally implicated in host-defense as a negative regulator of NF-κB signaling. Maternal loss of either Casp or it’s protein partner, Transitional endoplasmic reticulum 94 (TER94) leads to partial embryonic lethality correlated with aberrant centrosome behavior, cytoskeletal abnormalities, and defective gastrulation. Although ubiquitously distributed, both proteins are enriched in the primordial germ cells (PGCs), and in keeping with the centrosome problems, mutant embryos display a significant reduction in the PGC count. Moreover, the total number of pole buds is directly proportional to the level of Casp. Consistently, it’s ‘loss’ and ‘gain’ results in respective reduction and increase in the Oskar protein levels, the master determinant of PGC fate. To elucidate this regulatory loop, we analyzed several known components of mid-blastula transition and identify the translational repressor Smaug, a zygotic regulator of germ cell specification, as a potential critical target. We present a detailed structure-function analysis of Casp aimed at understanding its novel involvement during PGC development.
APOE3-R136Smutation confers resilience against tau pathology via cGAS-STING-IFN inhibition
Authors: Naguib Sarah , Lopez-Lee Chloe , Torres Eileen Ruth , Lee Se-In , Zhu Jingjie , Zhu Daphne , Ye Pearly , Norman Kendra , Zhao Mingrui , Wong Man Ying , Ambaw Yohannes A. , Castaneda Rodrigo , Wang Wei , Patel Tark , Bhagwat Maitreyee , Norinsky Rada , Mok Sue-Ann , Walther Tobias C. , Farese Robert V. , Luo Wenjie , Sinha Subhash , Wu Zhuhao , Fan Li , Gong Shiaoching , Gan Li
Published: April 2024

The Christchurch mutation (R136S) on theAPOE3(E3S/S) gene is associated with attenuation of tau load and cognitive decline despite the presence of a causalPSEN1mutation and high levels of amyloid beta pathology in the carrier1. However, the specific molecular mechanisms enabling theE3S/Smutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouseApoEwith wild-type humanE3orE3S/Son a tauopathy background. TheR136Smutation markedly decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in theta and gamma powers. Additionally, theR136Smutation reduced interferon response to tau pathology in both mouse and human microglia, suppressing cGAS-STING activation. Treating tauopathy mice carrying wild-typeE3with a cGAS inhibitor protected against tau-induced synaptic loss and induced similar transcriptomic alterations to those induced by theR136Smutation across brain cell types. Thus, suppression of microglial cGAS-STING-IFN pathway plays a central role in mediating the protective effects ofR136Sagainst tauopathy.

One-sentence summary

The R136S mutation on APOE3 enhances resistance to tau-related pathology and toxicity by downregulating the cGAS-STING-IFN signaling pathway.
The Role of Similarity of Stimuli and Responses in Learning by Nectar-Foraging Bumble Bees: A Test of Osgood’s Model
Authors: Baek Minjung , Papaj Daniel R.
Published: April 2024

Learning stimulus – response associations helps animals to adjust to changing environments. Sequentially learned associations may interact with each other, either reinforcing memory, a process referred to as ‘transfer’, or hindering memory, a process referred to as ‘interference.’ According to Osgood’s (1949) model, close similarity between new and previously learned stimuli can enhance the transfer of memory through a process of stimulus generalization. In contrast, the model proposes that if responses are different from those previously learned, generalizing stimuli may lead to confusion, resulting in the interference of memory. Except for some work in humans, the interaction between stimulus similarity and response similarity is poorly documented. Here, we tested Osgood’s model using bumble bees (Bombus impatiens) foraging for sucrose on artificial flowers with varied colours (= stimuli) that required either legitimate visitation or nectar robbing (= responses). Bees were first allowed to forage on one type of flower, were then switched to another, and finally were returned to the initial flower type. We measured learning performance via flower handling time and the number of failed visits. Consistent with Osgood’s model, bees made more failed visits when they switched between similarly coloured flowers requiring different foraging techniques but made fewer failed visits when switching between similarly coloured flowers with the same technique. Regardless of similarities in stimuli or responses, however, experienced bees were faster in handling flowers than were naïve bees. Results taken together thus provided mixed support for Osgood’s model. Possible explanations for the mixed results are discussed.
Effects of conceptus proteins on endometrium and blood leukocytes of dairy cattle using transcriptome and meta-analysis
Authors: Isabel da Silva Maria , Ott Troy
Published: April 2024

This study investigates the short and long-term effects of IFNT and PAG on the transcriptome of endometrium and blood leukocytes. Holstein heifers received intrauterine infusions of one of the following treatments: 20 mL of a 200 μg/mL bovine serum albumin solution (BSA; vehicle) from day 14 to 16 of the estrous cycle (BSA), vehicle + 10 μg/mL of IFNT from day 14 to 16 (IFNT3), vehicle + 10 μg/mL of IFNT from day 14 to 19 (IFNT6), and vehicle + 10 μg/mL of IFNT from day 14 to 16 followed by vehicle + 10 μg/mL of IFNT + 5 μg/mL of PAG from day 17 to 19 (IFNT+PAG). RNA-seq analysis was performed in endometrial biopsies and blood leukocytes collected after treatments. Acute IFNT signaling in the endometrium (IFNT3 vs BSA), induced differentially expressed genes (DEG) associated with interferon activation, immune response, inflammation, cell death, and inhibited vesicle transport and extracellular matrix remodeling. Prolonged IFNT signaling (IFNT6 vs IFNT3) altered gene expression related to cell invasion, retinoic acid signaling, and embryo implantation. In contrast, PAG induced numerous DEG in blood leukocytes but only 4 DEG in the endometrium. In blood leukocytes, PAG stimulated genes involved in development and TGFB signaling while inhibiting interferon signaling and cell migration. Overall, IFNT is a primary regulator of endometrial gene expression, while PAG predominantly affected the transcriptome of circulating immune cells during early pregnancy. Further research is essential to fully grasp the roles of identified DEG in both the endometrium and blood leukocytes.

Graphic abstract

Main findings

Acute IFNT signaling in the endometrium activates genes involved in inflammation while inhibiting vesicle transport in cells and ECM remodeling.

Prolonged IFNT signaling in the endometrium regulates genes involved in cell invasion and retinoic acid signaling.

PAG alter gene expression in blood leukocytes more than in endometrium and may stimulate leukocyte differentiation while inhibiting leukocyte extravasation.
Lactate transport inhibition therapeutically reprograms fibroblast metabolism in experimental pulmonary fibrosis
Authors: Ziehr David R. , Li Fei , Mark Parnell K. , Krah Nathan M. , Leahy Kevin J. , Guillermier Christelle , Varon Jack , Baron Rebecca M. , Maron Bradley A. , Philp Nancy J. , Hariri Lida P. , Kim Edy Y. , Steinhauser Matthew L. , Knipe Rachel S. , Rutter Jared , Oldham William M.
Published: April 2024

Myofibroblast differentiation, essential for driving extracellular matrix synthesis in pulmonary fibrosis, requires increased glycolysis. While glycolytic cells must export lactate, the contributions of lactate transporters to myofibroblast differentiation are unknown. In this study, we investigated how MCT1 and MCT4, key lactate transporters, influence myofibroblast differentiation and experimental pulmonary fibrosis. Our findings reveal that inhibiting MCT1 or MCT4 reduces TGFβ-stimulated pulmonary myofibroblast differentiationin vitroand decreases bleomycin-induced pulmonary fibrosisin vivo. Through comprehensive metabolic analyses, including bioenergetics, stable isotope tracing, metabolomics, and imaging mass spectrometry in both cells and mice, we demonstrate that inhibiting lactate transport enhances oxidative phosphorylation, reduces reactive oxygen species production, and diminishes glucose metabolite incorporation into fibrotic lung regions. Furthermore, we introduce VB253, a novel MCT4 inhibitor, which ameliorates pulmonary fibrosis in both young and aged mice, with comparable efficacy to established antifibrotic therapies. These results underscore the necessity of lactate transport for myofibroblast differentiation, identify MCT1 and MCT4 as promising pharmacologic targets in pulmonary fibrosis, and support further evaluation of lactate transport inhibitors for patients for whom limited therapeutic options currently exist.

Small molecule inhibitors of lactate transporters, including the novel MCT4 inhibitor VB253, reprogram fibroblast metabolism to prevent myofibroblast differentiation and decrease bleomycin-induced pulmonary fibrosis.
Intrinsically disordered membrane anchors of Rheb, RhoA and DiRas3 small GTPases: Molecular dynamics, membrane organization, and interactions
Authors: Hutchins Chase M. , Gorfe Alemayehu A.
Published: April 2024

Protein structure has been well established to play a key role in determining function; however, intrinsically disordered proteins and regions (IDPs and IDRs) defy this paradigm. IDPs and IDRs exist as an ensemble of structures rather than a stable 3D structure yet play essential roles in many cell signaling processes. Nearly all Ras Superfamily GTPases are tethered to membranes by a lipid tail at the end of a flexible IDR. The sequence of these IDRs are key determinants of membrane localization, and interactions between the IDR and the membrane have been shown to affect signaling in RAS proteins through modulation of dynamic membrane organization. Here we utilized atomistic molecular dynamics simulations to study the membrane interactions, conformational dynamics, and lipid sorting of three IDRs from small GTPases Rheb, RhoA and DiRas3 in model membranes representing their physiological target membranes. We found that complementarity between lipidated IDR sequence and target membrane lipid composition is a determinant of conformational plasticity. We also show that electrostatic interactions between anionic lipids and basic residues on IDRs generate semi-stable conformational sub-states, and a lack of these residues leads to greater conformational diversity. Finally, we show that small GTPase IDRs with a polybasic domain alter local lipid composition by segregating anionic membrane lipids, and, in some cases, excluding other lipids from their immediate proximity in favor of anionic lipids.
Generation and validation of a D1 dopamine receptor Flpo knock-in mouse
Authors: Oppman Alexis M. , Paradee William J. , Narayanan Nandakumar S. , Kim Young-cho
Published: April 2024

Background

Dopamine is a powerful neuromodulator of diverse brain functions, including movement, motivation, reward, and cognition. D1-type dopamine receptors (D1DRs) are the most prevalently expressed dopamine receptors in the brain. Neurons expressing D1DRs are heterogeneous and involve several subpopulations. Studying these neurons has been limited by current animal models, especially when considering their integration with conditional or intersectional genetic tools.

New method

To address this limitation, we developed a novel Drd1-P2A-Flpo (Drd1-Flpo) mouse line in which the Flpo gene was knocked in immediately after the Drd1 gene using CRISPR-Cas9. We validated the Drd1-Flpo line by confirming Flp expression and functionality specific to D1DR+ neurons.

Comparison with existing methods: The Drd1-Flpo line is useful resource for studying subpopulation of D1DR+ neurons with intersectional genetic tools.

Conclusions

We demonstrated brain-wide GFP expression driven by Drd1-Flpo, suggesting that this mouse line may be useful for comprehensive anatomical and functional studies in many brain regions. The Drd1-Flpo model will advance the study of dopaminergic signaling by providing a new tool for investigating the diverse roles of D1DR+ neurons and their subpopulations in brain disease.

Significance Statement

The roles of dopamine in the brain are mediated by dopamine receptors. D1-type dopamine receptors (D1DRs) and D1DR-expressing (D1DR+) neurons play important roles in various brain functions. We generated a Drd1-Flpo mouse line that expresses Flp recombinase in D1DR+ neurons. This novel Drd1-Flpo mouse facilitates investigation of specific roles of D1DR+ neurons in various brain areas including the striatum, frontal cortex, and cerebellum, and it provides an alternative to existing Drd1-Cre mice. In addition, the Drd1-Flpo mouse line provides a tool for intersectional genetic studies, when used with existing transgenic Cre lines. The Drd1-Flpo mouse line can help unravel the specific contributions of D1DR+ neuron subpopulations to brain function and dysfunction.
Identification and Characterization of Compounds that Improve Plant Photosynthesis and Growth under Light Stress Conditions
Authors: Qu Yuchen , Sakoda Kazuma , Wakabayashi Yu , Nakajima Masatoshi , Asami Tadao , Terashima Ichiro , Yamori Wataru
Published: April 2024

In order to satisfy the food and fuel demands of a growing population, global food production needs to increase by more than 50% before 2050. However, various environmental stresses in the natural environment inhibit plant growth and result in reduced yields. This is primarily caused by decreases in photosynthetic capacity. Thus, there is an urgent need to develop new strategies to improve agricultural productivity and ensure food security. In this study, a novel chemical-screening system with 96 well plates and leaf disks of tobacco was used to identify several anthraquinone derivatives that could relieve high light stress from plants. Treatments with these chemicals induced greater photosynthetic capacity after high light stress conditions for 20–72 hours (h) in tobacco and better plant growth after exposure to light stress for 96 hours in Arabidopsis and lettuces. The photoprotective effect of anthraquinone derivatives is closely related to chemical induced oxidation of PSI. Furthermore, there were no negative effects on plant growth in chemically treated plants under non-stressful conditions. Taken together, this study shows that anthraquinone derivatives can confer high light stress tolerance in plants, resulting in improved plant photosynthesis and growth in environments with light stress.
Predicting gene expression responses to environment inArabidopsis thalianausing natural variation in DNA sequence
Authors: Takou Margarita , Bellis Emily S , Lasky Jesse R
Published: April 2024

The evolution of gene expression responses are a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved forcisregulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlyingcis-regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverseArabidopsis thalianaaccessions. We first tested for evidence thatcisregulation plays a role in environmental response, finding 14 and 15 motifs that were significantly enriched within the up- and down-stream regions of cold-responsive differentially regulated genes (DEGs). We next applied convolutional neural networks (CNNs), which learnde novo cis-regulatory motifs in DNA sequences to predict expression response to environment. We found that CNNs predicted differential expression with moderate accuracy, with evidence that predictions were hindered by biological complexity of regulation and the large potential regulatory code. Overall, DEGs between specific environments can be predicted based on variation incis-regulatory sequences, although more information needs to be incorporated and better models may be required.
Heparan sulfate regulates amphiregulin signaling towards reparative lung mesenchymal cells during influenza A infection
Authors: Loffredo Lucas F. , Surpur Anmol , Ringham Olivia R. , Li Fangda , de los Santos-Alexis Kenia , Arpaia Nicholas
Published: April 2024

Amphiregulin (Areg), a growth factor produced by regulatory T (Treg) cells to facilitate tissue repair/regeneration, contains a heparan sulfate (HS) binding domain. How HS, a highly sulfated glycan subtype that alters growth factor signaling, influences Areg repair/regeneration functions is unclear. Here we report that inhibition of HS in various cell lines and primary lung mesenchymal cells (LMC) qualitatively alters downstream signaling and highlights the existence of HS-dependent vs. -independent Areg transcriptional signatures. Utilizing a panel of cell lines with targeted deletions in HS synthesis–related genes, we found that the presence of the glypican family of heparan sulfate proteoglycans is critical for Areg signaling and confirmed this dependency in primary LMC by siRNA-mediated knockdown. Furthermore, in the context of influenza A (IAV) infectionin vivo, we found that an Areg-responsive subset of reparative LMC upregulate glypican-4 and HS. Conditional deletion of HS primarily within this LMC subset resulted in reduced blood oxygen saturation following infection with IAV, with no changes in viral load. Finally, we found that co-culture of HS-knockout LMC with IAV-induced Treg cells results in reduced LMC responses. Collectively, this study reveals the essentiality of HS on a specific lung mesenchymal population as a mediator of Treg cell–derived Areg reparative signaling during IAV infection.
Epithelial IL-2 is critical for NK cell-mediated cancer immunosurveillance in mammary glands
Authors: Wang Lei , Maharjan Chandra K , Borcherding Nicholas , Master Rohan P , Mo Jiao , Tithi Tanzia Islam , Kim Myung-Chul , Carelock Madison E , Master Anuj P. , Gibson-Corley Katherine N. , Kolb Ryan H. , Smith Kendall A. , Zhang Weizhou
Published: April 2024

Interleukin 2 (IL-2) is the first identified cytokine and its interaction with receptors has been known to shape the immune responses in many lymphoid or non-lymphoid tissues for more than four decades. Active T cells are the primary cellular source for IL-2 production and epithelial cells have never been considered the major cellular source of IL-2 under physiological conditions. It is, however, tempting to speculate that epithelial cells could potentially express IL-2 that regulates the intricate interactions between epithelial cells and lymphocytes. Datamining our recently published single-cell RNAseq in the mouse mammary gland identified IL-2 expression in mammary epithelial cells, which is induced by prolactin via the STAT5 signaling pathway. Furthermore, epithelial IL-2 plays a crucial role in maintaining the physiological functions of natural killer (NK) cells within the mammary glands. IL-2 deletion in the mammary epithelial cells leads to a significant reduction in the number and function of NK cells, which in turn results in defective immunosurveillance, expansion of luminal epithelial cells, and tumor development. Interestingly, T cells in the mammary glands are not changed, indicating the specific regulation of NK cells by epithelial IL-2 production. In agreement, we also found that human epithelial cells express IL-2 and NK cells express the highest level of IL2RB among all the immune cells. Here, we provide the first evidence that epithelial cells produce IL-2, which is critical for maintaining the physiological functions of NK cells in immunosurveillance.
Management recommendations for Alpine protection forests: the importance of regeneration quality and initial stand composition
Authors: Schmid Ueli , Frehner Monika , Bugmann Harald
Published: April 2024

The protection of infrastructure against gravitational natural hazards is one of the most important ecosystem services (ES) of mountain forests in Alpine countries. For a continuous provision of this ES, forests need to have a high protective effect, e.g., high canopy cover and/or stem numbers, while being resistant to and resilient after disturbances by being well-structured and stable, having a species composition adapted to the local site conditions and sufficient regeneration, all on a relatively small spatial scale.

While “natural” forests may fulfill these prerequisites without human intervention, management history and high levels of ungulate browsing have produced unsustainable stand structures in many protection forests that need to be improved by management. The general principles of protection forest management are well established, but there are no quantitative, science-based recommendations for management regimes, i.e., specific sequences of interventions, that ensure a continuous protective quality. Our goal was to derive such recommendations for different stand types across three elevational zones, from mixed forests of the upper montane to spruce forests of the subalpine zone.

We used an updated version of the model ProForM to simulate stand development under different levels of ungulate browsing, testing a large number of management regimes that vary in the spatial aggregation of tree removal, the intensity and interval of the interventions. We investigated the influence of browsing pressure and management on the protective quality using Boosted Regression Trees and Beta regression.

High levels of ungulate browsing had such a strong negative effect on the protective quality that it could not be improved through forest management. This underlines the need for maintaining ungulate densities in Alpine forests at levels that allow for the successful regeneration of all key tree species. In stands that are influenced less by browsing, the protective quality can be improved through management in many cases, with specific management recommendations differing mostly depending on the initial stand conditions and, to a lesser extent, on the elevational zone. Well-structured stands provide a high protective quality without management interventions during at least a century across all elevational zones. In young and in mature stands, we generally recommend management regimes with relatively long return intervals of 30 to 40 years and low intervention intensities of 10 to 20% basal area removal.
Aging-associated decline of phosphatidylcholine synthesis is a malleable trigger of natural mitochondrial aging
Authors: Poliezhaieva Tetiana , Pernas Pol Alonso , Espada Lilia , Bayar Melike , Li Yuting , Dönertaş Handan Melike , Ermolaeva Maria A.
Published: April 2024

Mitochondrial dysfunction is a prominent hallmark of aging contributing to the functional decline of metabolic plasticity in late life. While genetic distortions of mitochondrial integrity elicit premature aging, the mechanisms leading to “natural” aging of mitochondria are less clear. Here we initially used proteomics, genetics and functional tests in wild typeC. elegansand long-livedclk-1(qm30)andisp-1(qm150)mitochondrial mutants to identify molecular pathways that safeguard longevity amid persistent mitochondrial inefficiency. Strikingly, these analyses and subsequent transcriptomic and functional tests in the human system revealed aging-associated decline of phosphatidylcholine (PC) synthesis as a trigger of mitochondrial network disruption, which contributes to mitochondrial dysfunction during normal aging. Moreover, we found that ectopic boosting of PC levels via diet restores late life mitochondrial integrityin vivoand rescues metabolic plasticity in cell culture tests. Our work thus uncovered a novel natural driver of mitochondrial aging that is malleable by dietary interventions.
MicroRNA 21 induces carcinogenesis in hepatic cells by modulating mitochondrial metabolism
Authors: Maurya Ashutosh Kumar , Edatt Lincy , Kumar V.B. Sameer
Published: April 2024

Mitochondria plays crucial role in cell’s survivability and normal functioning. But in the case of cancer, the mitochondrial machinery (ETC) is altered and glycolytic pathway is activated as an alternate source of energy. The main reason behind the reprogramming of mitochondrial machinery could be mutations in mitochondrial genes or suppression of genes involved in normal functioning of the mitochondria. MicroRNAs could be a key player in modulating the mitochondrial metabolism, as they have targets on various important mitochondrial genes involved in the Electron Transport Chain of the mitochondria. Any alteration in the expression pattern of the mitochondrial genes would directly contribute to the modulation of normal functioning of the mitochondrial machinery. Micro RNA 21 is an oncomiR, located at q arm of the 17thchromosome. MiR 21 has been reported to be involved in many types of cancer. MiR 21 is reported to have targets on many important genes, crucial for cell survivability and proliferation, most of which falls in the category of tumor suppressor genes. With our bioinformatics analysis, we found that miR 21 has targets on important mitochondrial genes involved in the ETC. So, we tried to elucidate the role of miR 21 in modulation of the mitochondrial machinery and role of this alteration in the mitochondrial mechanism in carcinogenesis. Our results revealed that miR 21 have targets on the Cytochrome C Oxidase 1 (Cox1), which is directly involved in the Complex 4 of the electron transport chain. Next we checked the phenotypic effects of this down regulation of Cox1 by measuring the oxygen consumption by the mitochondria and found that O2 consumption goes significantly down in miR 21 over expressing cells. Along with this, we also checked if exosomes from miR 21 overexpressing cancer cells could induce the carcinogenesis in the normal hepatic cells and found that miR 21 accelerates the rate of cellular migration and enhances the colony formation. The results together suggest that miR 21 posses carcinogenic property, possibly by modulating mitochondrial machinery.