bluuebunny/crossref_metadata_2025 huggingface dataset:
Calibration of instrumented treadmills using an instrumented pole; a modified version to use relatively smaller forces
Authors: Hosseini-Yazdi Seyed-Saleh
Published: July 2024

The instrumented treadmills’ quality of the generated Ground Reaction Forces (GRF) may degrade over time, as the original calibration matrix may not accurately represent the exerted forces. A cost-effective alternative to manufacturer recalibration is to use an instrumented pole for calibration. Collins et al. presented a simple method to collect multiple data points by exerting forces in various directions. The sensor on the instrumented pole provides instantaneous force magnitudes, while motion capture records the pole’s instantaneous directions. They recommended a relatively large force magnitude (1000N), requiring at least two individuals. Using an optimization method, the new calibration may be estimate by relating the exerted forces (pole) to the treadmill signals. Here, we attempted to simplify the process further, allowing a single individual to perform force exertion with additional force exertion direction. Thus, the calibrating forces were reduced to one-third of the prior recommendation. This maintained the structural integrity of the pole and helped avoid inducing bending moments that could affect calibration results. The cross-validation score for test data (prediction score) was at least 0.92. Additionally, comparing GRFs in posterior/anterior and vertical directions with a benchmark treadmill for even walking revealed an average cross-correlation of 0.97.
Interoceptive Signals Bias Decision Making in Rhesus Macaques
Authors: Cardenas Michael A. , Le Ryan P. , Champ Tess M. , O’Neill Derek , Fuglevand Andrew J. , Gothard Katalin M.
Published: July 2024

Several influential theories have proposed that interoceptive signals, sent from the body to the brain, contribute to neural processes that coordinate complex behaviors. We altered the physiological state of the body using compounds that have minimal effect on the brain and evaluated their effect on decision-making in rhesus monkeys. We used glycopyrrolate, a non-specific muscarinic (parasympathetic) antagonist, and isoproterenol, a beta-1/2 (sympathetic) agonist, to create a sympathetic-dominated state in the periphery, that was indexed by increased heart rate. Rhesus monkeys were trained on two variants of an approach-avoidance conflict task. The tasks offered a choice between enduring mildly aversive stimuli in exchange for a steady flow of rewards, or cancelling the aversive stimuli, forgoing the rewards. The delay to interrupt the aversive stimuli was used as a measure of monkeys’ tolerance for contact with a hot but not painful stimulus or airflow directed at their muzzle. Both drugs reduced tolerance for the aversive stimuli. To determine whether the drug-induced autonomic state reduced the subjective value of the reward, we tested the effects of glycopyrrolate on a food preference task. Food preference was unaltered, suggesting that the sympathetic dominated state in the periphery selectively reduces tolerance for aversive stimuli without altering reward-seeking behaviors. As the drugs used are expected to have little or no direct effect on the brain, the observed biases in decision making are likely induced by interoceptive afferents that signal to the brain the physiological state of the body.

Significance statement

The brain adjusts body physiology to the behavioral agenda of the organism through autonomic efferents; concomitantly interoceptive afferents carry signals that inform the brain about the physiological state of the body, closing a homeostatic regulatory loop. Persuasive theories proposed that interoceptive afferents contribute to higher cognitive functions, including emotion. Empirical evidence that these signals are sufficient to bias complex behavior has been limited by the difficulty of isolating interoceptive afferents from the rest of the homeostatic loop. Here we selectively manipulated the autonomic state of the body using drugs with limited penetrance of the brain in macaques performing decision-making tasks. Sympathetic-dominated peripheral states significantly altered decision making, suggesting that changes in interoceptive afferent signals are sufficient to bias behavior.
Smooth muscle expression of RNA editing enzymeADAR1controls activation of RNA sensor MDA5 in atherosclerosis
Authors: Weldy Chad S. , Li Qin , Monteiro João P. , Guo Hongchao , Galls Drew , Gu Wenduo , Cheng Paul P. , Ramste Markus , Li Daniel , Palmisano Brian T. , Sharma Disha , Worssam Matthew D. , Zhao Quanyi , Bhate Amruta , Kundu Ramendra K. , Nguyen Trieu , Li Jin Billy , Quertermous Thomas
Published: July 2024

Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 (IFIH1) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing by MDA5 to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specificAdar1deletion mouse model on a pro-atherosclerosis background with additional constitutive deletion of MDA5 (Ifih1), and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state by regulating Mda5 activation, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.

One Sentence Summary

Smooth muscle expression of RNA editing enzyme ADAR1 regulates activation of double strand RNA sensor MDA5 in novel mechanism of atherosclerosis.
Co-activation of selective nicotinic acetylcholine receptor subtypes is required to reverse hippocampal network dysfunction and prevent fear memory loss in Alzheimer’s disease
Authors: Lee Rahmi , Kim Gayeon , Kim Seonil
Published: July 2024

Alzheimer’s disease (AD) is the most common form of dementia with no known cause and cure. Research suggests that a reduction of GABAergic inhibitory interneurons’ activity in the hippocampus by beta-amyloid peptide (Aβ) is a crucial trigger for cognitive impairment in AD via hyperexcitability. Therefore, enhancing hippocampal inhibition is thought to be protective against AD. However, hippocampal inhibitory cells are highly diverse, and these distinct interneuron subtypes differentially regulate hippocampal inhibitory circuits and cognitive processes. Moreover, Aβ unlikely affects all subtypes of inhibitory interneurons in the hippocampus equally. Hence, identifying the affected interneuron subtypes in AD to enhance hippocampal inhibition optimally is conceptually and practically challenging. We have previously found that Aβ selectively binds to two of the three major hippocampal nicotinic acetylcholine receptor (nAChR) subtypes, α7- and α4β2-nAChRs, but not α3β4-nAChRs, and inhibits these two receptors in cultured hippocampal inhibitory interneurons to decrease their activity, leading to hyperexcitation and synaptic dysfunction in excitatory neurons. We have also revealed that co-activation of α7- and α4β2-nAChRs is required to reverse the Aβ-induced adverse effects in hippocampal excitatory neurons. Here, we discover that α7- and α4β2-nAChRs predominantly control the nicotinic cholinergic signaling and neuronal activity in hippocampal parvalbumin-positive (PV+) and somatostatin-positive (SST+) inhibitory interneurons, respectively. Furthermore, we reveal that co-activation of these receptors is necessary to reverse hippocampal network dysfunction and fear memory loss in the amyloid pathology model mice. We thus suggest that co-activation of PV+ and SST+ cells is a novel strategy to reverse hippocampal dysfunction and cognitive decline in AD.
Array Detection Enables Large Localization Range for Simple and Robust MINFLUX
Authors: Slenders Eli , Patil Sanket , Held Marcus Oliver , Zunino Alessandro , Vicidomini Giuseppe
Published: July 2024

The MINFLUX concept significantly enhances the spatial resolution of single-molecule localization microscopy (SMLM) by overcoming the limit imposed by the fluorophore’s photon counts. Typical MINFLUX microscopes localize the target molecule by scanning a zero-intensity focus around the molecule in a circular trajectory, with smaller trajectory diameters yielding lower localization uncertainties for a given number of photons. Since this approach requires the molecule to be within the scanned trajectory, MINFLUX typically relies on a photon-demanding iterative scheme with decreasing trajectory diameters. Although the iterative procedure does not substantially reduce the photon efficiency of MINFLUX, this approach is prone to misplacements of the trajectory and increases the system’s complexity. In this work, we introduce ISM-FLUX, a novel implementation of MINFLUX using image-scanning microscopy (ISM) with a single-photon avalanche diode (SPAD) array detector. ISM-FLUX provides precise MINFLUX localization within the trajectory while maintaining conventional photon-limited uncertainty outside it. The robustness of ISM-FLUX localization results in a larger localization range and greatly simplifies the architecture, which may facilitate broader adoption of MIN-FLUX.
Single-nanoparticle electrophoretic mobility determination and trapping using active-feedback 3D tracking
Authors: Johnson Alexis , Welsher Kevin D.
Published: July 2024

Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EM on a per-particle basis. Single-nanoparticle EM is determined by using active feedback to “lock on” to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EM in various ionic strengths (0.25-5 mM) and found decreased EM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.
Identifying foraging spatial cues in beehive sound activity using machine learning methods
Authors: Bocanegra David , Galvez Jorge , Di Nayan , Liu Fanglin , Wario Fernando
Published: July 2024

The beehive sound, a continuous signal produced by bees within the hive, has been found to correlate with different behavioral states of the colony, like being queenless and swarming. We investigated the possibility of identifying foraging spatial cues in this signal. We recorded a colony’s sound while foraging from food sources located at three different distances from the hive, one at a time. The recordings were split into frames to obtain six statistics of their Mel Frequency Cepstral Coefficients. Then, we evaluated different autoencoding networks to obtain a latent space that allowed frames from different foraging distances to be easily differentiable. The high accuracy, silhouette score, and F1 score shown in the obtained latent spaces strongly support our approach for identifying foraging spatial cues in beehive sound activity.
Temporal resolution of spike coding in feedforward networks with signal convergence and divergence
Authors: Mobille Zach , Sikandar Usama Bin , Sponberg Simon , Choi Hannah
Published: July 2024

Convergent and divergent structures in the networks that make up biological brains are found universally across many species and brain regions at various scales. Neurons in these networks fire action potentials, or "spikes", whose precise timing is becoming increasingly appreciated as large sources of information about both sensory input and motor output. While previous theories on coding in convergent and divergent networks have largely neglected the role of precise spike timing, our model and analyses place this aspect at the forefront. For a suite of stimuli with different timescales, we demonstrate that structural bottlenecks (small groups of neurons) post-synaptic to network convergence have a stronger preference for spike timing codes than expansion layers created by structural divergence. Additionally, we found that a simple network model with similar convergence and divergence ratios to those found experimentally can reproduce the relative contribution of spike timing information about motor output in the hawkmoth Manduca sexta. Our simulations and analyses suggest a relationship between the level of convergent/divergent structure present in a feedforward network and the loss of stimulus information encoded by its population spike trains as their temporal resolution decreases, which could be confirmed experimentally across diverse neural systems in future studies. We further show that this relationship can be generalized across different models and measures, implying a potentially fundamental link between network structure and coding strategy using spikes.
Prefrontal and ventral striatal dendritic morphology: effects of life-long complex housing and amphetamine administration
Authors: Kolb Bryan , Robinson Terry E.
Published: July 2024

Complex housing is one of the most effective experiences in producing plastic changes in the brain. For example, animals living in complex environments show widespread synaptic changes both in cerebral cortex and the striatum. Similarly, repeatedly treating animals with psychomotor stimulants such as amphetamine also induces changes in prefrontal cortex and the striatum. The purpose of the current study was to determine the effects of life-long housing in complex environments versus standard laboratory caging and this experience influenced the later effects of amphetamine. Both male and female Long-Evans rats were placed in complex environments for about 110 days, beginning at conception, until adulthood at which time they were administered saline or amphetamine daily (1 mg/kg, IP) for 14 days. A week later the brains were harvested and processed for Golgi-Cox staining to analyze dendritic length, branching, and spine density in prefrontal cortex (areas Cg3 and AID) and Nucleus Accumbens (NAcc). The results showed that the prolonged period of enriched housing produced significant synaptic changes in all three measures in all three areas measured, but the effects differed in the two sexes. Amphetamine produced large synaptic changes in Cg3 and NAcc in males but only spine changes in those regions in females. Complex housing did not interact with the later effects of amphetamine administration. Thus, both complex housing and amphetamine can produce a range of synaptic changes depending upon sex and area examined. Furthermore, the effect of complex housing varies depending on the details of when complex housing is begun and how long it lasts.
Computational Insights into the Molecular Dynamics of the Binding of Ligands in the Methanol Dehydrogenase
Authors: Lee One-Sun , Lee Sung Haeng
Published: July 2024

Methanol dehydrogenase (MDH) is a promising biocatalyst for industrial use, converting methanol to formaldehyde. Our molecular modeling revealed methanol binds to MDH with ∼7 kcal/mol free energy, while formaldehyde binds with ∼4 kcal/mol. This suggests methanol remains longer in the active site, and formaldehyde exits more readily post-reaction. These insights are crucial for designing more efficient MDH variants for industrial applications.

Graphical abstract

The left panel shows methanol and formaldehyde within the active site of methanol dehydrogenase, illustrating entry and release paths. The right panel presents the free energy profiles, indicating methanol’s stronger binding affinity and formaldehyde’s easier release post-reaction.
Cell-Type-Specific Regulation of Cocaine Reward by the E2F3a Transcription Factor in Nucleus Accumbens
Authors: Martínez-Rivera Freddyson J. , Yim Yun Young , Godino Arthur , Minier-Toribio Angélica , Tofani Solange , Holt Leanne M. , Torres-Berrío Angélica , Futamura Rita , Browne Caleb J. , Markovic Tamara , Hamilton Peter J. , Neve Rachael L. , Nestler Eric J.
Published: July 2024

The development of drug addiction is characterized by molecular changes in brain reward regions that lead to the transition from recreational to compulsive drug use. These neurobiological processes in brain reward regions, such as the nucleus accumbens (NAc), are orchestrated in large part by transcriptional regulation. Our group recently identified the transcription factor E2F3a as a novel regulator of cocaine’s rewarding effects and gene expression regulation in the NAc of male mice. Despite this progress, no information is available about the role of E2F3a in regulating cocaine reward at the sex- and cell-specific levels. Here, we used male and female mice expressing Cre-recombinase in either D1- or D2-type medium spiny neurons (MSNs) combined with viral-mediated gene transfer to bidirectionally control levels of E2F3a in a cell-type-specific manner in the NAc during conditioned place preference (CPP) to cocaine. Our findings show that selective overexpression of E2F3a in D1-MSNs increased cocaine CPP in both male and female mice, whereas opposite effects were observed under knockdown conditions. In contrast, equivalent E2F3a manipulations in D2-MSNs had no significant effects. To further explore the role of E2F3a in sophisticated operant and motivated behaviors, we performed viral manipulations of all NAc neurons in combination with cocaine self-administration and behavioral economics procedures in rats and demonstrated that E2F3a regulates sensitivity aspects of cocaine seeking and taking. These results confirm E2F3a as a central substrate of cocaine reward and demonstrate that this effect is mediated in D1-MSNs, thereby providing increased knowledge of cocaine action at the transcriptional level.
Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
Authors: Ravikrishnan Aarthi , Wijaya Indrik , Png Eileen , Chng Kern Rei , Pei Eliza Ho Xin , Qi Amanda Ng Hui , Naim Ahmad Nazri Mohamed , Gounot Jean-Sebastien , Ping Guan Shou , Lee Hanqing Jasinda , Lihuan Guan , Chenhao Li , Yu Jayce Koh Jia , Sessions Paola Florez de , Koh Woon-Puay , Feng Lei , Ng Tze Pin , Larbi Anis , Maier Andrea B. , Kennedy Brian , Nagarajan Niranjan
Published: July 2024

While rapid demographic changes in Asia are driving the incidence of chronic diseases related to aging, the limited availability of high-qualityin vivodata hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging the availability of a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun metagenomic sequencing to do high-resolution taxonomic and functional characterization of their gut microbiomes (n=234). Joint species-level analysis with other Asian cohorts identified a distinct age-associated shift in Asian gut metagenomes, characterized by a reduction in microbial richness, and enrichment of specificAlistipesandBacteroidesspecies (e.g.Alistipes shahiiandBacteroides xylanisolvens). Functional pathway analysis confirmed that these changes correspond to a metabolic potential expansion in aging towards alternate pathways that synthesize and utilize amino-acid precursors, relative to the dominant microbial guilds that typically produce butyrate in the gut from pyruvate (e.g.Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust gut microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species such asParabacteroides goldsteiniiand pathobionts such asKlebsiella pneumoniae, highlighting the role of the microbiome as biomarkers and potential intervention targets for promoting healthy aging.
Polycystin-1 loss of function increases susceptibility to atrial fibrillation through impaired DNA damage response
Authors: Hendrickson Troy , Abigail Giese Abigail , Fiedler Matthew , Perez William , Reyes-Sanchez Ernesto , Reyes-Lozano Monserrat , Wang Sufen , Venegas-Zamora Leslye , Provasek Vincent , El-Essawi Aschraf , Breitenbach Ingo , Fakuade Funsho E. , Kutschka Ingo , Schiattarella Gabriele G , Voigt Niels , Valderrabano Miguel , Altamirano Francisco
Published: July 2024

Background: The increasing prevalence of atrial fibrillation (AF) and chronic kidney diseases highlights the need for a deeper comprehension of the molecular mechanisms linking them. Mutations in PKD1, the gene encoding Polycystin-1 (PKD1 or PC1), account for 85% of autosomal dominant polycystic kidney disease (ADPKD) cases. This disease often includes cardiac complications such as AF. In cardiomyocytes, PC1 deletion reduces hypertrophic response to pressure overload but promotes baseline ventricular dysfunction, while deletion in fibroblasts ameliorates post-myocardial infarction fibrosis. Despite its known cardiac impact, the role of PC1 in atrial cardiomyocytes and arrhythmias is less understood. Here, we sought to investigate the role of PC1 in AF. Methods: We used intracardiac programmed stimulation and optical mapping to evaluate AF inducibility in two mouse models, Pkd1 R3277C, which recapitulates human ADPKD progression, and cardiomyocyte-specific Pkd1 deletion, and their respective controls. Isolated adult mouse atrial cardiomyocytes, human iPSC-derived atrial cardiomyocytes (hiPSC-aCM), and HL-1 cells served as in vitro cellular models. Molecular mechanisms were evaluated using optical mapping and molecular and biochemical approaches. Results: Loss-of-function PC1 mutations significantly increased AF susceptibility in vivo and facilitated local reentry in ex vivo left atrial appendages. Comprehensive in vitro experiments supported a direct effect of PC1 in atrial cardiomyocytes. PC1-deficient monolayers exhibited increased arrhythmic events, escalating into reentrant spiral waves post-tachypacing. Transcriptomics analysis revealed PC1-dependent regulation of DNA repair, with PC1 deficiency leading to increased DNA damage under stress. PARP1 inhibitors or nicotinamide riboside, which counteract DNA damage-related metabolic consequences, reduced in vitro arrhythmias PC1-deficient monolayers. Overexpression of the C-terminus of PC1 had the opposite effects in DNA repair genes, suggesting its regulatory effects in atrial cardiomyocytes through retinoblastoma/E2F. Analyses of human atrial tissue from non-ADPKD patients showed reduced levels of mature PC1, suggesting a broader relevance of impaired PC1 in AF. Conclusions: Impaired PC1 increases in vivo AF inducibility under programmed electrical stimulation and promotes in vitro arrhythmias in hiPSC-aCM and HL-1 cells. Our findings indicate that PC1 protects against DNA damage to reduce AF susceptibility.
Dietary fiber intervention modulates the formation of the cardiovascular risk factor trimethylamine-N-oxide after beef consumption
Authors: Haas Melanie , Brandl Beate , Neuhaus Klaus , Wudy Susanne , Kleigrewe Karin , Hauner Hans , Skurk Thomas
Published: July 2024

Objective: The gut-microbiota-dependent metabolite trimethylamine-N-oxide (TMAO) has emerged as a potential risk factor for cardiovascular disease (CVD). Conversely, dietary fiber has been associated with a reduced risk of CVD and been proposed to exhibit beneficial effects on gut health. Considering these associations, we conducted an intervention study to investigate the influence of fiber supplementation on intestinal TMAO formation and its response after beef consumption. Approach and Results: Our randomized, double blind, pilot study MEATMARK included thirteen volunteers who underwent a dietary fiber and placebo intervention over two weeks. We assessed the effect of fiber supplementation on the gut microbiota and expression of the enzyme cutC, a key enzyme for microbial TMA formation, a precursor for TMAO. We measured the TMAO response following beef consumption after the two-week intervention. We further investigated the impact of three human single nucleotide polymorphisms (SNPs) in the expression of the hepatic enzyme FMO3 on TMAO plasma levels, as this factor is responsible for the final oxidation step from TMA to TMAO. Conclusion: Our findings indicate that dietary fiber supplementation attenuated TMAO formation after beef intake, particularly in participants with habitual lower daily meat consumption. Furthermore, we observed a significant downregulation of cutC expression in response to the fiber intervention, suggesting a potential mechanism to reduce plasma TMAO. Considering these findings, a high fiber, low meat diet presents a promising dietary strategy for reducing this CVD risk factor.
GlyTrait Brings Insights into Functional Glycosylation
Authors: Fu Bin , Wang Guoli , Li Chenxin , Li Yueyue , Liu Xuejiao , Zhang Ying , Lu Haojie
Published: July 2024

Glycomics research often grapples with the interpretability and biological relevance of glycomics data. Using glycosylation derived traits are promising methods for more in-depth biological insights, yet no such bioinformatic tool exists for such task. Here, we developed GlyTrait, a Python-based framework designed to enhance glycomics analysis through the innovative calculation and interpretation of derived traits from N-glycome data. GlyTrait automates the derivation of biologically significant traits, shifting focus from mere glycan abundances to functional glycan properties such as branching and fucosylation. GlyTrait extends the well-established nomenclatures and definitions of derived traits in the N-glycomics community, allowing for fast exploration and analysis of N-glycome data effortlessly. Furthermore, with the well-designed formula grammar, custom derived traits could be materialized without any knowledge of coding. Besides, a two-step post-filtering process reduces information redundancy, maintaining only the most informative traits. Finally, subsequent statistical and interpretable machine learning analysis provide robust insights into the glycosylation patterns associated with disease states. This comprehensive approach not only improves the statistical power and sensitivity compared to traditional methods, but also enhances the interpretability of glycomics data. GlyTrait's efficacy is demonstrated through the re-analysis of published glycoengineered CHO cell lines and visceral leishmaniasis patient data, alongside a newly conducted pilot study for hepatocellular carcinoma (HCC) N-glycan biomarker discovery. We are confident in GlyTrait's potential to become an indispensable tool for the glycomics community.
Non-standard proteins in the lenses of AlphaFold3 - case study of amyloids
Authors: Wojciechowska Alicja W. , Wojciechowski Jakub W. , Kotulska Malgorzata
Published: July 2024

The recent release ofAlphaFold3raises a question about its powers and limitations. Here, we analyze the potential ofAlphaFold3for correct reproduction of amyloid structures, which are an example of multimeric proteins with low representation in protein structure databases, which may also be characterized by polymorphism. We show thatAlphaFold3is capable of producing amyloid-like assemblies that have significant similarity to experimental structures (TM-score>0.5), although its results are impacted by the number of monomers forming the predicted fibril and a protein of choice.AlphaFold3produces structurally diverse models of some amyloid proteins, which could reflect their polymorphism observed in nature. We hypothesize that the lower emphasis on multiple sequence analysis (MSA) inAlphaFold3improves the results quality, since for this class of proteins sequence homology may be misleading in their structural similarity. However, the structural landscape obtained from the modeling does not reflect the real one governed by thermodynamics. Finally,AlphaFold3enables for the first time, structural modeling of fibril-like structures to a certain extent, possibly including their polymorphic nature. Still individual benchmarking is necessary for optimal modeling.

Graphical Abstract
Activated SKN-1 alters the aging trajectories of long-lived C. elegans mutants
Authors: Curran Sean , Turner Chris
Published: July 2024

In the presence of stressful environments, the SKN-1 cytoprotective transcription factor is activated to induce the expression of gene targets that can restore homeostasis. However, chronic activation of SKN-1 results in diminished health and a reduction of lifespan. Here we demonstrate the necessity of modulating SKN-1 activity to maintain the longevity-promoting effects associated with genetic mutations that impairdaf-2/insulin receptor signaling, theeat-2model of caloric restriction, andglp-1-dependent loss of germ cell proliferation. A hallmark of animals with constitutive SKN-1 activation is the age-dependent loss of somatic lipids and this phenotype is linked to a general reduction in survival in animals harboring theskn-1gfallele, but surprisingly,daf-2lf; skn-1gfdouble mutant animals do not redistribute somatic lipids which suggests the insulin signaling pathway functions downstream of SKN-1 in the maintenance of lipid distribution. As expected, theeat-2lfallele, which independently activates SKN-1, continues to display somatic lipid depletion in older ages with and without theskn-1gfactivating mutation. In contrast, the presence of the skn-1gf allele does not lead to somatic lipid redistribution inglp-1lfanimals that lack a proliferating germline. Taken together, these studies support a genetic model where SKN-1 activity is an important regulator of lipid mobilization in response to nutrient availability that fuels the developing germline by engaging thedaf-2/insulin receptor pathway.
Nitrate activates a MKK3-dependent MAPK module via NLP transcription factors in Arabidopsis
Authors: Schenk Sebastian T. , Brehaut Virginie , Chardin Camille , Boudsocq Marie , Marmagne Anne , Colcombet Jean , Krapp Anne
Published: July 2024

Plant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via NIN-LIKE PROTEIN (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen-activated protein (MAP) kinase genes are among the early nitrate-responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen-depleted Arabidopsis (Arabidopsis thaliana) plants triggers, within minutes, a MAPK cascade that requires NLP-dependent transcriptional induction of MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 13 (MAP3K13) and MAP3K14. Importantly, nitrate reductase-deficient mutants exhibited nitrate-induced MAPK activities comparable to those observed in wild-type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate-stimulated gene expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that a MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency.
Blebs regulate phosphoinositides distribution and promote cell survival through the Septin-SH3KBP1-PI3K axis
Authors: Zhen Zifeng , Zhang Chunlei , Li Jiayi , Wu Congying
Published: July 2024

Cells rely on substrate adhesion to activate diverse signaling pathways essential for survival. In the absence of proper adhesion, cells undergo anoikis, a form of programmed cell death. Poorly attached cells often exhibit rounded morphologies and form small round protrusions called blebs. While the role of blebs in amoeboid migration is well-documented, recent studies have highlighted their function in anoikis resistance with the help of curvature-recognized proteins. However, little is known about whether the most abundant membrane components-phospholipids function in blebs-facilitated cell survival. Here, we found enriched PI(3,4,5)P3 and diluted PI(4,5)P2 at the bleb membrane, compared to non-bleb plasma membrane regions. Our experimental results showed that both phosphoinositides (PIs) have restricted diffusion pattern between the bleb and non-bleb membranes. Subsequently, we reveal SH3KBP1 to play a crucial role in recruiting PI3K and organizing the Septin-SH3KBP1-PI3K complex at the bleb necks. This process then contributes to differential PIs distribution and anoikis resistance. These novel insights into PIs dynamics elucidate their role in cell blebbing, cancer cell behavior and metastasis, presenting potential targets for new therapeutic interventions.
Perceptual and semantic deficits in face recognition in semantic dementia
Authors: Yadollahikhales Golnaz , Mandelli Maria Luisa , Ezzes Zoe , Pillai Janhavi , Ratnasiri Buddhika , Baquirin David Paul , Miller Zachary , de Leon Jessica , Tee Boon Lead , Seeley William , Rosen Howard , Miller Bruce , Kramer Joel , Sturm Virginia , Gorno-Tempini Maria Luisa , Montembeault Maxime
Published: July 2024

State of the art

Semantic dementia (SD) patients including semantic variant primary progressive aphasia (svPPA) and semantic behavioral variant frontotemporal dementia (sbvFTD) patients show semantic difficulties identifying faces and known people related to right anterior temporal lobe (ATL) atrophy. However, it remains unclear whether they also have perceptual deficits in face recognition.

Methodology

We selected 74 SD patients (54 with svPPA and predominant left ATL atrophy and 20 with sbvFTD and predominant right ATL atrophy) and 36 cognitively healthy controls (HC) from UCSF Memory and Aging Center. They underwent a perceptual face processing test (Benton facial recognition test-short version; BFRT-S), and semantic face processing tests (UCSF Famous people battery – Recognition, Naming, Semantic associations – pictures and words subtests), as well as structural magnetic resonance imaging (MRI). Neural correlates with the task’s performance were conducted with a Voxel-based morphometry approach using CAT12.

Results

svPPA and sbvFTD patients were impaired on all semantic face processing tests, with sbvFTD patients performing significantly lower on the famous faces’ recognition task in comparison to svPPA, and svPPA performing significantly lower on the naming task in comparison to sbvFTD. These tasks predominantly correlated with gray matter (GM) volumes in the right and left ATL, respectively. Compared to HC, both svPPA and sbvFTD patients showed preserved performance on the perceptual face processing test (BFRT-S), and performance on the BFRT-S negatively correlated with GM volume in the right posterior superior temporal sulcus (pSTS).

Conclusion

Our results suggest that early in the disease, with the atrophy mostly restricted to the anterior temporal regions, SD patients do not present with perceptual deficits. However, more severe SD cases with atrophy in right posterior temporal regions might show lower performance on face perception tests, in addition to the semantic face processing deficits. Early sparing of face perceptual deficits in SD patients, regardless of hemispheric lateralization, furthers our understanding of clinical phenomenology and therapeutical approaches of this complex disease.
Mitoregulin self-associates to form likely homo-oligomeric pore-like structures
Authors: Linzer Connor R. , Stein Colleen S. , Witmer Nathan H. , Xu Zhen , Schnicker Nicholas J. , Boudreau Ryan L.
Published: July 2024

We and others previously found that a misannotated long noncoding RNA encodes for a conserved mitochondrial transmembrane microprotein named Mitoregulin (Mtln). Beyond an established role for Mtln in lipid metabolism, Mtln has also been shown to more broadly influence mitochondria, boosting respiratory efficiency and Ca2+retention capacity, while lowering ROS, yet the underlying mechanisms remain unresolved. Prior studies have identified possible Mtln protein interaction partners; however, a lack of consensus persists, and no claims have been made about Mtln’s structure. We previously noted two key published observations that seemingly remained overlooked: 1) endogenous Mtln co-immunoprecipitates with epitope-tagged Mtln at high efficiency, and 2) Mtln primarily exists in a ∼66 kDa complex. To investigate if Mtln may self-oligomerize into higher-order complexes, we performed co-immunoprecipitation, protein modeling simulations, and native gel assessments of Mtln-containing complexes in cells and tissues, as well as tested whether synthetic Mtln protein itself forms oligomeric complexes. Our combined results provide strong support that Mtln self-associates and likely forms a hexameric pore-like structure.
An in vivo screen for proteolytic switch domains that can mediate Notch activation by force
Authors: Baker Frederick C. , Harman Jacob , Jordan Trevor , Walton Breana , Ajamu-Johnson Amber , Alashqar Rama F. , Bhikot Simran , Struhl Gary , Langridge Paul D.
Published: July 2024

Notch proteins are single pass transmembrane receptors activated by sequential extracellular and intramembrane cleavages that release their cytosolic domains to function as transcription factors in the nucleus. Upon binding, Delta/Serrate/LAG-2 (DSL) ligands activate Notch by exerting a “pulling” force across the intercellular ligand/receptor bridge. This pulling force is generated by Epsin-mediated endocytosis of ligand into the signal-sending cell, and results in the extracellular cleavage of the force-sensing Negative Regulatory Region (NRR) of the receptor by an ADAM10 protease [Kuzbanian (Kuz) inDrosophila]. Here, we have used chimeric Notch and DSL proteins to screen for other domains that can function as ligand-dependent proteolytic switches in place of the NRR in the developingDrosophilawing. While most of the tested domains are either refractory to cleavage or constitutively cleaved, we identify several that mediate Notch activation in response to ligand. These NRR analogues derive from widely divergent source proteins and have strikingly different predicted structures. Yet, almost all depend on force exerted by Epsin-mediated ligand endocytosis and cleavage catalyzed by Kuz. We posit that the sequence space of protein domains that can serve as force-sensing proteolytic switches in Notch activation is unexpectedly large, a conclusion that has implications for the mechanism of target recognition by Kuz/ADAM10 proteases and is consistent with a more general role for force dependent ADAM10 proteolysis in other cell contact-dependent signaling mechanisms. Our results also validate the screen for increasing the repertoire of proteolytic switches available for synthetic Notch (synNotch) therapies and tissue engineering.

One sentence summary

A scalable in vivo screen for Epsin and ADAM10 dependent proteolytic switches that can mediate Notch activation in response to force.
The Fc fragment of soluble IgMs binds C1q to activate the classical complement pathway, while inhibiting complement-dependent cytotoxicity
Authors: Pinto Andre J. , Chouquet Anne , Bally Isabelle , Thielens Nicole M. , Dumestre-Perard Chantal , Kunert Renate , Gaboriaud Christine , Ling Wai Li W , REISER Jean-Baptiste
Published: July 2024

Soluble type-M immunoglobulins (IgMs), among the most potent activators of the classical pathway, are key mediators of complement-dependent cytotoxicity, which render them promising candidates for developing alternative drugs in treating autoimmune or inflammatory diseases. In this study, we investigated the biochemical and in vitro functional properties of recombinant fragments from IgMs corresponding to the Fc-core in their two pentameric or hexameric forms. Biophysical experiments confirmed the crucial role of the IgM Joining chain (J) in favoring homogenous pentamers, while its absence led to heterogeneous population with a mixture of oligomeric forms. By combining size-exclusion chromatography with mass photometry, isolation of enriched samples with IgM hexamers or IgM pentamers without the J chain was possible. Biolayer interferometry demonstrated that both IgM-Fc forms bind C1q and ELISA showed that they induce the in vitro C4b deposition when in solid phase. Additionally, our data confirmed the higher efficacy of IgM hexamers compared to pentamers in activating the first component of the classical pathway. Finally, hemolytic assays demonstrate the ability of IgM-Fc constructs to inhibit Ig-induced complement-dependent cytotoxicity. These findings provide important information for the ultimate development of IgM-based molecules that target specifically complement activation.
Cytosol-living Trypanosoma cruzi amastigotes scavenge cholesterol from host ER and Golgi complex
Authors: Alcantara Carolina de Lima , Pereira Miria Gomes , De Souza Wanderley , Cunha-e-Silva Narcisa Leal
Published: July 2024

Chagas Disease, caused by the protozoan parasite Trypanosoma cruzi, stands as a prevalent neglected disease in Latin America. The amastigote stage, the replicant intracellular form of the parasite, is a crucial player in infection persistence within vertebrate hosts. The amastigotes exhibit remarkable adaptability regarding the cell type that they infect, being able to modulate their metabolism and growth based on the host cell resources availability. Lipid metabolism emerges as a key determinant of amastigote growth, with a dependency on the host cell's lipid resources. While the parasite can synthesize some sterols and fatty acids, it also scavenges these essential components, particularly cholesterol, from the host. Alterations in the host's cholesterol metabolism, potentially regulated by SREBPs, contribute to increased intracellular cholesterol levels, fostering parasite development. However, the mechanisms underlying cholesterol uptake by amastigotes remained elusive. Here, we investigate the cholesterol trafficking mechanism from host cells to amastigotes by employing a fluorescent cholesterol analog. Using advanced imaging techniques, such as confocal fluorescence microscopy and high-resolution volume electron microscopy we demonstrated that amastigotes internalize extracellular-derived cholesterol, defined the uptake kinetics for cholesterol by amastigotes, and demonstrated that cholesterol is important for amastigote development. Analysis of the interaction of host cell ER with the amastigotes revealed by the presence of membrane contact sites between this organelle and the amastigote plasma membrane. We also showed that amastigotes can take up host ER and Golgi proteins, probably by endocytosis, paving a new mechanism for host cell scavenging of molecules by the parasite.
Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage
Authors: Huang Zhiwei , Luo Songhao , Wang Zihao , Zhang Zhenquan , Jiang Benyuan , Nie Qing , Zhang Jiajun
Published: July 2024

Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of various external stimuli. One key cellular strategy that enables these functions is stochastic gene expression programs. However, understanding how transcriptional bursting, and consequently, cell fate, responds to DNA damage on a genome-wide scale poses a challenge. In this study, we propose an interpretable and scalable inference framework, DeepTX, that leverages deep learning methods to connect mechanistic models and scRNA-seq data, thereby revealing genome-wide transcriptional burst kinetics. This framework enables rapid and accurate solutions to transcription models and the inference of transcriptional burst kinetics from scRNA-seq data. Applying this framework to several scRNA-seq datasets of DNA-damaging drug treatments, we observed that fluctuations in transcriptional bursting induced by different drugs could lead to distinct fate decisions: IdU treatment induces differentiation in mouse embryonic stem cells by increasing the burst size of gene expression, while 5FU treatment with low and high dose increases the burst frequency of gene expression to induce cell apoptosis and survival in human colon cancer cells. Together, these results show that DeepTX can be used to analyze single-cell transcriptomics data and can provide mechanistic insights into cell fate decisions.
Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function
Authors: Paddar Masroor Ahmad , Wang Fulong , Trosdal Einar S , Hendrix Emily , He Yi , Salemi Michelle , Mudd Michal , Jia Jingyue , Duque Thabata L A , Javed Ruheena , Phinney Brett , Deretic Vojo
Published: July 2024

ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here we show that ATG5 associates with retromer’s core components VPS26, VPS29 and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.