Miracle-dz/UniFAR-FTUs huggingface dataset:
Ginsenoside Rg1 can reverse fatigue behavior in CFS rats by regulating EGFR and affecting Taurine and Mannose 6-phosphate metabolism

Background: Chronic fatigue syndrome (CFS) is characterized by significant and persistent fatigue. Ginseng is a traditional anti-fatigue Chinese medicine with a long history in Asia, as demonstrated by clinical and experimental studies. Ginsenoside Rg1 is mainly derived from ginseng, and its anti-fatigue metabolic mechanism has not been thoroughly explored. Methods: We performed non-targeted metabolomics of rat serum using LC-MS and multivariate data analysis to identify potential biomarkers and metabolic pathways. In addition, we implemented network pharmacological analysis to reveal the potential target of ginsenoside Rg1 in CFS rats. The expression levels of target proteins were measured by PCR and Western blotting. Results: Metabolomics analysis confirmed metabolic disorders in the serum of CFS rats. Ginsenoside Rg1 can regulate metabolic pathways to reverse metabolic biases in CFS rats. We found a total of 34 biomarkers, including key markers Taurine and Mannose 6-phosphate. AKT1, VEGFA and EGFR were identified as anti-fatigue targets of ginsenoside Rg1 using network pharmacological analysis. Finally, biological analysis showed that ginsenoside Rg1 was able to down-regulate the expression of EGFR. Conclusion: Our results suggest ginsenoside Rg1 has an anti-fatigue effect, impacting the metabolism of Taurine and Mannose 6-phosphate through EGFR regulation. This demonstrates ginsenoside Rg1 is a promising alternative treatment for patients presenting with chronic fatigue syndrome.
Effects of stance control via hidden Markov model-based gait phase detection on healthy users of an active hip-knee exoskeleton

Introduction: In the past years, robotic lower-limb exoskeletons have become a powerful tool to help clinicians improve the rehabilitation process of patients who have suffered from neurological disorders, such as stroke, by applying intensive and repetitive training. However, active subject participation is considered to be an important feature to promote neuroplasticity during gait training. To this end, the present study presents the performance assessment of the AGoRA exoskeleton, a stance-controlled wearable device designed to assist overground walking by unilaterally actuating the knee and hip joints. Methods: The exoskeleton’s control approach relies on an admittance controller, that varies the system impedance according to the gait phase detected through an adaptive method based on a hidden Markov model. This strategy seeks to comply with the assistance-as-needed rationale, i.e., an assistive device should only intervene when the patient is in need by applying Human-Robot interaction (HRI). As a proof of concept of such a control strategy, a pilot study comparing three experimental conditions (i.e., unassisted, transparent mode, and stance control mode) was carried out to evaluate the exoskeleton’s short-term effects on the overground gait pattern of healthy subjects. Gait spatiotemporal parameters and lower-limb kinematics were captured using a 3D-motion analysis system Vicon during the walking trials. Results and Discussion: By having found only significant differences between the actuated conditions and the unassisted condition in terms of gait velocity (ρ = 0.048) and knee flexion (ρ ≤ 0.001), the performance of the AGoRA exoskeleton seems to be comparable to those identified in previous studies found in the literature. This outcome also suggests that future efforts should focus on the improvement of the fastening system in pursuit of kinematic compatibility and enhanced compliance.
Uncursing winner’s curse: on-line monitoring of directed evolution convergence

Directed evolution (DE) is a versatile protein-engineering strategy, successfully applied to a range of proteins, including enzymes, antibodies, and viral vectors. However, DE can be time-consuming and costly, as it typically requires many rounds of selection to identify desired mutants. Next-generation sequencing allows monitoring of millions of variants during DE and can be leveraged to reduce the number of selection rounds. Unfortunately the noisy nature of the sequencing data impedes the estimation of the performance of individual variants. Here, we propose ACIDES that combines statistical inference and in-silico simulations to improve performance estimation in DE by providing accurate statistical scores. We tested ACIDES first on a novel random-peptide-insertion experiment and then on several public datasets from DE of viral vectors and phage-display. ACIDES allows experimentalists to reliably estimate variant performance on the fly and can aid protein engineering pipelines in a range of applications, including gene therapy.
Metformin regulates bone marrow stromal cells to accelerate bone healing in diabetic mice

Diabetes mellitus is a group of chronic diseases characterized by high blood glucose levels. Diabetic patients have a higher risk of sustaining osteoporotic fractures than non-diabetic people. The fracture healing is usually impaired in diabetics and our understanding of the detrimental effects of hyperglycemia on fracture healing is still inadequate. Metformin is the first-line medicine for type-2 diabetes (T2D). However, its effects on bone in T2D patients remain to be studied. To assess the impacts of metformin on fracture healing, we compared the healing process of closed wound fixed fracture, non-fixed radial fracture, and femoral drill-hole injury models in T2D mice with and without metformin treatment. Our results demonstrated that metformin rescued the delayed bone healing and remolding in T2D mice in all the three injury models. The proliferation, osteogenesis, chondrogenesis of the bone marrow stromal cells (BMSCs) derived from WT and T2D mice treated with or without metformin were compared in vitro and in vivo by assessing the subcutaneous ossicle formation of the BMSC implants in recipient T2D mice. In vivo treatment with metformin to T2D mice could effectively rescue the impaired differentiation potential and detrimental lineage commitment of BMSCs, caused by the hyperglycemic conditions. Moreover, the Safranin O staining of cartilage formation in the endochondral ossification under hyperglycemic condition significantly increased at day 14 post-fracture in T2D mice receiving metformin treatment. The chondrocyte transcript factor SOX9 and PGC1α, important to maintain chondrocyte homeostasis, were both significantly upregulated in callus tissue isolated at the fracture site of metformin-treated MKR mice on day 12 post-fracture. Metformin also rescued the chondrocyte disc formation of BMSCs isolated from T2D mice. Taken together, our study demonstrated that metformin facilitated bone healing, bone formation and chondrogenesis in T2D mouse models.
CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including the PTEN gene locus mimicking cancer profiles

The CRISPR-Cas9 system is a powerful tool for studying gene functions and has tremendous potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected deletion of a 287 kb region on Chromosome 10 (10q23.31) in chronic myelogenous leukemia HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN. We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently by the process of generating CRISPR-Cas9-modifed cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Overall, our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies, highlights the importance of assessing unintended genomic changes in CRISPR-Cas9-modified cells and may have clinical significance in cancer research. Highlights CRISPR-Cas9-modified HAP1 cells carry an unexpected large genomic deletion at 10q23.31 encompassing four protein-coding genes frequently expressed across various cell types. The 10q23.31 deletion is accompanied by global changes in histone modification and transcriptomes. The generation of CRISPR-Cas9-modified cells rather than Cas9 activity increases the frequencies of the deletion at 10q23.31. The 10q23.31 deletion identified in HAP1 cells resembles a commonly occurring deletion pattern in cancer patients.
Optogenetic control of medaka behavior with channelrhodopsin

Optogenetics enables the manipulation of neural activity with high spatiotemporal resolution in genetically defined neurons. The method is widely used in various model animals in the neuroscience and physiology fields. Channelrhodopsins are robust tools for optogenetic manipulation, but they have not yet been used for studies in medaka. In the present study, we used the CRISPR/Cas9-mediated knock-in approach to establish a transgenic medaka strain expressing the Chloromonas oogama channelrhodopsin (CoChR) in the ISL LIM homeobox 1 (isl1) locus. We demonstrated that light stimuli elicited specific behavioral responses such as bending or turning locomotion in the embryos and pectoral fin movements in the larvae and adults. The response probabilities and intensities of these movements could be controlled by adjusting the intensity, duration, or wavelength of each light stimulus. Furthermore, we demonstrated that the pectoral fin movements in the adult stage could be elicited using a laser pointer to irradiate only the hindbrain region. Our results indicate that CoChR allows for manipulation of medaka behaviors by activating targeted neurons, which will further our understanding of the detailed neural mechanisms of social behaviors in medaka.
Free energy landscapes of KcsA inactivation

The bacterial ion channel KcsA has become a useful model of complex K+-ion channels thanks to its single pore domain structure whose sequence shares many similarities with eukaryotic channels. Like many physiologically-relevant ion channels, KcsA inactivates after prolonged exposure to stimuli (in this case, a lowered pH). The inactivation mechanism has been heavily investigated, using structural, functional and simulations methods, but the molecular basis underlying the energetics of the process remains actively debated. In this work, we use the “string method with swarms of trajectories” enhanced sampling technique to characterize the free energy landscape lining the KcsA inactivation process. After channel opening following a pH drop, KcsA presents metastable open states leading to an inactivated state. The final inactivation step consists of a constriction of the selectivty filter and entry of three water molecules into binding sites behind each selectivity filter subunit. Based our simulations, we propose a key role for residue L81 in opening a gateway for water molecules to enter their buried sites, rather than for Y82 which has previously been suggested to act as a lid. In addition, since we found the energetically favored inactivation mechanism to be dependent on the force field, our results also address the importance of parameter choice for this type of mechanism. In particular, inactivation involves passing through the fully-open state only when using the AMBER force field. In contrast, using CHARMM, selectivity filter constriction proceeds directly from the partially open state. Finally, our simulations suggest that removing the co-purifying lipids stabilizes the partially open states, rationalizing their importance for the proper inactivation of the channel.
Early consequences of the phospholamban mutation PLN-R14del+/- in a transgenic mouse model

Aims The heterozygous phospholamban (PLN) mutation R14del (PLN R14del+/-) is associated with a severe arrhythmogenic cardiomyopathy (ACM) developing in the adult. “Superinhibition” of SERCA2a by PLN R14del is widely assumed to underlie the pathogenesis, but alternative mechanisms such abnormal energy metabolism have also been reported. This work aims to 1) to evaluate Ca2+ dynamics and energy metabolism in a transgenic (TG) mouse model of the mutation prior to cardiomyopathy development; 2) to test whether they are causally connected. Methods and Results Ca2+ dynamics, energy metabolism parameters, reporters of mitochondrial integrity, energy and redox homeostasis were measured in ventricular myocytes of 8-12 weeks-old, phenotypically silent, TG mice. Mutation effects were compared to pharmacological PLN antagonism and analysed during modulation of sarcoplasmic reticulum (SR) and cytosolic Ca2+ compartments. Transcripts and proteins of relevant signalling pathways were evaluated. The mutation was characterized by hyperdynamic Ca2+ handling, similar to that induced by PLN antagonism. Albeit all components of energy metabolism were depressed at rest, functional signs of mitochondrial damage or energy starvation were absent and cell energy charge was preserved. The response of mitochondrial O2 consumption to SERCA2a blockade was lost in mutant myocytes (SR-mitochondrial uncoupling) and ER-stress signalling was activated. Conclusions 1) PLN R14del+/- loses its ability to inhibit SERCA2a, which argues against SERCA2a superinhibition as a mechanism of ACM; 2) depression of resting energy metabolism may at least partly reflect impairment of SR-mitochondrial coupling; 3) ER-stress may be an early factor in the pathogenesis.
Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification

A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Further MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web-server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.
Xrp1 governs the stress response program to spliceosome dysfunction

Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 snRNPs in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects and the organismal lethality, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction.
Innate attraction and aversion to odors in locusts

Many animals display innate preferences for some odors, but the physiological mechanisms underlying these preferences are poorly understood. Here, with behavioral tests, we establish a model system well suited to investigating olfactory mechanisms, the locust Schistocerca americana. We conducted open field two-choice tests with purely olfactory stimuli. In these tests, newly hatched locusts navigated toward, and spent time near, the source of a food odor blend, crushed wheat grass. In similar tests, we found that hatchlings avoided moderate concentrations of major individual components of the food blend odor, 1-hexanol and hexanal. They were neither attracted nor repelled by a lower concentration of 1-hexanol, but were moderately attracted to a low concentration of hexanal. These results establish that hatchlings have a strong, innate preference for food odor blend, but the valence of the blend’s individual components may be different and may change depending on the concentration. This suggests innate odor preferences may emerge from more complex processing pathways than labeled lines. Our results provide a useful entry point for an analysis of physiological mechanisms underlying innate sensory preferences.
One-carbon metabolism is required for epigenetic stability in the mouse placenta

One-carbon metabolism, including the folate cycle, has a crucial role in fetal development though its molecular function is complex and unclear. The hypomorphic Mtrrgt allele is known to disrupt one-carbon metabolism, and thus methyl group availability, leading to several developmental phenotypes (e.g., neural tube closure defects, fetal growth anomalies). Remarkably, previous studies showed that some of the phenotypes were transgenerationally inherited. Here, we explored the genome-wide epigenetic impact of one-carbon metabolism in placentas associated with fetal growth phenotypes and determined whether specific DNA methylation changes were inherited. Firstly, methylome analysis of Mtrrgt/gt homozygous placentas revealed genome-wide epigenetic instability. Several DMRs were identified including at the Cxcl1 gene promoter and at the En2 gene locus, which may have phenotypic implications. Importantly, we discovered hypomethylation and ectopic expression of a subset of ERV elements throughout the genome of Mtrrgt/gt placentas with broad implications for genomic stability. Next, we determined that sperm DMRs in males from the Mtrrgt model were reprogrammed in the placenta with little evidence of direct or transgenerational germline DMR inheritance. However, some sperm DMRs were associated with placental gene misexpression despite normalisation of DNA methylation, suggesting the inheritance of an alternative epigenetic mechanism. Integration of published histone ChIP-seq datasets with sperm methylome and placenta transcriptome data from the Mtrrgt model point towards H3K4me3 deposition at key loci suggesting that histone modifications might play a role in epigenetic inheritance in this context. This study sheds light on the mechanistic complexities of one-carbon metabolism in development and epigenetic inheritance.
Structural Plasticity of GABAergic Pallidothalamic Terminals in MPTP-Treated Parkinsonian Monkeys: A 3D Electron Microscopic Analysis

The globus pallidus pars interna (GPi) is a major source of GABAergic inhibition upon the motor thalamus. GPi neurons are endowed with properties that allow them to fire at a high rate and maintain a tonic inhibitory influence upon thalamocortical neurons. In parkinsonism, the firing rate of GPi neurons is further increased and their firing pattern switches from a tonic to a bursty mode, two pathophysiological changes associated with increased GABAergic pallidothalamic activity. At the thalamic level, GPi terminals display ultrastructural features (large diameter, multiple synapses, large number of mitochondria) that allow them to maintain tonic synaptic inhibition at high firing rate upon thalamocortical neurons in the parvocellular ventral anterior nucleus (VApc) and the centromedian nucleus (CM), the two main GPi-recipient motor thalamic nuclei in nonhuman primates. To determine if changes of GPi neurons activity are associated with neuroplastic reorganization of GPi terminals and their synapses, we used a Single Block Facing/Scanning Electron Microscopy (SBF/SEM), high resolution 3D electron microscopic approach to compare the morphometry of GPi terminals between 2 control and 2 MPTP-treated parkinsonian monkeys. Our findings demonstrate that pallidothalamic terminals in VApc and CM undergo major ultrastructural changes in parkinsonian monkeys: (1) increased terminal volume in both nuclei, (2) increased surface area of synapses in both nuclei, (3) increased number of synapses/GPi terminals in the CM, but not VApc, (4) increased total volume of mitochondria/terminals in both nuclei but not in the number of mitochondria. In contrast, the ultrastructure of putative GABAergic terminals from the reticular thalamic nucleus was not affected in both the VApc and CM of parkinsonian monkeys. Our findings also show striking morphological differences in terminal volume, number/area of synapses and volume/number of mitochondria between GPi terminals in VApc and CM of control monkeys. In conclusion, results of this study demonstrate that GABAergic pallidothalamic terminals are endowed with a high level of structural plasticity that may contribute to the development and maintenance of the abnormal increase in pallidal GABAergic outflow to the thalamus in the parkinsonian state. Furthermore, the evidence for ultrastructural differences between GPi terminals in VApc and CM suggests that Morphologically distinct pallidothalamic terminals underlie specific physiological properties of pallidal inputs to VApc and CM in normal and diseased states.
Typical neural adaptation for familiar images in autistic adolescents

It has been proposed that autistic perception may be marked by a reduced influence of temporal context. Under this hypothesis, prior exposure to a stimulus should lead to a weaker or absent alteration of the behavioral and neural response to the stimulus in autism, compared to a typical population. To examine this hypothesis, we recruited two samples of human volunteers: a student sample (N=26), which we used to establish our analysis pipeline, and an adolescent sample (N=36), which consisted of a group of autistic (N=18) and a group of non-autistic (N=18) participants. All participants were presented with visual stimulus streams consisting of novel and familiar image pairs, while they attentively monitored each stream. We recorded task performance and used magnetoencephalography (MEG) to measure neural responses, and to compare the responses to familiar and novel images. We found behavioral facilitation as well as a reduction of event-related field (ERF) amplitude for familiar, compared to novel, images in both samples. Crucially, we found statistical evidence against between-group effects of familiarity on both behavioral and neural responses in the adolescent sample, suggesting that the influence of familiarity is comparable between autistic and non-autistic adolescents. These findings challenge the notion that perception in autism is marked by a reduced influence of prior exposure.