Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct Fastigial Output Channels and Their Impact on Temporal Lobe Seizures

Despite being canonically considered a motor control structure, the cerebellum is increasingly recognized for important roles in processes beyond this traditional framework, including seizure suppression. Excitatory fastigial neurons project to a large number of downstream targets, and it is unclear whether this broad targeting underlies seizure suppression, or whether a specific output may be sufficient. To address this question, we used the intrahippocampal kainic acid mouse model of temporal lobe epilepsy, male and female animals, and a dual-virus approach to selectively label and manipulate fastigial outputs. We examined fastigial neurons projecting to the superior colliculus, medullary reticular formation, and central lateral nucleus of the thalamus, and found that these comprise largely nonoverlapping populations of neurons that send collaterals to unique sets of additional, somewhat overlapping, thalamic and brainstem regions. We found that neither optogenetic stimulation of superior colliculus nor reticular formation output channels attenuated hippocampal seizures. In contrast, on-demand stimulation of fastigial neurons targeting the central lateral nucleus robustly inhibited seizures. Our results indicate that fastigial control of hippocampal seizures does not require simultaneous modulation of many fastigial output channels. Rather, selective modulation of the fastigial output channel to the central lateral thalamus, specifically, is sufficient for seizure control. More broadly, our data highlight the concept of specific cerebellar output channels, whereby discrete cerebellar nucleus neurons project to specific aggregates of downstream targets, with important consequences for therapeutic interventions. SIGNIFICANCE STATEMENT The cerebellum has an emerging relationship with nonmotor systems and may represent a powerful target for therapeutic intervention in temporal lobe epilepsy. We find, as previously reported, that fastigial neurons project to numerous brain regions via largely segregated output channels, and that projection targets cannot be predicted simply by somatic locations within the nucleus. We further find that on-demand optogenetic excitation of fastigial neurons projecting to the central lateral nucleus of the thalamus—but not fastigial neurons projecting to the reticular formation, superior colliculus, or ventral lateral thalamus—is sufficient to attenuate hippocampal seizures.
Long-term p21 and p53 trends regulate the frequency of mitosis events and cell cycle arrest

Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, two single cell datasets that monitored the time evolution of p21 and p53, one subjected to gamma irradiation and the other to x-ray irradiation, are analyzed to uncover the dynamics of this process. New insights into the biological mechanisms were found by decomposing the p53 and p21 signals into transient and oscillatory components. Through the use of dynamic time warping on the oscillatory components of the two signals, we found that p21 signaling lags behind its lead signal, p53, by about 3.5 hours with oscillation periods of around 6 hours. Additionally, through various quantification methods, we showed how p21 levels, and to a lesser extent p53 levels, dictate whether the cells are arrested in their cell cycle and how fast these cells divide depending on their long-term trend in these signals.
Deep tissue scattering compensation with three-photon F-SHARP

Optical imaging techniques are widely used in biological research, but their penetration depth is limited by tissue scattering. Wavefront shaping techniques are able to overcome this problem in principle, but are often slow and their performance depends on the sample. This greatly reduces their practicability for biological applications. Here we present a scattering compensation technique based on three-photon (3P) excitation, which converges faster than comparable two-photon (2P) techniques and works reliably even on densely labeled samples, where 2P approaches fail. To demonstrate its usability and advantages for biomedical imaging we apply it to the imaging of dendritic spines on GFP-labeled layer 5 neurons in an anesthetized mouse.
Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L

The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled to reversible changes in energy metabolism with key implications for life-long NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We found that a state-dependent rewiring of the mitochondrial proteome by the peptidase YME1L is required to preserve NSPC self-renewal in the adult brain. YME1L-mediated proteome rewiring regulates the rate of fatty acid oxidation (FAO) for replenishing Krebs cycle intermediates and dNTP precursors, which are required to sustain NSPC amplification. Yme1l deletion irreversibly shifts the metabolic profile of NSPCs away from a FAO-dependent state resulting in defective self-renewal, premature differentiation and NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.
The genome of stress tolerant crop wild relative Paspalum vaginatum leads to increased biomass productivity in the crop Zea mays

A number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum Paspalum vaginatum is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologous conserved in 6 related grass species placed paspalum as an outgroup of the maize-sorghum clade demonstrating paspalum as their closest sequenced wild relative. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibited significant increases in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, resulting in autophagy dependent increases in biomass accumulation.
Global and network functional connectivity of Nucleus Basalis of Meynert is strengthened in blind individuals

Vision loss causes dramatic changes in brain function which are thought to facilitate behavioral adaptation. One interesting prospect is that the cholinergic signals are involved in this blindness-induced plasticity. Critically, the nucleus basalis of Meynert is the principal source of the cholinergic signals, however, no studies have yet investigated whether the nucleus basalis of Meynert is altered in blindness. Therefore, here we examined its structure, cerebrovascular response, and the resting-state functional connectivity in blind individuals. We found that the global signal of the nucleus basalis of Meynert as well as its network connectivity with the visual, language, and default mode network is significantly enhanced in early blind individuals. On the other hand, its structure and cerebrovascular response remain unchanged in early blind individuals. Further, we observed that less visual experience predicts stronger global and network connectivity of the nucleus basalis of Meynert. These results suggest that the nucleus basalis of Meynert develops a stronger neuromodulatory influence on the cortex of blind individuals at both global and network levels.
Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer

Colorectal cancer (CRC) remains the third most common cancer in the US with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1 (c.1029C<G, p.Tyr343Ter). Our study incorporated a detailed molecular characterization of rhesus CRC for cross-comparison with human MMRd CRC. We performed PCR-based MSI testing, transcriptomic analysis, and reduced-representation bisulfite sequencing (RRBS) of rhesus CRC (n=41 samples) using next-generation sequencing (NGS). Systems biology pipelines were used for gene set enrichment analysis (GSEA) for pathway discovery, consensus molecular subtyping (CMS), and somatic mutation profiling. Overall, the majority of rhesus tumors displayed high levels of MSI (MSI-high) and differential gene expression profiles that were consistent with known deregulated pathways in human CRC. DNA methylation analysis exposed differentially methylated patterns among MSI-H, MSI-L (MSI-low)/MSS (MS-stable) and LS tumors with MLH1 predominantly inactivated among sporadic MSI-H CRCs. The findings from this study support the use of rhesus macaques as the preferred animal model to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans.
Integrated experimental-computational analysis of a HepaRG liver-islet microphysiological system for human-centric diabetes research

Microphysiological systems (MPS) are powerful tools for emulating human physiology and replicating disease progression in vitro. MPS could be better predictors of human outcome than current animal models, but mechanistic interpretation and in vivo extrapolation of the experimental results remain significant challenges. Here, we address these challenges using an integrated experimental-computational approach. This approach allows for in silico representation and predictions of glucose metabolism in a previously reported MPS with two organ compartments (liver and pancreas) connected in a closed loop with circulating medium. We developed a computational model describing glucose metabolism over 15 days of culture in the MPS. The model was calibrated on an experiment-specific basis using data from seven experiments, where single-liver or liver-islet cultures were exposed to both normal and hyperglycemic conditions resembling high blood glucose levels in diabetes. The calibrated models reproduced the fast (i.e. hourly) variations in glucose and insulin observed in the MPS experiments, as well as the long-term (i.e. over weeks) decline in both glucose tolerance and insulin secretion. We also investigated the behavior of the system under hypoglycemia by simulating this condition in silico, and the model could correctly predict the glucose and insulin responses measured in new MPS experiments. Last, we used the computational model to translate the experimental results to humans, showing good agreement with published data of the glucose response to a meal in healthy subjects. The integrated experimental-computational framework opens new avenues for future investigations toward disease mechanisms and the development of new therapies for metabolic disorders.
Semantic scene-object consistency modulates N300/400 EEG components, but does not automatically facilitate object representations

During natural vision, objects rarely appear in isolation, but often within a semantically related scene context. Previous studies reported that semantic consistency between objects and scenes facilitates object perception, and that scene-object consistency is reflected in changes in the N300 and N400 components in EEG recordings. Here, we investigate whether these N300/N400 differences are indicative of changes in the cortical representation of objects. In two experiments, we recorded EEG signals while participants viewed semantically consistent or inconsistent objects within a scene; in Experiment 1, these objects were task-irrelevant, while in Experiment 2, they were directly relevant for behavior. In both experiments, we found reliable and comparable N300/400 differences between consistent and inconsistent scene-object combinations. To probe the quality of object representations, we performed multivariate classification analyses, in which we decoded the category of the objects contained in the scene. In Experiment 1, in which the objects were not task-relevant, object category could be decoded from around 100 ms after the object presentation, but no difference in decoding performance was found between consistent and inconsistent objects. By contrast, when the objects were task-relevant in Experiment 2, we found enhanced decoding of semantically consistent, compared to semantically inconsistent, objects. These results show that differences in N300/N400 components related to scene-object consistency do not index changes in cortical object representations, but rather reflect a generic marker of semantic violations. Further, our findings suggest that facilitatory effects between objects and scenes are task-dependent rather than automatic.
Comparison of Two Multidisciplinary Occupational Rehabilitation Programs Based on Multimodal Cognitive Behavior Therapy on Self-Rated Health and Work Ability

Objective: Musculoskeletal pain and common mental disorders constitute the largest proportion of people who are on sick leave. This study investigated the efficacy of two multidisciplinary occupational rehabilitation programs on self-rated health and work-related outcomes. The interventions were identical in content but differed in length. It was hypothesized that a longer inpatient program would yield greater improvements than a shorter outpatient program. Methods: Patients were sick-listed workers referred to occupational rehabilitation by the Norwegian Labor and Welfare Administration. A non-randomized 2 Condition (20 days, n = 64 versus 12 days, n = 62) × 4 repeated measures (start, end, 3 months, 12 months) between-subject design was used. Both programs were based on multimodal cognitive behavior therapy with a return-to-work focus. Health-related questionnaires were the Subjective Health Complaints inventory, Hospital Anxiety and Depression Scale, and SF-36 Bodily Pain. Work-related questionnaires were the Work Ability Index, the Fear-Avoidance Beliefs Questionnaire, Return To Work Self-Efficacy, and Return To Work expectations. Intervention effects were estimated using linear mixed models and Cohen’s d. Results: The results revealed that both groups improved on the selected outcomes. Within-group contrasts and effect sizes showed that the inpatient group showed larger effect sizes at the end of rehabilitation and 12 months post-intervention for work-related outcomes than the outpatient group. Conclusion: Both programs were efficacious in improving health- and work-related outcomes during and after rehabilitation, but the inpatient group generally displayed stronger and more rapid improvements and was more stable at one-year postintervention.
The Evolution of Fluoroquinolone Resistance in Salmonella under Exposure to Sub-Inhibitory Concentration of Enrofloxacin

The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase of ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompF, ompC and ompD, were down-regulated first to rapidly adapt and develop resistance of ≤ 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. ‘de novo’ IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.
Positive Relationship Between Precompetitive Sympathetic Predominance and Competitive Performance in Elite Extreme Sports Athletes

Elite athletes achieve superior performance under high pressure in competitive situations. Although it is known that such situations affect the precompetitive activity of their autonomic nervous system (ANS), the relationship between precompetitive ANS activity and performance remains controversial. Especially in extreme sports, it has been shown that cardiac sympathetic tone occurs in athletes before competition attempts. However, the relationship between precompetitive sympathetic tone and performance is unclear. To investigate this relationship in extreme sports, we organized a freestyle snowboard jumping competition and examined competitors' physiological states and performance during this event. The electrocardiograms (ECGs) of 20 elite snowboarders were measured 10 min before each jump in different competitive situations: practice, qualifying, and final sessions. The mean heart rate (HR), the low-frequency to high-frequency component ratio (LF/HF ratio), the logarithm of the HF (lnHF) component of the frequency-domain of the heart rate variability (HRV), the ratio of the standard deviation of all R–R intervals to the root mean square of successive differences of R–R intervals (SDNN/rMSSD ratio), and the rMSSD of the time-domain of the HRV were calculated from the ECG data. The results showed a significant increase in the mean HR as well as significant decreases in the lnHF component and rMSSD of the HRV as the sessions progressed. Interestingly, the mean HR, LF/HF ratio and SDNN/rMSSD ratio of the HRV showed significant positive correlations with competitive scores, and the lnHF component and rMSSD of the HRV showed significant negative correlations with the scores. Our results indicate that precompetitive ANS activity becomes predominantly sympathetic in elite extreme athletes, such as freestyle snowboarders, when the competition intensifies, and that this sympathetic predominance is positively related to competitive performance.
Characterization of Compound-Specific, Concentration-Independent Biophysical Properties of Sodium Channel Inhibitor Mechanism of Action Using Automated Patch-Clamp Electrophysiology

We have developed an automated patch-clamp protocol that allows high information content screening of sodium channel inhibitor compounds. We have observed that individual compounds had their specific signature patterns of inhibition, which were manifested irrespective of the concentration. Our aim in this study was to quantify these properties. Primary biophysical data, such as onset rate, the shift of the half inactivation voltage, or the delay of recovery from inactivation, are concentration-dependent. We wanted to derive compound-specific properties, therefore, we had to neutralize the effect of concentration. This study describes how this is done, and shows how compound-specific properties reflect the mechanism of action, including binding dynamics, cooperativity, and interaction with the membrane phase. We illustrate the method using four well-known sodium channel inhibitor compounds, riluzole, lidocaine, benzocaine, and bupivacaine. Compound-specific biophysical properties may also serve as a basis for deriving parameters for kinetic modeling of drug action. We discuss how knowledge about the mechanism of action may help to predict the frequency-dependence of individual compounds, as well as their potential persistent current component selectivity. The analysis method described in this study, together with the experimental protocol described in the accompanying paper, allows screening for inhibitor compounds with specific kinetic properties, or with specific mechanisms of inhibition.
Proteome Analysis of Condensed Barley Mitotic Chromosomes

Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.
Loss of the ClpXP Protease Leads to Decreased Resistance to Cell-Envelope Targeting Antimicrobials in Bacillus anthracis Sterne

The ClpX ATPase is critical for resistance to cell envelope targeting antibiotics in Bacillus anthracis, however, it is unclear whether this is due to its function as an independent chaperone or as part of the ClpXP protease. In this study, we demonstrate that antibiotic resistance is due to formation of the ClpXP protease through construction of a ClpX complementation plasmid that is unable to interact with ClpP. Additionally, we genetically disrupted both clpP genes, clpP1 and clpP2, found in B. anthracis Sterne and find that the loss of either increases susceptibility to cell envelope targeting antimicrobials, although neither has as strong of a phenotype as loss of clpX and neither clpP gene is essential for virulence in a G. mellonella model of infection. Lastly, we looked at changes to cell envelope morphology that could contribute to increased antibiotic sensitivity. We find no difference in cell charge or cell lysis, although we do see increased hydrophobicity in the ΔclpX strain, decreased cellular density and slightly thinner cells walls. We also see significant cell division defects in ΔclpX, although only when cells are grown in the mammalian cell culture medium, RPMI. We conclude that the intrinsic resistance of B. anthracis to cell wall active antimicrobials is dependent on formation of the ClpXP protease and that this could be due, at least in part, to the role of ClpX in regulating cell envelope morphology.