Miracle-dz/UniFAR-FTUs huggingface dataset:
ATP and Substrate Binding Regulates Conformational Changes of Human Peroxisomal ABC Transporter ALDP

The malfunction of ABCD1 causes X-linked adrenoleukodystrophy (X-ALD), a rare neurodegenerative disease that affect all tissues in human. Residing in the peroxisome membrane, ABCD1 plays a role in the translocation of very long chain fatty acids (VLCFA) for their damage by β-oxidation. Here, we present five Cryo-Electron microscopy structures of ABCD1 in four conformational states. Combined with functional analysis, we found that substrate and ATP trigger the closing of two nucleotide binding domains (NBDs) over a distance of 40 Å and the rearrangement of the transmembrane domains. Each of the three inward-facing structure of ABCD1 has a vestibule opens to cytosol with variable size. Furthermore, the structure of ABCD1 in the outward-facing state supports that ATP molecules pull the two NBDs together and open the transmembrane domain to the peroxisomal lumen for substrate release. The five structures provide a snapshot of substrate transporting cycle and mechanistic implications for disease-causing mutations.
Alkyne modified purines for assessing activation of Plasmodium vivax hypnozoites and growth of pre-erythrocytic and erythrocytic stages in Plasmodium spp

Malaria is a major global health problem which predominantly afflicts developing countries. Although many antimalarial therapies are currently available, the protozoan parasite causing this disease, Plasmodium spp. , continues to evade eradication efforts. One biological phenomenon hampering eradication efforts is the parasite’s ability to arrest development, transform into a drug-insensitive form, and then resume growth post-therapy. Currently, the mechanisms by which the parasite enters arrested development, or dormancy, and later recrudesces or reactivates to continue development, are unknown and the malaria field lacks techniques to study these elusive mechanisms. Since Plasmodium spp. salvage purines for DNA synthesis, we hypothesized that alkyne-containing purine nucleosides could be used to develop a DNA synthesis marker which could be used to investigate mechanisms behind dormancy. Using copper-catalyzed click chemistry methods, we observe incorporation of alkyne modified adenosine, inosine, and hypoxanthine in actively replicating asexual blood stages of P. falciparum and incorporation of modified adenosine in actively replicating liver stage schizonts of P. vivax. Notably, these modified purines were not incorporated in dormant liver stage hypnozoites, suggesting this marker could be used as a tool to differentiate replicating and non-replicating liver forms and, more broadly, a tool for advancing our understanding Plasmodium dormancy mechanisms.
Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis

The use of short peptide tags in synthetic genetic circuits allows for the tuning of gene expression dynamics and release of amino acid resources through targeted protein degradation. Here, we use elements of the Escherichia coli and Mesoplasma florum transfer-messenger RNA (tmRNA) ribosome rescue systems to compare endogenous and foreign proteolysis systems in E. coli. We characterize the performance and burden of each and show that while both greatly shorten the half-life of a tagged protein, the endogenous system is approximately ten times more efficient. Based on these results, we then demonstrate using mathematical modelling and experiments how proteolysis can improve cellular robustness through targeted degradation of a reporter protein in auxotrophic strains, providing a limited secondary source of essential amino acids that help partially restore growth when nutrients become scarce. These findings provide avenues for controlling the functional lifetime of engineered cells once deployed and increasing their tolerance to fluctuations in nutrient availability.
Frugivore gut passage increases seed germination: an updated meta-analysis

Many plants rely on animal mutualists for reproduction. Quantifying how animal mutualists impact plant performance provides a foundation for modelling how change in animal communities affects the composition and functioning of plant communities. We performed a meta-analysis of 2539 experiments, 6 times more than the last comprehensive meta-analysis, examining how gut passage by frugivores influences seed germination. We simultaneously analyzed multiple predictor variables related to study methodology, location, and frugivore identity to disentangle methodological from ecological impacts on effect sizes. We found that gut passage by birds, fish, reptiles, bats, primates, and other mammals on average increased seed germination, but that the magnitude varied across vertebrate groups. The positive effects of gut passage were largely explained by the de-inhibitory effects of pulp removal rather than by the scarification of seed tissues. Some previous studies and meta-analyses that found no effect of gut passage only tested scarification or did not distinguish between these tests of scarification and pulp removal. We found that, for a typical fleshy-fruited plant species, the lack of gut passage reduces germination by 60%. From an evolutionary perspective, this indicates a large risk associated with reliance on animal mutualists that is balanced against the benefits of animal-mediated seed dispersal. From a conservation perspective, this highlights the potential for large demographic consequences of frugivore declines on plant populations. Our database and findings advance quantitative predictions for the role of fruit-frugivore interactions in shaping plant communities in the Anthropocene.
Cold atmospheric plasma differentially affects cell renewal and differentiation of stem cells and APC-deficient-derived tumor cells in intestinal organoids

Cold atmospheric plasma (CAP) treatment has been proposed as a potentially innovative therapeutic tool in the biomedical field, notably for cancer due to its proposed toxic selectivity on cancer cells versus healthy cells. In the present study, we addressed the relevance of three-dimensional organoid technology to investigate the biological effects of CAP on normal epithelial stem cells and tumor cells isolated from mouse small intestine. CAP treatment exerted dose-dependent cytotoxicity on normal organoids and induced major transcriptomic changes associated with the global response to oxidative stress, fetal-like regeneration reprogramming, and apoptosis-mediated cell death. Moreover, we explored the potential selectivity of CAP on tumor-like Apc-deficient versus normal organoids in the same genetic background. Unexpectedly, tumor organoids exhibited higher resistance to CAP treatment, correlating with higher antioxidant activity at baseline as compared to normal organoids. This pilot study suggests that the ex vivo culture system could be a relevant alternative model to further investigate translational medical applications of CAP technology.
Neuronal hemoglobin induces α-synuclein cleavage and loss of dopaminergic neurons

α-synuclein, a protein involved in the pathogenesis of several neurodegenerative disorders, is subjected to several post-translational modifications. Among them, C-terminal truncation seems to increase its aggregation propensity in vitro. Hemoglobin is the major protein in erythrocytes to carries oxygen and recently is found to be expressed in dopaminergic neurons and to be involved in the pathogenesis of neurodegenerative diseases such as Parkinson’s disease.To assess the role of hemoglobin in α-synuclein post-translational modification and in dopamine cells physiology, we over-expressed α and β-chains of Hb in iMN9D dopamine cells to evaluate its effect on α-synuclein truncation. Using an AAV9 we expressed α and β-chains of hemoglobin in dopamine neurons of Substantia Nigra pars compacta and evaluate its effect on α-synuclein post-translational modification, dopamine neurons survivals and behavioural outcome.The over-expression of α and β-chains of hemoglobin in iMN9D dopamine cells increased C-terminal truncation of α-synuclein when cells were treated with α-synuclein preformed fibrils. This cleavage was led at least in part by Calpain protease. Hemoglobin over-expression in Substantia Nigra pars compacta induced a similar pattern of α-synuclein truncation and a decrease in tyrosine hydroxylase expression, unveiling a decrease of dopamine neurons of about 50%. This dopamine cells loss led to a mild motor impairment and a deficit in recognition and spatial working memory.Our study reveals a novel role for hemoglobin in α-synuclein post-translational modification and in dopamine neurons homeostasis suggesting neuronal hemoglobin is an important modifier in synucleinopathies such as Parkinson’s disease.
Resilience of Nematode Connectomes Based on Network Dimension-reduced Method

The whole map of nematode connectomes provides important structural data for exploring the behavioral mechanism of nematodes, but to further reveal the functional importance and resilience pattern of nematode neurons, it is necessary to effectively couple the regulatory relationship between neurons and their topology. Here, with a typical signal excitation function we propose a model to capture the interacting relationship between the neurons, because a differential equation depicts the activity of a neuron, n neurons mean we need high-D differential equations to capture the neural network. With mean-field theory, we decouple this N-dimension question into a one-dimension problem mathematically. In our framework, we emphatically analyze the characteristics, similarities and differences of the structure and dynamical behaviors of the neuronal system for Caenorhabditis elegans and Pristionchus pacificus. The comparing results of simulating method and theoretical approach show that the most important homologous neurons between C.elegans and P.pacificus are I2 and NSM, which may lead to their different behavior characteristics of predation and prey. At the same time, we expect that the x eff index can be used to reveal the importance of neurons for the functional evolution and degeneration of neural networks from a dynamic perspective. In the hermaphroditic and male C.elegans, we test the control level of the intermediate neuron groups over the output neuron groups and the single neuron. These results suggest that our theoretical approach can be used to reveal the effects of bio-connectivity groups, potentially enabling us to explore the interaction relationship of neural networks in humans and animals.
Biomechanical Evaluation of the Effect of Minimally Invasive Spine Surgery Compared with Traditional Approaches in Lifting Tasks

Fusion of spinal vertebrae can be accomplished by different surgical approaches. We investigated Traditional Open Spine Surgery (TOSS) versus Minimally Invasive Spine Surgery (MISS). While TOSS sacrifices spine muscles originating or inserting on the affected vertebrae, MISS seeks to minimize the approach-related morbidity and preserve the tendon attachments of the muscles in the area. We captured 3-D motions of the full body of one healthy subject performing a variety of 10 kg box lifting operations representing activities-of-daily-living that are likely to challenge the spine biomechanically. The motion data were transferred to a full-body biomechanical model with a detailed representation of the biomechanics of the spine, and simulations of the internal spine loads and muscle forces were performed under a baseline configuration and muscle configurations typical for TOSS respectively MISS for the cases of L3/L4, L4/L5, L5/S1, L4/S1 and L3/L5 fusions. The computational model was then used to investigate the biomechanical differences between surgeries. The simulations revealed that joint reaction forces are more affected by both surgical approaches for lateral lifting motions than for sagittal plane motions, and there are indications that individuals with fused joints, regardless of the approach, should be particularly careful with asymmetrical lifts. The MISS and TOSS approaches shift the average loads of different muscle groups in different ways. TOSS generally leads to higher post-operative muscle loads than MISS in the investigated cases, but the differences are smaller than could be expected, given the differences of surgical technique.
Ypd1 Is an Essential Protein of the Major Fungal Pathogen Aspergillus fumigatus and a Key Element in the Phosphorelay That Is Targeted by the Antifungal Drug Fludioxonil

Aspergillus fumigatus is a major fungal pathogen causing life threatening infections in immunocompromised humans and certain animals. The HOG pathway is for two reasons interesting in this context: firstly, it is a stress signaling pathway that contributes to the ability of this pathogen to adapt to various stress conditions and secondly, it is the target of antifungal agents, such as fludioxonil or pyrrolnitrin. In this study, we demonstrate that Ypd1 is an essential protein in A. fumigatus. As the central component of the multistep phosphorelay it represents the functional link between the sensor histidine kinases and the downstream response regulators SskA and Skn7. A GFP-Ypd1 fusion was found to reside in both, the cytoplasm and the nucleus and this pattern was only slightly affected by fludioxonil. A strain in which the ypd1 gene is expressed from a tet-on promoter construct is unable to grow under non-inducing conditions and shows the characteristic features of A. fumigatus wild type hyphae treated with fludioxonil. Expression of wild type Ypd1 prevents this lethal phenotype, but expression of an Ypd1 mutant protein lacking the conserved histidine at position 89 was unable to do so, which confirms that A. fumigatus Ypd1 is a phosphotransfer protein. Generation of ypd1tet−on variants of several mutant strains revealed that the lethal phenotype associated with low amounts of Ypd1 depends on SskA, but not on TcsC or Skn7. The ΔsskA ypd1tet−on, but not the ΔsskAΔskn7 ypd1tet−on mutant, was sensitive to fludioxonil, which underlines the importance of Skn7 in this context. We finally succeeded to delete ypd1, but only if sskA and skn7 were both inactivated, not in a ΔsskA single mutant. Hence, a deletion of ypd1 and an inactivation of Ypd1 by fludioxonil result in similar phenotypes and the two response regulators SskA and Skn7 are involved in both processes albeit with a different relative importance.
Electroporation as an Efficacy Potentiator for Antibiotics With Different Target Sites

Antibiotic resistance is a global health threat, and there is ample motivation for development of novel antibacterial approaches combining multiple strategies. Electroporation is among the promising complementary techniques – highly optimizable, effective against a broad range of bacteria, and largely impervious to development of resistance. To date, most studies investigating electroporation as an efficacy potentiator for antibacterials used substances permissible in food industry, and only few used clinical antibiotics, as acceptable applications are largely limited to treatment of wastewaters inherently contaminated with such antibiotics. Moreover, most studies have focused mainly on maximal achievable effect, and less on underlying mechanisms. Here, we compare Escherichia coli inactivation potentiation rates for three antibiotics with different modes of action: ampicillin (inhibits cell wall synthesis), ciprofloxacin (inhibits DNA replication), and tetracycline (inhibits protein synthesis). We used concentrations for each antibiotic from 0 to 30× its minimum inhibitory concentration, a single 1-ms electric pulse with amplitude from 0 to 20 kV/cm, and post-pulse pre-dilution incubation either absent (≲1 min) or lasting 60 min, 160 min, or 24 h. Our data show that with incubation, potentiation is significant for all three antibiotics, increases consistently with pulse amplitude, and generally also with antibiotic concentration and incubation time. With incubation, potentiation for ampicillin was rather consistently (although with weak statistical significance) superior to both ciprofloxacin and tetracycline: ampicillin was superior to both in 42 of 48 data points, including 7 with significance with respect to both, while at 60- and 160-min incubation, it was superior in 31 of 32 data points, including 6 with significance with respect to both. This suggests that electroporation potentiates wall-targeting antibiotics more than those with intracellular targets, providing motivation for in-depth studies of the relationship between the mode of action of an antibiotic and its potentiation by electroporation. Identification of substances permissible in foods and targeting the cell wall of both Gram-negative and Gram-positive bacteria might provide candidate antibacterials for broad and strong potentiation by electroporation applicable also for food preservation.
DNA Vaccines Targeting Novel Cancer-Associated Antigens Frequently Expressed in Head and Neck Cancer Enhance the Efficacy of Checkpoint Inhibitor

HPV-independent head and neck squamous cell carcinoma (HNSCC) is a common cancer globally. The overall response rate to anti-PD1 checkpoint inhibitors (CPIs) in HNSCC is ~16%. One major factor influencing the effectiveness of CPI is the level of tumor infiltrating T cells (TILs). Converting TILlow tumors to TILhigh tumors is thus critical to improve clinical outcome. Here we describe a novel DNA vaccines to facilitate the T-cell infiltration and control tumor growth. We evaluated the expression of target antigens and their respective immunogenicity in HNSCC patients. The efficacy of DNA vaccines targeting two novel antigens were evaluated with or without CPI using a syngeneic model. Most HNSCC patients (43/44) co-expressed MAGED4B and FJX1 and their respective tetramer-specific T cells were in the range of 0.06-0.12%. In a preclinical model, antigen-specific T cells were induced by DNA vaccines and increased T cell infiltration into the tumor, but not MDSC or regulatory T cells. The vaccines inhibited tumor growth and improved the outcome alone and upon combination with anti-PD1 and resulted in tumor clearance in approximately 75% of mice. Pre-existence of MAGED4B and FJX1-reactive T cells in HNSCC patients suggests that these widely expressed antigens are highly immunogenic and could be further expanded by vaccination. The DNA vaccines targeting these antigens induced robust T cell responses and with the anti-PD1 antibody conferring excellent tumor control. This opens up an opportunity for combination immunotherapy that might benefit a wider population of HNSCC patients in an antigen-specific manner.
Comprehensive Analysis of Regulatory Factors and Immune-Associated Patterns to Decipher Common and BRCA1/2 Mutation-Type-Specific Critical Regulation in Breast Cancer

Background: BRCA1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1-mutant BC; N = 49 BRCA2-mutant BC; and N = 117 BRCA1/2-wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data (N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2-mutant BC but lacking correlations in BRCA1/2-wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK–STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15, BUB1, and TTK, were upregulated in several BRCA1/2-mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2-mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.
Preoperative Oral Gabapentin in the Management of Postoperative Catheter-Related Bladder Discomfort in Adults: A Systematic Review and Meta-Analysis

Objective: To evaluate the efficacy and safety of preoperative oral gabapentin in preventing postoperative Catheter-Related Bladder Discomfort (CRBD) in surgical patients. Methods: Randomized controlled trials in which gabapentin was used for the prevention of CRBD in surgical patients with transurethral catheterization were evaluated. The primary outcome was the incidence of moderate-to-severe CRBD at 0, 1, 2, and 6 h after surgery, and secondary outcomes included the incidence of any grade CRBD, postoperative pain, and adverse events. Pooled risk ratios (RRs) and mean difference (MD), 95% confidence intervals (CIs), and P values were estimated using fixed and random effects statistical models. The Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach was used to rate the levels of certainty for key results. Results: A total of 6 randomized controlled trials involving 679 participants were included in the meta-analysis. Gabapentin significantly reduced the risk of moderate-to-severe CRBD at 0, 1, 2, and 6 h (0 h: RR = 0.19, 95% CI: 0.11 to 0.31, p < 0.00001; 1 h: RR = 0.40, 95% CI: 0.25 to 0.66, p < 0.001; 2 h: RR = 0.38, 95% CI: 0.26 to 0.56, p < 0.00001; 6 h: RR = 0.20, 95% CI: 0.11 to 0.38, p < 0.00001). The overall incidence of CRBD at 1 h showed no statistical difference between the two groups (RR = 0.55, 95% CI: 0.30 to 1.00, p = 0.05). The risk of CRBD was significantly reduced in the gabapentin group at 0, 2, and 6 h after surgery (0 h: RR = 0.59, 95% CI: 0.46 to 0.74, p < 0.0001; 2 h: RR = 0.62, 95% CI: 0.51 to 0.75, p < 0.00001; 6 h: RR = 0.66, 95% CI: 0.52 to 0.83, p < 0.001). In addition, gabapentin was associated with low postoperative pain intensity without significant side effects. Conclusion: Preoperative oral gabapentin as an adjunct to surgery is effective in decreasing the risk and severity of CRBD over a short time after surgery, and it can decrease postoperative pain without significant side effects. Overall, the level of certainty was moderate to low. Systematic Review Registration: https://www.crd. york.ac. uk/prospero/#recordDetails, identifier: CRD42021228171.