Miracle-dz/UniFAR-FTUs huggingface dataset:
Elucidation of an anaerobic pathway for metabolism of l-carnitine–derived γ-butyrobetaine to trimethylamine in human gut bacteria

Significance Trimethylamine (TMA) is a disease-associated metabolite produced in the human body exclusively by microbes. Gut microbes generate TMA from essential nutrients consumed in the human diet, including l-carnitine. However, our understanding of the biochemical mechanisms involved in these transformations is incomplete. In this work, we define the biochemical pathway and genetic components in gut bacteria required for anaerobic production of TMA from γ-butyrobetaine, a metabolite derived from l-carnitine. This discovery identifies a new type of TMA-producing enzyme and fills a critical gap in our knowledge of l-carnitine metabolism to TMA in the anaerobic environment of the human gut. This knowledge will enable evaluation of the link between l-carnitine metabolism and human disease and the design of potential therapeutics. Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient l-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent l-carnitine–metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the l-carnitine–derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis. We identify a set of genes up-regulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a putative flavin cofactor to catalyze a redox-neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from l-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of l-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.
Intrauterine Nitric Oxide Deficiency Weakens Differentiation of Vascular Smooth Muscle in Newborn Rats

Nitric oxide (NO) deficiency during pregnancy is a key reason for preeclampsia development. Besides its important vasomotor role, NO is shown to regulate the cell transcriptome. However, the role of NO in transcriptional regulation of developing smooth muscle has never been studied before. We hypothesized that in early ontogeny, NO is important for the regulation of arterial smooth muscle-specific genes expression. Pregnant rats consumed NO-synthase inhibitor L-NAME (500 mg/L in drinking water) from gestational day 10 till delivery, which led to an increase in blood pressure, a key manifestation of preeclampsia. L-NAME reduced blood concentrations of NO metabolites in dams and their newborn pups, as well as relaxations of pup aortic rings to acetylcholine. Using qPCR, we demonstrated reduced abundances of the smooth muscle-specific myosin heavy chain isoform, α-actin, SM22α, and L-type Ca2+-channel mRNAs in the aorta of newborn pups from the L-NAME group compared to control pups. To conclude, the intrauterine NO deficiency weakens gene expression specific for a contractile phenotype of arterial smooth muscle in newborn offspring.
Antiviral Potential of Plants against Noroviruses

Human noroviruses, which belong to the enterovirus family, are one of the most common etiological agents of food-borne diseases. In recent years, intensive research has been carried out regarding the antiviral activity of plant metabolites that could be used for the preservation of fresh food, because they are safer for consumption when compared to synthetic chemicals. Plant preparations with proven antimicrobial activity differ in their chemical compositions, which significantly affects their biological activity. Our review aimed to present the results of research related to the characteristics, applicability, and mechanisms of the action of various plant-based preparations and metabolites against norovirus. New strategies to combat intestinal viruses are necessary, not only to ensure food safety and reduce infections in humans but also to lower the direct health costs associated with them.
Effect of Seasonal Variation during Annual Cyclist Training on Somatic Function, White Blood Cells Composition, Immunological System, Selected Hormones and Their Interaction with Irisin

The aim of this study was to evaluate somatic, hormonal and immunological changes during the macrocycle of cyclists (9 well-trained men, age 25.6 ± 5.2 years and body weight 72.4 ± 7.35 kg). During the training macrocycle, four exercise control tests were carried out, and biochemical markers were measured in the laboratory. Seasonal training changes did not significantly disturb resting somatic and functional parameters, physical capacity (VO2max), body weight, the number of leukocytes and selected hormones. The secretory system of the organism did not respond significantly to the exercise stress in the training process, even with the increasing share of anaerobic processes in the subsequent periods of the macrocycle. Irisin and other parameters globally did not correlate with training volume. Irisin showed a significant correlation only with cortisol in the first period and human growth hormone in the second, and it showed a weak correlation in the third period with body mass and BMI. The lack of interactions between irisin level and other variables practically excludes its use in monitoring cyclist training. Future research would be complemented by the assessment of stress and postexercise changes in the cyclists’ macrocycle and expanding the research group to other athletes, including women.
Phytochemicals in Malignant Pleural Mesothelioma Treatment—Review on the Current Trends of Therapies

Malignant pleural mesothelioma (MPM) is a rare but highly aggressive tumor of pleura arising in response to asbestos fibers exposure. MPM is frequently diagnosed in the advanced stage of the disease and causes poor prognostic outcomes. From the clinical perspective, MPM is resistant to conventional treatment, thus challenging the therapeutic options. There is still demand for improvement and sensitization of MPM cells to therapy in light of intensive clinical studies on chemotherapeutic drugs, including immuno-modulatory and targeted therapies. One way is looking for natural sources, whole plants, and extracts whose ingredients, especially polyphenols, have potential anticancer properties. This comprehensive review summarizes the current studies on natural compounds and plant extracts in developing new treatment strategies for MPM.
Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases

Glycogen synthase kinase-3 beta (GSK-3β) is an enzyme pertinently linked to neurodegenerative diseases since it is associated with the regulation of key neuropathological features in the central nervous system. Among the different kinds of inhibitors of this kinase, the allosteric ones stand out due to their selective and subtle modulation, lowering the chance of producing side effects. The mechanism of GSK-3β allosteric modulators may be considered still vague in terms of elucidating a well-defined binding pocket and a bioactive pose for them. In this context, we propose to reinvestigate and reinforce such knowledge by the application of an extensive set of in silico methodologies, such as cavity detection, ligand 3D shape analysis and docking (with robust validation of corresponding protocols), and molecular dynamics. The results here obtained were consensually consistent in furnishing new structural data, in particular by providing a solid bioactive pose of one of the most representative GSK-3β allosteric modulators. We further applied this to the prospect for new compounds by ligand-based virtual screening and analyzed the potential of the two obtained virtual hits by quantum chemical calculations. All potential hits achieved will be subsequently tested by in vitro assays in order to validate our approaches as well as to unveil novel chemical entities as GSK-3β allosteric modulators.
Investigation of the role of the Golgi resident GGA1 coat protein in CD4 down-modulation by HIV-1 Nef

1 Nederlandse samenvatting 3 Introduction 5 About HIV-1 5 CD4 receptor down-modulation 6 The HIV-1 Nef protein and CD4 down-modulation 7 Adaptor protein complexes 10 Introduction to the experiments 11 Materials and methods 13 Cell culture 13 CD4+ primary blood lymphocytes isolation from buffy coat 13 Thawing cells 14 Viral production and transduction using Nef coding retroviruses 14 Preparation of RetroNectin-coated plates 15 Viral production and transduction using Nef-coding lentiviruses 15 Flow Cytometry 16 Fixation and permeabilisation of cells and intracellular staining 16 Bafilomycin A1 treatment 17 PMN-elastase and cathepsin G 17 RNAisolation 18 cDNA synthesis 19 Polymerase Chain Reaction (PCR) 20 Agarose gel electrophoresis and DNA purification from the gel 21 DNA sequencing 22 Quantitative reverse transcriptionpolymerase chain reaction 24 Results 28 Investigation of intracellular CD4 31 Investigation of intracellular CD4 in cells treated with bafilomycin A1 and expressing Nef . 31 Investigation of intracellular CD4 in cells expressing Nef and treated with cathepsin G and PMNelastase 33 Investigation of the influence of shRNA mediated knockdown of GGA1 on the expression of GGA2 and GGA3 36 Investigation shRNA-mediated knock-down efficiency via qRT-PCR 38 Discussion 41 References 44
Neobavaisoflavone May Modulate the Activity of Topoisomerase Inhibitors towards U-87 MG Cells: An In Vitro Study

Despite many advances in therapy, glioblastoma (GB) is still characterized by its poor prognosis. The main reason for this is unsuccessful treatment, which slightly extends the duration of remission; thus, new regimens are needed. One of many types of chemotherapeutics that are being investigated in this field is topoisomerase inhibitors, mainly in combination therapy with other drugs. On the other hand, the search for new anti-cancer substances continues. Neobavaisoflavone (NBIF) is a natural compound isolated from Psoralea corylifolia L. , which possesses anti-oxidant, anti-inflammatory, and anti-cancer properties. The aim of this study was to evaluate the effect of NBIF in human U-87 MG glioblastoma cells in comparison to normal human NHA astrocytes, and to examine if it influences the activity of irinotecan, etoposide, and doxorubicin in this in vitro model. We demonstrated that NBIF decreases U-87 MG cells viability in a dose-dependent manner. Furthermore, we found that it inhibits cell growth and causes glutathione (GSH) depletion more intensely in U-87 MG cells than in astrocytes. This study also provides, for the first time, evidence of the potentialization of the doxorubicin effect by NBIF, which was shown by the reduction in the viability in U-87 MG cells.
The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer.

The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune-based strategies to combat this disease have been largely unsuccessful to date. We corroborate prior reports that a substantial portion of PDAC harbors predicted high-affinity MHC class I-restricted neoepitopes and extend these findings to advanced/metastatic disease. Using multiple preclinical models of neoantigen-expressing PDAC, we demonstrate that intratumoral neoantigen-specific CD8+ T cells adopt multiple states of dysfunction, resembling those in tumor-infiltrating lymphocytes of PDAC patients. Mechanistically, genetic and/or pharmacologic modulation of the CD155/TIGIT axis was sufficient to promote immune evasion in autochthonous neoantigen-expressing PDAC. Finally, we demonstrate that the CD155/TIGIT axis is critical in maintaining immune evasion in PDAC and uncover a combination immunotherapy (TIGIT/PD-1 co-blockade plus CD40 agonism) that elicits profound anti-tumor responses in preclinical models, now poised for clinical evaluation.
Polysaccharide Structures and Their Hypocholesterolemic Potential

Several classes of polysaccharides have been described to have hypocholesterolemic potential, namely cholesterol bioaccessibility and bioavailability. This review will highlight the main mechanisms by which polysaccharides are known to affect cholesterol homeostasis at the intestine, namely the effect (i) of polysaccharide viscosity and its influence on cholesterol bioaccessibility; (ii) on bile salt sequestration and its dependence on the structural diversity of polysaccharides; (iii) of bio-transformations of polysaccharides and bile salts by the gut microbiota. Different quantitative structure–hypocholesterolemic activity relationships have been explored depending on the mechanism involved, and these were based on polysaccharide physicochemical properties, such as sugar composition and ramification degree, linkage type, size/molecular weight, and charge. The information gathered will support the rationalization of polysaccharides’ effect on cholesterol homeostasis and highlight predictive rules towards the development of customized hypocholesterolemic functional food.
Sex Differences in the Triad of Acquired Sensorineural Hearing Loss

The triad of noise-generated, drug-induced, and age-related hearing loss is the major cause of acquired sensorineural hearing loss (ASNHL) in modern society. Although these three forms of hearing loss display similar underlying mechanisms, detailed studies have revealed the presence of sex differences in the auditory system both in human and animal models of ASNHL. However, the sexual dimorphism of hearing varies among noise-induced hearing loss (NIHL), ototoxicity, and age-related hearing loss (ARHL). Importantly, estrogen may play an essential role in modulating the pathophysiological mechanisms in the cochlea and several reports have shown that the effects of hormone replacement therapy on hearing loss are complex. This review will summarize the clinical features of sex differences in ASNHL, compare the animal investigations of cochlear sexual dimorphism in response to the three insults, and address how estrogen affects the auditory organ at molecular levels.
Nutritional Studies On Fermented, Germinated And Baked Soya Bean(Glycine Max) Preparations

AbstractThe nutritional quality and protein efficiency ratio (PER) of shoyu a fermentedsoya bean product, ferment ed soya milk drink, germinated soya bean andgerminated soya bean bread were studied. Nutritional quality was determinedby chemical analysis and PER by animal feeding studies. Results indicate aslight change in the protein content of the processed products with no adversechanges in essential amino acid content. Ash content was greatest in germinatedsoya beans. Trypsin inhibitor activity was markedly reduced on germination.Animal feeding studies indicate a slight increase in protein quality on germinationand fermentation. However, a slight decrease was noted in soya bean breadwhich may be due to the Maiilard reaction rendering lysine unavailable.
Fully Automated Colorimetric Analysis of the Optic Nerve Aided by Deep Learning and Its Association with Perimetry and OCT for the Study of Glaucoma

Background: Laguna-ONhE is an application for the colorimetric analysis of optic nerve images, which topographically assesses the cup and the presence of haemoglobin. Its latest version has been fully automated with five deep learning models. In this paper, perimetry in combination with Laguna-ONhE or Cirrus-OCT was evaluated. Methods: The morphology and perfusion estimated by Laguna ONhE were compiled into a “Globin Distribution Function” (GDF). Visual field irregularity was measured with the usual pattern standard deviation (PSD) and the threshold coefficient of variation (TCV), which analyses its harmony without taking into account age-corrected values. In total, 477 normal eyes, 235 confirmed, and 98 suspected glaucoma cases were examined with Cirrus-OCT and different fundus cameras and perimeters. Results: The best Receiver Operating Characteristic (ROC) analysis results for confirmed and suspected glaucoma were obtained with the combination of GDF and TCV (AUC: 0.995 and 0.935, respectively. Sensitivities: 94.5% and 45.9%, respectively, for 99% specificity). The best combination of OCT and perimetry was obtained with the vertical cup/disc ratio and PSD (AUC: 0.988 and 0.847, respectively. Sensitivities: 84.7% and 18.4%, respectively, for 99% specificity). Conclusion: Using Laguna ONhE, morphology, perfusion, and function can be mutually enhanced with the methods described for the purpose of glaucoma assessment, providing early sensitivity.
The Diagnostic Approach to Mitochondrial Disorders in Children in the Era of Next-Generation Sequencing: A 4-Year Cohort Study

Mitochondrial diseases (MDs) are a large group of genetically determined multisystem disorders, characterized by extreme phenotypic heterogeneity, attributable in part to the dual genomic control (nuclear and mitochondrial DNA) of the mitochondrial proteome. Advances in next-generation sequencing technologies over the past two decades have presented clinicians with a challenge: to select the candidate disease-causing variants among the huge number of data provided. Unfortunately, the clinical tools available to support genetic interpretations still lack specificity and sensitivity. For this reason, the diagnosis of MDs continues to be difficult, with the new “genotype first” approach still failing to diagnose a large group of patients. With the aim of investigating possible relationships between clinical and/or biochemical phenotypes and definitive molecular diagnoses, we performed a retrospective multicenter study of 111 pediatric patients with clinical suspicion of MD. In this cohort, the strongest predictor of a molecular (in particular an mtDNA-related) diagnosis of MD was neuroimaging evidence of basal ganglia (BG) involvement. Regression analysis confirmed that normal BG imaging predicted negative genetic studies for MD. Psychomotor regression was confirmed as an independent predictor of a definitive diagnosis of MD. The findings of this study corroborate previous data supporting a role for neuroimaging in the diagnostic approach to MDs and reinforce the idea that mtDNA sequencing should be considered for first-line testing, at least in specific groups of children.
Controlled Human Exposures to Concentrated Ambient Fine Particles and Ozone: Individual and Combined Effects on Cardiorespiratory Outcomes

Epidemiological studies have shown strong and consistent associations between exposure to air pollution and increases in morbidity and mortality. Key air pollutants that have been identified include fine particulate matter (PM) and ozone (O3), both major contributors to smog. However, there is a lack of understanding of the mechanisms involved and the relative contributions of individual pollutants. A controlled human exposure facility was used to carry out inhalation studies of concentrated ambient fine particles (CAP), O3, CAP+O3 and filtered air following a randomized design. Exposures were 2 hrs in duration at rest. Subjects included mild asthmatics and non-asthmatics. This thesis focuses on acute cardiovascular responses including blood pressure (BP), brachial artery reactivity (flow-mediated dilatation [FMD]) and markers of systemic inflammation (blood neutrophils and interleukin [IL]-6). Results showed that for CAP-containing exposures (CAP, CAP+O3) there were small but significant transient increases in diastolic BP (DBP) during exposures. Furthermore, neutrophils and IL-6 increased 1 3 hrs after and FMD decreased 20 hrs after CAP-containing exposures. Responses to O3 were smaller, comparable to filtered air. The data suggests that adverse responses were mainly driven by PM. The DBP increase was rapid-developing and quick to dissipate, which points to an autonomic irritant response. The magnitude of the DBP increase was strongly negatively associated with the high frequency
Interactive comment on “Air quality and health benefits from ultra-low emission control policy indicated by continuous emission monitoring: A case study in the Yangtze River Delta region, China” by Yan Zhang et al

Author: Yan Zhang, Yu Zhao, Meng Gao, Xin Bo, Chris P. Nielsen We thank very much for the valuable comments from the reviewer, which help us improve our manuscript. The comments were carefully considered and revisions have been made in response to suggestions. Following are our point-by-point responses to the comments and corresponding revisions. Please note that the line numbers mentioned following refer to the clean version of manuscript. Reviewer #3 [Report #2] (the Interactive Discussion stage): 0. This paper evaluated the potential benefit of the ultra-low emission policy on both air quality and human health in the YRD region. No novel technique was developed, or new scientific finding was reported. The results can still provide some scientific reference for related emission control policy and health burden caused by air pollution over the YRD region. Overall, this paper is well written, but more description in the methodology is still needed. A major revision is suggested, and my specific comments are listed as follows. Response and revisions: We appreciate the reviewer’s remarks and have revised the manuscript according to the reviewer’s specific comments, as summarized below. 1. Line 55, in the abstract section, "874 years", but according to on paper Table6, it should be "8744 years of life loss". Response and revisions: We thank the reviewer’s reminder and the error has been corrected. 2. In the methodology section, please generally introduce the method of how to incorporate the CEMS data and cite the references which have the detailed description. Response and revisions:
Culture Clash: Incompatible Reputation Systems and Intergroup Conflict∗

Under which conditions does intergroup contact lead to conflict? We provide a novel answer to this question by highlighting the role of reputation mechanisms in sustaining cooperation. Punishment-based reputation (a “culture of honor”) and reputation based on image scoring (indirect reciprocity) can both deter defection in one-time interactions within groups. Yet these reputation mechanisms can be incompatible in intergroup interactions. Using a game theoretic model, we show that injecting pools of individuals from a punishment-based culture into a culture of image scoring can lead to widespread intergroup conflict. Cooperation is a more likely outcome if the cultures that interact use a similar reputation mechanism. The theoretical framework helps us explain a variety of phenomena, such as variation in immigrant crime rates and patterns of outgroup discrimination.