Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuronal cholesterol synthesis is essential for repair of chronically demyelinated lesions in mice

Astrocyte-derived cholesterol supports brain cells under physiological conditions. However, in demyelinating lesions, astrocytes downregulate cholesterol synthesis and the cholesterol that is essential for remyelination has to originate from other cellular sources. Here, we show that repair following acute versus chronic demyelination involves distinct processes. In particular, we found that in chronic myelin disease, when recycling of lipids is often defective, de novo neuronal cholesterol synthesis is critical for regeneration. By gene expression profiling, genetic loss of function experiments and comprehensive phenotyping, we provide evidence that neurons increase cholesterol synthesis in chronic myelin disease models and MS patients. In mouse models, neuronal cholesterol facilitated remyelination specifically by triggering OPC proliferation. Our data contribute to the understanding of disease progression and have implications for therapeutic strategies in MS patients.
Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements

Polycomb Repressive Complex 2 (PRC2) maintains transcriptionally silent genes in a repressed state via deposition of histone H3 K27 trimethyl (me3) marks. PRC2 has also been implicated in silencing transposable elements (TEs) yet how PRC2 is targeted to TEs remains unclear. To address this question, we performed tandem affinity purification combined with mass spectrometry and identified proteins that physically interact with the Paramecium Enhancer-of-zeste Ezl1 enzyme, which catalyzes H3K9me3 and H3K27me3 deposition at TEs. We show that the Paramecium PRC2 core complex comprises four subunits, each required in vivo for catalytic activity. We also identify PRC2 cofactors, including the RNA interference (RNAi) effector Ptiwi09, which are necessary to target H3K9me3 and H3K27me3 to TEs. We find that the physical interaction between PRC2 and the RNAi pathway is mediated by a RING finger protein and that small RNA recruitment of PRC2 to TEs is analogous to the small RNA recruitment of H3K9 methylation SU(VAR)3-9 enzymes.
MODEL BASED OPTIMIZACION OF THE TERPENOIDS BIOSYNTHESIS IN E. coli

Terpenoids are a family of compounds with high industrial interest and the development of biotechnological production methods is essential to achieve more sustainable alternatives to traditional extraction and synthesis methods. The modification and engineering of the catalytic activity (kcat) have been shown to be a feasible strategy in the biotechnological realm. Accordingly, we introduce a novel optimization strategy based in the modification of the kcat of the enzymes and applied it to the maximization of the terpenoids synthesis in E. coli. This approach is fairly general and can be applied alone or in conjunction with classic optimization strategies such as the modification of enzymatic specific activities. For this purpose we first build up a reliable dynamic mathematical model of the alternative mevalonate pathway synthesis leading terpenoids biosynthesis in E. coli through the methyl-D-erythritol 4-phosphate (MEP) pathway. This model includes the 2-C-methyl-D-erythritol 2, 4-diphosphate (MEC) pumps that mediate MEC extracellular extrusion. Although the physiological significance of the MEC extrusion is still discussed and their biological function is not clear, we find that this process is a must to guarantee bacteria homeostasis and cell viability. We have identified the enzyme IspA as a bottleneck of the terpenoids biosynthesis, which is dual substrate for the two bisubstrate final reactions. Here are presented different ways to overcome this enzymatic flux restriction by modification of the IspA kcat or by introduction of new enzymes with parallel function. Our results show that the MEP pathway optimized solutions for kcat can yield a maximum of 17.68 fold increment in the terpenoids biosynthetic flux when the kcat are modified. This maximal solution involves the modification of 8 kcat and the corresponding Km’s and Kd’s. Remarkably, this increase doesn’t imply a change in the total enzyme concentration of the cell. This is favorable output since enzyme overproduction can compromise cell functionality. We also apply the overexpression of the enzyme activity approach and then we have compared and combined both strategies including scenarios as the deletion or import of the genes expressing enzymes not naturally present in E. coli. A combined strategy of enzymes concentrations and kcat modifications with changes up ti six enzyme levels allows a flux increment of 21.22 fold the basal value. It involves the incorporation of two IspA with similar GPP and IPP bisubstrate functions than the native one but low affinity for the DMAPP as substrate.
Across functional boundaries: making non-neutralizing antibodies to neutralize HIV-1 and mediate Fc-mediated effector killing of infected cells

In HIV-1 infection, many antibodies (Abs) are elicited to Envelope (Env) epitopes that are conformationally masked in the native trimer and are only available for antibody recognition after the trimer binds host cell CD4. Among these are epitopes within the Co-Receptor Binding Site (CoRBS) and the constant region 1 and 2 (C1-C2 or Cluster A region). In particular, C1-C2 epitopes map to the gp120 face interacting with gp41 in the native, ‘closed’ Env trimer present on HIV-1 virions or expressed on HIV-1 infected cells. Antibodies targeting this region are therefore non-neutralizing and their potential as mediators of antibody depended cellular cytoxicity (ADCC) of HIV-1 infected cells diminished by a lack of available binding targets. Here we present the design of Ab-CD4 chimeric proteins that consist of the Ab-IgG1 of a CoRBS or Cluster A specificity to the extracellular domain 1 and 2 of human CD4. Our Ab-CD4 hybrids induce potent ADCC against infected primary CD4+ T cells and neutralize tier 1 and 2 HIV-1 viruses. Furthermore, competition binding experiments reveal that the observed biological activities rely on both the antibody and CD4 moieties confirming their cooperativity in triggering conformational rearrangements of Env. Our data indicate the utility of these Ab-CD4 hybrids as antibody therapeutics effective in eliminating HIV-1 through the combined mechanisms of neutralization and ADCC. This is also the first report of single-chain-Ab-based molecules capable of opening ‘closed’ Env trimers on HIV-1 particles/infected cells to expose the Cluster A region and activate ADCC and neutralization against these non-neutralizing targets. Importance Highly conserved epitopes within the co-receptor binding site (CoRBS) and constant region 1 and 2 (C1C2 or Cluster A) are only available for antibody recognition after the HIV-1 Env trimer binds host cell CD4, therefore they are not accessible on virions and infected cells where the expression of CD4 is downregulated. Here we have developed new antibody fusion molecules in which domains 1 and 2 of soluble human CD4 are linked with monoclonal antibodies of either the CoRBS or Cluster A specificity. We optimized the conjugation sites and linker lengths to allow each of these novel bispecific fusion molecules to recognize native “closed” Env trimers and induce the structural rearrangements required for exposure of the epitopes for antibody binding. Our in vitro functional testing shows that our Ab-CD4 molecules can efficiently target and eliminate HIV-1 infected cells through antibody depended cellular cytoxicity (ADCC) and inactivate HIV-1 virus through neutralization.
Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E−5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E−5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E−5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.
Deep Convolutional Neural Networks With Ensemble Learning and Generative Adversarial Networks for Alzheimer’s Disease Image Data Classification

Recent advancements in deep learning (DL) have made possible new methodologies for analyzing massive datasets with intriguing implications in healthcare. Convolutional neural networks (CNN), which have proven to be successful supervised algorithms for classifying imaging data, are of particular interest in the neuroscience community for their utility in the classification of Alzheimer’s disease (AD). AD is the leading cause of dementia in the aging population. There remains a critical unmet need for early detection of AD pathogenesis based on non-invasive neuroimaging techniques, such as magnetic resonance imaging (MRI) and positron emission tomography (PET). In this comprehensive review, we explore potential interdisciplinary approaches for early detection and provide insight into recent advances on AD classification using 3D CNN architectures for multi-modal PET/MRI data. We also consider the application of generative adversarial networks (GANs) to overcome pitfalls associated with limited data. Finally, we discuss increasing the robustness of CNNs by combining them with ensemble learning (EL).
Acceptability of COVID-19 Certificates: A Qualitative Study in Geneva, Switzerland, in 2020

Immunity certificates related to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been under discussion since the beginning of the pandemic with conflicting opinions. In order to identify arguments in favor of and against the possible implementation of documents certifying immunity of an individual based on serological testing, we developed a qualitative study in Geneva, Switzerland. The study took place between two lockdowns with a sense of semi-normalcy during summer 2020 in Switzerland but at a time when no vaccine was available and seroprevalence was below 21%. Eleven focus groups with members of the public and 14 semi-structured interviews with stakeholders were conducted between July and November 2020, with a total of 68 participants with an age range between 24 and 77 years. Interviews and focus groups transcripts were coded with the ATLAS.ti CAQDAS. Few participants considered immunity certificates based on serological testing as an acceptable public health measure. Major concerns included the reliability of scientific data related to COVID-19 immunity and serological testing potential re-infection as well as the possibility that the use of certificates could result in deleterious outcomes. Discrimination, counterfeiting, incitement for self-infection, invasion of the private sphere, violation of personal integrity, and violation of medical secrecy were perceived as the major risks. Benefits of immunity certificates were more perceived when in relation to vaccination, and included gains in medical knowledge and protection in certain contexts involving leisure or work-related activities. The consequences of implementing immunity certificates are numerous, and the acceptability by the general population has to be considered when engaging in such policy. Even if the results provide a snapshot of arguments discussed around immunity certificates based on serological testing before the implementation of the COVID-19 vaccine, most of the issues discussed are central in the current debates about vaccination certificates.
A Significant Genetic Admixture in Farmed Populations of the Noble Scallop Chlamys nobilis Revealed by Microsatellite DNA Analysis in Southern China

The noble scallop, Chlamys nobilis, is an important bivalve mollusk with high commercial value and is usually farmed in the waters of southern China. To date, very little is known about the genetic diversity and population structure of C. nobilis. In this study, 10 microsatellite loci of four farmed C. nobilis populations were compared with one another and compared wild population in southern China. A total of 83 alleles were found. Surprisingly, the level of genetic diversity of the farmed C. nobilis populations was higher than that of the wild population. Although the population genetic of wild population was completely in the Hardy–Weinberg equilibrium, due to heterozygote deficiency, significant deviations from the Hardy–Weinberg equilibrium were found in all farmed populations, suggesting a genetic admixture caused by the mixing of seeds from various hatcheries. The Fst and AMOVA values showed significant genetic differences between wild and farmed populations. The Bayesian assignment also confirmed that genetic admixture was significant and widespread in artificial breeding of C. nobilis. Furthermore, the UPGMA tree topology and PCA demonstrated that the genetic diversity of wild population can be clearly distinguished from farmed populations. In a nutshell, the findings of this study not only fill the knowledge gaps in genetic diversity of wild and farmed C. nobilis populations, but also serve as a guide for maintaining the genetic diversity of C. nobilis in both farmed and wild populations.
Precision N-Glycoproteomic Profiling of Murine Peritoneal Macrophages After Different Stimulations

Macrophages are important immune cells that participate in both innate and adaptive immune responses, such as phagocytosis, recognition of molecular patterns, and activation of the immune response. In this study, murine peritoneal macrophages were isolated and then activated by LPS, HSV and VSV. Integrative proteomic and precision N-glycoproteomic profiling were conducted to assess the underlying macrophage activation. We identified a total of 587 glycoproteins, including 1239 glycopeptides, 526 monosaccharide components, and 8326 intact glycopeptides in glycoproteomics, as well as a total of 4496 proteins identified in proteomic analysis. These glycoproteins are widely involved in important biological processes, such as antigen presentation, cytokine production and glycosylation progression. Under the stimulation of the different pathogens, glycoproteins showed a dramatic change. We found that receptors in the Toll-like receptor pathway, such as Tlr2 and CD14, were increased under LPS and HSV stimulation. Glycosylation of those proteins was proven to influence their subcellular locations.
Hill Runner's Physiology, Performance and Nutrition: A Descriptive Study

Objectives: The aim of this descriptive study was to characterise anthropometric variables, aerobic capacity, running performance and energy intake and expenditure of hill runners in free-living conditions, and to investigate the relationship between age, anthropometric variables, aerobic capacity and running performance. Methods: Twenty-eight hill runners participated in this study (17 males and 11 females; aged 18–65 years). Body fat percentage estimate, sum of eight skinfolds (triceps, subscapular, biceps, iliac crest, supraspinale, abdominal, front thigh and medial calf) and maximal oxygen capacity (VO2max) were assessed in a laboratory setting. Participants also completed a timed hill run (Dumyat Hill, Scotland, ascent: 420 m, distance: 8 km) while wearing a portable gas analyzer to assess oxygen consumption (VO2). Energy intake and energy expenditure were assessed in free-living conditions over three consecutive days different from the testing days through self-reported food diaries and accelerometers. Results: VO2max assessed in the lab (51.2 ± 7.6 ml·min−1·kg−1) showed a weak negative relationship with age [rs(23) = −0.38, p = 0.08]. Neither body fat percentage (median 12.4; IQR 10.1–17.1) nor the sum of skinfolds (median 81.8; IQR 62.4–97.8 mm) correlated with age [rs(28) = 0.001, p = 0.10 and 26 rs(28) = −0.02, p = 0.94, respectively]. The observed intensity of the hill run was 89 ± 6% of the age predicted maximum heart rate and 87 ± 9% of the VO2max observed in the lab. Hill running performance correlated with VO2max [r(21) = 0.76, p < 0.001], age [rs(26) = −0.44, p = 0.02] and with estimated body fat percentage and sum of skinfolds [rs(26) = −0.66, p < 0.001 and rs(26) = −0.49, p = 0.01, respectively]. Energy intake negatively correlated with age [rs(26) = −0.43, p = 0.03], with the overall energy intake being significantly lower than the total energy expenditure (2273 ± 550 vs. 2879 ± 510 kcal·day−1; p < 0.001; d = 1.05). Conclusion: This study demonstrated that hill running performance is positively associated with greater aerobic capacity and negatively associated with increases in adiposity and age. Further, the study highlights that hill runners are at risk of negative energy balance.
Prevalence of Behavioral Addictions and Their Relationship With Stress and Anxiety Among Medical Students in Saudi Arabia: A Cross-Sectional Study

Behavioral addiction is identified as any compulsive, repeated, and persistent behavior that leads to significant and functionally impairing harm or distress. The aim of this study is to determine the prevalence of internet, video-gaming, and pornography addictions among medical students in Western region. In addition, we intend to investigate the relationship between these behavioral addictions with stress and anxiety. Our study was a cross-sectional study with a sample size of 225. The study participants were medical students in their 3rd, 4th, and 5th academic years from five different medical colleges in Western region. The questionnaire included demographics and adapted five different pre-validated scales: Young's Internet Addiction Test – Short Version (IAT-SV), Internet Gaming Disorder Scale 9 – Short Form (IGDS9-SF), (PPC scale), Perceived Stress Scale (PSS), and Generalized Anxiety Disorder 7-item scale (GAD-7). The IAT-SV scale showed: 71 (31.6%) of the participants had normal internet usage, 51 (22.7%) participants showed problematic usage, and 103 (45.8%) used the internet pathologically. The IGDS9-SF scale had observed the following values: 220 participants (97.8%) were non-disordered, and 5 participants (2.2%) were found to be disordered. Statistical analysis showed a highly significant association between stress and problematic pornography consumption (P < 0.01), and internet addiction (P <0.001). Moreover, there was a significant association between anxiety and internet gaming disorder (P < 0.01). This study showed high prevalence of internet addiction and low prevalence of internet gaming disorder. Also, it gave more understanding to a possible association between these behavioral addictions with stress and anxiety.
Simultaneous Multiplex Genome Engineering via Accelerated Natural Transformation in Bacillus subtilis

Multiplex engineering at the scale of whole genomes has become increasingly important for synthetic biology and biotechnology applications. Although several methods have been reported for engineering microbe genomes, their use is limited by their complex procedures using multi-cycle transformations. Natural transformation, involving in species evolution by horizontal gene transfer in many organisms, indicates its potential as a genetic tool. Here, we aimed to develop simultaneous multiplex genome engineering (SMGE) for the simple, rapid, and efficient design of bacterial genomes via one-step of natural transformation in Bacillus subtilis. The transformed DNA, competency factors, and recombinases were adapted to improved co-editing frequencies above 27-fold. Single to octuplet variants with genetic diversity were simultaneously generated using all-in-one vectors harboring multi-gene cassettes. To demonstrate its potential application, the tyrosine biosynthesis pathway was further optimized for producing commercially important resveratrol by high-throughput screening of variant pool in B. subtilis. SMGE represents an accelerated evolution platform that generates diverse multiplex mutations for large-scale genetic engineering and synthetic biology in B. subtilis.
Production of Biodiesel From Croton gratissimus Oil Using Sulfated Zirconia and KOH as Catalysts

Optimization studies for the esterification and transesterification of oil extracted from Croton gratissimus grains were carried out using the response surface methodology (RMS) that utilizes the central composite design (CCD) and the analysis of variance (ANOVA). A 23 full-factorial rotatable CCD for three independent variables at five levels was developed in each case, giving a total of 20 experiments needed per study. The three design factors chosen for study were the catalyst concentration, methanol-to-oil ratio, and the reaction temperature. The values of the acid value of oil (in esterification) and the percentage FAME yield and FAME purity (in transesterification) were taken as the responses of the designed experiments. In the optimization of the esterification and transesterification processes, the ANOVA showed that both quadratic regression models developed were significant. The optimum operating conditions for the esterification process that could give an optimum acid value of 2.693 mg KOH/g of oil were found to be 10.96 mass% SO4 2–/ZrO2 catalyst concentration, 27.60 methanol-to-oil ratio, and 64°C reaction temperature. In the optimization of the transesterification process, the model revealed that the catalyst concentration and the methanol-to-oil ratio were the terms that had the most influence on the % FAME yield and the % FAME purity of the final biodiesel product. From the combined regression model, it was established that optimum responses of the 84.51% FAME yield and 90.66% FAME purity could be achieved when operating the transesterification process at 1.439 mass% KOH catalyst concentration, 7.472 methanol-to-oil ratio, and at a temperature of 63.50°C. Furthermore, in the two-step biodiesel synthesis, a predominantly monoclinic-phased sulfated zirconia (SO4 2–/ZrO2) catalyst exhibited high activity in the esterification of high free fatty acid oil extracted from Croton gratissimus grains. A 91% reduction in the acid value of the Croton gratissimus oil from 21.46 mg KOH/g of oil to 2.006 mg KOH/g of oil, well below the 4 mg KOH/g of oil maximum limit, was achieved. This resulted in the high FAME yield and purity of the biodiesel produced in the subsequent catalytic transesterification of oil using KOH.