Neuronal reprogramming of mouse and human fibroblasts using transcription factors involved in suprachiasmatic nucleus development.

The hypothalamic suprachiasmatic nucleus (SCN) is composed of heterogenous populations of neurons that express signaling peptides such as vasoactive intestinal polypeptide (VIP) and arginine vasopressin (AVP) and regulate circadian rhythms in behavior and physiology. SCN neurons acquire functional and morphological specializations from waves of transcription factors (TFs) that are expressed during neurogenesis. However, the in vitro generation of SCN neurons has never been achieved. Here we supplemented a highly efficient neuronal conversion protocol with TFs that are expressed during SCN neurogenesis, namely Six3, Six6, Dlx2, and Lhx1. Neurons induced from mouse and human fibroblasts predominantly exhibited neuronal properties such as bipolar or multipolar morphologies, GABAergic neurons with expression of VIP. Our study reveals a critical contribution of these TFs to the development of vasoactive intestinal peptide (Vip) expressing neurons in the SCN, suggesting the regenerative potential of neuronal subtypes contained in the SCN for future SCN regeneration and in vitro disease remodeling.

Diurnal expression of Dgat2 induced by time-restricted feeding maintains cardiac health in the Drosophila model of circadian disruption.

Circadian disruption is associated with an increased risk of cardiometabolic disorders and cardiac diseases. Time-restricted feeding/eating (TRF/TRE), restricting food intake within a consistent window of the day, has shown improvements in heart function from flies and mice to humans. However, whether and how TRF still conveys cardiac benefits in the context of circadian disruption remains unclear. Here, we demonstrate that TRF sustains cardiac performance, myofibrillar organization, and regulates cardiac lipid accumulation in Drosophila when the circadian rhythm is disrupted by constant light. TRF induces oscillations in the expression of genes associated with triglyceride metabolism. In particular, TRF induces diurnal expression of diacylglycerol O-acyltransferase 2 (Dgat2), peaking during the feeding period. Heart-specific manipulation of Dgat2 modulates cardiac function and lipid droplet accumulation. Strikingly, heart-specific overexpression of human Dgat2 at ZT 0-10 significantly improves cardiac performance in flies exposed to constant light. We have demonstrated that TRF effectively attenuates cardiac decline induced by circadian disruption. Moreover, our data suggests that diurnal expression of Dgat2 induced by TRF is beneficial for heart health under circadian disruption. Overall, our findings have underscored the relevance of TRF in preserving heart health under circadian disruptions and provided potential targets, such as Dgat2, and strategies for therapeutic interventions in mitigating cardiac aging, metabolic disorders, and cardiac diseases in humans.

Energy balance drives diurnal and nocturnal brain transcriptome rhythms.

Plasticity in daily timing of activity has been observed in many species, yet the underlying mechanisms driving nocturnality and diurnality are unknown. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance and switch mice to be nocturnal or diurnal. Here, we present the rhythmic transcriptome of 21 tissues, including 17 brain regions, sampled every 4 h over a 24-h period from nocturnal and diurnal male CBA/CaJ mice. Rhythmic gene expression across tissues comprised different sets of genes with minimal overlap between nocturnal and diurnal mice. We show that non-clock genes in the suprachiasmatic nucleus (SCN) change, and the habenula was most affected. Our results indicate that adaptive flexibility in daily timing of behavior is supported by gene expression dynamics in many tissues and brain regions, especially in the habenula, which suggests a crucial role for the observed nocturnal-diurnal switch.

Ultrastructure of Synaptic Connectivity within Subregions of the Suprachiasmatic Nucleus Revealed by a Genetically Encoded Tag and Serial Blockface Electron Microscopy.

The hypothalamic suprachiasmatic nucleus (SCN) is the central circadian pacemaker in vertebrates. The SCN receives photic information exclusively through melanopsin-expressing retinal ganglion cells (mRGCs) to synchronize circadian rhythms with the environmental light cycles. The SCN is composed of two major peptidergic neuron types in the core and shell regions of the SCN. Determining how mRGCs interact with the network of synaptic connections onto and between SCN neurons is key to understand how light regulates the circadian clock and to elucidate the relevant local circuits within the SCN. To map these connections, we used a newly developed Cre-dependent electron microscopy (EM) reporter, APEX2, to label the mitochondria of mRGC axons. Serial blockface scanning electron microscopy was then used to resolve the fine 3D structure of mRGC axons and synaptic boutons in the SCN of a male mouse. The resulting maps reveal patterns of connectomic organization in the core and shell of the SCN. We show that these regions are composed of different neuronal subtypes and differ with regard to the pattern of mRGC input, as the shell receives denser mRGC synaptic input compared with the core. This finding challenges the present view that photic information coming directly from the retina is received primarily by the core region of the SCN.

Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.

Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention that involves a daily cycle of feeding and fasting. In both animals and humans, TRF has pleiotropic health benefits that arise from multiple organ systems, yet the molecular basis of TRF-mediated benefits is not well understood. Here, we subjected mice to isocaloric ad libitum feeding (ALF) or TRF of a western diet and examined gene expression changes in samples taken from 22 organs and brain regions collected every 2 h over a 24-h period. We discovered that TRF profoundly impacts gene expression. Nearly 80% of all genes show differential expression or rhythmicity under TRF in at least one tissue. Functional annotation of these changes revealed tissue- and pathway-specific impacts of TRF. These findings and resources provide a critical foundation for future mechanistic studies and will help to guide human time-restricted eating (TRE) interventions to treat various disease conditions with or without pharmacotherapies.

Household Dietary Diversity among the Ethnic Minority Groups in the Mekong Delta: Evidence for the Development of Public Health and Nutrition Policy in Vietnam.

Poor household dietary diversity has been linked to malnutrition in individuals, households, and cumulatively in populations. High rates of malnutrition among Khmer ethnic children aged five years and younger have been reported in Tri Ton district, Vietnam. This paper aims to further investigate household dietary diversity and associated factors among Khmer ethnic minority populations in Vietnam. A cross sectional study was conducted from October 2018 to April 2019 in Tri Ton District, An Giang Province. By employing a multistage sampling technique, a total of 402 (99.8% response rate) participants were interviewed to measure household dietary diversity using a structured and validated questionnaire developed by FAO. Both bivariate and multivariate logistic regression analyses were carried out to identify factors associated with household dietary diversity. The results showed that the prevalence of low, medium and high dietary diversity scores were 21.4%, 70.4% and 8.2%, respectively. Male-headed households, literacy level, household income, exposure to mass media on nutrition and health information, and frequency of eating were positively associated with household dietary diversity (p < 0.05). However, owning a vegetable and rice farm was not statistically related to households' dietary diversification. The paper concludes that the magnitude of household diversified dietary intakes was essentially low to medium in participants' households. These findings have provided evidence to inform the development of the National Nutrition Strategy­2021−2030 in Vietnam, to be revised in 2045. This national strategy proposes appropriate interventions, programs and policies to improve socioeconomic status in ethnic groups and in mountainous areas to enhance populations' health and well-being including controlling childhood malnutrition. In order to improve population health and wellbeing in Tri Ton District, further actions to address effective dietary practices including strengthening nutrition and health communication about the need to improve household dietary diversity to high levels are recommended.

Time-restricted feeding promotes muscle function through purine cycle and AMPK signaling in Drosophila obesity models.

Obesity caused by genetic and environmental factors can lead to compromised skeletal muscle function. Time-restricted feeding (TRF) has been shown to prevent muscle function decline from obesogenic challenges; however, its mechanism remains unclear. Here we demonstrate that TRF upregulates genes involved in glycine production (Sardh and CG5955) and utilization (Gnmt), while Dgat2, involved in triglyceride synthesis is downregulated in Drosophila models of diet- and genetic-induced obesity. Muscle-specific knockdown of Gnmt, Sardh, and CG5955 lead to muscle dysfunction, ectopic lipid accumulation, and loss of TRF-mediated benefits, while knockdown of Dgat2 retains muscle function during aging and reduces ectopic lipid accumulation. Further analyses demonstrate that TRF upregulates the purine cycle in a diet-induced obesity model and AMPK signaling-associated pathways in a genetic-induced obesity model. Overall, our data suggest that TRF improves muscle function through modulations of common and distinct pathways under different obesogenic challenges and provides potential targets for obesity treatments.

Time-restricted eating alters the 24-hour profile of adipose tissue transcriptome in men with obesity.

OBJECTIVE: Time-restricted eating (TRE) restores circadian rhythms in mice, but the evidence to support this in humans is limited. The objective of this study was to investigate the effects of TRE on 24-hour profiles of plasma metabolites, glucoregulatory hormones, and the subcutaneous adipose tissue (SAT) transcriptome in humans. METHODS: Men (n = 15, age = 63 [4] years, BMI 30.5 [2.4] kg/m2 ) were recruited. A 35-hour metabolic ward stay was conducted at baseline and after 8 weeks of 10-hour TRE. Assessment included 24-hour profiles of plasma glucose, nonesterified fatty acid (NEFA), triglyceride, glucoregulatory hormones, and the SAT transcriptome. Dim light melatonin onset and cortisol area under the curve were calculated. RESULTS: TRE did not alter dim light melatonin onset but reduced morning cortisol area under the curve. TRE altered 24-hour profiles of insulin, NEFA, triglyceride, and glucose-dependent insulinotropic peptide and increased transcripts of circadian locomotor output cycles protein kaput (CLOCK) and nuclear receptor subfamily 1 group D member 2 (NR1D2) and decreased period circadian regulator 1 (PER1) and nuclear receptor subfamily 1 group D member 1 (NR1D1) at 12:00 am. The rhythmicity of 450 genes was altered by TRE, which enriched in transcripts for transcription corepressor activity, DNA-binding transcription factor binding, regulation of chromatin organization, and small GTPase binding pathways. Weighted gene coexpression network analysis revealed eigengenes that were correlated with BMI, insulin, and NEFA. CONCLUSIONS: TRE restored 24-hour profiles in hormones, metabolites, and genes controlling transcriptional regulation in SAT, which could underpin its metabolic health benefit.

Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients.

Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.

Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression.

In mammals, the circadian oscillator generates approximately 24-h rhythms in feeding behavior, even under constant environmental conditions. Livers of mice held under constant darkness exhibit circadian rhythm in abundance in up to 15% of expressed transcripts. Therefore, oscillations in hepatic transcripts could be driven by rhythmic food intake or sustained by the hepatic circadian oscillator, or a combination of both. To address this question, we used distinct feeding and fasting paradigms on wild-type (WT) and circadian clock-deficient mice. We monitored temporal patterns of feeding and hepatic transcription. Both food availability and the temporal pattern of feeding determined the repertoire, phase, and amplitude of the circadian transcriptome in WT liver. In the absence of feeding, only a small subset of transcripts continued to express circadian patterns. Conversely, temporally restricted feeding restored rhythmic transcription of hundreds of genes in oscillator-deficient mouse liver. Our findings show that both temporal pattern of food intake and the circadian clock drive rhythmic transcription, thereby highlighting temporal regulation of hepatic transcription as an emergent property of the circadian system.

Comparative Analysis of Complete Mitogenomes of Two Oxyurichthys Gobies and Their Phylogenetic Implication.

Oxyurichthys is a genus of goby that is widespread in the tropical Indo-West Pacific region. Oxyurichthys species are usually found in estuarine and coastal marine habitats. In Southeast Asia, they are commercial fishes and often collected by trawling to serve the market's demand. The mitogenome serves as a good marker for investigating the systematics and evolution of fishes, but the mitogenome of Oxyurichthys species remains unknown. In this study, mitogenomes of two Oxyurichthys gobies, O. ophthalmonema and O. microlepis, were characterized and compared. The sizes of the mitogenomes were 16,504 bp and 16,506 bp for O. ophthalmonema and O. microlepis, respectively. Mitogenomes of these two species were similar in gene content and structure. Both included 37 genes and a control region. The two Oxyurichthys mitogenomes shared similar gene features and base composition with other recorded gobies. Typical conserved blocks (CSB-1, CSB-2, CSB-3 and CSB-D) were found in the control region of both species. Phylogenetic analyses based on concatenation of 13 protein-coding genes and 2 rRNAs revealed that the two Oxyurichthys species clustered together and were sister to species of the genera Sicydium, Sicyopterus and Stiphodon. The findings of the present study support previous evolutionary studies of gobies using other molecular markers.

Time-restricted eating improves glycemic control and dampens energy-consuming pathways in human adipose tissue.

OBJECTIVE: We sought to examine the effects of 8 wk of time-restricted eating (TRE) on glucose metabolism and the adipose tissue transcriptome during a metabolic ward stay in men with obesity. METHODS: In a single-arm, pre-post trial, 15 men (ages 63 ± 4 y, body mass index = 30.5 ± 2.4 kg/m2, waist circumference = 113 ± 4 cm) with obesity but no history of diabetes were enrolled and underwent 2 wk of baseline monitoring before they were instructed to eat their regular diets within a contiguous 10-h time frame each day for 8 wk. Metabolic testing was performed at baseline and week 8 during a 35-h metabolic ward stay, during which all food intake was strictly timed and controlled. Identical meal-tolerance tests were performed at breakfast and dinner. Blood glucose, glucoregulatory hormones, and subjective appetite score were measured. Subcutaneous adipose tissue biopsies were performed and the transcriptome was assessed. RESULTS: The primary outcome, plasma glucose area under the curve, was altered by TRE, being unchanged at breakfast but increased at dinner. However, TRE reduced fasting glucose, glycated hemoglobin, body weight, and body fat, and increased glucose-dependent insulinotropic peptide area under the curve at dinner. In subcutaneous adipose tissue, 117 genes were up-regulated and 202 genes down-regulated by TRE. Pathway analysis revealed down-regulation of genes involved in proteasome function and mitochondrial regulation. CONCLUSIONS: TRE had a net effect of reducing glycemia and dampening energy-consuming pathways in adipose tissue.

Groundwater Potential Mapping Using GIS-Based Hybrid Artificial Intelligence Methods.

Groundwater is one of the major valuable water resources for the use of communities, agriculture, and industries. In the present study, we have developed three novel hybrid artificial intelligence (AI) models which is a combination of modified RealAdaBoost (MRAB), bagging (BA), and rotation forest (RF) ensembles with functional tree (FT) base classifier for the groundwater potential mapping (GPM) in the basaltic terrain at DakLak province, Highland Centre, Vietnam. Based on the literature survey, these proposed hybrid AI models are new and have not been used in the GPM of an area. Geospatial techniques were used and geo-hydrological data of 130 groundwater wells and 12 topographical and geo-environmental factors were used in the model studies. One-R Attribute Evaluation feature selection method was used for the selection of relevant input parameters for the development of AI models. The performance of these models was evaluated using various statistical measures including area under the receiver operation curve (AUC). Results indicated that though all the hybrid models developed in this study enhanced the goodness-of-fit and prediction accuracy, but MRAB-FT (AUC = 0.742) model outperformed RF-FT (AUC = 0.736), BA-FT (AUC = 0.714), and single FT (AUC = 0.674) models. Therefore, the MRAB-FT model can be considered as a promising AI hybrid technique for the accurate GPM. Accurate mapping of the groundwater potential zones will help in adequately recharging the aquifer for optimum use of groundwater resources by maintaining the balance between consumption and exploitation.

Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19.

The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the 'active cistrome,' offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID- 19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.

Removal performance and optimisation of pharmaceutical micropollutants from synthetic domestic wastewater by hybrid treatment.

Occurrence of pharmaceutical micropollutants in aquatic environments has been one amongst serious environmental problems. During this study, two reactors, including a sequencing batch reactor (SBR) + powdered composite adsorbent (CA) (first reactor, SBR + CA) and a sequencing batch reactor (second reactor, SBR), were designed to treat synthetic wastewater. Powdered CA was added with a dosage of 4.8 g L-1 to the first reactor. Tap water was contaminated with chemical oxygen demand (COD), ammonia and three pharmaceuticals, namely, atenolol (ATN), ciprofloxacin (CIP) and diazepam (DIA) to produce synthetic wastewater. The SBR + CA illustrated a better performance during synthetic municipal wastewater treatment. Up to 138.6 mg L-1 (92.4%) of COD and up to 114.2 mg L-1 (95.2%) of ammonia were removed by the first reactor. Moreover, optimisation of pharmaceuticals removal was conducted through response surface methodology (RSM) and artificial neural network (ANN). Based on the RSM, the best elimination of ATN (90.2%, 2.26 mg L-1), CIP (94.0%, 2.35 mg L-1) and DIA (95.5%, 2.39 mg L-1) was detected at the optimum initial concentration of MPs (2.51 mg L-1) and the contact time (15.8 h). In addition, ANN represented a high R2 value (>0.99) and a rational mean squared error (<1.0) during the optimisation of micropollutants removal by both reactors. Moreover, adsorption isotherm study showed that the Freundlich isotherm could justify the abatement of micropollutants by using CA better than the Langmuir isotherm.

Human development index in a context of human development: Review on the western Balkans countries.

INTRODUCTION: The Human Development Index (HDI), as one of the more complex composite indicators of the level of human potential and quality of life, is a combination of three dimensions (indicators, factors): life expectancy at birth, the middle number of years of education and the expected number of years of schooling combined into a single education index and economic benefits expressed by production, or GDP (gross domestic product) according to purchasing power (PPP US $). METHODS: The same measures and average achievements in the field of health, education, and living standards are presented. The HDI was first developed in 1990 under the United Nations Development Program (UNDP) and is published as Human Development Reports (HDR). At present, it has become the most widely used complex indicator suitable for international comparisons and assessments of the achieved development level of a particular country or region. RESULTS: The paper deals specifically with the more perspective view of human development in the Western Balkans, with a series of socio-economic implications for the development policy of the countries under observation. CONCLUSION: The particular significance of the conducted research stems from the fact that in the countries of the Western Balkans are identified factors at the beginning of the transition period were often marginalized in the creation of macroeconomic policies, but in recent years there have been more positive developments in that regard.

Author Correction: Time-restricted feeding restores muscle function in Drosophila models of obesity and circadian-rhythm disruption.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Groundwater Potential Mapping Combining Artificial Neural Network and Real AdaBoost Ensemble Technique: The DakNong Province Case-study, Vietnam.

: The main aim of this study is to assess groundwater potential of the DakNong province, Vietnam, using an advanced ensemble machine learning model (RABANN) that integrates Artificial Neural Networks (ANN) with RealAdaBoost (RAB) ensemble technique. For this study, twelve conditioning factors and wells yield data was used to create the training and testing datasets for the development and validation of the ensemble RABANN model. Area Under the Receiver Operating Characteristic (ROC) curve (AUC) and several statistical performance measures were used to validate and compare performance of the ensemble RABANN model with the single ANN model. Results of the model studies showed that both models performed well in the training phase of assessing groundwater potential (AUC ≥ 0.7), whereas the ensemble model (AUC = 0.776) outperformed the single ANN model (AUC = 0.699) in the validation phase. This demonstrated that the RAB ensemble technique was successful in improving the performance of the single ANN model. By making minor adjustment in the input data, the ensemble developed model can be adapted for groundwater potential mapping of other regions and countries toward more efficient water resource management. The present study would be helpful in improving the groundwater condition of the area thus in solving water borne disease related health problem of the population.

Time-Restricted Feeding Prevents Obesity and Metabolic Syndrome in Mice Lacking a Circadian Clock.

Increased susceptibility of circadian clock mutant mice to metabolic diseases has led to the idea that a molecular clock is necessary for metabolic homeostasis. However, these mice often lack a normal feeding-fasting cycle. We tested whether time-restricted feeding (TRF) could prevent obesity and metabolic syndrome in whole-body Cry1;Cry2 and in liver-specific Bmal1 and Rev-erbα/ß knockout mice. When provided access to food ad libitum, these mice rapidly gained weight and showed genotype-specific metabolic defects. However, when fed the same diet under TRF (food access restricted to 10 hr during the dark phase) they were protected from excessive weight gain and metabolic diseases. Transcriptome and metabolome analyses showed that TRF reduced the accumulation of hepatic lipids and enhanced cellular defenses against metabolic stress. These results suggest that the circadian clock maintains metabolic homeostasis by sustaining daily rhythms in feeding and fasting and by maintaining balance between nutrient and cellular stress responses.

Time-restricted feeding restores muscle function in Drosophila models of obesity and circadian-rhythm disruption.

Pathological obesity can result from genetic predisposition, obesogenic diet, and circadian rhythm disruption. Obesity compromises function of muscle, which accounts for a majority of body mass. Behavioral intervention that can counteract obesity arising from genetic, diet or circadian disruption and can improve muscle function holds untapped potential to combat the obesity epidemic. Here we show that Drosophila melanogaster (fruit fly) subject to obesogenic challenges exhibits metabolic disease phenotypes in skeletal muscle; sarcomere disorganization, mitochondrial deformation, upregulation of Phospho-AKT level, aberrant intramuscular lipid infiltration, and insulin resistance. Imposing time-restricted feeding (TRF) paradigm in which flies were fed for 12 h during the day counteracts obesity-induced dysmetabolism and improves muscle performance by suppressing intramuscular fat deposits, Phospho-AKT level, mitochondrial aberrations, and markers of insulin resistance. Importantly, TRF was effective even in an irregular lighting schedule mimicking shiftwork. Hence, TRF is an effective dietary intervention for combating metabolic dysfunction arising from multiple causes.