In silico identification of multi-target inhibitors from medicinal fungal metabolites against the base excision repair pathway proteins of African swine fever virus

African swine fever virus (ASFV) has emerged as a serious threat to the pork industry resulting in significant economic losses and heightened concerns about food security. With no known cure presently available, existing control measures center on animal quarantine and culling. Considering the severity and challenges posed by ASFV, it is imperative to discover new treatment strategies and implement additional measures to prevent its further spread. This study recognized the potential of 1830 fungal metabolites from medicinal fungi as antiviral compounds against base excision repair (BER) proteins of ASFV, specifically ASFVAP, ASFVPolX, and ASFVLig. A wide array of computer-aided drug discovery techniques were employed to carry out the virtual screening process: ADMET profiling revealed 319 molecules with excellent bioavailability and toxicity properties; consensus docking identified the 10 best-scoring ligands against all targets; molecular dynamics simulation elucidated the stability of the protein-ligand complexes; and MM/PB(GB)SA energy calculations predicted the binding energies of the compounds as well as the key residues integral to binding. Through in silico methods, we identified two theoretical lead candidates against ASFVAP, four against ASFVLig, and five against ASFVPolX. Two compounds, methyl ganoderate E and antcamphin M, exhibited potential multi-target inhibitory characteristics against ASFVPolX and ASFVLig, while compound cochlactone A showed promising antagonistic results against all three BER proteins. It is recommended to prioritize these hit compounds in future in vitro and in vivo studies to validate their potential as antiviral drugs against ASFV.

A systematic review and meta-analysis of the SIRT1 response to exercise

Sirtuin 1 (SIRT1) is a key physiological regulator of metabolism and a target of therapeutic interventions for cardiometabolic and ageing-related disorders. Determining the factors and possible mechanisms of acute and adaptive SIRT1 response to exercise is essential for optimising exercise interventions aligned to the prevention and onset of disease. Exercise-induced SIRT1 upregulation has been reported in animals, but, to date, data in humans have been inconsistent. This exploratory systematic review and meta-analysis aims to assess various exercise interventions measuring SIRT1 in healthy participants. A total of 34 studies were included in the meta-analysis (13 single bout exercise, 21 training interventions). Studies were grouped according to tissue sample type (blood, muscle), biomarkers (gene expression, protein content, enzyme level, enzyme activity), and exercise protocols. A single bout of high-intensity or fasted exercise per se increases skeletal muscle SIRT1 gene expression as measured by qPCR or RT-PCR, while repeated resistance training alone increases blood SIRT1 levels measured by ELISA. A limited number of studies also show a propensity for an increase in muscle SIRT1 activity as measured by fluorometric or sirtuin activity assay. In conclusion, exercise acutely upregulates muscle SIRT1 gene expression and chronically increases SIRT1 blood enzyme levels.

Wilson disease-causing mutations in the carboxyl terminus of ATP7B regulates its localization and Golgi exit selectively in the unpolarized cells

Mutational inactivation of the P-type Cu-ATPase ATP7B interferes with its cellular functions to varying extent leading to varied cellular phenotypes. Wilson's disease (WD) primarily affects organs composed of polarized/differentiated epithelial cells. Therefore, phenotypic variability might differ depending on the polarization/differentiation of the cells. The present study investigates the intracellular stability and localization of ATP7B harboring WD mutations in both unpolarized/undifferentiated and polarized/differentiated cell-based models. Green fluorescent protein (GFP)-ATP7B harboring the WD causing mutations, N41S, S653Y, R778Q, G1061E, H1069Q, S1423N, S1426I, and T1434M, are included for investigation. The C-terminal WD mutations (S1423N, S1426I, and T1434M), exhibit distinct localization and Cu(I) responsive anterograde and retrograde trafficking in undifferentiated/unpolarized vs. differentiated/polarized cells. While basal localization of the S1423N mutant gets corrected in the differentiated glia, its Cu(I) responsive anterograde and retrograde trafficking behavior is not identical to the wild-type. But localization and trafficking properties are completely rescued for the S1426I and T1434M mutants in the differentiated cells. Comprehensive meta-analysis on the effect of the reported C-terminal mutations on patient phenotype and cultured cells demonstrate discrete regions having distinct effects. While mutations in the proximal C-terminus affect ATP7B stability, the present study shows that the distal region dictates cell-specific Trans Golgi Network (TGN) localization and exit. The localization and export properties are corrected in the differentiated cells, which is a plausible mechanism for the milder phenotype exhibited by these mutations. It highlights the critical role of the C-terminus in cell-specific TGN retention and exit of ATP7B.

Coconut power: a sustainable approach for the removal of Cr6+ ions using a new coconut-based polyurethane foam/activated carbon composite in a fixed-bed column

To attain efficient removal of hexavalent chromium (Cr⁶⁺) from aqueous solutions, a novel polyurethane foam-activated carbon (PUAC) adsorbent composite was developed. The composite material was synthesized by the binding of coconut shell-based activated carbon (AC) onto a coconut oil-based polyurethane matrix. To thoroughly characterize the physicochemical properties of the newly developed material, various analytical techniques including FTIR spectroscopy, SEM, XRD, BET, and TGA analyses were conducted. The removal efficiency of the PUAC composite in removing Cr⁶⁺ ions from aqueous solutions was evaluated through column experiments with the highest adsorption capacity of 28.41 mg g^-1 while taking into account variables such as bed height, flow rate, initial Cr⁶⁺ ion concentration, and pH. Experimental data were fitted using Thomas, Yoon-Nelson, and Adams-Bohart models to predict the column profiles and the results demonstrate high breakthrough and exhaustion time dependence on these variables. Among the obtained R² values of the models, a better fit was observed using the Thomas and Yoon-Nelson models, indicating their ability to effectively predict the adsorption of Cr⁶⁺ ions in a fixed bed column. Significantly, the exhausted adsorbent can be conveniently regenerated without any noteworthy loss of adsorption capability. Based on these findings, it can be concluded that this new PUAC composite material holds significant promise as a potent sorbent for wastewater treatment backed by its excellent performance, cost-effectiveness, biodegradability, and outstanding reusability.

Effect of Buffalo Milk Consumption on the Growth of 10 to 12 years Old Schoolgirls in Magdalena, Laguna, Philippines

Background

Milk contains essential nutrients that help can improve the growth and development of adolescent girls.

Objectives

The study determined the effect of milk consumption on the nutritional status of schoolgirls ages 10 to 12 years old in Magdalena, Laguna, Philippines.

Methodology

A quasi-experimental study design was used to determine the impact of daily consumption of 200 ml buffalo milk on the prevalence of undernutrition among the 57 schoolgirl participants before and after 160 days. One sample t-test and paired t-test were used to compare the actual and expected total increment and monthly changes in the height and body mass index (BMI) of the participants, while a one-way analysis of variance was used to compare the actual total changes in height and BMI by age. Factors that are correlated with these measurements were identified based on Spearman's correlation coefficients.

Results

The percentage of stunting (31.6%-22.8%) and thinness (21.1%-15.8%) decreased after the milk feeding. Significant differences were observed in the means of total actual and expected changes in height (P < .00) and BMI (P < .00). While there were significant differences in the means of actual and expected monthly changes in height every month, this was only observed in the first 2 months for BMI. Only the mean actual changes in height had significant differences when compared by age (P = .04). Lastly, the age and education of the father were found to be correlated with the height of the schoolgirls.

Conclusion

Buffalo milk consumption can improve the growth outcomes of schoolgirls.

Enhanced photo-reactivity of polyanthracene in the VIS region

The wavelength-dependent photo-reactivity of polyanthracene was explored upon UV-C and VIS light irradiation. The material was prepared via one-pot chemical oxidation route using FeCl₃ as oxidizing agent. A decrease in surface hydrophobicity of a polyanthracene-coated poly(methylmethacrylate) substrate from 109.11° to 60.82° was observed upon UV-C exposure for 48 hrs which was attributed to increase in oxygen content at the surface, as validated by energy dispersive X-ray spectroscopy. Upon exposure to ultraviolet-visible LEDs, photo-dimerization of polyanthracene in solution occurred and was monitored using UV-VIS spectroscopy. The photo-dimer product formation decreased from 381 nm to 468 nm and was found to be higher for the polyanthracene material compared to the monomer anthracene. At 381 nm, photo-dimerization of the material was found to be approx. 4x more efficient than the non-substituted monomer counterpart. Results obtained show that photo-dimerization of polyanthracene will proceed upon exposure with visible light LEDs with reduction in efficiency at longer wavelengths. To compensate, irradiation power of the light source and irradiation time were increased.

Amenity counts significantly improve water consumption predictions

Anticipating the increase in water demand in an urban area requires us to properly understand daily human movement driven by population size, land use, and amenity types among others. Mobility data from phones can capture human movement, but not only is this hard to obtain, but it also does not tell where the population is going. Previous studies have shown that amenity types can be used to predict people’s movement patterns; thus, we propose using crowd-sourced amenity data and other open data sources as reasonable proxies for human mobility. Here we present a framework for predicting water consumption in areas with established service water connections and generalize it to underserved areas. Our work used features such as geography, population, and domestic consumption ratio and compared the prediction performance of various machine learning algorithms. We used 44 months of monthly water consumption data from January 2018 to July 2021, aggregated across 1790 district metering areas (DMAs) in the east service zone of Metro Manila. Results show that amenity counts reduce the mean absolute error (MAE) of predictions by 1,440 m³/month or as much as 5.73% compared to just using population and topology features. Predicted consumption during the pandemic also improved by as much as 1,447 m³/month or nearly 16% compared to just using population and topology features. We find that Gradient Boosting Trees are the best models to handle the data and feature set used in this work. Finally, the developed model is robust to disruptions in human mobility, such as lockdowns, indicating that amenities are sufficient to predict water consumption.

Impact of vaccine supplies and delays on optimal control of the COVID-19 pandemic: mapping interventions for the Philippines

BACKGROUND

Around the world, controlling the COVID-19 pandemic requires national coordination of multiple intervention strategies. As vaccinations are globally introduced into the repertoire of available interventions, it is important to consider how changes in the local supply of vaccines, including delays in administration, may be addressed through existing policy levers. This study aims to identify the optimal level of interventions for COVID-19 from 2021 to 2022 in the Philippines, which as a developing country is particularly vulnerable to shifting assumptions around vaccine availability. Furthermore, we explore optimal strategies in scenarios featuring delays in vaccine administration, expansions of vaccine supply, and limited combinations of interventions.

METHODS

Embedding our work within the local policy landscape, we apply optimal control theory to the compartmental model of COVID-19 used by the Philippine government's pandemic surveillance platform and introduce four controls: (a) precautionary measures like community quarantines, (b) detection of asymptomatic cases, (c) detection of symptomatic cases, and (d) vaccinations. The model is fitted to local data using an L-BFGS minimization procedure. Optimality conditions are identified using Pontryagin's minimum principle and numerically solved using the forward-backward sweep method.

RESULTS

Simulation results indicate that early and effective implementation of both precautionary measures and symptomatic case detection is vital for averting the most infections at an efficient cost, resulting in [Formula: see text] reduction of infections compared to the no-control scenario. Expanding vaccine administration capacity to 440,000 full immunizations daily will reduce the overall cost of optimal strategy by [Formula: see text], while allowing for a faster relaxation of more resource-intensive interventions. Furthermore, delays in vaccine administration require compensatory increases in the remaining policy levers to maintain a minimal number of infections. For example, delaying the vaccines by 180 days (6 months) will result in an [Formula: see text] increase in the cost of the optimal strategy.

CONCLUSION

We conclude with practical insights regarding policy priorities particularly attuned to the Philippine context, but also applicable more broadly in similar resource-constrained settings. We emphasize three key takeaways of (a) sustaining efficient case detection, isolation, and treatment strategies; (b) expanding not only vaccine supply but also the capacity to administer them, and; (c) timeliness and consistency in adopting policy measures.

Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta

Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.

Spatio-temporal assessment and economic analysis of a grid-connected island province toward a 35% or greater domestic renewable energy portfolio: a case in Bohol, Philippines

The year 2020 marks the start of the implementation of the Renewable Portfolio Standards in the Philippines. To raise the country’s renewable energy (RE) share to 35% by 2030 (aspirational target), an annual minimum incremental RE of 1% has been imposed to all mandated participants. This local-level policy implementation has allowed the assessment of RE resource adequacy to be carried out on a smaller geographical scale (i.e., province level). The case for grid-connected island provinces, such as our study area, can be more interesting because of the opportunity to self-sustainable energy production. In this paper, we assess the adequacy of domestic RE resources of Bohol province to reach this target by estimating the technical potential of solar, wind, biomass, and hydropower using spatio-temporal datasets. Then, for every identified potential RE project, we calculate the busbar levelized cost. We also evaluate the province's base RE share to assess the extent to which the technical potential can improve its RE penetration in four distinct domestic and imported energy generation scenarios. With 20 different scenarios of additional RE capacity, we generate RE portfolios for the minimum target RE share (35%), as well as the 50% and maximum. The results revealed that, when the country’s RE penetration continues, Bohol’s hydropower potential is not enough to meet the 35% target. Seasonal renewables are also insufficient for a 50% target. In several scenarios, the province’s energy self-sustainability can be possible at reasonable costs when variable RE technologies are included in the portfolio.

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

BACKGROUND

The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions.

FINDINGS

By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial "hubs" and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities.

CONCLUSION

We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

Genetic dissection of developmental responses of agro-morphological traits under different doses of nutrient fertilizers using high-density SNP markers

The production and productivity of rice (Oryza sativa L.) are primarily influenced by the application of the critical nutrients nitrogen (N), phosphorus (P), and potassium (K). However, excessive application of these fertilizers is detrimental to the environment and increases the cost of production. Hence, there is a need to develop varieties that simultaneously increase yields under both optimal and suboptimal rates of fertilizer application by maximizing nutrient use efficiency (NuUE). To unravel the hidden genetic variation and understand the molecular and physiological mechanisms of NuUE, three different mapping populations (MPs; BC1F5) derived from three donors (Haoannong, Cheng-Hui 448, and Zhong 413) and recipient Weed Tolerant Rice 1 were developed. A total of three favorable agronomic traits (FATs) were considered as the measure of NuUE. Analysis of variance and descriptive statistics indicated the existence of genetic variation for NuUE and quantitative inheritance of FATs. The genotypic data from single-nucleotide polymorphism (SNP) markers from Tunable Genotyping-By-Sequencing (tGBS) and phenotypic values were used for locating the genomic regions conferring NuUE. A total of 19 quantitative trait loci (QTLs) were detected, out of which 11 QTLs were putative on eight chromosomes, which individually explained 17.02% to 34.85% of the phenotypic variation. Notably, qLC-II_1 and qLC-II_11 detected at zero fertilizer application showed higher performance for LC under zero percentage of NPK fertilizer. The remarkable findings of the present study are that the detected QTLs were associated in building tolerance to low/no nutrient application and six candidate genes on chromosomes 2 and 5 within these putative QTLs were found associated with low nutrient tolerance and related to several physiological and metabolic pathways involved in abiotic stress tolerance. The identified superior introgressed lines (ILs) and trait-associated genetic regions can be effectively used in marker-assisted selection (MAS) for NuUE breeding programs.