Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Comparison of growth performance among channel-blue hybrid catfish, ccGH transgenic channel catfish, and channel catfish in a tank culture system

Fish is an essential source of high-quality protein for people worldwide. The present study was designed to compare the growth performance among the channel-blue hybrid catfish, channel catfish transgenic for the channel catfish growth hormone (ccGH) cDNA driven by the antifreeze protein promoter from an ocean pout Zoarces americanus (opAFP-ccGH), and non-transgenic channel catfish control. Mean body weight of channel-blue hybrid catfish was 15.80 and 24.06% larger than non-transgenic channel catfish control at 4 and 18 months of age, respectively. However, transgenic opAFP-ccGH channel catfish were 5.52 and 43.41% larger than channel-blue hybrid catfish and 22.19 and 77.91% larger than their controls at 4 and 18 months of age, respectively. Significant differences in mean body weight between the sexes within all genetic types were found. Males were larger than females (P < 0.001). However, mean body weight of non-transgenic males was not larger than transgenic opAFP-ccGH females or male and female hybrid catfish. Condition factor of transgenic opAFP-ccGH channel catfish was higher (P < 0.05) than that of full-sibling, non-transgenic channel catfish and hybrid catfish. The mean percentage body weight gain of GH transgenic channel catfish was 559%, the channel-blue hybrid catfish was 384.9% and their non-transgenic controls channel catfish was 352.6%.

Modeling the Contribution of Milk to Global Nutrition

Nutrient-rich foods play a major role in countering the challenges of nourishing an increasing global population. Milk is a source of high-quality protein and bioavailable amino acids, several vitamins, and minerals such as calcium. We used the DELTA Model, which calculates the delivery of nutrition from global food production scenarios, to examine the role of milk in global nutrition. Of the 29 nutrients considered by the model, milk contributes to the global availability of 28. Milk is the main contributing food item for calcium (49% of global nutrient availability), Vitamin B2 (24%), lysine (18%), and dietary fat (15%), and contributes more than 10% of global nutrient availability for a further five indispensable amino acids, protein, vitamins A, B5, and B12, phosphorous, and potassium. Despite these high contributions to individual nutrients, milk is responsible for only 7% of food energy availability, indicating a valuable contribution to global nutrition without necessitating high concomitant energy intakes. Among the 98 food items considered by the model, milk ranks in the top five contributors to 23 of the 29 nutrients modeled. This quantification of the importance of milk to global nutrition in the current global food system demonstrates the need for the high valuation of this food when considering future changes to the system.

Diet Supplementation with Madagascar Cockroach Flour (Gromphadorhina portentosa) Improved Malnourished Mice Metabolism and Ameliorated Liver Inflammatory Markers

Background: Malnutrition and accessible high-quality protein food sources are two of the world’s alimentary challenges. Edible insects are nowadays recognized as a possible functional food solution with lower environmental impacts and beneficial health effects. Objective: In this context, the aim of the present study is to evaluate Madagascar cockroach (Gromphadorhina portentosa) flour supplementation effects on a malnourished mice model, considering its effects on metabolism, adiposity, and inflammatory liver profiles. Method: Male Swiss mice are divided into five groups and fed with experimental diets for eight weeks, including a standard diet (ST) ad libitum, AIN93 ad libitum (AIN), insect flour-enriched AIN93 (AIN+IM), AIN-40% feed restriction (AIN-FR), and insect flour-enriched AIN-40% of feed restriction (AIN-FR+IM). The metabolic profiles, adipose tissue, biochemical parameters, and liver IL-6 and IL-10 expression are evaluated. Results: The main findings show a body weight and metabolism improvement followed by an increased recovery of the adipocyte area in the AIN-FR+IM group when compared to the AIN-FR malnourished group. Reduced hepatic IL-6 and increased IL-10 expression are also detected in the AIN-FR+IM group. Conclusion: The results show that insect flour supplementation enhances both body weight and adiposity gain/recovery. The results also show hepatic improvement of inflammatory markers.

Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here we present SalmoNet2, a major update to SalmoNet, the first multi-layered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory and enzyme-enzyme interactions. The new version extends the number of Salmonella genomes from 11 to 20, including strains such as Salmonella Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. The database now uses strain specific metabolic models instead of a generalised model to highlight differences between strains. This has increased the coverage of high-quality protein-protein interactions, and enhances interoperability with other computational resources by adopting standardised formats. The resource website has been updated with tutorials to help researchers analyse their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/.</SPAN>

Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean

Soybean is one of the most important legumes, providing high-quality protein for humans. The caffeic acid O-methyltransferase (COMT) gene has previously been demonstrated to be a critical gene that regulates lignin production in plant cell walls and plays an important function in plant growth and development. However, the COMT gene family has not been studied in soybeans. In this study, 55 COMT family genes in soybean were identified by phylogenetic analysis and divided into two groups, I and II. The analysis of conserved domains showed that all GmCOMTs genes contained Methyltransferase-2 domains. Further prediction of cis-acting elements showed that GmCOMTs genes were associated with growth, light, stress, and hormonal responses. Eventually, based on the genomic data of soybean under different stresses, the results showed that the expression of GmCOMTs genes was different under different stresses, such as salt and drought stress. This study has identified and characterized the COMT gene family in soybean, which provides an important theoretical basis for further research on the biological functions of COMT genes and promotes revealing the role of GmCOMTs genes under stress resistance.

Molecular Survey of Viral Poultry Diseases with an Indirect Public Health Significance in Central Ethiopia

The importance of poultry production is globally increasing, in Ethiopia as well, where high-quality protein and contained costs make poultry a valuable food resource. However, this entails some problems linked to rural, backyard and intensively reared flock proximity and pathogen circulation. This study is aimed at monitoring the presence of important viral pathogens in poultry (infectious bronchitis virus (IBV), avian metapneumovirus (aMPV), infectious bursal disease virus (IBDV) and Newcastle disease virus (NDV)) in Ethiopia. Respiratory and cloacal swabs and bursa of Fabricius and kidney imprints on FTA cards were collected in 2021 from 16 farms and tested for IBV, aMPV, NDV and IBDV. One farm was positive for IBDV, resulting in strains similar to those present in vaccines, belonging to genogroup A1a; two farms were positive for IBV but, due to sensitivity limits, only one sample was sequenced, resulting in a 4/91-like strain (GI-13); a layer farm tested positive for NDV with a Lasota-like vaccine strain. These findings suggest a low presence of these pathogens, probably due to the implementation of vaccination strategies, which is also testified by the detection of vaccine strains. A close diagnostic activity should be implemented on a routine basis in order to monitor pathogen circulation, ameliorate biosecurity measures and protect animal health and production levels.

Mealworm (Tenebrio molitor) potencial in fish nutrition: a review

The creation of aquatic organisms it is constantly growing and with this comes the need to meet this demand with the increased production of inputs such as feed for aquaculture. Fish nutrition is mainly characterized by the use of fish meal and oil for the manufacture of rations for their food. Soybean bran is the second most used ingredient as a source of protein in the production of feed for aquaculture. However, these ingredients compete with other feed segments, increasing cost or reducing market availability. Therefore, alternative sources of protein must be studied and developed to meet this demand. In this sense, insects present themselves as sources of high quality protein, in addition to fatty acids, vitamins and minerals. Although there is a problem with large-scale production to meet the demand of the feed market, the ease of breeding certain species of insects is capable of making this reality possible. Thus, insects can be a likely alternative protein source in fish feed, replacing conventional sources. This review aims to evaluate the inclusion of mealworm in the fish diet, in terms of performance and discuss the results obtained.

Microalgae as Sources of High-Quality Protein for Human Food and Protein Supplements

As a result of population growth, an emerging middle-class, and a more health-conscious society concerned with overconsumption of fats and carbohydrates, dietary protein intake is on the rise. To address this rapid change in the food market, and the subsequent high demand for protein products, agriculture, aquaculture, and the food industry have been working actively in recent years to increase protein product output from both production and processing aspects. Dietary proteins derived from animal sources are of the highest quality, containing well-balanced profiles of essential amino acids that generally exceed those of other food sources. However, as a result of studies highlighting low production efficiency (e.g., feed to food conversion) and significant environmental impacts, together with the negative health impacts associated with the dietary intake of some animal products, especially red meats, the consumption of animal proteins has been remaining steady or even declining over the past few decades. To fill this gap, researchers and product development specialists at all levels have been working closely to discover new sources of protein, such as plant-based ingredients. In this regard, microalgae have been recognized as strategic crops, which, due to their vast biological diversity, have distinctive phenotypic traits and interactions with the environment in the production of biomass and protein, offering possibilities of production of large quantities of microalgal protein through manipulating growing systems and conditions and bioengineering technologies. Despite this, microalgae remain underexploited crops and research into their nutritional values and health benefits is in its infancy. In fact, only a small handful of microalgal species are being produced at a commercial scale for use as human food or protein supplements. This review is intended to provide an overview on microalgal protein content, its impact by environmental factors, its protein quality, and its associated evaluation methods. We also attempt to present the current challenges and future research directions, with a hope to enhance the research, product development, and commercialization, and ultimately meet the rapidly increasing market demand for high-quality protein products.

iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean

Adzuki bean is an important legume crop due to its high-quality protein, fiber, vitamins, minerals as well as rich bioactive substances. However, it is vulnerable to drought at the germination stage. However, little information is available about the genetic control of drought tolerance during seed germination in adzuki bean. In this study, some differential expression proteins (DEPs) were identified during seed germination between the drought-tolerant variety 17235 and drought-sensitive variety 17033 in adzuki bean using iTRAQ method. A total of 2834 proteins were identified in the germinating seeds of these two adzuki beans. Compared with the variety 17033, 87 and 80 DEPs were increased and decreased accumulation in variety 17235 under drought, respectively. Meanwhile, in the control group, a few DEPs, including 9 up-regulated and 21 down-regulated proteins, were detected in variety 17235, respectively. GO, KEGG, and PPI analysis revealed that the DEPs related to carbohydrate metabolism and energy production were significantly increased in response to drought stresses. To validate the proteomic function, the ectopic overexpression of V-ATPase in tobacco was performed and the result showed that V-ATPase upregulation could enhance the drought tolerance of tobacco. The results provide valuable insights into genetic response to drought stress in adzuki bean, and the DEPs could be applied to develop biomarkers related to drought tolerant in adzuki bean breeding projects.