Amino Acid Research Articles

Computational study of phytochemical derived bioactive compounds of Vernonia amygdalina as a potential inhibitor of Topoisomerase IV in pneumonia

Several of the bacteria responsible for pneumonia had become resistant to available antibiotics. According to the WHO, the resistance of Klebsiella pneumonia to Ciprofloxacin is 79.4%, making infections such as pneumonia and several diseases more difficult, if not impossible to treat. The prevalence of antimicrobial resistance is a global problem and among the 10 top global health threats facing humanity. With the projection of 10 million deaths per year by 2050 due to bacterial infections associated with antibiotic resistance according to WHO, there is an urgent need to identify an alternative approach to curb the incessant antimicrobial resistance and a complementary approach is to employ the use of naturally occurring compounds with potent antibacterial activities. We employed structural bioinformatics and theoretical chemistry techniques via molecular docking, and pharmacokinetic study, to identify novel S. pneumoniae topoisomerase IV inhibitors. The stringent molecular docking identified Arg140, Arg81, Glu55, Pro84, Met83, and Asn51, as principal amino acid residues for topoisomerase IV ligand interactions. Ten of the bioactive compounds found in Vernonia amygdalina showed a higher binding energy when compared to the reference compound (Ciprofloxacin). The overall analysis of MD results and binding free energy calculations reveal that Luteolin and 7-O-methylwogonin displayed stable trajectories with acceptable RMSD values and sufficient high negative energies throughout the MD simulation run of 100ns. These identified bioactive compounds in this study can be taken further for in vitro and In vivo studies to examine their efficacy against Pneumonia.

Changes in tumor microbiome and underlying value according to response to neoadjuvan chemotherapy for in patients with gastric cancer

Objective: To investigate the relationship between efficacy of neoadjuvant chemotherapy (NACT) for gastric cancer and gastric microecology. Methods: This was a retrospective observational study using fresh frozen operative specimens. The specimens had been stored in the tumor sample bank of the Department of Gastrointestinal Surgery of the Affiliated Hospital of Qingdao University from January 2017 to January 2023 after having been collected from 31 patients with pathologically diagnosed gastric cancer who had no metastases and had received only neoadjuvant chemotherapy preoperatively. The study patients had all successfully undergone radical gastric cancer surgery. Patients with metastases or other primary tumor foci and/or had received other therapies within 1 month prior to surgery, including immunotherapy, targeted therapies and probiotics, were excluded. The tumors were graded and grouped in accordance with the 8th edition of the American Joint Committee on Cancer staging system and the Tumor Regression Grading System (TRG) of the College of American Pathologists. Those with TRG Grades 0-1, ypT0-1 and ypN0 were classified as responsive (Group R, 12 cases), whereas those with TRG Grades 2-3 and ypT2-4 or ypN+ were classified as non-responsive (Group NR, 19 cases). The fresh frozen samples were processed and analyzed using 16S rRNA sequencing. Alpha and beta diversity analyses were performed using the Q2-diversity plug-in for QIIME2 and STAMP was used to determine the default parameters and differentially enriched bacterial taxa in the two groups. High-dimensional class comparisons were performed by effect size linear discriminant analysis, and potential functional distributions of microbiomes were predicted using PICRUST2 (v2.3.0-b) software. Results: Groups R and NR did not differ significantly in sex, age, body mass index, smoking history, tumor location, cTNM stage before NACT, and neoadjuvant chemotherapy (all P>0.05), whereas tumor size and ypTNM stage after NACT differed significantly between the two groups (both P=0.001). Alpha and beta diversity analysis of the gastric microbiota did not reveal a statistically significant difference in alpha diversity between the two groups (P>0.05), whereas there was a statistically significant difference in beta diversity between the two groups (P=0.004). Four family-level bacterial taxa, namely Coriobacteriaceae, Ruminococcaceae, Veillonellaceae, and Lachnospiraceae, were enriched in the R group, whereas four bacterial taxa dominated by phylum Proteobacteria were enriched in the NR group. Metabolic pathways of various amino acids, including citric acid cycle and alanine, were found to be potentially predictive. Conclusions: There are significant differences in the abundance and composition of gastric microecology in gastric cancer patients with different responses to NACT.

Cloning and functional characterization of the pinoresinol-lariciresinol reductase gene IiPLR2 in Isatis indigotica

The pinoresinol-lariciresinol reductase (PLR), a crucial enzyme in the biosynthesis of lignans in plants, catalyzes a two-step reaction to produce lariciresinol and secoisolariciresinol. Lignans such as lariciresinol are the effective components of traditional Chinese medicine Radix Isatidis in exerting antiviral activity. In order to study the function of the key enzyme PLR in the biosynthesis of lariciresinol in Isatis indigotica, the original plant of Radix Isatidis, IiPLR2 was cloned from I. indigotica, with a full length of 954 bp, encoding 317 amino acids. Multiple sequence alignment showed that IiPLR2 contained a conserved nicotinamide adenine dinucleotide phosphate (NADPH)-binding motif. The phylogenetic tree showcased that IiPLR2 shared the same clade with AtPrR1 from Arabidopsis thaliana. The prokaryotic expression vector pET32a-IiPLR2 was constructed and then transformed into Escherichia coli BL21(DE3) competent cells for protein expression. The purified enzyme IiPLR2 could catalyze the conversion of pinoresinol to lariciresinol and the conversion of lariciresinol to secoisolariciresinol. The cloning, sequencing, and catalytic functional analysis of IiPLR2 in this study enrich the understanding of this kind of functional proteins in I. indigotica and supplement the biosynthesis pathways of lignans. Moreover, this study provides a functional module for further research on metabolic regulation and synthetic biology and lays a foundation for comprehensively revealing the relationship between the spatial structures and catalytic functions of such proteins.

Biosynthesis of a clickable pyoverdine via in vivo enzyme engineering of an adenylation domain

The engineering of non ribosomal peptide synthetases (NRPS) for new substrate specificity is a potent strategy to incorporate non-canonical amino acids into peptide sequences, thereby creating peptide diversity and broadening applications. The non-ribosomal peptide pyoverdine is the primary siderophore produced by Pseudomonas aeruginosa and holds biomedical promise in diagnosis, bio-imaging and antibiotic vectorization. We engineered the adenylation domain of PvdD, the terminal NRPS in pyoverdine biosynthesis, to accept a functionalized amino acid. Guided by molecular modeling, we rationally designed mutants of P. aeruginosa with mutations at two positions in the active site. A single amino acid change results in the successful incorporation of an azido-l-homoalanine leading to the synthesis of a new pyoverdine analog, functionalized with an azide function. We further demonstrated that copper free click chemistry is efficient on the functionalized pyoverdine and that the conjugated siderophore retains the iron chelation properties and its capacity to be recognized and transported by P. aeruginosa. The production of clickable pyoverdine holds substantial biotechnological significance, paving the way for numerous downstream applications.

Metabolomics analysis of human spermatozoa reveals impaired metabolic pathways in asthenozoospermia.

Infertility is a major health issue, affecting 15% of reproductive-age couples with male factors contributing to 50% of cases. Asthenozoospermia (AS), or low sperm motility, is a common cause of male infertility with complex aetiology, involving genetic and metabolic alterations, inflammation and oxidative stress. However, the molecular mechanisms behind low motility are unclear. In this study, we used a metabolomics approach to identify metabolic biomarkers and pathways involved in sperm motility. We compared the metabolome and lipidome of spermatozoa of men with normozoospermia (n = 44) and AS (n = 22) using untargeted LC-MS and the metabolome of seminal fluid using 1H-NMR. Additionally, we evaluated the seminal fluid redox status to assess the oxidative stress in the ejaculate. We identified 112 metabolites and 209 lipids in spermatozoa and 27 metabolites in the seminal fluid of normozoospermic and asthenozoospermic men. PCA analysis of the spermatozoa's metabolomics and lipidomics data showed a clear separation between groups. Spermatozoa of asthenozoospermic men presented lower levels of several amino acids, and increased levels of energetic substrates and lysophospholipids. However, the metabolome and redox status of the seminal fluid was not altered inAS. Our results indicate impaired metabolic pathways associated with redox homeostasis and amino acid, energy and lipid metabolism in AS. Taken together, these findings suggest that the metabolome and lipidome of human spermatozoa are key factors influencing their motility and that oxidative stress exposure during spermatogenesis or sperm maturation may be in the aetiology of decreased motility in AS.

Effects of Individual and Combined Applications of Seaweed Extracts and Plant Growth-Promoting Rhizobacteria (PGPR) on Plant Growth and Physio-Biochemical Properties of Soft Wheat and Faba Bean

ABSTRACT The research on carbon materials and plants primarily focuses on their use in soil, showing variable effects. However, significant gaps exist regarding their impact under stress conditions (such as drought, salinity, etc.) and their interactions with plant physiological processes. Long-term effects on plant health and ecosystems are understudied, as are their interactions with other biofertilizers like algae extracts and plant growth-promoting rhizobacteria (PGPR). The aim of the present study was to evaluate the effects of seaweed extracts and PGPR on plant growth and some physio-biochemical properties of soft wheat (Triticum aestivum L.) and faba bean (Vicia faba L.). Two concentrations of aqueous extract from two seaweeds, Fucus spiralis (F) and Ulva rigida (U), and the PGPR bacillus strain solution S48 (S48S) were used either individually or in combination. All treatments were applied as foliar sprays. The findings showed that the combined application of Fucus spiralis extract [25%] (F), Ulva rigida extract [50%] (U), along with the PGPR S48 bacillus strain solution (S48S) promoted plant growth (50.93 cm for faba bean) and root development (17.90 cm for wheat). This treatment also resulted in increased chlorophyll content (3.25 mg/g Fresh Weight (FW) in soft wheat and 3.93 mg/g FW in faba bean), proteins (14.66 µg/mg FW in soft wheat and 23.79 µg/mg FW in faba bean), amino acids (0.46 mg/g FW in soft wheat and 0.56 mg/g FW in faba bean), and total carbohydrates (529.8 µg/ml in soft wheat and 340.7 µg/ml in faba bean) as compared to controls. On the other hand, the nitrate reductase activity was enhanced by seaweed extract application in both crops. Phosphorus (P) uptake by soft wheat and faba bean was significantly improved following the application of Ulva rigida extract [50%] (U), the PGPR S48 bacillus strain solution (S48S), and the co-treatment of Fucus spiralis extract [25%] (F) with the PGPR S48 bacillus strain solution (S48S). The findings suggest that the combined application of Fucus spiralis extract (F) and Ulva rigida extract (U) with the PGPR S48 bacillus strain solution (S48S) can significantly improve plant growth and nutrient absorption in durum wheat and faba bean. This offers a sustainable alternative to chemical fertilizers, reducing pollution and promoting healthier ecosystems. Furthermore, these biological treatments enhance plant resilience to abiotic stresses, potentially increasing yields in challenging conditions. By reducing reliance on chemical fertilizers, these practices can save money for farmers and advance sustainable agriculture.

On farm precision feeding of gestating sows based on energy and amino acids on farrowing performances and feeding behavior over three consecutive gestations.

Gestating sows are often fed a single diet throughout their gestation cycle, leading to situations of nutrients deficiency or excess at the individual level. The purpose of this study was to characterize, over 3 consecutive cycles, the impact of a precision feeding (PF), i.e. dietary supplies adjusted at individual level in terms of quantity (energy intake) and quality (standardized ileal digestible (SID) lysine (Lys) intake), on gestating sows' productive performance, feeding behavior, environmental outputs and health status compared with sows fed a conventional feeding (CF, i.e. fixed SID Lys intake). At the start of the trial, 2 batches of 20 Landrace × Large White gestating sows were allocated to one of the 2 feeding strategies (PF vs. CF), based on their parity (1, 2 or 3 and more), body weight (BW), and backfat thickness (BT) 3 days after insemination. The PF strategy consisted in mixing with automatic feeders 2 iso-energetic diets (9.8 MJ/kg of net energy with 3.3 and 8.5g SID Lys / kg, respectively) in variable proportions at individual and daily levels, whereas for the CF strategy these proportions remained constant throughout gestation (73% and 27%, respectively, resulting in a SID Lys concentration of 4.7g/kg). Sows were followed over 3 consecutive gestations and the sows remained allocated to the same strategy throughout the study. Some sows were culled before the end of the study and were replaced by other sows who therefore performed only 1 or 2 gestations during the study. Thus, 106 gestations and lactations from 51 sows were fully studied and their data analyzed. The PF strategy allowed the sows to reach more closely the expected BT values at farrowing across cycles than the CF strategy (P < 0.001). The PF sows consumed 16% less SID Lys per gestation than the CF sows (P < 0.001), resulting in a 4% improvement in N efficiency (P < 0.001), with no impact on performance at farrowing (P > 0.10). The sows consumed their daily ration in a single visit whatever the feeding strategy (P = 0.41), but CF sows spent more time in the feeder in cycle 2 and 3 (P < 0.001). Thus, compared to the CF strategy implemented by farmers, the individual and daily nutritional supplies implemented with the PF strategy were more efficient in enabling sows to achieve body condition objectives at farrowing over the long-term, also with a reduced SID Lys intake and an improved N efficiency without negative impact on farrowing performances.

Effects of alloferon and its analogues on reproduction and development of the Tenebrio molitor beetle

As the most numerous group of animals on Earth, insects are found in almost every ecosystem. Their useful role in the environment is priceless; however, for humans, their presence may be considered negative or even harmful. For years, people have been trying to control the number of pests by using synthetic insecticides, which eventually causes an increased level of resistance to applied compounds. The effects of synthetic insecticides have encouraged researchers to search for alternatives and thus develop safe compounds with high specificity. Using knowledge about the physiology of insects and the functionality of compounds of insect origin, a new class of bioinsecticides called peptidomimetics, which are appropriately modified insect analogues, was created. One promising compound that might be successfully modified is the thirteen amino acid peptide alloferon (HGVSGHGQHGVHG), which is obtained from the hemolymph of the blue blowfly Calliphora vicinia. Our research aimed to understand the physiological properties of alloferon and the activity of its peptidomimetics, which will provide the possibility of using alloferon or its analogues in the pharmaceutical industry, as a drug or adjuvant, or in agriculture as a bioinsecticide. We used alloferon and its three peptidomimetics, which are conjugates of the native peptide with three unsaturated fatty acids with various chain lengths: caprylic, myristic, and palmitic. We tested their effects on the morphology and activity of the reproductive system and the embryogenesis of the Tenebrio molitor beetle. We found that the tested compounds influenced the growth and maturation of ovaries and the expression level of the vitellogenin gene. The tested compounds also influenced the process of egg laying, embryogenesis, and offspring hatching, showing that alloferon might be a good peptide for the synthesis of effective bioinsecticides or biopharmaceuticals.

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Knotted proteins are present in nature, but there is still an open issue regarding the existence of a universal role for these remarkable structures. To address this question, we used classical molecular dynamics (MD) simulations combined with in vitro experiments to investigate the role of the Gordian knot in the catalytic activity of UCH-L1. To create an unknotted form of UCH-L1, we modified its amino acid sequence by truncating several residues from its N-terminus. Remarkably, we find that deleting the first two N-terminal residues leads to a partial loss of enzyme activity with conservation of secondary structural content and knotted topological state. This happens because the integrity of the N-terminus is critical to ensure the correct alignment of the catalytic triad. However, the removal of five residues from the N-terminus, which significantly disrupts the native structure and the topological state, leads to a complete loss of enzymatic activity. Overall, our findings indicate that UCH-L1's catalytic activity depends critically on the integrity of the N-terminus and the secondary structure content, with the latter being strongly coupled with the knotted topological state.

Single-molecule analysis reveals the phosphorylation of FLS2 governs its spatiotemporal dynamics and immunity.

The Arabidopsis thaliana FLAGELLIN-SENSITIVE2 (FLS2), a typical receptor kinase, recognizes the conserved 22 amino acid sequence in the N-terminal region of flagellin (flg22) to initiate plant defense pathways, which was intensively studied in the past decades. However, the dynamic regulation of FLS2 phosphorylation at the plasma membrane after flg22 recognition needs further elucidation. Through single-particle tracking, we demonstrated that upon flg22 treatment the phosphorylation of Ser-938 in FLS2 impacts its spatiotemporal dynamics and lifetime. Following Förster resonance energy transfer-fluorescence lifetime imaging microscopy and protein proximity indexes assays revealed that flg22 treatment increased the co-localization of GFP-tagged FLS2/FLS2S938D but not FLS2S938A with AtRem1.3-mCherry, a sterol-rich lipid marker, indicating that the phosphorylation of FLS2S938 affects FLS2 sorting efficiency to AtRem1.3-associated nanodomains. Importantly, we found that the phosphorylation of Ser-938 enhanced flg22-induced FLS2 internalization and immune responses, demonstrating that the phosphorylation may activate flg22-triggered immunity through partitioning FLS2 into functional AtRem1.3-associated nanodomains, which fills the gap between the FLS2S938 phosphorylation and FLS2-mediated immunity.

Enhancing the Rigidity of the Catalytic Pocket Entrance to Improve Catalytic Efficiency and Thermal Stability of Alginate Lyase from Pseudoalteromonas

Alginate lyase plays a critical role in the production of alginate oligosaccharides (AOS), necessitating efficient activity and a certain level of thermal stability for industrial AOS production. In this study, through sequence alignment and structural analysis, a non-catalytic amino acid residue, Ala195, located at the entrance of the catalytic pocket was identified. This residue is crucial for the catalytic efficiency and thermal stability of Alg2944, a member of the polysaccharide lyase family 18. The specific activities of A195F, A195I, and A195L were enhanced by 1.84-, 1.39-, and 1.98-fold, respectively, while the thermal stability of mutants A195L and A195I showed significant improvements at 35°C and 40°C compared to the wild-type (WT) enzyme. Furthermore, molecular docking, structural analysis, and molecular dynamics (MD) simulations revealed that the enhanced specific activity and thermal stability of the A195L mutant can be attributed to the creation of a hydrophobic pocket, increased rigidity in the loop region, and a notably lower binding free energy of the A195L mutant (-45.96 ± 7.69 kcal/mol) compared to the WT (-38.40 ± 4.25 kcal/mol). These findings underscore the essential role of rigidity and hydrophobicity at the entrance of the catalytic pocket in ensuring both catalytic efficiency and thermal stability of alginate lyase.

Emergence of a novel FRI-type carbapenemase; blaFRI-12 in Enterobacter asburiae located on an IncR plasmid.

Carbapenem-resistance in Enterobacter spp due to acquisition of mobile carbapenemases is of concern. An Enterobacter spp grew on ChromID CARBA medium and was positive for the mCIM carbapenemase detection assay. Susceptibility testing showed resistance to aztreonam and reduced susceptibility to imipenem. Conventional PCR using FRI primers detected a blaFRI gene. Whole genome sequencing reveled a new variant; blaFRI-12 was closest in sequence to blaFRI-5 differing by 13 amino acids and was found on a unique 110Kb IncR plasmid. Given the intrinsic nature of Enterobacter spp. to be carbapenem non-susceptible, blaFRI-types may be under reported globally.

Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.

α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.

Variation in protein and amino acids in global collection of pearl millet (Pennisetum glaucum) germplasm

Pearl millet is a major source of daily protein intake in south Asia and sub-Saharan Africa. Despite considerable importance, the extent of variation in protein and amino acids in pearl millet global germplasm is unknown. The present study assessed 165 genotypes from within the Pearl Millet Inbred Germplasm Association Panel (PMiGAP), that includes breeding lines, landraces and improved cultivars randomly drawn from a core collection from 23 countries, for protein content and 18 amino acids. The results showed considerable variation for protein content (10.06 – 20.31%) and amino acids in PMiGAP. Diverse patterns were observed across the geographical distribution and clustered the germplasm into 7 clusters, with one cluster (“2”) containing most of the superior properties. Most amino acid levels were positively correlated but these were negatively correlated with protein content. A set of twelve genotypes was identified having higher protein with better amino acid compositions. These superior genotypes could directly feed into global and regional pearl millet improvement programs to counter hidden hunger in developing countries. We propose that these findings can be combined with the starches, lipids, antioxidants, micronutrients, and other healthful traits for which the PMiGAP resource has been extensively studied.

Identification of amino acids restricting HBV receptor function in porcine NTCP

With 254 million chronically infected patients, hepatitis B virus (HBV) continues to be a severe health threat. While animal models play a crucial role in developing new therapies, the availability of preclinical HBV models is very limited. Therefore, novel in vivo infection models are urgently needed. The bona fide HBV receptor, sodium-taurocholate cotransporting polypeptide (NTCP), determines HBV’s species and cell-type specificity. Recent studies have indicated that the expression of human NTCP is the only limiting factor for HBV infection in selected species, such as macaques or pigs. Here, we confirm HBV infection of pig hepatocytes expressing human NTCP and show that porcine NTCP does not support HBV binding. By gradually humanizing porcine NTCP and site-directed mutagenesis, we identified amino acids 158 and 167 in porcine NTCP, limiting HBV interaction. In a proof-of-concept experiment, we showed that the expression of porcine NTCP with humanized amino acids 157-167 renders primary porcine hepatocytes fully susceptible to HBV. These results pave the way for generating transgenic pigs with humanized porcine chimeric NTCP as a novel, fully immunocompetent infection model for developing and validating new curative HBV therapies.

Binary Catalytic Hydrogen/Deuterium Exchange of Free α-Amino Acids and Derivatives.

The increasing demand for deuterium-labeled amino acids and derivatives has heightened interest in direct hydrogen/deuterium exchange reactions of free amino acids. Existing methods, including biocatalysis and metal catalysis, typically require expensive deuterium sources or excessive use of deuterium reagents and often struggle with site selectivity. In contrast, our pioneering binary catalysis system, employing benzaldehyde and Cs2CO3 in the presence of inexpensive D2O with minimal stoichiometric quantities, facilitates efficient hydrogen/deuterium exchange at the α-position of amino acids without the need for protecting groups in the polar aprotic solvent DMSO. The process is highly compatible with most natural and non-natural α-amino acids and derivatives, even those with potentially reactive functionalities. This advancement not only addresses the cost and efficiency concerns of existing methods but also significantly broadens the applicability and precision of deuterium labeling in biochemical research.

Exploring the Nutritional Profiles and Dietary Value of Indigenous Fish Species from the Mathabanga River in Bangladesh

The study aimed to address the pervasive issue of inadequate nutrition in Bangladesh by analyzing eight distinct fish species, a pivotal step toward developing fish powder as a promising dietary supplement for nutritional enhancement. Samples from the Mathabhanga River in Chuadanga were rigorously processed and oven-dried to assess their nutritional properties, focusing on proximate composition, mineral content, and amino acid profile. Among the studied fish species, C. reba demonstrated the highest energy content (198.56 Kcal/100 g, p < 0.001), with notably elevated crude protein content (16.99 g/100 g, p < 0.001) compared to all except N. notopterus. The mineral composition order in fish powders was Ca > P > Fe > Na > Mg. Leucine emerged as the predominant essential amino acid (EAA) (6.84 to 32.15 mg/g, p < 0.001) among the species. O. pabo exhibited notably higher total EAA (∑EAA) levels (124.30 mg/g, p < 0.05) compared to other species. P. ticto showed a significantly higher ratio of total essential and non-essential amino acid content (∑EAA/∑NEAA) (0.41, p < 0.05) compared to other species. These findings underscored the nutritional value of the studied fish species, advocating their utilization as a dietary supplement to address malnutrition in Bangladesh.

Application of Protein Hydrolysate Improved the Productivity of Soybean under Greenhouse Cultivation

Protein hydrolysates are plant biostimulants containing amino acids, oligopeptides, and peptides in their composition. When supplied to plants, protein hydrolysates (HPs) have been identified to improve nitrogen metabolism, enhance the activity of antioxidant enzymes, boost plant defense response to stresses, and positively impact the quantity and quality of products. Soybean is a crucial global commodity, with nitrogen being the primary nutrient for crop development as it directly affects productivity. This study aimed to evaluate the effect of an HP-based biostimulant on the N metabolism in nodulated soybean plants and their productivity. A greenhouse experiment was conducted to test two modes of application of the 0.20% HP-based biostimulant. Soybean plants, growing in pots, were treated with 0.20% HP either via seed treatment or foliar application (at growth stages V3 and V5). Activities of enzymes and compounds related to N metabolism, gene expression, and productivity components were analyzed. It was observed that the mode of application did not significantly influence the results. The application of HPs increased the concentration of nitrate, amino acids, and ureides in soybean leaves. It also positively altered the expression of genes such as nitrate reductase, urease, and asparagine. Additionally, it enhanced productivity, resulting in plants with a greater number and weight of pods and grains. Therefore, it is possible to consider HPs as a stimulator for increasing soybean productivity, even under non-stressing conditions.

Construction of the Glycolysis Metabolic Pathway Inside an Artificial Cell for the Synthesis of Amino Acid and Its Reversible Deformation.

The bottom-up construction of artificial cells is beneficial for understanding cell working mechanisms. The glycolysis metabolism mimicry inside artificial cells is challenging. Herein, the glycolytic pathway (Entner-Doudoroff pathway in archaea) is reconstituted inside artificial cells. The glycolytic pathway comprising glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxygluconate aldolase (KDGA) converts glucose molecules to pyruvate molecules. Inside artificial cells, pyruvate molecules are further converted into alanine with the help of alanine dehydrogenase (AlaDH) to build a metabolic pathway for synthesizing amino acid. On the other hand, the pyruvate molecules from glycolysis stimulate the living mitochondria to produce ATP inside artificial cells, which further trigger actin monomers to polymerize to form actin filaments. With the addition of methylcellulose inside the artificial cell, the actin filaments form adjacent to the inner lipid bilayer, deforming the artificial cell from a spherical shape to a spindle shape. The spindle-shaped artificial cell reverses to a spherical shape by depolymerizing the actin filament upon laser irradiation. The glycolytic pathway and its further extension to produce amino acids (or ATP) inside artificial cells pave the path to build functional artificial cells with more complicated metabolic pathways.

Dietary protein re-alimentation following restriction improves protein deposition via changing amino acid metabolism and transcriptional profiling of muscle tissue in growing beef bulls

This study aimed to develop a compensatory growth model using growing beef cattle by changing dietary protein and to investigate the underlying mechanisms of compensatory protein deposition in muscle tissue. Twelve Charolais bulls were randomly assigned to one of two groups with two periods: 1) a control group (CON) fed a 13% crude protein (CP) diet for 6 weeks; 2) a treatment group (REC) fed a 7% CP diet for 4 weeks (restriction period) and fed a 13% CP diet in the following 2 weeks (re-alimentation period). Growth performance, digestibility, nitrogen balance, targeted metabolomics of amino acids (AA) in plasma, and transcriptional profiling in muscle tissue were analyzed. Protein restriction decreased average daily gain (ADG; P < 0.05), while protein re-alimentation increased ADG relative to the CON (P < 0.05). Compared to the CON, REC reduced retained N (P < 0.05), and protein re-alimentation increased retained N and N utilization efficiency (P < 0.05), due to reduced urinary urea, hippuric acid, and creatinine excretions (P < 0.05). Ruminal NH3-N in the REC was lower than that in the CON in the protein re-alimentation period (P < 0.05). However, there was no difference in microbial protein and plasma urea nitrogen concentrations. Dietary protein restriction decreased plasma valine and aspartic acid concentrations relative to the CON (P < 0.05), and increased proline and 3-methyl-L-histidine concentrations (P < 0.05). After dietary protein re-alimentation, REC increased plasma citrulline concentrations (P < 0.05). The transcriptional profiling revealed that REC upregulated the AA transporter SLC3A1, and protein re-alimentation downregulated SLC7A8 in the muscle cell membrane. Within the muscle cell, upregulated cytosolic arginine sensor for mTORC1 subunit 2 (CASTOR2) inhibited protein synthesis by inhibiting the mammalian target of rapamycin complex 1 phosphorylation in the protein restriction period, while DNA-damage-inducible transcript 4 (DDIT4) activated the mTOR signaling pathway and promoted protein synthesis in the protein re-alimentation period. In summary, the targeted metabolomics and transcriptomics analyses demonstrated that protein re-alimentation following restriction can promote protein synthesis and reduce muscle breakdown by regulating AA metabolism and functional transcripts related to AA transporters and the mTOR signaling pathway.