Glutamate Research Articles

Motif mapping during chickpea germination reveals a complex sequential activation of different proteolytic activities.

Despite the importance of grains and legumes in the human diet, little is known regarding peptide release and the temporal changes of protease activities during seed germination. LC/MS-MS peptidomic analysis of two cultivars of germinating chickpea followed by computational analyses indicated cleavage dominated by proteases with a single position preference (mainly before (P1) or after cleavage (P1'): L at P2 (cysEP-like); R or K at P1 (vignain-like), N or Q at P1 (legumain-like); and previously unidentified K, R, A and S at P1'; A at P2'). While P1 N cleavages were relatively constant, P1' K/R preferences were high in soaked garbanzo (kabuli) seeds, declined by four days, and returned at six days, but were much rarer in the brown (desi) cultivar. Late Embryogenesis Associated (LEA) peptides were markedly released during early germination. Vicilin peptides rich in glutamic acid near their N-termini markedly increased with germination, consistent with strong proteolytic resistance, even to human digestion, as indicated by analyses of separate datasets. Thus, this first peptidomics study of seed germination proteolytic profiles unveils a complex cultivar-specific programme of sequential activation and inactivation of a series of proteases, associated with the differential release of peptides from different protein groups.

Preliminary study on the potential impact of probiotic combination therapy on Helicobacter pylori infection in children using 16S gene sequencing and untargeted metabolomics approach.

The purpose of this study was to explore the potential mechanism of Helicobacter pylori (Hp) eradication by probiotic therapy through 16S rRNA gene sequencing technology and untargeted metabolomics. Twenty four Hp-infected children were recruited from the Shanxi Bethune Hospital, and 24 healthy children were recruited as a blank control group. Group A: fecal samples from 24 healthy children. Group B: fecal samples of 24 children with Hp infection. Group B1 (n = 15): fecal samples of group B treated with probiotic therapy for 2 weeks. Group B2 (n = 19): fecal samples of group B treated with probiotic therapy for 4 weeks. The above fecal samples were analyzed by 16S rRNA gene sequencing technology and untargeted metabolomics. There was no significant difference in alpha diversity and beta diversity among the four groups, but many bacteria with statistical difference were found in each group at the bacterial genus level and phylum level. LEfSe results showed that in group B, Porphyromonadaceae, Shigella and other microorganisms related to intestinal microecological dysbiosis were enriched. And in group B2, abundant characteristic microorganisms were found, namely Bacillales and Prevotella. KEGG metabolic pathway enrichment analysis showed that groups B1 and B2 were involved in 10 metabolic pathways potentially related to probiotic treatment: purine metabolism, nitrogen metabolism, arginine biosynthesis, alanine, aspartic acid and glutamate metabolism, glyoxylic acid and dicarboxylic acid metabolism, unsaturated fatty acid biosynthesis, fatty acid extension, fatty acid degradation, pyrimidine metabolism, fatty acid biosynthesis. Probiotic therapy can inhibit Hp to some extent and can relieve gastrointestinal symptoms, making it a preferred therapy for children with Hp infection and functional abdominal pain. Hp infection can reduce the diversity of intestinal microbes, resulting in the disturbance of intestinal microbiota and changes in the relative abundance of microbiota in children, while probiotic therapy can restore the diversity of intestinal microbes and intestinal microecological balance.

Xanthohumol Protects Against Neuronal Excitotoxicity and Mitochondrial Dysfunction in APP/PS1 Mice: An Omics-Based Study.

Background: Neuronal excitotoxicity and metabolic decline, which begin in the early stages of Alzheimer's disease (AD), pose challenges for effective amelioration. Our previous work suggested that the natural compound xanthohumol, the most abundant prenylated flavonoid in hops, prevents memory deficits in APP/PS1 mice; however, the underlying mechanisms remain unclear. Methods: This study utilized APP/PS1 mice and cutting-edge omics techniques to investigate the effects of xanthohumol on hippocampal proteome, serum metabolome, and microbiome. Results: Our findings revealed that xanthohumol reduces the postsynaptic overexpression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, N-methyl-D-aspartate, and metabotropic glutamate receptors, but enhances ATP synthesis and mitophagy in the young AD hippocampus. Further mechanistic analyses suggested systemic regulatory effects, particularly on the decreasing glutamate synthesis in the blood and intestines of AD mice following xanthohumol administration. Conclusions: These results underscore the potential of xanthohumol in mitigating AD pathology through multifaceted mechanisms, sparking interest and curiosity in its preventive and therapeutic potential in AD.

Quantitative proteomics and multi-omics analysis identifies potential biomarkers and the underlying pathological molecular networks in Chinese patients with multiple sclerosis

Multiple sclerosis (MS) is an autoimmune disorder caused by chronic inflammatory reactions in the central nervous system. Currently, little is known about the changes of plasma proteomic profiles in Chinese patients with MS (CpwMS) and its relationship with the altered profiles of multi-omics such as metabolomics and gut microbiome, as well as potential molecular networks that underlie the etiology of MS. To uncover the characteristics of proteomics landscape and potential multi-omics interaction networks in CpwMS, Plasma samples were collected from 22 CpwMS and 22 healthy controls (HCs) and analyzed using a Tandem Mass Tag (TMT)-based quantitative proteomics approach. Our results showed that the plasma proteomics pattern was significantly different in CpwMS compared to HCs. A total of 90 differentially expressed proteins (DEPs), such as LAMP1 and FCG2A, were identified in CpwMS plasma comparing to HCs. Furthermore, we also observed extensive and significant correlations between the altered proteomic profiles and the changes of metabolome, gut microbiome, as well as altered immunoinflammatory responses in MS-affected patients. For instance, the level of LAMP1 and ERN1 were significantly and positively correlated with the concentrations of metabolite L-glutamic acid and pro-inflammatory factor IL-17 (Padj < 0.05). However, they were negatively correlated with the amounts of other metabolites such as L-tyrosine and sphingosine 1-phosphate, as well as the concentrations of IL-8 and MIP-1α. This study outlined the underlying multi-omics integrated mechanisms that might regulate peripheral immunoinflammatory responses and MS progression. These findings are potentially helpful for developing new assisting diagnostic biomarker and therapeutic strategies for MS.

Effects of MDA-19 on Zebrafish Larval Behavior: Perspectives From Neurodevelopment, Oxidative Stress, and Metabolomics.

As global regulations on synthetic cannabinoids tighten, illicit vendors increasingly turn to new structures of synthetic cannabinoids to evade legal scrutiny. MDA-19, a novel synthetic cannabinoid, exhibited significant agonistic effects on type 2 cannabinoid receptors invivo and showed emerging trends of abuse in illicit markets. However, research on the toxicological effects of MDA-19 remains scarce. In this study, we examined the effects of MDA-19 on neurodevelopment, behavior, oxidative stress, and metabolomics by exposing zebrafish embryos to MDA-19 solutions with concentrations of 1, 10, and 20 mg/L over 5 days. Results revealed that exposure to 10 and 20 mg/L of MDA-19 accelerated hatching in zebrafish embryos but led to reduced body length without affecting mortality or malformation. Furthermore, exposure to all concentrations of MDA-19 resulted in diminished swimming ability and reduced activity time in zebrafish. Transgenic zebrafish (hb9-GFP) exposed to MDA-19 exhibited impaired development of spinal motor neurons. Notably, exposure to 20 mg/L MDA-19 increased the levels of reactive oxygen species (ROS) in zebrafish and elevated the activity of antioxidant enzymes such as superoxide dismutase (SOD) and catalase (CAT), while the levels of the lipid oxidation product malondialdehyde (MDA) remained unaffected. Nontargeted metabolomics analyses showed that MDA-19 interfered with multiple metabolic pathways affecting energy metabolism, such as alanine, aspartate, and glutamate metabolism; the citric acid cycle (TCA cycle), pantothenate, and coenzyme A biosynthesis; and purine metabolism. In conclusion, the present study provided the essential evidence for the neurotoxic effects of MDA-19, which was associated with impaired neurodevelopment, dysregulation of oxidative stress homeostasis, and altered energy metabolism.

Two Novel Variants in the CHRNA2 and SCN2A Genes in Italian Patients with Febrile Seizures.

Febrile seizures (FSs) are the most common form of epilepsy in children aged between six months and five years. The exact cause is unknown, but several studies have demonstrated the importance of genetic predisposition, with increasing involvement of receptors and ion channels. The present study aims to identify novel pathogenic variants in Italian patients with FSs. We performed targeted panel sequencing in a cohort of 21 patients with FSs. In silico analysis was performed to predict the pathogenic role of the resulting variants. We found two novel variants segregating in two families with FSs: c.1021C>G (p.Leu341Val) in the CHRNA2 gene and c.140A>G (p.Glu47Gly) in SCN2A. The c.1021C>G (p.Leu341Val) variant leads to a codon change of highly conserved leucine to valine at position 341 and is located in segments M3 of the subunit, which is important for channel gating. The c.140A>G (p.Glu47Gly) variant causes a substitution of glutamic acid with glycine at position 47 of the protein, which is highly conserved across the species. Moreover, it is located in the N-terminal domain, a region commonly affected in ASD, which impacts the inactivation kinetics and voltage dependence of steady-state activation. Further analyses are needed to better explain the role of CHRNA2 and SCN2A in the development of febrile seizures.

Recognition of a salivary effector by the TNL protein RCSP promotes effector-triggered immunity and systemic resistance in Nicotiana benthamiana.

Insects secret chemosensory proteins (CSPs) into plant cells as potential effector proteins during feeding. The molecular mechanisms underlying how CSPs activate plant immunity remain largely unknown. We show that CSPs from six distinct insect orders induce dwarfism when overexpressed in Nicotiana benthamiana. Agrobacterium-mediated transient expression of Nilaparvata lugens CSP11 (NlCSP11) triggered cell death and plant dwarfism, both of which were dependent on ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), neuregulin 1 (NRG1) and SENESCENCE-ASSOCIATED GENE 101 (SAG101), indicating the activation of effector-triggered immunity (ETI) in N. benthamiana. Overexpression of NlCSP11 led to stronger systemic resistance against Pseudomonas syringae DC3000 lacking effector HopQ1-1 and tobacco mosaic virus, and induced higher accumulation of salicylic acid (SA) in uninfiltrated leaves compared to another effector XopQ that is recognized by a Toll-interleukin-1 receptor (TIR) domain nucleotide-binding leucine-rich repeat receptor (TNL) called ROQ1 in N. benthamiana. Consistently, NlCSP11-induced dwarfism and systemic resistance, but not cell death, were abolished in N. benthamiana transgenic line expressing the SA-degrading enzyme NahG. Through large-scale virus-induced gene silencing screening, we identified a TNL protein that mediates the recognition of CSPs (RCSP), including aphid effector MP10 that triggers resistance against aphids in N. benthamiana. Co-immunoprecipitation, bimolecular fluorescence complementation and AlphaFold2 prediction unveiled an interaction between NlCSP11 and RCSP. Interestingly, RCSP does not contain the conserved catalytic glutamic acid in the TIR domain, which is required for TNL function. Our findings point to enhanced ETI and systemic resistance by a TNL protein via hyperactivation of the SA pathway. Moreover, RCSP is the first TNL identified to recognize an insect effector.

Seizure solver- pyridoxine dependent seizures

Pyridoxine dependency is a rare cause of seizures. Pyridoxine dependent seizures (PDS) occur despite normal vitamin B6 levels and is due to defective binding of pyridoxine to its apoenzyme, glutamate decarboxylase, which converts glutamic acid to gamma aminobutyric acid (GABA). Pyridoxine-dependent seizure is a rare autosomal recessive disorder that usually presents with neonatal intractable seizures. Parenteral pyridoxine injection test is a highly effective and reproducible test in confirming the diagnosis. Hunt, et al.(l) described the first case of PDS with autosomal recessive inheritance. Since then, several cases have been reported with onset of seizures after neonatal period (2-6). Pyridoxine-dependent epilepsy – ALDH7A1 (PDE-ALDH7A1) is characterized by seizures not well controlled with anti-seizure medication that are responsive clinically and electrographically to large daily supplements of pyridoxine (vitamin B6). This is true across a phenotypic spectrum that ranges from classic to atypical PDE-ALDH7A1. Intellectual disability is common, particularly in classic PDE-ALDH7A1.(7)

Metabolomics based on GC-MS combined with chemometrics for geographical discrimination of garlic (Allium sativum L.)

Ensuring the geographic origin of products helps protect consumers against fraud and mislabeling. This study investigates the metabolomic profiles of garlic (Allium sativum L.) samples from Brazil and China using gas chromatography-mass spectrometry (GC-MS). Multivariate analysis Partial Least Squares Discriminant Analysis (PLS-DA) and Orthogonal PLS-DA (Ortho PLS-DA) revealed clear metabolic distinctions between the two sample groups with high classification accuracy. Brazilian garlic samples showed higher levels of sulfur compounds, such as allyl propyl sulfide, cysteine sulfonic acid, and S-carboxymethyl-L-cysteine, which contribute to its pungency and potential health benefits. Amino acids L-arginine, L-glutamic acid, and L-cysteine were also significantly increased in garlic from Brazil. In contrast, Chinese garlic exhibited higher intensities of sugars (e.g., D-fructose, D-mannose) and essential amino acids (L-tryptophan, L-valine, and L-leucine). These differences in metabolism are the result of distinct metabolic profiles. GC-MS-based untargeted metabolomic and chemometric analysis were able to differentiate the geographical origin of Brazilian and Chinese garlics and remain valuable to food authentication and quality control. Further studies are needed to confirm the biomarkers for origin verification here stated.

Optimization of extraction for efficient recovery of kenaf seed protein isolates: evaluation of physicochemical and techno-functional characteristics.

Kenaf seeds are a rich source of protein; however, finding the best extraction method is crucial to obtaining high-quality protein from these underutilized seeds. This research devised an optimized extraction process for best recovery of kenaf seeds protein using response surface methodology. The key parameters affecting the yield and protein content were optimized, including extraction pH (2-11), seed:water ratio (5:1-50:1), temperature (30-90 °C), and duration (20-360 min). The physicochemical and techno-functional properties of kenaf seed protein isolates (KSPIs) were examined. A maximum protein yield of 12.05 g/100 g with purity level 91.94 g/100 g was obtained using an optimized extraction with pH 11.0, seed:water ratio 50:1, 360 min duration, and temperature 50 °C. The oil and water retention capacities of KSPI were 1.14 mL g-1 and 1.37 mL g-1 respectively. After 30 min at pH 7, KSPIs demonstrated remarkable emulsion capacity (83.12%) and stability (75.63%), along with high foaming capacity (106%) and stability (18.3%). As per high-performance liquid chromatography analysis, arginine, glutamic acid, leucine, phenylalanine, and lysine were the most abundant amino acids detected in KPSIs. The KSPIs' globular protein structure was successfully verified using analytical approaches, including Fourier transform infrared spectroscopy, protein fraction ratios, and differential scanning calorimetry. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis revealed that KPSI has a molecular weight distribution ranging from 10 kDa to 50 kDa. The results of this study support the application of the proposed response-surface-methodology-optimized extraction method for efficient recovery of high-quality kenaf seed proteins that meet the necessary physicochemical and techno-functional requirements. © 2024 Society of Chemical Industry.

Effect of synchronicity of amino acid supply on the synthesis of protein in C2C12 myotubes cultured in vitro.

Previous studies inferred that the synthesis rate/efficiency of protein in body tissue is probably affected by synchronicity of different amino acid (AA) supply in its metabolic pool. In order to further observe the influence of synchronicity of AA supply on the synthesis of protein in cell level, a cell culture experiment in vitro was conducted with C2C12 myotubes. C2C12 myotubes were cultured for 24 h, meanwhile the culture medium was replaced for each 8 h. Those myotubes were subjected to 3 treatments (1 for controlled and 2 for tested), control myotubes were cultured with same normal complete medium within the whole 24 h, and the 2 tested myotubes were cultured with asynchronous amino acid supply medium in which the levels of different AAs (Lysine, threonine, methionine, leucine, valine and glutamic acid) either increased and then decreased or decreased and then increased, at different replaced medium time point (at 0, 8, and 16 h). However, during the whole experiment period all the 3 treated myotubes received same amount of each AA. The sample of the myotubes were used for myotube morphology, protein, AA, and proteomic analysis. The results showed that asynchronous AA nutrition affect the synthesis and degradation of myotube proteins, and the AAAS in the medium increase, thus decreasing the synthesis rate of myotube proteins (p < 0.05) and decreasing the diameter of myotubes (p < 0.05). The process of reduced protein synthesis affects the PI3K-AKT and FoxO signaling pathway by downregulating the levels of IRS1 and EGFR, and the degradation amplitude is greater than the synthesis amplitude. Therefore, this study further revealed the effect of the asynchronous supply of amino acids on myotube protein synthesis and the underlying mechanism and provided a theoretical reference for the precision of nutrition to animals.

Physiological and pathogenic T cell autoreactivity converge in type 1 diabetes

Autoimmune diseases result from autoantigen-mediated activation of adaptive immunity; intriguingly, autoantigen-specific T cells are also present in healthy donors. An assessment of dynamic changes of this autoreactive repertoire in both health and disease is thus warranted. Here we investigate the physiological versus pathogenic autoreactive processes in the context of Type 1 diabetes (T1D) and one of its landmark autoantigens, glutamic acid decarboxylase 65 (GAD65). Using single cell gene expression profiling and tandem T cell receptor (TCR) sequencing, we find that GAD65-specific true naïve cells are present in both health and disease, with GAD65-specific effector and memory responses showing similar ratios in healthy donors and patients. Deeper assessment of phenotype and TCR repertoire uncover differential features in GAD65-specific TCRs, including lower clonal sizes of healthy donor-derived clonotypes in patients. We thus propose a model whereby physiological autoimmunity against GAD65 is needed during early life, and that alterations of these physiological autoimmune processes in predisposed individuals trigger overt Type 1 diabetes.

Food additive monosodium glutamate and risk of cardiovascular diseases - NutriNet-Santé cohort

Abstract Background One may add monosodium glutamate (MSG) to food for its flavour-enhancing properties. However, its implication in long-term cardiovascular health is uncertain due to a lack of precise epidemiological evidence. This study aimed to investigate the associations between food additive glutamate exposures and cardiovascular disease (CVD) risk, including cerebrovascular disease (CVA) and coronary heart disease (CHD) risks in a large prospective cohort of French adults. Methods Participants (n = 108,932, 79.3% women, mean age=42.4 years, SD = 14.5) were 15 years old and above from the French NutriNet-Santé prospective cohort (2009-2023). We assessed dietary intakes using repeated 24h-dietary records and exposure to food additive glutamate using food composition databases and laboratory assays. We characterised associations between cumulative time-dependent continuous exposures to total glutamate, natural glutamic acid, MSG and risk of CVD, CVA, and CHD using multivariable proportional hazards Cox models adjusted for known risk factors for standardised increments of glutamate intake. Results During follow-up (median 7.92 years), 2397, 1113, and 1284 participants were diagnosed with CVD, CVA, and CHD respectively. Higher intakes of naturally occurring glutamic acid (HR per 3000 mg/d increment=1.08, 95% CI [1.01-1.16], p-value=0.03), food additive MSG (HR per 200 mg/d increment=1.05, 95% CI [1.01-1.09], p-value=0.03), and total glutamate (HR per 3000 mg/d increment=1.09, 95% CI [1.01-1.17], p-value=0.02) were associated with higher risks of CHD (p-value for non-linearity&amp;gt;0.6). Conclusions This large prospective cohort study revealed positive associations between exposure to the widely used glutamate food additives, especially MSG (E621) and CVD, CVA, and CHD risks. Key messages • This large prospective cohort study revealed positive associations between exposure to the widely used glutamate food additives, especially MSG (E621) and CVD, CVA, and CHD risks. • If confirmed, our findings regarding MSG could lead to a re-evaluation of the safety of these food additives by European and international public health agencies to improve consumer protection.

Composition of raw and roasted runner, Spanish and Valencia market type peanuts

Spanish, Valencia, and runner are three peanut market-types which have distinct physical and chemical profiles that can affect flavor and industry uses. Market-type and roast treatment (raw/roasted) were evaluated for physical and chemical differences between raw (skin removed) and dry roasted seeds. Samples were analyzed for seed weight, moisture content, water activity, total oil, fatty acid profiles, tocopherols, protein, sugars, and free amino acids. Runner-types had the largest seed weight relative to Spanish and Valencia seeds. Roasting significantly affected moisture content and water activity. Total oil ranged from 49.66 % to 55.63 % with the runner samples having the highest content. Oleic, palmitic, and linoleic fatty acids were the most abundant in the samples and significantly differed between market-types with ranges between 54.74 % and 82.65 %, 5.82–9.04 %, and 2.63–3.06 % respectively. Samples were discriminated by market-type for alpha, beta, and gamma tocopherols. The Valencia-types were highest in protein. Sucrose was the major sugar quantified, but market-type and roasting had no effect on the content. Glucose and fructose levels significantly decreased after roasting. Several free amino acids were differentiated by market-type, but glutamic acid and phenylalanine were the most abundant in all the samples. Roasting demonstrated a significant effect on several free amino acids.

Evaluation of Xanthone and Cinnamoylbenzene as Anticancer Agents for Breast Cancer Cell Lines through In Vitro and In Silico Assays

Breast cancer is a severe global disease for women as the number of deaths increases annually. Therefore, attempts to find new anticancer agents are critical and inevitable. In this work, we report the investigation on the anticancer activity of xanthone and cinnamoylbenzene compounds against two breast cancer cell lines, i.e., T47D and MCF-7, through experimental in vitro and theoretical in silico assays. Xanthone and cinnamoylbenzene exhibit anticancer activity with a half-maximal inhibitory concentration (IC50) of 136.7–194.3 and 235.8–262.4 µg/mL against T47D and MCF-7 cancer cells, respectively. Cinnamoylbenzene generates less cytotoxicity to normal Vero cells with a selectivity index of 1.095–2.102. The molecular docking studies agree with the experimental data in which cinnamoylbenzene is more active against T47D with an IC50 of 136.7 µg/mL due to Topoisomerase II inhibition through π-π stacked interactions with Adenine12 and Guanine13 nitrogen bases. Meanwhile, xanthone is more active against MCF-7 with an IC50 of 235.8 µg/mL due to EGFR inhibition through van der Waals interaction and hydrogen bond with Glutamic acid767 and Methionine769 amino acid residues, respectively. Additionally, the pharmacokinetic parameters of xanthone and cinnamoylbenzene are predicted through absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis, and they show better suitability than doxorubicin as the commercial anticancer drug.

Effects of Black Soldier Fly Larvae Oil on Growth Performance, Blood Biochemical Parameters, Carcass Quality, and Metabolomics Profile of Breast Muscle of Thai Native Chickens.

This study aimed to evaluate the effects of the replacement of rice bran oil (RBO) with black soldier fly larvae oil (BSFLO) on growth performance, blood biochemicals, carcass quality, and metabolomics profile of breast muscle of Thai native chickens. A total of 192 1-day-old, mixed-sex, Pradu Hang Dam (Mor Kor 55) chickens were randomly allocated to one of three dietary groups. Each treatment had four replicates with 16 chicks per replicate (8 males and 8 females). Three dietary treatments were used: (T1) the control group, based on a corn-soybean meal with RBO, and two treatment groups that replaced 50% (T2) and 75% (T3) of RBO in the basal diet with BSFLO, respectively. Results showed that BSFLO inclusion at 50% and 75% did not adversely affect the productive performance of Thai native chickens (p > 0.05). Regarding blood profiles, on day 28, chickens fed 75% BSFLO exhibited significant increases in hemoglobin, hematocrit, and MCHC (mean corpuscular hemoglobin concentration) with lower eosinophil percentages compared to the control group (p < 0.05). Additionally, BSFLO supplementation raised glucose levels but decreased globulin and total protein levels (p < 0.05). On day 63, BSFLO inclusion primarily affected MCV (mean corpuscular volume), with higher values in the 50% BSFLO group (p < 0.05). It also increased globulin and HDL (high-density lipoprotein) levels while lowering AST (aspartate transaminase) concentrations (p < 0.05). For carcass and meat quality, BSFLO supplementation did not affect dressing percentage or edible meat yield (p > 0.05). However, it influenced meat pH and shear force (p < 0.05), with a higher pH at 24 h post-mortem in BSFLO-fed chickens. Metabolomics showed that arginine biosynthesis; phenylalanine, tyrosine, and tryptophan metabolism; alanine, aspartate, and glutamate metabolism; arginine and proline metabolism; and taurine and hypotaurine metabolism were the most differentially abundant. These findings suggest that BSFLO can be used for a partial replacement (50 to 75%) for RBO in Thai native chicken diets, potentially offering benefits for animal health and meat quality without compromising growth performance.

A classical peptide coupling approach for the total synthesis of simnotrelvir

The total synthesis of an oral small-molecule antiviral agent; a structure based developmental drug simnotrelvir has been accomplished. The synthesis involves readily accessible commercial amino acids L-tert-leucine, 4-hydroxy-l-proline and l-glutamic acid that are easily converted to the key intermediates and are coupled together following classical peptide coupling technique using HATU and NMM. One of the crucial step in the synthesis involved a one pot Boc-deprotection and trifluoroacetylation of tert-leucine amino acid moiety mediated by ZnCl2.

Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.

All-atom constant pH molecular dynamics simulations offer a powerful tool for understanding pH-mediated and proton-coupled biological processes. As the protonation equilibria of protein sidechains are shifted by electrostatic interactions and desolvation energies, pKa values calculated from the constant pH simulations may be sensitive to the underlying protein force field and water model. Here we investigated the force field dependence of the all-atom particle mesh Ewald (PME) continuous constant pH (PME-CpHMD) simulations of a mini-protein BBL. The replica-exchange titration simulations based on the Amber ff19SB and ff14SB force fields with the respective water models showed significantly overestimated pKa downshifts for a buried histidine (His166) and for two glutamic acids (Glu141 and Glu161) that are involved in salt-bridge interactions. These errors (due to undersolvation of neutral histidines and overstabilization of salt bridges) are consistent with the previously reported \pka's based on the CHARMM c22/CMAP force field, albeit in larger magnitudes. The pKa calculations also demonstrated that ff19SB with OPC water is significantly more accurate than ff14SB with TIP3P water, and the salt-bridge related pKa downshifts can be partially alleviated by the atom-pair specific Lennard-Jones corrections (NBFIX). Together, these data suggest that the accuracies of the protonation equilibria of proteins from constant pH simulations can significantly benefit from improvements of force fields.

Association of the GRIK4 rs1954787 polymorphism with clinical response in antidepressant-treated depressed patients: results from a prospective cohort and meta-analysis.

Major Depressive Disorder (MDD) is the leading cause of disability worldwide. Genetic factors influence the effect of its main treatment option, antidepressant drugs (ATD). The GRIK4 rs1954787(T>C) genetic polymorphism was associated with response following 1-3 months of ATD treatment in some studies, but not others. We aimed to analyze its association with clinical outcomes in a cohort of 6-month ATD-treated patients and meta-analysis. Clinical data were obtained at baseline and after 1 (M1), 3 (M3), and 6 (M6) months of ATD treatment in 390 patients of the METADAP cohort. Mixed-effects models were used to assess the association of the GRIK4 rs1954787 polymorphism with the Hamilton Depression Rating Scale (HDRS) score and response and remission rates across time. Meta-analyses of ATD treatment response were performed with previously meta-analyzed data and METADAP. Compared to C allele carriers at M3 (n = 200), TT homozygotes at M3 (n = 66) had higher HDRS scores (coef = 3.37, 95% CI [1.30-5.54], Padj = 0.0046) and lower remission rates (OR = 0.36, 95% CI [0.16-0.76], Padj = 0.029). At M6, greater differences between TT homozygotes (n = 53) and C allele carriers (n = 152) were observed for HDRS scores (coef = 4.68, 95% CI [2.17-7.18], Padj = 0.00091) and remission rates (OR = 0.26, 95% CI [0.12-0.54], Padj = 0.0016). Meta-analyses of response were significant when comparing C vs T alleles (OR = 1.31, 95% CI [1.06-1.62], P = 0.014) and CC vs TT genotypes (OR = 1.63, 95% CI [1.10-2.38], P = 0.019). Altogether, our results support an association of the GRIK4 rs1954787(T>C) polymorphism with clinical improvement following ATD treatment. This association should be further assessed in other longitudinal studies. Its position within the glutamatergic system may help in understanding the mechanism of ATD action.

Systematic characterization and efficient prediction of cobalamin C deficiency clinical phenotypes using network analysis and deep learning on multi-omics data

As a monogenic disease, cobalamin C (cblC) deficiency lacks a clear correlation between gene pathogenic mutations and its spectrum of disease phenotypes, necessitating the understanding of molecular mechanisms how diverse clinical phenotypes emerge. This work aimed to disentangle the phenotypic complexity of cblC deficiency via network analysis and deep learning on multi-omics (proteomics and metabolomics) data. For this purpose, a novel computational framework was developed to systematically characterize and efficiently predict clinical phenotypes of cblC deficiency utilizing a Connect the Dots (CTD)-based Hybrid data Structural Representation of each patient and graph convolutional network (GCN)-based Multi-Omics Learning (CTDHSR-GCNMOL). CTD algorithm enabled the identification of relevant perturbed proteins or metabolites and the construction of clinical phenotype-specific co-perturbation network. GCN allowed efficient learning of subtle change patterns across clinical phenotypes not only depending on the hybrid feature description (Euclidean structure hybridized with non-Euclidean structure) of each patient but on the interaction exploration between patients offered by sample similarity network. Investigated by three clinical phenotypes (epilepsy, developmental delay and metabolic syndrome), the results showed that CTDHSR-GCNMOL identified the subsets of perturbed proteins or metabolites highly specific to each clinical phenotype and established each main disease module (network) for systematic characterization. For proteomics, epilepsy was characterized by the dysregulation of reported TAGLN2, SH3BGRL3 and LTA4H, and developmental delay was characterized by the dysregulation of reported HSP90AB1, PRDX1, GDI2, VIM, PNP and BLVRA with high confidence (selection frequencies). For untargeted metabolomics in negative ion mode, the disease status of metabolic syndrome could be well interpreted by the disturbed pathways of the top-ranked 20 perturbed metabolites all of which have been reported to be closely related with its pathogenesis in previous studies. These disturbed pathways involved butanoate metabolism, purine metabolism, alanine, aspartate and glutamate metabolism, pyrimidine metabolism, fructose and mannose metabolism, galactose metabolism, amino sugar and nucleotide sugar metabolism, and steroid hormone biosynthesis. Based on the hybridization of the abundances of perturbed proteins and metabolites with the topological structures of patient-specific perturbation network, CTDHSR-GCNMOL yielded desired prediction performance across three clinical phenotypes and outperformed the traditional block PLSDA. All these findings verified the effectiveness of CTDHSR-GCNMOL in gaining useful insights into the phenotypic complexity of cblC deficiency and guiding its targeted treatment strategies.