Type 1 diabetes (T1D) is mediated by autoreactive T cells targeting pancreatic β-cell antigens, with CD8+ T cells specific for islet autoantigens playing a central role. CD8+ T cell reactivity to glutamic acid decarboxylase 65 (GAD65) in HLA-A*02:01 individuals has been reported to focus on the immunogenic region around residues 114-122 (VMNILLQYV). Here, we design GAD65114-122 mimotopes with enhanced human leukocyte antigen (HLA) binding as potential T1D vaccine candidates. Using all-atom molecular dynamics (MD) simulation and free energy perturbation (FEP), we evaluate single, double, and swap mutations on HLA-A*02:01-GAD65114-122 binding. Our results identify positions 3 and 7 as key sites for affinity enhancement. Position 3 favors negatively charged residues aspartic acid (N3D) and glutamic acid (N3E) over native asparagine (ASN), suggesting favorable electrostatic interactions, while position 7 prefers hydrophobic residues methionine (Q7M) and isoleucine (Q7I) over native glutamine (GLN), enhancing binding stability. Double mutations at both positions 3 and 7 display an overall additive or even synergistic effect, with N3D_Q7M, N3D_Q7I, N3E_Q7M, and N3E_Q7I double mutants identified as strong candidates for further experimental validation of T cell activation. This work highlights key insights for optimizing antigen-based vaccine design and optimization for T1D.

Different types of biochar reduce N2O emissions by mediating the interplay of multiple factors during composting

Retraction notice to "Growth of L-asparagine monohydrate organic single crystals: An experimental and DFT computational approach for nonlinear optical applications" [Heliyon 10 (2024) e39842

Background: The study’s main objective was to quantify the acrylamide (ACR) content in potato, plantain, and cassava crisps—products widely consumed in Costa Rica. ACR, a possible carcinogen according to various global organizations, is generated during the Maillard reaction when foods rich in asparagine (ASN) and reducing sugars are subjected to temperatures above 120 °C. Methods: Using GC-MS analysis on n = 54 samples (24 potatoes, 18 plantains, and 12 cassavas), it was determined that ACR levels were within the ranges established by international organizations such as Codex Alimentarius (CODEX) and the Food and Drug Administration (FDA). The reducing sugra and ASN content of the raw materials was quantified to correlate them with the ACR in the final product. Results: One potato product was identified with an ACR concentration that significantly exceeded the 750 μg kg-1 limit stipulated in Recommendation (EU) 2019/1888. For plantain and cassava chips, which currently have no specific regulations, the results showed ACR content to be significantly lower compared to potato crisps. The findings demonstrated a significant correlation between the initial asparagine content and ACR formation in potato crisps, a relationship not observed with reducing sugars. In contrast, no direct correlation was found between precursors and ACR in plantain chips. The analysis also revealed that, in addition to asparagine concentration, the crisps’s surface-to-volume ratio is a crucial physical parameter for minimizing ACR formation. Conclusion: The data obtained on daily ACR intake will serve as a valuable input for future risk studies in the Costa Rican population, suggesting that plantain and cassava chips are a safer alternative due to their lower ACR content.

L-Asparagine monohydrate (LAM) is grown by solution growth method is nucleation by the slow evapouration technique. Grown crystal has characterized by the various studies they are Powder XRD, FTIR, UV-vis, EDAX, CHN, Photoluminescence, 1H&13C FT-NMR, TG-DTA, SEM, LDT and Z scan. Powder XRD used to identify the Space group, Lattice parameters and crystal structure. X pert high score is the research tool which help to find the FWHM, Crystalline size and strain(ղ). FTIR is mainly identify the functional group of various assignments and Functional groups. DTA was used to study the thermal behaviour of the material, which provides insights into the stability and decomposition behaviour of the crystal under varying temperatures, including the determination of the glass transition temperature (TG). The thermal kinetic parameters such as Entropy j/mol.k, Enthalpy j/mol and Gibbs free energy j/mol is the technique which is used to find the Broidos method. In UV-Vis the optical property of the LAM compound which are find out the Transmittance (%), Linear Band gap (Eg) and Refractive index (no).The Z scan technique is generally helps for Third harmonic generation of Nonlinear absorption coefficient (β), Nonlinear refractive index (n2) and Third order susceptibility X (3).The LAM sample had the different elements of carbon, nitrogen, and oxygen, according to EDAX. Elemental analysis verifies the chemical makeup of growing samples. A Prominent peak in the Fluorescence spectrum, recorded from 200-800 nm, was seen at 467 nm. The LDT was experimentally determined as 24.8 GW/cm2 . The FT-NMR method verified the molecular structure. The SEM image was captured the particle and minutes crack. SEM Reveals the information about growth quality and defect level.

Adoption of conservation agriculture (CA) based crop establishment methods involving legumes enhances soil organic nitrogen and carbon fractions by promoting microbial activity and residue retention, thereby improving nutrient availability and crop productivity in alluvial soils. A field experiment was conducted at Bihar Agricultural University, Sabour, in 2023 to evaluate the effects of eight crop establishment methods combining DSR or transplanted puddled rice (TPR), followed by CTW (conventionally tilled wheat) or ZTW (zero tilled wheat) and Fallow (F) or Green Gram (GG). The treatments were laid out in a factorial randomized block design. Soil samples were analyzed for labile and stable SOC and organic and inorganic nitrogen fractions after the rice harvest. Results showed significant improvement in very labile carbon (29.34 %) and labile carbon (27.17 %) under Dry DSR-ZTW-GG (T4) over conventional TPR-CTW-F (T5). Similarly, T4 recorded the highest nitrate-N (31.91 mg kg-1) and hydrolysable ammoniacal-N (149.53 mg kg-1). The rice grain yield ranged from 4276.67 to 5193.33 kg ha-1, with T8 (TPR-ZTW-GG) and T7 (TPR-CTW-GG) outperforming others, but statistically at par with T4. The rice yield was found to be strongly and positively correlated (p=0.01) with hydrolysable NH4+-N (r = 0.879), amino acid-N (r = 0.893), very labile carbon (r = 0.914) and labile carbon (r = 0.872), indicating that these fractions contribute the most towards yield performance. Integration of DSR, zero tillage wheat and legume in rotation significantly improves SOC and N dynamics while enhancing productivity, suggesting a promising alternative to conventional puddled rice systems which ultimately leads to sustainable alluvial soil management.

Abstract Extracellular enzymes that catalyze the hydrolysis of proteinaceous and chitinaceous forms of organic nitrogen (N) inputs into N-bearing monomers limit downstream N mineralization, though depolymerization rates are also modulated by organic N chemistry and soil fertility status. We evaluated the short-term (28 d) sensitivity of N-hydrolytic enzyme activities and N pool concentrations to chitinaceous (chitin, chitosan, cricket, mealworm) and proteinaceous (soy, wheat, casein) substrate additions to two soils under contrasting long-term (145 y) fertility management practices that differed markedly in nutrient status and organic matter content. We found that chitin and chitosan additions increased chitinase activities substantially in both soils (> 7-fold), but unexpectedly, chitinaceous substrates also increased protease (chitin) and aminopeptidase (chitin and mealworm) activities in the fertilized soil under a diverse crop rotation with fertilization (high fertility soil) but not in the unfertilized soil under continuous maize (low fertility soil). Although proteinaceous substrates consistently decreased aminopeptidase activities in both soils, large magnitude increases in downstream free amino acid-N and ammonium-N (low fertility soil) and nitrate-N (high fertility soil) indicated amino acid production and mineralization likely occurred shortly after substrate additions (< 28 d). In addition to short-term augmentation of hydrolytic soil enzyme activities and downstream N pools, most substrates increased soil respiration more in the low versus high fertility soil– without concurrent increases in microbial biomass carbon or N. Thus, our study demonstrates that long-term management practices can yield metabolically distinct soils that exhibit divergent, and often unexpected, responses to organic N additions.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Long COVID are complex multisystem conditions that pose significant challenges in healthcare. Accumulated research evidence suggests that ME/CFS and Long COVID exhibit overlapping metabolic symptoms, indicating potential shared metabolic dysfunctions. This study aims to systematically explore shared metabolic disturbances in the muscle tissue of patients. Utilizing genome-wide metabolic modeling, we identified key metabolic irregularities in the muscle of patients with ME/CFS, notably the downregulation of the alanine and aspartate metabolism pathway and the arginine and proline metabolism pathway. Further, in silico knockout analyses suggested that supplementation with aspartate (ASP) or asparagine (ASN) could potentially ameliorate these metabolic deficiencies. In addition, assessments of metabolomic levels in Long COVID patients also showed the significant downregulation of ASP during post-exertional malaise (PEM) in both muscle and blood. Consequently, we propose that a combination of l-ornithine and l-aspartate (LOLA) is a potential candidate to alleviate metabolic symptoms in ME/CFS and Long COVID for future clinical trials.

Parameter sensitivity analysis is being currently used in the modeling of physical phenomena in almost all engineering areas. The computational effort required to assess the importance of the uncertain parameters in a model is of utmost importance. In this article, a five-step process for parameter sensitivity analysis is proposed based on an efficient sigma point (SP) method. The SP method uses only ( 2 n + 1 ) function evaluations for n number of uncertain input parameters. Several practical engineering problems, including two population balance models for the crystallization process of L-asparagine monohydrate and pyrazinamide, are evaluated to demonstrate the effectiveness of the proposed sensitivity approach. For the validation of sensitivity results obtained from the SP method, the polynomial chaos expansion (PCE) and optimal sparse PCE (OSPCE) methods are used as references. Before this, SP, PCE, and OSPCE methods are compared with the Monte Carlo simulations to check the accuracy of the three methods in approximating the mean and variance of the model outcomes. The results clearly indicate that the proposed SP-based sensitivity analysis approach is highly beneficial for complex dynamic models involving a huge number of uncertain parameters.

Biochar application can increase soil carbon (C) and nitrogen (N) storage. However, the short- and long-term effects of biochar application on soil organic N fractions remain poorly understood in tropical areas. Hence, an in situ combined laboratory incubation study was investigated to determine changes in soil organic N fractions and related chemical biological properties under 1 month (BF) and 3 years (BA) of different biochar application rates (1% and 2%). The results showed that biochar application significantly increased the hydrolysable ammonium N (HAN) by 8.67–18.90% (BF) and 9.45–17.32% (BA). Amino acid N (AAN) significantly increased by 6.08–12.90% (BF) and 5.32–12.16% (BA) compared to CK. The hydrolysable unknown N decreased significantly in BF. The HAN and AAN under the higher biochar application rate were significantly higher than those under the lower application rate. Total N, HAN, and AAN contents were positively correlated with MBN. The structural equation model results showed that soil pH directly promoted AAN, and indirectly promoted soil MBC and MBN. Our results implied that the 3-year biochar application had a more stable effect on the organic N fraction. Therefore, it is possible to increase and maintain soil organic N fractions by appropriate amounts of long-term biochar application in tropical areas.

L-asparaginase (L-ASNase) functions as a chemotherapeutic enzyme with antitumor properties. It facilitates the degradation of L-asparagine (L-ASN), a vital amino acid required for the proliferation of tumor cells. In this study, we have isolated 177 L-ASNase-producing strains from the aquatic environment of the Arabian-Persian Gulf. The most potent isolate, ASP-J1-4, was an endophyte recovered from the seablite Suaeda maritima and was molecularly identified as B. xiamenensis (accession number PQ593941). The enzyme purified through DEAE-Sepharose displayed a molecular weight of 37 kDa based on the SDS-PAGE profile and lacked detectable L-glutaminase (L-GTNase) activity. Optimal enzyme activity was at 40 °C and pH 9.0, with stability at pH 7-9. The maximum stimulation effect was found in the presence of Fe3+, Mn2+, and Na+ ions, respectively. The enzyme demonstrated a Vmax of 35.71 U/mL and a Km of 0.15 mM. Interestingly, ASP-J1-4 L-ASNase showed a dose-dependent inhibition against human colon carcinoma (HCT-116) and cervical Henrietta Lacks (HeLa) cell lines, with IC50 values of 15.42 µg/mL and 12.13 µg/mL, respectively. These findings collectively suggest a biocompatible, efficient, and robust enzyme for potential applications in tumor therapy after validation of in vivo studies and clinical trials. This study introduces the first deep screening program for L-ASNase-producing bacteria harboring in the Arabian-Persian Gulf region. In addition, it launches B. xiamenensis and other species as new sources of L-ASNase.

L-asparagine monohydrate at high temperatures: transformations and negative thermal expansion. A study by thermal analysis and synchrotron X-ray diffraction

Exploring the temporal evolution dynamics of different soil organic nitrogen (N) components under different water–N management practices is a useful approach to accurately assessing N supply and soil fertility. This information can provide a scientific basis for precise water and N management methods for greenhouse vegetable production. The objective of this study was to investigate the effects of optimized irrigation and nitrogen management on the dynamics of soil organic nitrogen fractions, soil properties, and crop growth. This research was conducted from 2017 to 2023 in a greenhouse vegetable field in North China. Four treatments were applied: (1) high chemical N application with furrow irrigation (farmers’ practice, FP); (2) no chemical N application with drip irrigation (DN0); (3) 50% N of FP with drip irrigation (DN1); and (4) 75% N of FP with drip irrigation (DN2). The volume in drip irrigation is 70% of that in furrow irrigation. The results showed that in 2023 (after seven years of field trials), compared with FP, the soil organic carbon (SOC), total N, and water use efficiency of the DN1 and DN2 treatments increased by 15.9%, 11.4%, and 11.3% and 7.7%, 47.2% and 44.6%, respectively. However, there was no significant difference in the total crop yield except in the DN0 treatment. Soil organic N was mostly in the form of acid-hydrolyzed N (AHN). After seven years of optimized irrigation and N management, the DN1 treatment significantly increased the content of ammonium N (AN) and amino sugar N (ASN) in AHN compared with the FP treatment. The results of further analysis demonstrated that SOC was the main factor in regulating AHN and non-hydrolyzable N (NHN), while the main regulatory factors for amino acid N (AAN) and ASN in the AHN component were dry biomass and water use efficiency, respectively. From a time scale perspective, optimization of the water and N scheduling, especially in DN1 (reducing the total irrigation volume by 30% and the amount of N applied by 50%), is crucial for the sustainable improvement of soil fertility and the maintenance of vegetable production.

Root exudation of N is a plant input to the soil environment and may be differentially regulated by the plant during drought. Organic N released by root systems has important implications in rhizosphere biogeochemical cycling considering the intimate coupling of C and N dynamics by microbial communities. Besides amino acids, diverse molecules exuded by root systems constitute a significant fraction of root exudate organic N but have yet to receive a metabolomic and quantitative investigation during drought. To observe root exudation of N during drought, mature cotton plants received progressive drought and recovery treatments in an aeroponic system throughout their reproductive stage and were compared to control plants receiving full irrigation. Root exudates were nondestructively sampled from the same plants at 9 timepoints over 18 days. Total organic C and N were quantified by combustion, inorganic N with spectrophotometric methods, free amino acids by high performance liquid chromatography (HPLC), and untargeted metabolomics by Fourier-transform ion cyclotron resonance-mass spectrometry (FT-ICR-MS). Results indicate that organic N molecules in root exudates were by far the greatest component of root exudate total N, which accounted for 20-30% of root exudate mass. Drought increased root exudation of organic N (62%), organic C (6%), and free amino acid-N (562%), yet free amino acids were <5% of the N balance. Drought stress significantly increased root exudation of serine, aspartic acid, asparagine, glutamic acid, tryptophan, glutamine, phenylalanine, and lysine compared to the control. There was a total of 3,985 molecules detected across root exudate samples, of which 41% contained N in their molecular formula. There were additionally 349 N-containing molecules unique to drought treatment and 172 unique to control. Drought increased the relative abundance and redistributed the molecular weights of low molecular weight N-containing molecules. Time-series analysis revealed root exudation of organic N was stimulated by drought and was sensitive to the degree of drought stress.

Background: Emerging data reveal the importance of metabolomics in identifying specific amino acids and their metabolites as markers of hypercoagulability and stroke. Hypercoagulability, measured by a global hemostasis assay, is associated with thrombotic risk in patients with acute ischemic stroke (AIS). Hypothesis: AIS Patients undergoing coronary intervention compared to healthy controls (HC) exhibit dysregulated amino acid metabolomics that is associated with coagulation. Methods: Serum samples were collected from HC and AIS patients during the intervention. Untargeted metabolomics was performed using a Thermo-Scientific Q Exactive Plus Orbitrap mass spectrometer with Vanquish Horizon Binary UPLC. Metabolomics results were normalized relative to control subjects and compared to patients with AIS. Whole blood samples were used for the TEG assay, and the results were compared between patients with AIS and HC. Hypercoagulability was defined as platelet-fibrin clot strength (P-FCS) &gt;66.5 mm. Results: AIS patients undergoing interventional procedures (n=12) and HC (n=17) were included. Among AIS patients, 50% were black, 67% were male, and 67% were obese. AIS patients vs. controls had elevated levels of P-FCS (67±3mm vs. 62±2mm) and a higher prevalence of hypercoagulability (83% vs. 0%) (p&lt;0.05 for both). Compared to HC, patients with AIS had negative correlation with histidine (his), glutamine (Glu), arginine, lysine (Lys), asparagine (ASP), homoarginine (Harg), ornithine (orn), valine (Val), homocysteine (Hcyc), anthranilate (Ant), serotonin (Ser), tryptophan (Trp), proline (Prl), alanine (Ala), and beta-alanine (Bala). They positively correlated with kynurenine (Kyn), xanthine (Xan), and xanthosine (Xanth) (P&lt;0.05 for all, Figur ). Conclusions: This hypothesis-generating study of untargeted metabolomics revealed that patients with AIS at the time of intervention were characterized by significant hypercoagulability and dysregulation of amino acids associated with coagulation. Further studies are planned to analyze the relationship between these amino acids and AIS risk and to identify them as novel prognostic risk factors.

APR-246 Overcomes Resistance to Asparaginase in Lymphoid Malignancies By Targeting Metabolic Cell Vulnerabilities

Good optical quality of L-asparagine monohydrate (C4H8N2O3.H2O) organic single crystal has been grown by adopting natural slow evaporation process at room temperature from aqueous solutions. The lattice parameters obtained by powder X-ray diffraction data revealed orthorhombic crystal system of the harvested crystal. The morphology and planes of the crystal have been identified. The molecular vibrations and functional groups have been specified by Fourier transform infrared (FTIR) spectroscopy studies. Energy dispersive X-ray (EDX) study has been availed to find out the elements constituting the crystal. Scanning electron microscopy, (SEM), provided the surface morphology of the crystal. The dependence of dielectric properties on frequency and temperature have been investigated and the electronic polarizability (α) has been determined. UV–vis spectral analysis shows that the crystal possesses good optical transmittance in the visible part of the energy spectrum. The optical band gap and the Urbach energy have been determined from lower absorption edge. Third order nonlinear susceptibility χ(3), nonlinear refractive index (n2), and linear susceptibility χ(1) have been calculated by Miller's generalized rule. The first-principle computation of band structure of electrons and the electron density of states have been discussed, which suggest that the crystals possess direct band gap. Density Functional Theory (DFT) with B3LYP function by Gaussian09W software was utilized to calculate HOMO-LUMO energy gap as well as non-linear optical parameters namely, linear polarizability (α), hyperpolarizability (β and γ) and dipole moment (μ) of L-asparagine monohydrate crystal. All the findings prove that L-asparagine monohydrate is a promising NLO crystal.

Solubility, molecular simulation, and dissolution thermodynamic of L-asparagine monohydrate in twelve pure solvents

Single crystal of L-Asparagine monohydrate admixtured with DL- malic acid (LAMDLM) has been grown by slow evaporation solution growth technique by using deionized water as solvent at room temperature. Optically clear single crystals having dimensions up to 4mm x 3mm x 1mm. Powder X-ray diffraction analysis reveals that LAMDLM crystal crystallizes by Orthorhombic system with the space group of P212121. The physical phase of the product was confirmed by powder x-ray diffraction analysis. The Fourier Transform Infrared (FTIR) spectra of all grown crystals have been recorded in the wavenumber range of 500-4500 cm-1 by KBr pellet technique and the associated functional groups of the grown crystals. The optical parameters, such as optical band gap energy, transparency (%) and absorbance were calculated parameters using UV-Vis Transmittance data in the spectral range of wavelength 190-1100 nm. The Multilayer plate-like pattern of growth was observed by Scanning electron microscopy. The presence of L-Asparagine malate was confirmed by EDAX analysis. Incorporation of Various elements present in L-Asparagine malate in the crystal was confirmed by Energy Dispersive X-ray Analysis (EDX). The laser damage threshold for the grown crystal was measured using Nd:YAG Laser. The laser damage threshold value was found to be 3.6 GW/cm2.

Among the 20 proteinogenic amino acids, glutamine (GLN) and asparagine (ASN) represent a unique cohort in containing a terminal amide in their side chain, and share a direct metabolic relationship, with glutamine generating asparagine through the ATP-dependent asparagine synthetase (ASNS) reaction. Circulating glutamine levels and metabolic flux through cells and tissues greatly exceed those for asparagine, and "glutamine addiction" in cancer has likewise received considerable attention. However, historic and recent evidence collectively suggest that in spite of its modest presence, asparagine plays an outsized regulatory role in cellular function. Here, we present a unifying evidence-based hypothesis that the amides constitute a regulatory signaling circuit, with glutamine as a driver and asparagine as a second messenger that allosterically regulates key biochemical and physiological functions, particularly cell growth and survival. Specifically, it is proposed that ASNS serves as a sensor of substrate sufficiency for S-phase entry and progression in proliferating cells. ASNS-generated asparagine serves as a subsequent second messenger that modulates the activity of key regulatory proteins and promotes survival in the face of cellular stress, and serves as a feed-forward driver of S-phase progression in cell growth. We propose that this signaling pathway be termed the amide signaling circuit (ASC) in homage to the SLC1A5-encoded ASCT2 that transports both glutamine and asparagine in a bidirectional manner, and has been implicated in the pathogenesis of a broad spectrum of human cancers. Support for the ASC model is provided by the recent discovery that glutamine is sensed in primary cilia via ASNS during metabolic stress.