Search Results (42)

The purpose of this study was to investigate the physiological and biochemical changes of the hepatopancreas and intestinal microbial structure of Penaeus vannamei under various levels of carbonate alkalinity stress. After Penaeus vannamei (body length 14.24 ± 2.13 cm, body weight 26.31 ± 3.26 g) was subjected to 96 h carbonate alkalinity stress, the alkalinity stress levels were E8 (8 mmol/L), E18 (18 mmol/L) and E28 (28 mmol/L), respectively. The activity of antioxidant enzymes was determined by enzyme markers, and then the intestinal microorganisms of Penaeus vannamei were analyzed by high-throughput sequencing technology. The results showed that, under the stress of high carbonate alkalinity, the mortality rate of Penaeus vannamei was as high as 75%, and hepatopancreas cells showed obvious deformation, abnormal nuclear shapes, and serious cell vacuolation. Under high carbonate alkalinity stress, superoxide dismutase activity, catalase activity and glutathione peroxidase activity in the Penaeus vannamei hepatopancreas were significantly lower than those in control group (p < 0.05), and malondialdehyde content was significantly lower than that in the control group (p < 0.05). Alkaline phosphatase activity in the experimental group was significantly different from that in the control group (p < 0.05). Moreover, the 16SrDNA high-throughput sequencing results showed that the intestinal abundance of Proteobacteria in Penaeus vannamei was significantly decreased (p < 0.05) under high carbonate alkalinity stress, and the abundance of Bacteroides was significantly increased (p < 0.05). At the genus level, the abundance of Chrysobacteria was significantly increased (p < 0.05). The functional prediction results of COG and KEGG showed that the functional abundance of RNA polymerase sigma-70 factor is direct bacterial or plastid core RNA polymerase and is specific to promoter elements that are situated 10 and 35 base-pairs upstream of transcription-initiation points—in the high carbonate alkalinity treatment group, this was higher than that in the control group. The functional abundance of signal transduction histidine kinase was lower than that of the control group. The results of this study not only indicated that Penaeus vannamei cell structure would change and mortality would increase under high carbonate alkalinity culture environment, but they also analyzed the changes of the intestinal microbial structure under carbonate alkalinity stress. This study could provide theoretical reference for Penaeus vannamei saline–alkali land culture. Full article

French beans are tender, immature, edible pods that are harvested early in the plant’s growth cycle and are usually eaten cooked. The growth habits of French beans were studied for the first time in a Citizen Science experiment, and 19 pod samples were collected for further nutritional analysis. Various macronutrients (e.g., protein, ash, fat, carbohydrates, amino acids) and multi-element profiles were determined. A survey of their growing habits revealed that beans are usually planted once or twice a year in May and June at a length of 5–10 m, with a predominance of dwarf beans cultivation over climbing varieties, and pest resistance and stringless pods are the most important characteristics when deciding on a bean. Homogenised freeze-dried pod samples contained 16.1–23.1% protein, 4.5–8.2% ash, 0.1–1.1% fat, and 62.0–70.6% carbohydrates and had a caloric value of 337–363 kcal/100 g. Of the 17 free amino acids identified, 8 were essential (histidine, threonine, methionine, valine, lysine, isoleucine, leucine, phenylalanine) and 9 were non-essential (cysteine, aspartic acid, serine, glutamic acid, glycine, arginine, alanine, proline, tyrosine); meanwhile, of the 12 elements, 5 were macroelements and 7 were microelements. The predominant free amino acids were aspartic acid, glutamic acid, and serine. In the multiple comparisons (Box and Whisker plot), the parameters caloric value and iron showed the strongest response. A very strong positive significant Pearson correlation (≥0.95) was found for five pairs of variables within the free amino acids. Comparison of the nutrient data obtained in the pods showed near-perfect or high complementarity (85.2–103.4%) with the food composition databases for half of the parameters, suggesting that the home-grown French beans from the Citizen Science experiment are a highly nutritious vegetable. Full article

Biogenic amines (BAs) are biologically active substances found in the cells of microorganisms, plants, and animals. These BAs serve many vital functions in the body. However, an excessive amount can be toxic, especially for individuals taking monoamine oxidase (MAO) and diamine oxidase (DAO) inhibitors. They primarily form in products rich in amino acids, the primary substrates for BA formation. The aim of this study was to determine the formation of BAs and their precursor amino acids in chicken breast and leg muscles stored under chilling conditions. Analyses of BA and AA determinations were conducted on days 1, 3, 5, 7, and 10 of muscle storage. There was a noted increase in BAs with the storage of both muscle types (p < 0.05). Distinct levels of BAs were detected (p < 0.05) in the muscles, except for putrescine (p > 0.05). Interactions emerged between the two factors for various Bas, including histamine (p = 0.001), tyramine (p < 0.001), BAI index (p < 0.001), tryptamine (p < 0.001), agmatine (p = 0.001), spermidine (p < 0.001), TOTAL BA-1 (p < 0.001), and TOTAL BA-2 (p = 0.016). There was no evident interaction between the type of meat and storage time concerning amino acid content (p > 0.05). Correlations in breast muscles were observed for biogenic amine–amino acid pairs such as putrescine–ornithine (r = −0.57) (p < 0.05), spermidine–ornithine (r = −0.73) (p < 0.05), and phenylethylamine–phenylethylalanine (r = −0.50) (p < 0.05). In leg muscles, significant correlations were found for histamine–histidine (r = −0.87) (p < 0.05), putrescine–ornithine (r = −0.96) (p < 0.05), and phenylethylamine–phenylethylalanine (r = −0.65) (p < 0.05). The results obtained can be used in the future to estimate the levels of BAs with knowledge of the levels of individual amino acids and inversely. Full article

This study aims to explore the relationship between macrosomia and amino acids in maternal and cord sera. Methods: In the case-control study, 78 pairs of mothers and newborns were recruited from December 2016 to November 2019. Participants were divided into the macrosomia group (BW ≥ 4000 g, n = 39) and the control group (BW between 2500 g and 3999 g, n = 39) according to the birth weight (BW) of newborns. Maternal vein blood samples were collected before delivery and cord vein blood samples were collected after birth. The levels of amino acids in maternal and cord sera were measured by liquid chromatography and mass spectrometry (LC-MS/MS) in the year 2021. The difference in amino acid levels in maternal and cord sera between the two groups was compared, and the contribution of each amino acid to the difference between the two groups was analyzed. Unconditional logistic regression analysis was used to test the relationship between macrosomia and amino acids. Results: In maternal serum during the antepartum, the levels of asparagine, glutamine, methionine, alanine, and threonine in the macrosomia group were higher but arginine was lower than that in the control group (p < 0.05). In cord serum, the levels of lysine, histidine, phenylalanine, arginine, tryptophan, valine, isoleucine, glutamate, tyrosine, and total essential amino acid (EAA) in the macrosomia group were lower while glutamine was higher than that in the control group (p < 0.05). The ratios of EAA, valine, threonine, methionine, tryptophan, and alanine in maternal serum to those in cord serum were higher, while the ratio of glutamine was lower in the macrosomia group (p < 0.05). Arginine and threonine in maternal serum and glutamate, glutamine, and histidine in cord serum were associated with macrosomia (p < 0.05). Conclusion: Most of the amino acid levels in the maternal sera of the macrosomia group are higher than those in the control group, while most of the amino acids’ levels in the cord sera of the macrosomia group are lower than those in the control group. The ratios of some amino acids in maternal serum to those in cord serum were different between the two groups. Arginine and threonine in maternal serum and glutamate, glutamine, and histidine in cord serum are closely related to macrosomia. Full article

The histidine-containing phosphocarrier (HPr) is a monomeric protein conserved in Gram-positive bacteria, which may be of mesophilic or thermophilic nature. In particular, the HPr protein from the thermophilic organism B. stearothermophilus is a good model system for thermostability studies, since experimental data, such as crystal structure and thermal stability curves, are available. However, its unfolding mechanism at higher temperatures is yet unclear at a molecular level. Therefore, in this work, we researched the thermal stability of this protein using molecular dynamics simulations, subjecting it to five different temperatures during a time span of 1 μs. The analyses of the structural parameters and molecular interactions were compared with those of the mesophilic homologue HPr protein from B. subtilis. Each simulation was run in triplicate using identical conditions for both proteins. The results showed that the two proteins lose stability as the temperature increases, but the mesophilic structure is more affected. We found that the salt bridge network formed by the triad of Glu3-Lys62-Glu36 residues and the salt bridge made up of Asp79-Lys83 ion pair are key factors to keep stable the thermophilic protein, maintaining the hydrophobic core protected and the structure packed. In addition, these molecular interactions neutralize the negative surface charge, acting as “natural molecular staples”. Full article

The suppressor of TCR signaling (Sts) proteins, Sts-1 and Sts-2, are a pair of closely related signaling molecules that belong to the histidine phosphatase (HP) family of enzymes by virtue of an evolutionarily conserved C-terminal phosphatase domain. HPs derive their name from a conserved histidine that is important for catalytic activity and the current evidence indicates that the Sts HP domain plays a critical functional role. Sts-1_HP has been shown to possess a readily measurable protein tyrosine phosphatase activity that regulates a number of important tyrosine-kinase-mediated signaling pathways. The in vitro catalytic activity of Sts-2_HP is significantly lower than that of Sts-1_HP, and its signaling role is less characterized. The highly conserved unique structure of the Sts proteins, in which additional domains, including one that exhibits a novel phosphodiesterase activity, are juxtaposed together with the phosphatase domain, suggesting that Sts-1 and -2 occupy a specialized intracellular signaling niche. To date, the analysis of Sts function has centered predominately around the role of Sts-1 and -2 in regulating host immunity and other responses associated with cells of hematopoietic origin. This includes their negative regulatory role in T cells, platelets, mast cells and other cell types, as well as their less defined roles in regulating host responses to microbial infection. Regarding the latter, the use of a mouse model lacking Sts expression has been used to demonstrate that Sts contributes non-redundantly to the regulation of host immunity toward a fungal pathogen (C. albicans) and a Gram-negative bacterial pathogen (F. tularensis). In particular, Sts-/- animals demonstrate significant resistance to lethal infections of both pathogens, a phenotype that is correlated with some heightened anti-microbial responses of phagocytes derived from mutant mice. Altogether, the past several years have seen steady progress in our understanding of Sts biology. Full article

Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA polymerase transcription complex containing a temperature-sensitive bacterial σ factor, σ³² (σ³²-RPo). The structure of σ³²-RPo reveals key interactions essential for the assembly of E. coli σ³²-RNAP holoenzyme and for promoter recognition and unwinding by σ³². Specifically, a weak interaction between σ³² and −35/−10 spacer is mediated by T128 and K130 in σ³². A histidine in σ³², rather than a tryptophan in σ⁷⁰, acts as a wedge to separate the base pair at the upstream junction of the transcription bubble, highlighting the differential promoter-melting capability of different residue combinations. Structure superimposition revealed relatively different orientations between βFTH and σ₄ from other σ-engaged RNAPs and biochemical data suggest that a biased σ₄–βFTH configuration may be adopted to modulate binding affinity to promoter so as to orchestrate the recognition and regulation of different promoters. Collectively, these unique structural features advance our understanding of the mechanism of transcription initiation mediated by different σ factors. Full article

Previous works have shown the existence of protein partnership, belonging to a MultiStep Phosphorelay (MSP), potentially involved in osmosensing in Populus. The first actor of this signalling pathway belongs to the histidine-aspartate kinase (HK) family, which also includes the yeast osmosensor Sln1, as well as the Arabidopsis putative osmosensor AHK1. In poplar, the homologous AHK1 protein corresponds to a pair of paralogous proteins, HK1a and HK1b, exhibiting an extracellular domain (ECD), as in Sln1 and AHK1. An ECD alignment of AHK1-like proteins, from different plant species, showed a particularly well conserved ECD and revealed the presence of a cache domain. This level of conservation suggested a functional role of this domain in osmosensing. Thus, we tested this possibility by modelling assisted mutational analysis of the cache domain of the Populus HK1 proteins. The mutants were assessed for their ability to respond to different osmotic stress and the results point to an involvement of this domain in HK1 functionality. Furthermore, since HK1b was shown to respond better to stress than HK1a, these two receptors constituted a good system to search for osmosensing determinants responsible for this difference in efficiency. With domain swapping experiments, we finally demonstrated that the cache domain, as well as the second transmembrane domain, are involved in the osmosensing efficiency of these receptors. Full article

Effects of different feeding strategies on meat quality and intestinal development in pigeon squabs were investigated. 120 pairs of pigeons with two squabs each were assigned to five groups (four free-choice feeding systems and one complete feeding system): T1 (corn, pea, wheat, and pelleted feed), T2 (corn, wheat, and pelleted feed), T3 (corn, pea, and pelleted feed), T4 (corn and pelleted feed), and T5 (complete pelleted feed). Compared with T5, the diet in T4 made the breast meat redder and more yellow (p < 0.05). T2 and T4 resulted in an enhanced total superoxide dismutase activity of meat. Breast muscle in T1 and T2 was determined to have higher contents of nonessential amino acids, glycine, alanine, and glutamic acid (p < 0.05). The contents of the essential amino acids, lysine, threonine, valine, histidine, and arginine were also higher in T1 (p < 0.05). Villus height, surface area, and alkaline phosphatase activity of the duodenum and jejunum in T2 were the highest among the treatments (p < 0.05). In conclusion, free-choice feeding system can improve the meat quality and intestinal development of pigeon squabs, but which combination method of whole grains to use in the production depends on the feeding purpose. Full article

The antimicrobial activity of the novel coordination polymers obtained by co-crystallizing the amino acids arginine or histidine, as both enantiopure L and racemic DL forms, with the salts Cu(NO₃)₂ and AgNO₃ has been investigated to explore the effect of chirality in the cases of enantiopure and racemic forms. The compounds [Cu·AA·(NO₃)₂]_CPs and [Ag·AA·NO₃]_CPs (AA = L-Arg, DL-Arg, L-His, DL-His) were prepared by mechanochemical, slurry, and solution methods and characterized by X-ray single-crystal and powder diffraction in the cases of the copper coordination polymers, and by powder diffraction and by solid-state NMR spectroscopy in the cases of the silver compounds. The two pairs of coordination polymers, [Cu·L-Arg·(NO₃)₂·H₂O]_CP and [Cu·DL-Arg·(NO₃)₂·H₂O]_CP, and [Cu·L-Hys·(NO₃)₂·H₂O]_CP and [Cu·DL-His·(NO₃)₂·H₂O]_CP, have been shown to be isostructural in spite of the different chirality of the amino acid ligands. A similar structural analogy could be established for the silver complexes on the basis of SSNMR. The activity against the bacterial pathogens Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus was assessed by carrying out disk diffusion assays on lysogeny agar media showing that, while there is no significant effect arising from the use of enantiopure or chiral amino acids, the coordination polymers exert an appreciable antimicrobial activity comparable, when not superior, to that of the metal salts alone. Full article

Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations. Full article

This study evaluates the effects of carbon, nitrogen, and sulfur dopants on the photocatalytic activity of TiO₂ for degradation of oxytetracycline (OTC) and chemical oxygen demand (COD) removal from licorice extraction plant wastewater (LEPW). Three novel visible-light-responsive nanostructures, including L-Histidine-TiO₂, L-Methionine-TiO₂ and L-Asparagine-TiO₂, were successfully synthesized. The results showed that the modification of TiO₂ with these three amino acids made the catalyst active in the visible light region and reduced the recombination rate of e⁻/h⁺ pairs according to PL analysis. The photodegradation efficiency of L-Histidine (2 wt.%)-TiO₂ was 100% and 94% for OTC and COD, respectively. It showed the highest photocatalytic activity under illumination, compared to L-Methionine (1.5 wt.%)-TiO₂ and L-Asparagine (2 wt.%)-TiO₂. Synthesized composites were characterized with SEM, XRD, FTIR, DRS, and PL analyses. The biological oxygen demand to COD (BOD₅/COD) ratio for treated LEPW was determined to be 0.5–0.6, confirming the enhanced biodegradability of the treated effluent. The effect of the independent variables, namely, initial concentration of OTC and COD, catalyst dosage, irradiation time, pH of solution, and light intensity, on the photocatalytic process was evaluated by Response Surface Methodology (RSM), and the optimum value of each independent parameter for maximum degradation of OTC and COD by L-Histidine (2 wt.%)-TiO₂ was determined. The radical trapping experiment was performed with various scavengers in order to propose a photocatalytic mechanism, showing that hydroxyl radicals were the main active species. L-Histidine (2 wt.%)-TiO₂ showed a stable and reusable structure even after four cycles of COD removal under the following optimal conditions of [COD]: 300 mg/L, [catalyst]: 1 g/L, light intensity: 25 W/cm² at pH = 4 after 180 min irradiation. Full article

In this paper we study two lysine-based peptide dendrimers with Lys-His-Arg and Lys-Arg-His repeating units and terminal lysine groups. Combination of His and Arg properties in a dendrimer could be important for biomedical applications, especially for prevention of dendrimer aggregation and for penetration of dendrimers through various cell membranes. We describe the synthesis of these dendrimers and the confirmation of their structure using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. NMR spectroscopy and relaxation are used to study the structural and dynamic properties of these macromolecules and to compare them with properties of previously studied dendrimers with Lys-2Arg and Lys-2His repeating units. Our results demonstrate that both Lys-His-Arg and Lys-Arg-His dendrimers have pH sensitive conformation and dynamics. However, properties of Lys-His-Arg at normal pH are more similar to those of the more hydrophobic Lys-2His dendrimer, which has tendency towards aggregation, while the Lys-Arg-His dendrimer is more hydrophilic. Thus, the conformation with the same amino acid composition of Lys-His-Arg is more pH sensitive than Lys-Arg-His, while the presence of Arg groups undoubtedly increases its hydrophilicity compared to Lys-2His. Hence, the Lys-His-Arg dendrimer could be a more suitable (in comparison with Lys-2His and Lys-Arg-His) candidate as a pH sensitive nanocontainer for drug delivery. Full article

Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks. Full article

Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability. Full article