Glutamine-derived peptides: Current progress and future directions.

Glutamine, the most abundant amino acid in the body, plays a critical role in preserving immune function, nitrogen balance, intestinal integrity, and resistance to infection. However, its limited solubility and instability present challenges for its use a functional nutrient. Consequently, there is a preference for utilizing glutamine-derived peptides as an alternative to achieve enhanced functionality. This article aims to review the applications of glutamine monomers in clinical, sports, and enteral nutrition. It compares the functional effectiveness of monomers and glutamine-derived peptides and provides a comprehensive assessment of glutamine-derived peptides in terms of their classification, preparation, mechanism of absorption, and biological activity. Furthermore, this study explores the potential integration of artificial intelligence (AI)-based peptidomics and synthetic biology in the de novo design and large-scale production of these peptides. The findings reveal that glutamine-derived peptides possess significant structure-related bioactivities, with the smaller molecular weight fraction serving as the primary active ingredient. These peptides possess the ability to promote intestinal homeostasis, exert hypotensive and hypoglycemic effects, and display antioxidant properties. However, our understanding of the structure-function relationships of glutamine-derived peptides remains largely exploratory at current stage. The combination of AI based peptidomics and synthetic biology presents an opportunity to explore the untapped resources of glutamine-derived peptides as functional food ingredients. Additionally, the utilization and bioavailability of these peptides can be enhanced through the use of delivery systems in vivo. This review serves as a valuable reference for future investigations of and developments in the discovery, functional validation, and biomanufacturing of glutamine-derived peptides in food science.

Evaluating inter-rater reliability in the context of "Sysmex UN2000 detection of protein/creatinine ratio and of renal tubular epithelial cells can be used for screening lupus nephritis": a statistical examination.

BACKGROUND: The evaluation of inter-rater reliability (IRR) is integral to research designs involving the assessment of observational ratings by two raters. However, existing literature is often heterogeneous in reporting statistical procedures and the evaluation of IRR, although such information can impact subsequent hypothesis testing analyses. METHODS: This paper evaluates a recent publication by Chen et al., featured in BMC Nephrology, aiming to introduce an alternative statistical approach to assessing IRR and discuss its statistical properties. The study underscores the crucial need for selecting appropriate Kappa statistics, emphasizing the accurate computation, interpretation, and reporting of commonly used IRR statistics between two raters. RESULTS: The Cohen's Kappa statistic is typically used for two raters dealing with two categories or for unordered categorical variables having three or more categories. On the other hand, when assessing the concordance between two raters for ordered categorical variables with three or more categories, the commonly employed measure is the weighted Kappa. CONCLUSION: Chen and colleagues might have underestimated the agreement between AU5800 and UN2000. Although the statistical approach adopted in Chen et al.'s research did not alter their findings, it is important to underscore the importance of researchers being discerning in their choice of statistical techniques to address their specific research inquiries.

Kappa statistic considerations in evaluating inter-rater reliability between two raters: which, when and context matters.

BACKGROUND: In research designs that rely on observational ratings provided by two raters, assessing inter-rater reliability (IRR) is a frequently required task. However, some studies fall short in properly utilizing statistical procedures, omitting essential information necessary for interpreting their findings, or inadequately addressing the impact of IRR on subsequent analyses' statistical power for hypothesis testing. METHODS: This article delves into the recent publication by Liu et al. in BMC Cancer, analyzing the controversy surrounding the Kappa statistic and methodological issues concerning the assessment of IRR. The primary focus is on the appropriate selection of Kappa statistics, as well as the computation, interpretation, and reporting of two frequently used IRR statistics when there are two raters involved. RESULTS: The Cohen's Kappa statistic is typically utilized to assess the level of agreement between two raters when there are two categories or for unordered categorical variables with three or more categories. On the other hand, when it comes to evaluating the degree of agreement between two raters for ordered categorical variables comprising three or more categories, the weighted Kappa is a widely used measure. CONCLUSION: Despite not substantially affecting the findings of Liu et al.?s study, the statistical dispute underscores the significance of employing suitable statistical methods. Rigorous and accurate statistical results are crucial for producing trustworthy research.

Microbial community succession during crude oil-degrading bacterial enrichment cultivation and construction of a degrading consortium.

Microbial community succession during the enrichment of crude-oil-degrading bacteria was analyzed using Illumina high-throughput sequencing to guide bacterial isolation and construction of a bacterial consortium. Community change occurred in 6 days; the most abundant phylum changed from Proteobacteria to Actinobacteria; the most abundant genera were Dietzia and unspecified_Idiomarinaceae. Two crude oil-degrading strains, Rhodococcus sp. OS62-1 and Dietzia sp. OS33, and one weak-crude-oil-degrading strain, Pseudomonas sp. P35, were isolated. A consortium comprising Rhodococcus sp. OS62-1 and Pseudomonas sp. P35 showed the highest crude-oil-degrading efficiency, reaching 85.72 ± 3.21% within 7 days, over a wide pH range (5-11) and salinity (0-80 g·L-1). Consumption of saturated hydrocarbons, aromatic hydrocarbons, and resins was greater by the consortium than by a single strain, as was degradation of short-chain-alkanes (C13-C17) according to gas-chromatography. The bacterial consortium provides technical support for bioremediation of crude oil pollution.

Sphingopyxis yananensis sp. nov., a novel 2-nitropropane degrading bacterium isolated from a microbial fermentation bed substrate.

A rod-shaped, Gram-negative staining strain, FBM22T, was isolated from a microbial fermentation bed substrate from a pig farm. Its colonies appeared yellow and were 0.5-1.2 mm in diameter. Cells were 0.3-0.5 µm wide, 0.5-0.83 µm long. Optimal growth occurred at 30 °C and pH 7.0-8.0; NaCl was not required for growth. The strain performed denitrification and nitrate reduction functions. And it could produce catalase. FBM22-1T utilized the following organic substrates for growth: tyrosine, glutamic acid, D-glucose, and galactose. The novel isolate could degrade 2-nitropropane as carbon and nitrogen source. The dominant respiratory quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. C18:1 ω7c, C16:1 ω7c and/ or C16:1 ω6c, and C14:0 2-OH were the major (≥ 8%) fatty acids. The G+C content was 56.8 mol%. FBM22T was found to be a member of the genus Sphingopyxis in the family Sphingomonadaceae of the class Alphaproteobacteria. It had the highest sequence similarity with the type strains Sphingopyxis terrae subsp. ummariensis UI2T (96.47%) and Sphingopyxis terrae subsp. terrae NBRC 15098T (96.40%). Furthermore, FBM22T had 18.7% and 18.4% relatedness (based on digital DNA-DNA hybridization) with its two relatives (S. terrae subsp. ummariensis UI2T and S. terrae subsp. terrae NBRC 15098T). The morphological, physiological, and genotypic differences identified in this study support the classification of FBM22T as a novel species within the genus Sphingopyxis, for which the name Sphingopyxis yananensis sp. nov. is proposed. The type strain is FBM22T (= KCTC 82290T = CCTC AB2020286T).

Interactions between Autophagy and DNA Viruses.

Autophagy is a catabolic biological process in the body. By targeting exogenous microorganisms and aged intracellular proteins and organelles and sending them to the lysosome for phagocytosis and degradation, autophagy contributes to energy recycling. When cells are stimulated by exogenous pathogenic microorganisms such as viruses, activation or inhibition of autophagy is often triggered. As autophagy has antiviral effects, many viruses may escape and resist the process by encoding viral proteins. At the same time, viruses can also use autophagy to enhance their replication or increase the persistence of latent infections. Here, we give a brief overview of autophagy and DNA viruses and comprehensively review the known interactions between human and animal DNA viruses and autophagy and the role and mechanisms of autophagy in viral DNA replication and DNA virus-induced innate and acquired immunity.

Immunologic cross-reactivity between Muscovy duck parvovirus and goose parvovirus on the basis of epitope prediction.

Through bioinformatic prediction, between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV), there were one epitope AA503-509 (RANEPKE) on non-structural protein and three epitopes AA426-430 (SQDLD), 540-544 (DPYRS), 685-691 (KENSKRW) on structural protein might cross-react with each other. Furthermore, the four epitops were expressed in Escherichia coli. All the four recombinant proteins could react with GPV-antisera and MDPV-antisera in Western blot.

Immunologic cross-reactivity between Muscovy duck parvovirus and goose parvovirus on the basis of epitope prediction

Through bioinformatic prediction, between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV), there were one epitope AA503-509 (RANEPKE) on non-structural protein and three epitopes AA426-430 (SQDLD), 540-544 (DPYRS), 685-691 (KENSKRW) on structural protein might cross-react with each other. Furthermore, the four epitops were expressed in Escherichia coli. All the four recombinant proteins could react with GPV-antisera and MDPV-antisera in Western blot.

Monoclonal antibodies against NS1 protein of Goose parvovirus.

In the present study, monoclonal antibodies (MAbs) against NS1 protein of Goose parvovirus (GPV) were generated. The secreted MAbs were obtained by fusing mouse myeloma cells and spleen cells of BALB/c mice, which were immunized with the plasmid pcDNA3.1-GPV-NS1 and recombinant protein of GPV-NS1. With indirect ELISA, six hybridoma cell lines against GPV-NS1 were screened. The subtypes of the two MAbs were IgG2a; the others were IgM. The light chain was κ. Western blot analysis showed that six MAbs reacted with recombinant protein GPV-NS1. GPV-NS1 was dissected into 15 overlapping epitopes, which were used to react with MAbs in Western blot. Results showed that six MAbs recognized NS1 protein linear B-cell epitopes located at the C-terminus 453-514 aa, 485-542 aa, and 533-598 aa.

Localization of linear B-cell epitopes on goose parvovirus structural protein.

Goose parvovirus (GPV), a small non-enveloped ssDNA virus, can cause Derzsy's disease, a highly contagious and lethal disease in goslings and muscovy ducklings, leading to a huge economic loss. However, little is known about the localization of B-cell epitopes on GPV structural protein. To address the issue, the structural protein of GPV was dissected into sets of partially overlapping fragments and expressed in Escherichia coli. Then Western blot reactivity of these glutathione S-transferase (GST) fusion short peptides to viral infected sera was surveyed. The results showed linear immunodominant epitopes, which were found in seven fragments covering amino acid residues 35-71, 123-198, 423-444, 474-491, 531-566, 616-669, 678-732. Our findings may provide the basis for the development of immunity-based prophylactic, therapeutic, and diagnostic clinical techniques for Derzsy's disease.