Acid Changes Research Articles

Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections.

Significant variations have been observed in viral copies generated during SARS-CoV-2 infections. However, the factors that impact viral copies and infection dynamics are not fully understood, and may be inherently dependent upon different viral and host factors. Here, we conducted virus whole genome sequencing and measured viral copies using RT-qPCR from 9,902 SARS-CoV-2 infections over a 2-year period to examine the impact of virus genetic variation on changes in viral copies adjusted for host age and vaccination status. Using a genome-wide association study (GWAS) approach, we identified multiple single-nucleotide polymorphisms (SNPs) corresponding to amino acid changes in the SARS-CoV-2 genome associated with variations in viral copies. We further applied a marginal epistasis test to detect interactions among SNPs and identified multiple pairs of substitutions located in the spike gene that have non-linear effects on viral copies. We also analyzed the temporal patterns and found that SNPs associated with increased viral copies were predominantly observed in Delta and Omicron BA.2/BA.4/BA.5/XBB infections, whereas those associated with decreased viral copies were only observed in infections with Omicron BA.1 variants. Our work showcases how GWAS can be a useful tool for probing phenotypes related to SNPs in viral genomes that are worth further exploration. We argue that this approach can be used more broadly across pathogens to characterize emerging variants and monitor therapeutic interventions.

Analysis of volatile compounds, α-dicarbonyl compounds, and acetic acid in Robusta coffee by soaking with D-xylose and D-ribose

BackgroundThe study investigated the impact of D-xylose and D-ribose soaking methods (autoclaved and non-autoclaved) on Robusta coffee's volatile compounds, α-dicarbonyl compounds (α-DCs), and acetic acid. Robusta coffees were soaked with D-xylose and D-ribose solutions, and the beans were dried until constant moisture content and lightly roasted.ResultsThe sugar treatment led to an 85.6% reduction in pyrazine levels and a 64.4% decrease in pyridine, while pyrroles and furans increased significantly by 84.4% and 16.4%, respectively (p < 0.05). The total concentration of α-DCs was decreased by 24.6–69.2%, with the autoclaved D-xylose sample exhibiting the lowest among all samples. Acetic acid concentration was lower in non-autoclaved samples compared to autoclaved samples (p < 0.05). Principal component analysis indicated autoclave-treated pentose pretreatment reduced pyrazines and increased in the levels of 1-furfurylpyrrole, methyl furfuryl disulfide, 4-ethyl-2-methoxy-phenol, 2-methoxyphenol, 2-acetylpyrrole, pyridine, furfuryl acetate, and acetic acid.ConclusionThis study, utilizing GC–MS, GC–NPD, and HPLC–UV for compound quantification, offers valuable insights into the changes of volatiles, α-DCs, and acetic acid in Robusta coffee soaking with D-xylose and D-ribose, suggesting potential applications in the coffee industry to modulate flavor profiles.Graphical

Long-term changes in phospholipids and free fatty acids and the possible subcellular origins for phospholipid degradation in kainic acid-damaged mouse hippocampus

Kainic acid (KA)-induced excitotoxicity induces acute degradation of phospholipids and release of free fatty acids (FFAs) in rodent hippocampus, but the long-term changes in phospholipids or the subcellular origins of liberated FFAs remain unclarified. Phospholipids and FFAs were determined in KA-damaged mouse hippocampus by enzyme-coupled biochemical assays. The evolution of membrane injuries in the hippocampus was examined by a series of morphological techniques. The levels of phospholipids in the hippocampus decreased shortly after KA injection but recovered close to the control levels at 24 h. The decline in phospholipids was accelerated again from 72 to 120 after KA treatment. The levels of FFAs were negatively related to those of phospholipids, exhibiting a similar but opposite trend of changes. KA treatment caused progressively severe damage to vulnerable neurons, which was accompanied by increased permeability in the cell membrane and increased staining of membrane-bound dyes in the cytoplasm. Double fluorescence staining showed that the latter was partially overlapped with abnormally increased endocytic and autophagic components in damaged neurons. Our results revealed intricate and biphasic changes in phospholipid and FFA levels in KA-damaged hippocampus. Disrupted endomembrane system may be one of the major origins for KA-induced FFA release.

The Liver-Protective Effects of the Essential Oil from Amomum villosum in Tilapia (Oreochromis niloticus): Antioxidant, Transcriptomic, and Metabolomic Modulations.

This study investigates the effects of the essential oil from Amomum villosum (EOA) on liver-protective effects in Nile tilapia (Oreochromis niloticus), utilizing a multidisciplinary approach that integrates physiological assessments and transcriptomic and metabolomic analyses. Fish were fed diets containing 2 g/kg of EOA over a 56-day trial, with a no-EOA diet serving as the control. The results demonstrate that EOA supplementation improves liver histology, enhances antioxidant capacities, and reduces inflammation in tilapia. The transcriptomic analysis revealed significant alterations in gene expression profiles related to RNA splicing, metabolism, and disease pathways. The identification of differential genes and disease databases identified key target genes associated with the primary component of EOA for its anti-hepatobiliary disease effects. Furthermore, a molecular docking analysis of EOA major components with core differentially expressed genes in the hepatobiliary syndrome indicated that α-pinene is a potential Hsp90 inhibitor, which may prevent inflammation. A metabolomic analysis further demonstrated that EOA supplementation leads to notable changes in liver phospholipids, fatty acids, and carbohydrate metabolism. These findings underscore the potential of EOA as a natural additive for improving liver health in tilapia, offering valuable insights to the aquaculture industry for enhancing fish health and welfare in intensive farming systems.

Modeling the Change in Amino Acid and Peptide Contents during the Aging of Bottled-Fermented Sparkling Wines by Image Processing Methods

In this study, natural sparkling wine was produced using a mixture (1:1) of Emir and Dimrit grapes harvested (Around the Urgup District of Turkey). The change of free amino acid and peptide contents in sparkling wine depending on the aging time and yeasts (free and immobilized forms of the Saccharomyces bayanus and Saccharomyces oviformis) used in the second fermentation stage were examined by image processing methods. The immobilized yeasts were determined as more than the free ones along the second fermentation. It was also determined that the yeast type does not have a significant effect on both the peptides and free amino acid contents of sparkling wines and these contents were divided into 3 classes from high to low by measuring separately along the aging time. The amino acid contents of sparkling wines reached the highest level between the 335th and 365th days of aging time and also exceeded the amino acid contents of base wine.

A pleiotropic recurrent dominant ITPR3 variant causes a complex multisystemic disease.

Inositol 1,4,5-trisphosphate (IP3) receptor type 1 (ITPR1), 2 (ITPR2), and 3 (ITPR3) encode the IP3 receptor (IP3R), a key player in intracellular calcium release. In four unrelated patients, we report that an identical ITPR3 de novo variant-NM_002224.3:c.7570C>T, p.Arg2524Cys-causes, through a dominant-negative effect, a complex multisystemic disorder with immunodeficiency. This leads to defective calcium homeostasis, mitochondrial malfunction, CD4+ lymphopenia, a quasi-absence of naïve CD4+ and CD8+ cells, an increase in memory cells, and a distinct TCR repertoire. The calcium defect was recapitulated in Jurkat knock-in. Site-directed mutagenesis displayed the exquisite sensitivity of Arg2524 to any amino acid change. Despite the fact that all patients had severe immunodeficiency, they also displayed variable multisystemic involvements, including ectodermal dysplasia, Charcot-Marie-Tooth disease, short stature, and bone marrow failure. In conclusion, unlike previously reported ITPR1-3 deficiencies leading to narrow, mainly neurological phenotypes, a recurrent dominant ITPR3 variant leads to a multisystemic disease, defining a unique role for IP3R3 in the tetrameric IP3R complex.

Biofilm Formation by Lactobacillus Strains of Modern Probiotics and Their Antagonistic Activity against Opportunistic Bacteria.

The species identity of the studied lactobacillus strains was confirmed by matrix-activated laser desorption/ionization with time-of-flight ion separation (MALDI-TOF mass spectrometry). Lactobacillus strains differed in the dynamics of lactic acid accumulation and changes in the pH of the culture medium. The culture medium affected adhesion ability of lactobacilli. The ability to adhere does not affect the formation of biofilms by lactobacillus strains except for the L. acidophilus La5 strain, which has low adhesion ability and fewer microbial cells detected after mechanical destruction of the biofilm. The metabiotics of the lactobacillus culture medium have an antagonistic effect on conditionally pathogenic microorganisms. Adhesion, biofilm formation, and antagonistic activity of probiotic lactobacillus strains are strain-specific properties.

Development and validation of machine-learning models of diet management for hyperphenylalaninemia: a multicenter retrospective study

BackgroundAssessing dietary phenylalanine (Phe) tolerance is crucial for managing hyperphenylalaninemia (HPA) in children. However, traditionally, adjusting the diet requires significant time from clinicians and parents. This study aims to investigate the development of a machine-learning model that predicts a range of dietary Phe intake tolerance for children with HPA over 10 years following diagnosis.MethodsIn this multicenter retrospective observational study, we collected the genotypes of phenylalanine hydroxylase (PAH), metabolic profiles at screening and diagnosis, and blood Phe concentrations corresponding to dietary Phe intake from over 10 years of follow-up data for 204 children with HPA. To incorporate genetic information, allelic phenotype value (APV) was input for 2965 missense variants in the PAH gene using a predicted APV (pAPV) model. This model was trained on known pheno-genotype relationships from the BioPKU database, utilizing 31 features. Subsequently, a multiclass classification model was constructed and trained on a dataset featuring metabolic data, genetic data, and follow-up data from 3177 events. The final model was fine-tuned using tenfold validation and validated against three independent datasets.ResultsThe pAPV model achieved a good predictive performance with root mean squared error (RMSE) of 1.53 and 2.38 on the training and test datasets, respectively. The variants that cause amino acid changes in the region of 200–300 of PAH tend to exhibit lower pAPV. The final model achieved a sensitivity range of 0.77 to 0.91 and a specificity range of 0.8 to 1 across all validation datasets. Additional assessment metrics including positive predictive value (0.68–1), negative predictive values (0.8–0.98), F1 score (0.71–0.92), and balanced accuracy (0.8–0.92) demonstrated the robust performance of our model.ConclusionsOur model integrates metabolic and genetic information to accurately predict age-specific Phe tolerance, aiding in the precision management of patients with HPA. This study provides a potential framework that could be applied to other inborn errors of metabolism.

Methyl jasmonate induced tolerance effect of Pinus koraiensis to Bursaphelenchus xylophilus.

Methyl jasmonate (MeJA) can affect the balance of hormones and regulate the disease resistance of plants. Exploring the application and mechanism of MeJA in inducing the tolerance of Pinus koraiensis to pine wood nematode (PWN) infection is of great significance for developing new strategies for pine wilt disease control. Different concentrations (0.1, 1, 5 and 10 mm) of MeJA treatment groups showed differences in relative tolerance index and relative anti-nematode index of P. koraiensis seedlings to PWN infection. The treatment of 5 mm MeJA solution induced the best tolerance effect, followed by the 1 mm MeJA solution. Transcriptome analysis indicated that many plant defense-related genes upregulated after treatment with 1, 5 and 10 mm MeJA solutions. Among them, genes such as jasmonate ZIM domain-containing protein, phenylalanine ammonia-lyase and peroxidase also continuously upregulated after PWN infection. Metabolome analysis indicated that jasmonic acid (JA) was significantly increased at 7 days postinoculation with PWN, and after treatment with both 1 and 5 mm MeJA solutions. Integrated analysis of transcriptome and metabolome indicated that differences in JA accumulation might lead to ubiquitin-mediated proteolysis, and expression changes in trans-caffeic acid and trans-cinnamic acid-related genes, leading to the abundance differences of these two metabolisms and the formation of multiple lignin and glucosides. MeJA treatment could activate the expression of defense-related genes that correlated with JA, regulate the abundance of defense-related secondary metabolites, and improve the tolerance of P. koraiensis seedlings to PWN infection. © 2024 Society of Chemical Industry.

Study the implication of different SiO2/Al2O3 ratios on the pore size and acidity of Beta zeolite and its catalytic pyrolysis mechanism of Kraft lignin

This study employed a one-step synthesis method to prepare Beta zeolites (BZs) with various SiO2/Al2O3 ratios and applied them as catalysts in the process of producing bio-oil from Kraft lignin (KL). The research investigated the changes in acidity and pore size of BZs under different SiO2/Al2O3 ratios and their impact on the catalytic pyrolysis products of KL. Characterization and a series of physicochemical analyses of BZ with different SiO2/Al2O3 ratios as well as catalytic pyrolysis products were carried out. The Pearson correlation coefficient was also used to correlate BZ SiO2/Al2O3 ratios and the acidity/pore size of BZ as well as the distribution of the products and the deoxygenation effect. The results indicate that BZs with different SiO2/Al2O3 ratios can effectively catalyze the upgrading of KL during pyrolysis. BZ with SiO2/Al2O3 ratios of 45 exhibited stronger acidity, a more prominent layered porous structure, and a more orderly distribution of mesopores. It showed the best catalytic upgrading effect on KL, achieving a product yield of 58.4 %. More prominently, the oxygen content is reduced to 14.19 % and the deoxygenation extent of the heavy oil reached 37.1 %.

Genomic surveillance of SARS-CoV-2 in Russia: insights from the VGARus platform

Introduction. In response to the COVID-19 pandemic in the Russian Federation, comprehensive response measures were taken. One of these measures was the development of a viral genome aggregation platform (VGARus) to monitor virus variability. The aim of this paper is to describe the role of the VGARus platform in tracking genetic variation in SARS-CoV-2. Materials and methods. VGARus utilizes sequencing data and bioinformatics tools to monitor genetic variations in SARS-CoV-2. The viral genomes were aligned using NextClade, which also translated them into amino acids and identified mutations. The viral variability over time was analyzed by counting the number of amino acid changes compared to the reference sequence. Results. The analysis of data within VGARus enabled the identification of new virus variants, contributing to improved diagnostic tests and vaccine development. The platform allowed for the prediction of epidemiologic trends, facilitating a rapid response to changes in the epidemiologic situation. For example, using VGARus, an increase in COVID-19 incidence was accurately predicted in the summer of 2022 and early 2023, which were associated with the emergence of Omicron subvariants BA.5 and XBB. Data from the platform helps validate the effectiveness of primers and DNA probes to ensure high diagnostic accuracy and reduce the risk of false negatives. Conclusion. VGARus demonstrates the growing role of genomic surveillance in combating COVID-19 and improving preparedness for future infectious disease outbreaks. The platform is a powerful tool for generating evidence-based solutions to combat a pandemic and mitigate its health, economic and societal impacts. It provides the ability to promptly obtain information on the epidemiologic situation in a particular region of the Russian Federation, use genomic data for phylogenetic analysis, compare the mutational spectrum of SARS-CoV-2 sequences with foreign samples. VGARus data allow for both retrospective analysis and predictive hypotheses. For example, we can clearly see the dynamics of the change of different virus variants: sequences belonging to the Alpha, Beta, Delta, Omicron lineages and many less common ones, clearly form the upsurges of morbidity, the interaction of which is reflected in the epidemiological picture. It is also currently being expanded to monitor other pathogens, increasing its public health relevance.

SARS-CoV-2 Genotyping Highlights the Challenges in Spike Protein Drift Independent of Other Essential Proteins.

As of 2024, SARS-CoV-2 continues to propagate and drift as an endemic virus, impacting healthcare for years. The largest sequencing initiative for any species was initiated to combat the virus, tracking changes over time at a full virus base-pair resolution. The SARS-CoV-2 sequencing represents a unique opportunity to understand selective pressures and viral evolution but requires cross-disciplinary approaches from epidemiology to functional protein biology. Within this work, we integrate a two-year genotyping window with structural biology to explore the selective pressures of SARS-CoV-2 on protein insights. Although genotype and the Spike (Surface Glycoprotein) protein continue to drift, most SARS-CoV-2 proteins have had few amino acid alterations. Within Spike, the high drift rate of amino acids involved in antibody evasion also corresponds to changes within the ACE2 binding pocket that have undergone multiple changes that maintain functional binding. The genotyping suggests selective pressure for receptor specificity that could also confer changes in viral risk. Mapping of amino acid changes to the structures of the SARS-CoV-2 co-transcriptional complex (nsp7-nsp14), nsp3 (papain-like protease), and nsp5 (cysteine protease) proteins suggest they remain critical factors for drug development that will be sustainable, unlike those strategies targeting Spike.

Map-based cloning of LPD, a major gene positively regulates leaf prickle development in eggplant.

A critical gene for leaf prickle development (LPD) in eggplant was mapped on chromosome E06 and was confirmed to be SmARF10B through RNA interference using a new genetic transformation technique called SACI developed in this study Prickles on eggplant pose challenges for agriculture and are undesirable in cultivated varieties. This study aimed to uncover the genetic mechanisms behind prickle formation in eggplant. Using the F2 and F2:3 populations derived from a cross between the prickly wild eggplant, YQ, and the prickle-free cultivated variety, YZQ, we identified a key genetic locus (LPD, leaf prickle development) on chromosome E06 associated with leaf prickle development through BSA-seq and QTL mapping. An auxin response factor gene, SmARF10B, was predicted as the candidate gene as it exhibited high expression in YQ's mature leaves, while being significantly low in YZQ. Downregulating SmARF10B in YQ through RNAi using a simple and efficient Agrobacterium-mediated genetic transformation method named Seedling Apical Cut Infection (SACI) developed in this study substantially reduced the size and density of leaf prickles, confirming the role of this gene in prickle development. Besides, an effective SNP was identified in SmARF10B, resulting in an amino acid change between YQ and YZQ. However, this SNP did not consistently correlate with prickle formation in eight other eggplant materials examined. This study sheds light on the pivotal role of SmARF10B in eggplant prickle development and introduces a new genetic transformation method for eggplant, paving the way for future research in this field.

INTRA- AND INTER-HOST EVOLUTION OF HUMAN NOROVIRUS IN HEALTHY ADULTS.

Human noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults. We used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method. Complete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes. These data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.

Comprehensive modulatory effects of whole grain consumption on immune-mediated inflammation in middle-aged and elderly community residents: A real-world randomized controlled trial

Background and aimsWhole grain consumption is widely recognized as a vital component of a balanced diet. Dietary fiber has been well-documented to play a crucial role in these health benefits attributed to whole grain intake. However, population-based evidence directly linking whole grain consumption to anti-inflammatory effects, especially in the context of immune-mediated inflammation, remains limited. We hypothesized that whole grain consumption promotes health by modulating immune-mediated inflammation. Methods and resultsThis study was designed as a real-world, population-based randomized controlled trial. We compared the effects of whole grain versus refined grain consumption on immune-mediated inflammation through staple food substitution, while participants maintained their usual dietary practices. The results demonstrated that whole grain consumption significantly reduced circulating levels of pro-inflammatory cytokines IL-22 and IL-23 compared to refined grain consumption. These reductions were associated with optimized short-chain fatty acid profiles and changes in CD4+ T cell subset distributions. ConclusionsThe findings suggest that the anti-inflammatory effects of whole grain consumption in middle-aged and elderly populations are mediated by targeting specific CD4+ T cell subsets, in addition to modulating both upstream short-chain fatty acid composition and downstream expression of the pro-inflammatory cytokines IL-22 and IL-23.

Plasmodium berghei HMGB1 controls the host immune responses and splenic clearance by regulating the expression of pir genes

High mobility group box (HMGB) proteins belong to high mobility group (HMG) superfamily of non-histone nuclear proteins that are involved in chromatin remodeling, regulation of gene expression and DNA repair. When extracellular, HMGBs serve as alarmins inducing inflammation and this is attributed to the proinflammatory activity of box B. Here, we show that Plasmodium HMGB1 has key amino acid changes in box B resulting in the loss of TNF-α stimulatory activity. Site-directed mutagenesis of the critical amino acids in box B with respect to mouse HMGB1 renders recombinant Plasmodium berghei (Pb) HMGB1 capable of inducing TNF-α release. Targeted deletion of PbHMGB1 and a detailed in vivo phenotyping show that PbHMGB1 knockout (KO) parasites can undergo asexual stage development. Interestingly, Balb/c mice-infected with PbHMGB1KO parasites display a protective phenotype with subsequent clearance of blood parasitemia, and develop long-lasting protective immunity against the challenges performed with Pb wildtype parasites. The characterization of splenic responses show prominent germinal centres leading to effective humoral responses and enhanced T follicular helper cells. There is also a complete protection from experimental cerebral malaria in CBA/CaJ mice susceptible for cerebral pathogenesis with subsequent parasite clearance. Transcriptomic studies suggest the involvement of PbHMGB1 in pir expression. Our findings highlight the gene regulatory function of parasite HMGB1 and its in vivo significance in modulating the host immune responses. Further, clearance of asexual stages in PbHMGB1KO-infected mice underscores the important role of parasite HMGB1 in host immune evasion. These findings have implications in developing attenuated blood-stage vaccine for malaria.

Construction of amino acids reduced alphabets from molecular descriptors for interpretation of N-carbamylase, luciferase and PI3K mutations

The classification of amino acids has proven to be a useful tool for understanding the importance of sequence in protein function. The reduced amino acid alphabets are an example of these classifications, which, when built from physicochemical, structural and quantum characteristics of the amino acids, allow it to simplify the representation of the sequences, being useful in the modelling, design and understanding of proteins. So, an objective selection of amino acids properties is important, due classes formed in a reduced alphabet depend on the descriptors used for classification. In this research, based on a careful selection of descriptors for the 20 amino acids, through techniques such as the information content index and hierarchical cluster analysis with ties in proximity, 20,871,586 reduced amino acid alphabets were constructed. This large collection of reduced alphabets was been used to interpret alterations in the function of three proteins: N-carbamylase, Luciferase, and PI3K, caused by amino acid changes in their sequences. For this, the similar and different descriptors linked to these mutations were studied. Properties such as volume, hydrophobicity, charge and autocorrelation can be associated with variations in the behaviour of these proteins, while the frequency in specific secondary structures, the Gibbs free energy and some topological and quantum properties can be considered as the causes of preventing the deactivation of protein function. This work offers the most complete collection of reduced alphabets that promise to be a useful tool for the interpretation of alterations caused by amino acid mutations in the protein sequence.

Infection‑associated bile acid disturbance contributes to macrophage activation in patients with cirrhosis.

Cirrhosis impairs macrophage function and disrupts bile acid homeostasis. Although bile acids affect macrophage function in patients with sepsis, whether and how the bile acid profile is changed by infection in patients with cirrhosis to modulate macrophage function remains unclear. The present study aimed to investigate the changes in the bile acid profile of patients with cirrhosis and infection and their effects on macrophage function. Serum was collected from 20 healthy subjects, 18 patients with cirrhosis and 39 patients with cirrhosis and infection. Bile acid profiles were detected using high‑performance liquid chromatography‑triple time‑of‑flight mass spectrometer. The association between bile acid changes and infection was analysed using receiver operating characteristic (ROC) curves. Infection‑altered bile acids were used in combination with lipopolysaccharides (LPS) to stimulate RAW264.7/THP‑1 cells in vitro. The migratory capacity was evaluated using wound healing and Transwell migration assays. The expression of Arg‑1, iNOS, IκBα, phosphorylated (p‑)IκBα and p65 was examined with western blotting and immunofluorescence, Tnfα, Il1b and Il6 mRNA was examined with RT‑qPCR, and CD86, CD163 and phagocytosis was measured with flow cytometry. The ROC curves showed that decreased hyodeoxycholic acid (HDCA) and deoxycholic acid (DCA) levels were associated with infection. HDCA or DCA combined with LPS enhanced the phagocytic and migratory ability of macrophages, accompanied by upregulation of iNOS and CD86 protein expression as well as Tnfα, Il1b, and Il6 mRNA expression. However, neither HDCA nor DCA alone showed an effect on these phenotypes. In addition, DCA and HDCA acted synergistically with LPS to increase the expression of p‑IκBα and the intranuclear migration of p65. Infection changed the bile acid profile in patients with cirrhosis, among which the reduction of DCA and HDCA associated most strongly with infection. HDCA and DCA enhanced the sensitivity of macrophage function loss to LPS stimulation. These findings suggested a potential role for monitoring the bile acid profile that could help manage patients with cirrhosis and infection.

Determination of solid-state acidity of lyophilized trehalose containing citrate, phosphate, and histidine buffers using UV/VIS diffuse reflectance and solid-state NMR spectroscopy

Changes in the protonation state of lyophilized proteins can impact structural integrity, chemical stability, and propensity to aggregate upon reconstitution. When a buffer is chosen, the freezing/drying process may result in dramatic changes in the protonation state of the protein due to ionization shift of the buffer. In order to determine whether protonation shifts are occurring, ionizable probes can be added to the formulation. Optical probes (dyes) have shown dramatic ionization changes in lyophilized products, but it is unclear whether the pH indicator is uniform throughout the matrix and whether the change in the pH indicator actually mirrors drug ionization changes. In solid-state NMR (SSNMR) spectroscopy, the chemical shift of the carbonyl carbon in carboxylic acids is very sensitive to the ionization state of the acid. Therefore, SSNMR can be used to measure ionization changes in a lyophilized matrix by employing a small quantity of an isotopically-labeled carboxylic acid species in the formulation. This paper compares the apparent pH of six trehalose-containing lyophilized buffer systems using SSNMR and UV-Vis diffuse reflectance spectroscopy (UVDRS). Both SSNMR and UVDRS results using two different ionization probes (butyric acid and bromocresol purple, respectively) showed little change in apparent acidity compared to the pre-lyophilized solution in a sodium citrate buffer, but a greater change was observed in potassium phosphate, sodium phosphate, and histidine buffers. While the trends between the two methods were similar, there were differences in the numerical values of equivalent pH (pHeq) observed between the two methods. The potential causes contributing to the differences are discussed.

Insight into critical water quality factors and gill function of large yellow croaker (Larimichthys crocea) during packaging bag transport

To investigate the effects of the interaction between water quality and gill function of large yellow croaker during transportation in packaging bags, a total of 186 large yellow croakers weighing 120.0 ± 28.0 g were randomly divided into two groups: a control group (tanks with a water treatment system to maintain normal water quality) and treatment groups subjected to simulated transport for 0, 6, 12, 18, and 24 hours at a temperature of 20°C. The results revealed that prolonging the transport duration (beyond 6 hours) caused significant changes in dissolved oxygen (DO), total ammonia nitrogen (TAN) and pH levels in the water. Beyond 6 hours of transport, gill tissue damage increased, and the histomorphological characteristics of the gills were altered. Regarding osmoregulation, the activities of Ca2+/Mg2+-ATPase and Na+/K+-ATPase were notably reduced in the treatment groups, indicating compromised osmoregulatory function of the gill tissue during transport. However, changes in lactic acid (LD) and lactate dehydrogenase (LDH) were not statistically significant, and fish did not experience hypoxia during packaging bag transport. In terms of antioxidant activity, the treatment groups exhibited significantly lower activities of catalase (CAT) and superoxide dismutase (SOD) after 24 hours, as well as increased malondialdehyde (MDA) content after 18 hours. This reduction in antioxidant capacity led to cellular membrane damage in the gill tissue. Furthermore, acid phosphatase (ACP) activity showed a notable decline from 12 hours onwards in immune indicators, while lysozyme (LZM) activity experienced a substantial decrease at 24 hours. Correlation analysis revealed a significant correlation between the osmoregulation, antioxidant capacity, and immune response of gill tissue with elevated TAN levels and reduced pH. In conclusion, the levels of TAN and pH experience notable alterations after 6 hours of transportation, which may lead to impairment of gill function in large yellow croakers. Hence, we advise limiting the transportation of large yellow croakers to less than 6 hours at 20°C.