A genomic association study revealing subphenotypes of childhood steroid-sensitive nephrotic syndrome in a larger genomic sequencing cohort.

Dissecting the genetic components that contribute to the two main subphenotypes of steroid-sensitive nephrotic syndrome (SSNS) using genome-wide association studies (GWAS) strategy is important for understanding the disease. We conducted a multicenter cohort study (360 patients and 1835 controls) combined with a GWAS strategy to identify susceptibility variants associated with the following two subphenotypes of SSNS: steroid-sensitive nephrotic syndrome without relapse (SSNSWR, 181 patients) and steroid-dependent/frequent relapse nephrotic syndrome (SDNS/FRNS, 179 patients). The distribution of two single-nucleotide polymorphisms (SNPs) in ANKRD36 and ALPG was significant between SSNSWR and healthy controls, and that of two SNPs in GAD1 and HLA-DQA1 was significant between SDNS/FRNS and healthy controls. Interestingly, rs1047989 in HLA-DQA1 was a candidate locus for SDNS/FRNS but not for SSNSWR. No significant SNPs were observed between SSNSWR and SDNS/FRNS. Meanwhile, chromosome 2:171713702 in GAD1 was associated with a greater steroid dose (>0.75 mg/kg/d) upon relapse to first remission in patients with SDNS/FRNS (odds ratio = 3.14; 95% confidence interval, 0.97-9.87; P = 0.034). rs117014418 in APOL4 was significantly associated with a decrease in eGFR of greater than 20% compared with the baseline in SDNS/FRNS patients (P = 0.0001). Protein-protein intersection network construction suggested that HLA-DQA1 and HLA-DQB1 function together through GSDMA. Thus, SSNSWR belongs to non-HLA region-dependent nephropathy, and the HLA-DQA/DQB region is likely strongly associated with disease relapse, especially in SDNS/FRNS. The study provides a novel approach for the GWAS strategy of SSNS and contributes to our understanding of the pathological mechanisms of SSNSWR and SDNS/FRNS.

Are children with IgA nephropathy different from adult patients?

BACKGROUND: Previously, several studies have indicated that pediatric IgA nephropathy (IgAN) might be different from adult IgAN, and treatment strategies might be also different between pediatric IgAN and adult IgAN. METHODS: We analyzed two prospective cohorts established by pediatric and adult nephrologists, respectively. A comprehensive analysis was performed investigating the difference in clinical and pathological characteristics, treatment, and prognosis between children and adults with IgAN. RESULTS: A total of 1015 children and 1911 adults with IgAN were eligible for analysis. More frequent gross hematuria (88% vs. 20%, p < 0.0001) and higher proteinuria (1.8 vs. 1.3 g/d, p < 0.0001) were seen in children compared to adults. In comparison, the estimated glomerular filtration rate (eGFR) was lower in adults (80.4 vs. 163 ml/min/1.73 m2, p < 0.0001). Hypertension was more prevalent in adult patients. Pathologically, a higher proportion of M1 was revealed (62% vs. 39%, p < 0.0001) in children than in adults. S1 (62% vs. 28%, p < 0.0001) and T1-2 (34% vs. 8%, p < 0.0001) were more frequent in adults. Adjusted by proteinuria, eGFR, and hypertension, children were more likely to be treated with glucocorticoids than adults (87% vs. 45%, p < 0.0001). After propensity score matching, in IgAN with proteinuria > 1 g/d, children treated with steroids were 1.87 (95% CI 1.16-3.02, p = 0.01) times more likely to reach complete remission of proteinuria compared with adults treated with steroids. CONCLUSIONS: Children present significantly differently from adults with IgAN in clinical and pathological manifestations and disease progression. Steroid response might be better in children.

Identification of novel pathogenic variants of CUBN in patients with isolated proteinuria.

BACKGROUND: Although proteinuria is long recognized as an independent risk factor for progressive chronic kidney diseases, not all forms of proteinuria are detrimental to kidney function, one of which is isolated proteinuria caused by cubilin (CUBN)-specific mutations. CUBN encodes an endocytic receptor, initially found to be responsible for the Imerslund-Gräsbeck syndrome (IGS; OMIM #261100) characterized by a combined phenotype of megaloblastic anemia and proteinuria. METHODS: After analyzing their clinical and pathological characterizations, next-generation sequencing for renal disease genes or whole-exome sequencing (WES) was performed on four patients with non-progressive isolated proteinuria. CUBN biallelic pathogenic variants were identified and further analyzed by cDNA-PCR sequencing, immunohistochemistry, minigene assay, and multiple in silico prediction tools, including 3D protein modeling. RESULTS: Here, we present four patients with isolated proteinuria caused by CUBN C-terminal biallelic pathogenic variants, all of which showed no typical IGS symptoms, such as anemia and vitamin B12 deficiency. Their urine protein levels fluctuated between +~++ and estimated glomerular filtration rate (eGFR) were normal or slightly higher. Mild mesangial hypercellularity was found in three children's renal biopsies. A homozygous splice-site variant of CUBN (c.6821+3 (IVS44) A>G) was proven to result in the exon 44 skipping and premature translation termination by cDNA sequencing and immunohistochemistry. Compound heterozygous mutations were identified among the other three children, including another novel splice-site variant (c.10764+1 (IVS66) G>A) causing the retention of first 4 nucleotides in intron 66 by minigene assay, two unreported missense mutations (c.4907G>A (p.R1636Q); c. 9095 A>G (p.Y3032C)), and two reported missense mutations in China (c.8938G>A (p.D2980N); c. 9287T>C (p.L3096P)), locating behind the vitamin B12-binding domain, affecting CUB11, CUB16, CUB22, CUB23, and CUB27 domains, respectively. CONCLUSION: These results demonstrate that above CUBN mutations may cause non-progressive and isolated proteinuria, expanding the variant spectrum of CUBN and benefiting our understanding of proteinuria and renal function.

Three-way decisions in generalized intuitionistic fuzzy environments: survey and challenges.

Enhancing decision-making under risks is crucial in various fields, and three-way decision (3WD) methods have been extensively utilized and proven to be effective in numerous scenarios. However, traditional methods may not be sufficient when addressing intricate decision-making scenarios characterized by uncertain and ambiguous information. In response to this challenge, the generalized intuitionistic fuzzy set (IFS) theory extends the conventional fuzzy set theory by introducing two pivotal concepts, i.e., membership degrees and non-membership degrees. These concepts offer a more comprehensive means of portraying the relationship between elements and fuzzy concepts, thereby boosting the ability to model complex problems. The generalized IFS theory brings about heightened flexibility and precision in problem-solving, allowing for a more thorough and accurate description of intricate phenomena. Consequently, the generalized IFS theory emerges as a more refined tool for articulating fuzzy phenomena. The paper offers a thorough review of the research advancements made in 3WD methods within the context of generalized intuitionistic fuzzy (IF) environments. First, the paper summarizes fundamental aspects of 3WD methods and the IFS theory. Second, the paper discusses the latest development trends, including the application of these methods in new fields and the development of new hybrid methods. Furthermore, the paper analyzes the strengths and weaknesses of research methods employed in recent years. While these methods have yielded impressive outcomes in decision-making, there are still some limitations and challenges that need to be addressed. Finally, the paper proposes key challenges and future research directions. Overall, the paper offers a comprehensive and insightful review of the latest research progress on 3WD methods in generalized IF environments, which can provide guidance for scholars and engineers in the intelligent decision-making field with situations characterized by various uncertainties.

A novel pathogenic variant c.262delA in PBX1 causing oligomeganephronia identified using whole-exome sequencing and a literature review.

Oligomeganephronia (OMN) is a rare congenital renal hypoplasia reported more often in children than in adults. The diagnosis of OMN relies on renal biopsy and exhibits a significant reduction in the number of glomeruli and pronounced glomerular hypertrophy. Here, we report the case of an 8-year-old boy with recurrent proteinuria and abnormal external ears. A renal biopsy revealed large and rare glomeruli. The histological findings confirmed the diagnosis of OMN. Whole-exome sequencing of the patient revealed a new pathogenic variant in PBX1 (hg19, NM_002585, c.262delA, p.Thr88Glnfs*3). The PBX1 gene encodes a transcription factor whose pathogenic variants can result in congenital renal and urinary system anomalies, with or without hearing loss, abnormal ears, and developmental retardation (CAKUTED). This is the first report to detect PBX1 pathogenic variants in children with OMN, a novel phenotype of human PBX1 pathogenic variants. We performed functional prediction analyses of deletions in the corresponding structural domains. We summarized 27 cases of PBX1 single pathogenic variants reported between 2003 and 2023 in terms of truncating and missense pathogenic variants, which can deepen our understanding of the PBX1 structural domain and expand our knowledge of the PBX1 genotype and phenotype.

High Production of γ-Aminobutyric Acid by Activating the xyl Operon of Lactobacillus brevis.

γ-Aminobutyric acid (GABA) is an inhibitory neurotransmitter with important physiological functions such as sleep assistance and anti-depression. In this study, we developed a fermentation process for the high-efficiency production of GABA by Lactobacillus brevis (Lb. brevis) CE701. First, xylose was found as the optimal carbon source that could improve the GABA production and OD600 in shake flasks to 40.35 g/L and 8.64, respectively, which were 1.78-fold and 1.67-fold of the glucose. Subsequently, the analysis of the carbon source metabolic pathway indicated that xylose activated the expression of the xyl operon, and xylose metabolism produced more ATP and organic acids than glucose, which significantly promoted the growth and GABA production of Lb. brevis CE701. Then, an efficient GABA fermentation process was developed by optimizing the medium components using response surface methodology. Finally, the production of GABA reached 176.04 g/L in a 5 L fermenter, which was 336% higher than that in a shake flask. This work enables the efficient synthesis of GABA using xylose, which will provide guidance for the industrial production of GABA.

Psychological research of the children with chronic kidney disease and their guardians during the COVID-19 pandemic.

Background: There is great mental stress due to the coronavirus disease 2019 (COVID-19) pandemic. However, there are no detailed psychological studies of the children with chronic kidney disease (CKD) and their guardians during the COVID-19 pandemic. Objective: This study explores the psychological pressure on children with CKD and their guardians. Methods: An online survey was conducted at 20 of the largest pediatric nephropathy departments in China, including the Rutter Parent Questionnaire, Self-rating Anxiety Scale (SAS), and Self-rating Depression Scale (SDS). Overall, 885 children (589 children with CKD associated with 296 children of the control group) completed the survey together with their guardians. Results: There was no statistical difference between CKD children and control children regarding their Rutter behavior scores and abnormal behaviors. Nevertheless, the abnormal behavior of children might aggravate the anxiety and depression of guardians in both CKD and control groups (p < 0.05). We confirmed that the anxiety and depression of guardians in the CKD group were both significantly higher than those in the control group (p < 0.05). The guardians in the CKD group with lower annual income were more likely to experience anxiety (p < 0.05). Furthermore, the guardians whose children were older than 11 years old might be more anxious than those who were 6-11 years old. Besides, the guardians in the CKD group who watched the news for 30-60 min daily were less likely to have depression than those who watched < 10 min (p < 0.05). The subgroup results showed that the gender, the time of watching the news, the annual income of guardians, and children's age might be the most critical factors influencing guardians' psychological burden. Conclusion: The guardians in the CKD group have more severe anxiety and depression during the pandemic. The children's abnormal behavior, adolescents' pressure, low household income, and the panic about the pandemic may be the main reasons for the anxiety and depression of guardians.

Genetic testing enables a precision medicine approach for nephrolithiasis and nephrocalcinosis in pediatrics: a single-center cohort.

OBJECTIVE: Hereditary factors are the main cause of pediatric nephrolithiasis (NL)/nephrocalcinosis (NC). We summarized the genotype-phenotype correlation of hereditary NL/NC in our center, to evaluate the role of genetic testing in early diagnosis. METHODS: The clinical data of 32 NL/NC cases, which were suspected to have an inherited basis, were retrospectively analyzed from May 2017 to August 2020. The trio-whole exome sequencing was used as the main approach for genetic testing, variants were confirmed by Sanger sequencing, and pathogenicity analysis according to protein function was predicted with custom-developed software. RESULTS: Causative monogenic mutations were detected in 24 of 32 NL/NC patients, and copy number variation was detected in one patient. A summary of manifestations in patients with inherited diseases revealed a significant degree of growth retardation, increased urinary excretion of the low-molecular weight protein, hypercalciuria, electrolyte imbalances, and young age of onset to be common in heredity disease. In addition, some patients had abnormal renal function (3 ppm 25). The most frequent pathology identified was distal renal tubular acidosis (with inclusion of SLC4A1, ATP6V1B1, and ATP6VOA4 genes), followed by Dent disease (CLCN5 and OCRL1 genes), primary hyperoxaluria (PH) (AGXT and HOGA1 genes) and Kabuki syndrome (KMT2D gene), which was more likely to present as NC or recurrent stone and having a higher correlation with a specific biochemical phenotype and extrarenal phenotype. CONCLUSION: The etiology of NL/NC is heterogeneous. This study explored in depth the relationship between phenotype and genotype in 32 patients, and confirmed that genetic testing and clinical phenotype evaluation enable the precision medicine approach to treating patients.

Rational design of 17ß-hydroxysteroid dehydrogenase type3 for improving testosterone production with an engineered Pichia pastoris.

Testosterone (TS) is a critical androgenic steroid that regulates human metabolism and maintains secondary sexual characteristics. The biotransformation from 4-androstene-3,17-done (4-AD) to TS is limited by the poor catalytic activity of 17ß-hydroxysteroid dehydrogenase type 3 (17ß-HSD3). Herein, we explored the structural characteristics and catalytic mechanism of 17ß-HSD3 and adopted the rational design strategy to improve its catalytic activity. Molecular docking and molecular dynamics simulations revealed the substrate-binding pocket and the binding mode of 4-AD to 17ß-HSD3. We located the pivotal residues and regulated their hydrophobicity and polarity. The obtained G186R/Y195W variant formed additional electrostatic interaction and hydrogen bond with 4-AD, increasing the binding affinity between the variant and 4-AD. Therefore, the G186R/Y195W variant produced 3.98 g/L of TS, which increased to 297%. The combination of structural and mechanism resolution drives the implementation of the rational design strategy, which provides guidance for bioproduction of TS catalyzed by 17ß-HSD3.

Bifunctional utilization of whey powder as a substrate and inducer for ß-farnesene production in an engineered Escherichia coli.

ß-Farnesene can replace petroleum products as specialty fuel to solve the global fuel energy crisis, but its production by Escherichia coli (E.coli) using glucose and isopropyl ß-D-1-thiogalactopyranoside (IPTG) is costly. Hence, we developed a new strategy to produce ß-farnesene by engineered E.coli strain F13 with bifunctional utilization of whey powder. The utilization of whey powder as a substrate ensured the growth of the strain F13, while whey powder could also replace IPTG to induce the production of ß-farnesene. In shake flasks, ß-farnesene production reached 2.41 g/L by the bifunctional utilization of whey powder as a substrate and inducer, 65.1% higher than that with IPTG and glucose. In the 7 L bioreactor, ß-farnesene production reached 4.74 g/L using whey powder, which was 197% of that in shake flasks. Therefore, this new strategy might be an attractive route to broaden the applications of whey powder and achieve the economical production of ß-farnesene.

Detection of Nocardia by 16S Ribosomal RNA Gene PCR and Metagenomic Next-Generation Sequencing (mNGS).

In this study, the aim was to investigate the discriminatory power of molecular diagnostics based on mNGS and traditional 16S ribosomal RNA PCR among Nocardia species. A total of fourteen clinical isolates from patients with positive Nocardia cultures and clinical evidence were included between January 2017 and June 2020 in HeNan Provincial People's Hospital. DNA extraction and 16S rRNA PCR were performed on positive cultures, and pathogens were detected by mNGS in these same samples directly. Among the 14 Nocardia isolates, four species were identified, and N. cyriacigeorgica (8 cases) is the most common species. Twelve of the 14 Nocardia spp. isolates were identified by the two methods, while two strains of N. cyriacigeorgica were not identified by mNGS. All tested isolates showed susceptibility to trimethoprim-sulfamethoxazole (SXT), amikacin and linezolid. Apart from Nocardia species, other pathogens such as Acinetobacter baumannii, Klebsiella pneumonia, Aspergillus, Enterococcus faecalis, Human herpesvirus, etc., were detected from the same clinical samples by mNGS. However, these different pathogens were considered as colonization or contamination. We found that it is essential to accurately identify species for determining antibiotic sensitivity and, consequently, choosing antibiotic treatment. 16S rRNA PCR was useful for identification of nocardial infection among species, while this technique needs the clinicians to make the pre-considerations of nocardiosis. However, mNGS may be a putative tool for rapid and accurate detection and identification of Nocardia, beneficial for applications of antimicrobial drugs and timely adjustments of medication.

Increased CO2 and light intensity regulate growth and leaf gas exchange in tomato.

Carbon dioxide concentration (CO2 ) and light intensity are known to play important roles in plant growth and carbon assimilation. Nevertheless, the underlying physiological mechanisms have not yet been fully explored. Tomato seedlings (Solanum lycopersicum Mill. cv. Jingpeng No. 1) were exposed to two levels of CO2 and three levels of light intensity and the effects on growth, leaf gas exchange and water use efficiency were investigated. Elevated CO2 and increased light intensity promoted growth, dry matter accumulation and pigment concentration and together the seedling health index. Elevated CO2 had no significant effect on leaf nitrogen content but did significantly upregulate Calvin cycle enzyme activity. Increased CO2 and light intensity promoted photosynthesis, both on a leaf-area basis and on a chlorophyll basis. Increased CO2 also increased light-saturated maximum photosynthetic rate, apparent quantum efficiency and carboxylation efficiency and, together with increased light intensity, it raised photosynthetic capacity. However, increased CO2 reduced transpiration and water consumption across different levels of light intensity, thus significantly increasing both leaf-level and plant-level water use efficiency. Among the range of treatments imposed, the combination of increased CO2 (800 µmol CO2 mol-1 ) and high light intensity (400 µmol m-2 s-1 ) resulted in optimal growth and carbon assimilation. We conclude that the combination of increased CO2 and increased light intensity worked synergistically to promote growth, photosynthetic capacity and water use efficiency by upregulation of pigment concentration, Calvin cycle enzyme activity, light energy use and CO2 fixation. Increased CO2 also lowered transpiration and hence water usage.

Comparative Transcriptome Analysis of Gene Expression Patterns in Tomato Under Dynamic Light Conditions.

Plants grown under highly variable natural light regimes differ strongly from plants grown under constant light (CL) regimes. Plant phenotype and adaptation responses are important for plant biomass and fitness. However, the underlying regulatory mechanisms are still poorly understood, particularly from a transcriptional perspective. To investigate the influence of different light regimes on tomato plants, three dynamic light (DL) regimes were designed, using a CL regime as control. Morphological, photosynthetic, and transcriptional differences after five weeks of treatment were compared. Leaf area, plant height, shoot /root weight, total chlorophyll content, photosynthetic rate, and stomatal conductance all significantly decreased in response to DL regimes. The biggest expression difference was found between the treatment with the highest light intensity at the middle of the day with a total of 1080 significantly up-/down-regulated genes. A total of 177 common differentially expressed genes were identified between DL and CL conditions. Finally, significant differences were observed in the levels of gene expression between DL and CL treatments in multiple pathways, predominantly of plant-pathogen interactions, plant hormone signal transductions, metabolites, and photosynthesis. These results expand the understanding of plant development and photosynthetic regulations under DL conditions by multiple pathways.

Extra metabolic burden by displaying over secreting: Growth, fermentation and enzymatic activity in cellobiose of recombinant yeast expressing ß-glucosidase.

ß-Glucosidase was selected to be a reporter to study metabolic burden imposed by its expression in yeast. Cell growth, fermentation yield and enzymatic activity were used as indicators of the metabolic burden borne by 14 recombinant yeast strains. Various factors were found to affect metabolic burden, including BGLI gene source, gene dose, trafficking of the enzyme (either cell-surface display or secretion), and oxygen supply. While BGLI gene from Aspergillus aculeatus provided better performance for the host cells than that from Saccharomycopsis fibuligera, displaying ß-glucosidase on the cell surface generally led to lower µm, total activity and ethanol titer, and longer lag period, lower (aerobic condition) or higher (anaerobic condition) biomass yield than that of secreting ß-glucosidase. The negative effect on growth increased with gene dose level until a final failure to grow. This growth difference implies that displaying ß-glucosidase on the cell surface imposes an extra metabolic burden. The molecular basis and mechanisms for this phenomenon need to further be investigated in order to develop better strategies for utilizing displayed and secreted enzymes in biotechnology and yeast breeding.

A simply enzymatic hydrolysis pretreatment for ß-mannanase production from konjac powder.

Currently, the traditional fermentation using konjac powder for ß-mannanase production presents operational difficulties and high energy consumption, because of the individual hot air sterilization for konjac powder. A simply enzymatic hydrolysis pretreatment for konjac powder was developed to solve the problems of the traditional process in a 7-L fermenter. In the new process, when hydrolysis yield of konjac powder was above 50%, the media became liquid state from gelatinous state and could be sterilized immediately, avoiding the hot air sterilization and solving the operational difficulties. Interestingly, the new process didn't have negative influence on ß-mannanase production. Additionally, it could save close to 23% of power consumption during the whole fermentation. For another example, it did work well using locust bean gum for ß-mannanase production in a 7-L fermenter. Therefore, the new process might be scaled up for industrial production using mannan-based bioresource as substrate.

Optimized generation of survivin-specific cytotoxic T lymphocytes against lung cancer.

Cancer immunotherapy based on dendritic cells (DCs) that target survivin is a promising strategy with potential clinical applications. However, the translation of survivin-specific cytotoxic T-lymphocyte (CTL) immunotherapy into the clinical setting has numerous challenges, including the low efficiency of the treatment. The present study aimed to improve the efficiency of the treatment, and found that treatment with interleukin 4 (IL-4)/granulocyte macrophage colony-stimulating factor (GM-CSF) and a combination of proinflammatory cytokines significantly increased the antigen-presenting and -capture abilities of DCs that expressed exogenous survivin. Furthermore, lipopolysaccharide (LPS) stimulation enhanced the DC response to subsequent T-cell signals and the extent of T-cell activation. In addition, the efficiency of surviving-specific CTLs was examined, and high cytotoxicity against surviving-expressing A549 lung cancer cells was observed. However, the cytotoxicity of CTLs was significantly reduced in A549 cells with silenced survivin expression. The present study provides a novel method to optimize the generation of surviving-specific CTLs against lung cancer cells, which may advance the translation of surviving-specific CTL immunotherapy into clinical use for the treatment of cancer.