Novel variants in PDE6A and PDE6B genes and its phenotypes in patients with retinitis pigmentosa in Chinese families

Background Retinitis pigmentosa (RP) is a genetically heterogeneous disease with 89 causative genes identified to date. However, only approximately 60% of RP cases genetically solved to date, predicating that many novel disease-causing variants are yet to be identified. The purpose of this study is to identify novel variants in PDE6A and PDE6B genes and present its phenotypes in patients with retinitis pigmentosa in Chinese families. Methods Five retinitis pigmentosa patients with PDE6A variants and three with PDE6B variants were identified through a hereditary eye disease enrichment panel (HEDEP), all patients’ medical and ophthalmic histories were collected, and ophthalmological examinations were performed, followed by an analysis of the possible causative variants. Sanger sequencing was used to verify the variants. Results We identified 20 variants in eight patients: 16 of them were identified in either PDE6A or PDE6B in a compound heterozygous state. Additional four heterozygous variants were identified in the genes ADGRA3, CA4, OPTN, RHO. Two novel genetic changes in PDE6A were identified (c.1246G > A and c.1747 T > A), three novel genetic changes in PDE6B were identified (c.401 T > C, c.2293G > C and c.1610-1612del), out of the novel identified variants one was most probably non-pathogenic (c.2293G > C), all other novel variants are pathogenic. Additional variant was identified in CA4 and RHO, which can cause ADRP (c.243G > A, c.688G > A). In addition, a novel variant in ADGRA3 was identified (c.921-1G > A). Conclusions This study reveals novel and known variants in PDE6A and PDE6B genes in Chinese families with autosomal recessive RP, and expands the clinical and genetic findings of photoreceptor-specific enzyme deficiencies.

One-Pot Ionic Liquid-Mediated Bioprocess for Pretreatment and Enzymatic Hydrolysis of Rice Straw with Ionic Liquid-Tolerance Bacterial Cellulase

Ionic liquid (IL) pretreatment of lignocellulose is an efficient method for the enhancement of enzymatic saccharification. However, the remaining residues of ILs deactivate cellulase, therefore making intensive biomass washing after pretreatment necessary. This study aimed to develop the one-pot process combining IL pretreatment and enzymatic saccharification by using low-toxic choline acetate ([Ch][OAc]) and IL-tolerant bacterial cellulases. Crude cellulases produced from saline soil inhabited Bacillus sp. CBD2 and Brevibacillus sp. CBD3 were tested under the influence of 0.5–2.0 M [Ch][OAc], which showed that their activities retained at more than 95%. However, [Ch][OAc] had toxicity to CBD2 and CBD3 cultures, in which only 32.85% and 12.88% were alive at 0.5 M [Ch][OAc]. Based on the specific enzyme activities, the sugar amounts produced from one-pot processes using 1 mg of CBD2 and CBD3 were higher than that of Celluclast 1.5 L by 2.0 and 4.5 times, respectively, suggesting their potential for further application in the biorefining process of value-added products.

Genetic variation of CAST gene in Local Karnobat and Karnobat merino sheep breeds

Karnobat sheep plays an important role in the development of sheep breeding in Southeastern region of Bulgaria. They are valuable source of genetic material. The aim of present experiment was to determine the allele variation of CAST gene in Local Karnobat and Karnobat Merino sheep breeds. A total of 60 blood samples were collected – 30 per breed. DNA was extracted and genotypes of all animals were identified by means of PCR-RFLP technique. The restriction reactions were accomplished by specific enzyme MspI. As expected both breeds were characterized with low level of genetic diversity due to the fact that mostly maintaining selection has been implemented. In Local Karnobat sheep breed was identified only one heterozygous individual from all 30. In Karnobat merino were identified allele M with frequency 0,97 and allele N with frequency 0,03. Genotypes MM and MN were revealed with frequencies 0,93 and 0,07, respectively. According to the statistical analysis both breeds were in HWE equilibrium.

Saturation mutagenesis at Ser196 in BaCsn46A from Bacillus Amyloliquefaciens Enhances Enzyme Activity and Thermostability

The chitosanase (BaCsn46A) was extracted from Bacillus amyloliquefaciens (GenBank: QEK97559.1) and synthesized after codon optimization. The saturation mutation site was determined by analyzing the sequence and three-dimensional protein model. WT and mutant chitosanase genes were cloned and expressed in E. coli BL21 (DE3). The enzymatic properties of WT and mutants were compared, including the optimal reaction pH, temperature and thermostability. Three mutants S196F, S196Y and S196A with the highest specific enzyme activity were selected for further study. Compared with WT, the specific enzyme activity of S196Y increased by 144.76% (more than other two mutants), and the thermostability was not significantly improved. While the specific enzyme activity of S196A increased by 118.79%, and the thermostability of S196A was much higher than WT. From the perspective of industrial production, S196A is more in line with the requirements of industrial production because of its excellent thermal stability at 60°C. From the results of circular dichroism spectrum, the mutation of chitosanase at Ser196 did not change the secondary protein structure. In addition, CD analysis showed that the secondary structure of WT and mutants did not change significantly, indicating that the improvement of thermostability of S196A was not related to the secondary structure.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.

Myo-Inositol Oxygenase as a Predictor of Acute Kidney Injury in Critically ill Patients

Background Acute kidney injury (AKI) affects 45% of critically ill patients, resulting in increased morbidity and mortality. The diagnostic standard, plasma creatinine, is nonspecific and may not increase until days after injury. Aim of the work to assess myo inositol oxygenase as noval marker in early detection of acute kidney injury critically ill patients. Patients and Methods In this prospective study, 40 critically ill patients were followed up in ICU up regarding development of Aki in ICU according to KDIGO definition. They were categorized into two subgroups; 20 patients developed AKI in and 20 patients who did not develop AKI. In addition, a control group of 20 individuals in Ain Shams Hospital during the period from 2018 to 2019, we did myoinositol oxygenase level test at time of admission and repeated in patients group which develop AKI within 24-48 hours. Results MIOX for the diagnosis of AKI When the cut-off value was taken as above 800, the diagnostic sensitivity and specificity of MIOX for AKI were 100%). For creatinine, at the cut-off value of above 0.9, the sensitivity for AKI were found 90% and specificity for AKI were found 65%. Conclusion The measurement of serum MIOX is valuable for the diagnosis of AKI. Further research is needed for the evaluation of the potential use of MIOX as a kidney-specific enzyme in the early diagnosis of AKI.

Seroprevalence of Equine Herpesvirus 1 (EHV-1) and Equine Herpesvirus 4 (EHV-4) in the Northern Moroccan Horse Populations

This study reports the first equine herpesvirus-1 (EHV-1) and equine herpesvirus-4 (EHV-4) seroprevalence investigation in horse populations of Morocco in 24 years. It also aims to determine antibody titers in horses vaccinated under field conditions with a monovalent EHV-1 vaccine. Blood samples were collected from 405 horses, including 163 unvaccinated and 242 vaccinated animals. They were tested using a commercial type-specific enzyme-linked immunosorbent assay (ELISA) and a virus neutralization test (VNT). Overall, 12.8% unvaccinated, and 21.8% vaccinated horses were positive for EHV-1. All samples were positive for EHV-4 when tested with the type-specific ELISA. In the vaccinated group, the VNT revealed a mean antibody titer of 1:49 for EHV-1 and 1:45 for EHV-4.

Microspectroscopic visualization of how biochar elevates the soil organic carbon ceiling

The soil carbon saturation concept suggests an upper limit to store soil organic carbon (SOC), set by the mechanisms that protect soil organic matter from decomposition. Biochar has the capacity to protect new C including rhizodeposits and microbial necromass. However, the decadal scale mechanisms by which biochar influences the molecular diversity, spatial heterogeneity, and temporal changes of SOC persistence remain unresolved. Here we show that the soil C saturation ceiling of a Ferralsol under subtropical pasture could be elevated by 2 Mg (new) C ha-1 by the application of Eucalyptus saligna biochar 8.2 years after the first application. Using one, two-, and three-dimensional analyses, significant increases were observed in the spatial distribution of root-derived 13C in microaggregates (53-250 µm, 11 %) and new C protected in mineral fractions (<53 µm, 5 %). Microbial C-use efficiency was concomitantly improved by lowering specific enzyme activities, contributing to the decreased mineralization of native SOC by 18 %. We provide evidence that the global SOC ceiling can be elevated using biochar in Ferralsols by 0.01-0.1 Pg new C yr-1.