Unraveling the immunogenetic landscape of autism spectrum disorder: a comprehensive bioinformatics approach.

Background: Autism spectrum disorder (ASD) is a disease characterized by social disorder. Recently, the population affected by ASD has gradually increased around the world. There are great difficulties in diagnosis and treatment at present. Methods: The ASD datasets were obtained from the Gene Expression Omnibus database and the immune-relevant genes were downloaded from a previously published compilation. Subsequently, we used WGCNA to screen the modules related to the ASD and immune. We also choose the best combination and screen out the core genes from Consensus Machine Learning Driven Signatures (CMLS). Subsequently, we evaluated the genetic correlation between immune cells and ASD used GNOVA. And pleiotropic regions identified by PLACO and CPASSOC between ASD and immune cells. FUMA was used to identify pleiotropic regions, and expression trait loci (EQTL) analysis was used to determine their expression in different tissues and cells. Finally, we use qPCR to detect the gene expression level of the core gene. Results: We found a close relationship between neutrophils and ASD, and subsequently, CMLS identified a total of 47 potential candidate genes. Secondly, GNOVA showed a significant genetic correlation between neutrophils and ASD, and PLACO and CPASSOC identified a total of 14 pleiotropic regions. We annotated the 14 regions mentioned above and identified a total of 6 potential candidate genes. Through EQTL, we found that the CFLAR gene has a specific expression pattern in neutrophils, suggesting that it may serve as a potential biomarker for ASD and is closely related to its pathogenesis. Conclusions: In conclusion, our study yields unprecedented insights into the molecular and genetic heterogeneity of ASD through a comprehensive bioinformatics analysis. These valuable findings hold significant implications for tailoring personalized ASD therapies.

Enhancing the thermostability of phospholipase D from Streptomyces halstedii by directed evolution and elucidating the mechanism of a key amino acid residue using molecular dynamics simulation.

To enhance the thermostability of phospholipase D (PLD), error-prone polymerase chain reaction method was used to create mutants of PLD (PLDsh) from Streptomyces halstedii. One desirable mutant (S163F) with Ser to Phe substitution at position 163 was screened with high-throughput assay. S163F exhibited a 10 °C higher optimum temperature than wild-type (WT). Although WT exhibited almost no activity after incubating at 50 °C for 40 min, S163F still displayed 27% of its highest activity after incubating at 50 °C for 60 min. Furthermore, the half-life of S163F at 50 °C was 3.04-fold higher than that of WT. The analysis of molecular dynamics simulation suggested that the Ser163Phe mutation led to the formation of salt bridge between Lys300 and Glu314 and a stronger hydrophobic interaction of Phe163 with Pro341, Leu342, and Trp460, resulting in an increased structural rigidity and overall enhanced stability at high temperature. This study provides novel insights on PLD tolerance to high temperature by investigating the structure-activity relationship. In addition, it provides strong theoretical foundation and preliminary information on the engineering of PLD with improved characteristics to meet industrial demand.

Characterization and application of a novel laccase derived from Bacillus amyloliquefaciens.

As the copper-containing enzymes, laccases demonstrate a promising potential in various environmental and industrial applications. In this study, a bacterial strain isolated from soil exhibited the laccase activity, which was subsequently characterized and named as Bacillus amyloliquefaciens TCCC 111018. The novel gene encoding CotA-laccase (lac) was amplified using the genome of B. amyloliquefaciens TCCC 111018 as the template and efficiently and actively expressed in Escherichia coli. The recombinant LAC (rLAC) exhibited its highest activity at 80 °C and pH 5.5 for 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) oxidization and 80 °C and pH 7.0 for 2,6-dimethoxyphenol (2,6-DMP) oxidization. rLAC was stable at up to 60 °C and within the pH ranging from 3.0 to 9.0 when using the substrate ABTS. Furthermore, rLAC demonstrated the relatively high tolerance to NaCl, SDS, and most metal ions. Moreover, rLAC was capable of decolorizing the structurally different azo, anthraquinone, and triphenylmethane with different mediator at 60 °C under pH 5.5, 7.0, and 9.0. Therefore, rLAC would be an ideal candidate for lots of biotechnological and industrial applications due to its stability in the extreme conditions, including but not limit to pH, high temperature, halides, heavy metals and detergents.

Transcriptomic Analysis of the Influence of Methanol Assimilation on the Gene Expression in the Recombinant Pichia pastoris Producing Hirudin Variant 3.

Hirudin and its variants, as strong inhibitors against thrombin, are present in the saliva of leeches and are recognized as potent anticoagulants. However, their yield is far from the clinical requirement up to now. In this study, the production of hirudin variant 3 (HV3) was successfully realized by cultivating the recombinant Pichia pastoris GS115/pPIC9K-hv3 under the regulation of the promoter of AOX1 encoding alcohol oxidase (AOX). The antithrombin activity in the fermentation broth reached the maximum value of 5000 ATU/mL. To explore an effective strategy for improving HV3 production in the future, we investigated the influence of methanol assimilation on the general gene expression in this recombinant by transcriptomic study. The results showed that methanol was partially oxidized into CO2, and the rest was converted into glycerone-P which subsequently entered into central carbon metabolism, energy metabolism, and amino acid biosynthesis. However, the later metabolic processes were almost all down-regulated. Therefore, we propose that the up-regulated central carbon metabolism, energy, and amino acid metabolism should be beneficial for methanol assimilation, which would accordingly improve the production of HV3.

Environmental Assessment of a Hybrid Solar-Biomass Energy Supplying System: A Case Study.

Local energy supply by renewable energy, such as solar energy and biomass, using distributed energy systems plays an important role in global energy structure. This study investigated the environmental performance of a hybrid solar-biomass energy supplying system by life-cycle assessment method. The results showed that in terms of environmental and energy impacts, the construction stage and the disassembly and recycling stage of the system contribute little to the whole life-cycle environmental impacts. According to the results of most of the selected impact categories, the solar subsystem contributed the most environmental emissions during construction stage, followed by the two anaerobic reactors; therefore, the excessive pursuit of high solar energy proportion can correspondingly lead to even more serious environmental problems. The integrated energy supplying system significantly reduces non-renewable energy consumption, climate change impacts, acidification as well as eutrophication effects due to the replacement of alternatives such as lignite coal, and from fertilizer production. The present hybrid solar-biomass energy supplying system not only produces clean thermal energy but also reduces the disposal of organic wastes and produces valuable agricultural products.

Improvement of the alkali stability of Penicillium cyclopium lipase by error-prone PCR

BACKGROUND: Lipases are extensively exploited in lots of industrial fields; cold-adapted lipases with alkali-resistance are especially desired in detergent industry. Penicillium cyclopium lipase I (PCL) might be suitable for applications of detergent industry due to its high catalytic efficiency at low temperature and relatively good alkali stability. In this study, to better meet the requirements, the alkali stability of PCL was further improved via directed evolution with error-prone PCR. RESULTS: The mutant PCL (N157F) with an improved alkali stability was selected based on a high-throughput activity assay. After incubating at pH 11.0 for 120 min, N157F retained 70% of its initial activity, which was 23% higher than that of wild type PCL. Combined with the three-dimensional structure analysis, N157F exhibited an improved alkali stability under the high pH condition due to the interactions of hydrophilicity and ß-strand propensity. Conclusions: This work provided the theoretical foundation and preliminary data for improving alkali stability of PCL to meet the industrial requirements, which is also beneficial to improving alkali-tolerance ability of other industrial enzymes via molecular modification.

A novel process for phosphatidylserine production using a Pichia pastoris whole-cell biocatalyst with overexpression of phospholipase D from Streptomyces halstedii in a purely aqueous system.

This work was aimed to develop a novel phosphatidylserine (PS) production process for the food industry. The pldsh gene, encoding phospholipase D from Streptomyces halstedii (PLDsh) was cloned, and the codon optimized pldmsh gene was freely expressed by Pichia pastoris GS115 and successfully overexpressed on the cell surface of P. pastoris GS115 as displayed PLDMsh (dPLDMsh) - a whole-cell biocatalyst for PS synthesis from phosphatidylcholine and l-serine. dPLDMsh was stable over a broad range of temperatures (20-60 °C) and pH values (4.0-8.0), indicating significant improvement in stability compared with its free counterpart expressed by P. pastoris GS115. Under the optimum conditions, the conversion yield of PS was 53%, and the relative yield remained above 40% after 4 repeated batch cycles of dPLDMsh catalysis in an aqueous system. Thus, dPLDMsh and the associated reaction system provided a novel strategy for efficient PS production for the food industry.

Development of a Pichia pastoris whole-cell biocatalyst with overexpression of mutant lipase I PCLG47I from Penicillium cyclopium for biodiesel production.

Penicillium cyclopium lipase I (PCL) is a thermolabile triacylglycerol lipase with very low activity against monoacylglycerols, and there have been no reports on the transesterification of oil to produce biodiesel. A mutant PCLG47I with an improved thermostability was previously obtained through replacing Gly47 with Ile in PCL. In this study, a novel Pichia pastoris whole-cell biocatalyst (WCB) with overexpression of PCLG47I was constructed and characterized for biodiesel production from soybean oil. The optimum conditions for biodiesel preparation were 1 g soybean oil, 1 : 2 initial oil/methanol molar ratio with 3 times methanol addition of 1 : 0.75 oil/methanol molar ratio at 4 h intervals, 7% water content, 400 U lipase, temperature of 25 °C, and reaction time of 20 h. Under the optimum conditions, the FAME yield reached 60.7% and remained 47.3% after 4 batch cycles, and no glycerol was generated as a byproduct. These findings indicated that this WCB is a promising biocatalyst for biodiesel production in a relatively cost-effective manner. Additionally, the resulting enzymatic process may provide a potential method for biodiesel production at an industrial scale.