Hydrogenases, accessory genes and the regulation of [NiFe] hydrogenase biosynthesis in Thiocapsa roseopersicina

The purple (Sulphur) phototrophic bacterium, Thiocapsa roseopersicina BBS contains several [NiFe] hydrogenases, of which two are membrane bound. Mutant T. roseopersicina cells, carrying deletions in both gene clusters showed hydrogenase activity. This activity was located in the cytoplasm. The structural gene cluster hoxEFUYH was identified and sequenced. In addition, genes homologous to hupUV/hoxBC, the hydrogen sensing hydrogenase have been identified and sequenced.Regulation of hydrogenase biosynthesis was studied in detail for HydSL (renamed HynSL). A random mutagenesis system was optimised for T. roseopersicina. One of the mutations was in a gene similar to that coding for the HypF proteins in other organisms. Inactivation of the hypF gene resulted in a 60-fold increase in hydrogen evolution under nitrogen fixing conditions. In addition to hypF, the following accessory genes were identified: hydD, hupK, hypC1, hypC2, hypDE. Characterisation of the corresponding gene products and search for additional accessory genes are in progress.     

<i>In Silico</i> analysis and linking of metabolism-related genes with the immune landscape in head and neck squamous cell carcinoma

Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma (HNSCC). The integrative analysis of all the metabolism-related genes (MRGs) in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms. Therefore, this study was designed to establish a prognostic signature based on all the MRGs in HNSCC. Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study. Ultimately 4 prognostic MRGs were selected to construct a model possessing robust prognostic value and accuracy in TCGA cohorts. The favorable reproducibility of this model was confirmed in validation cohorts from GEO databases. The risk score calculated by this model was an independent prognostic factor that further classified these HNSCC patients into high-/low-risk groups. GSEA analyses and somatic mutations indicated the low-risk group could activate several anti-tumor pathways and possessed lower TP53 mutation. The results of ESTIMATE, single-sample GSEA, CIBERSORT, and some immune-related molecules analyses suggested the low-risk group exhibited lower metabolic activities and higher immune characteristics. The Spearman correlation test implied most metabolic pathways with tumor-promoting function were negatively correlated with the immune activity, indicating a plausible approach of combining the anti-metabolism and the immunotherapy drugs in the high-risk group to enhance therapeutic effects than applied separately. In conclusion, this prognostic signature linking MRGs with the immune landscape could promote the individualized treatment for HNSCC patients.     

Effect of omega fatty acid-rich oil blend supplementation on the growth,carcass, meat quality,and gene expression of Barbari goats

This study investigated the effect of supplementing omega fatty acids-rich oil blend, composed of sunflower oil (1.5% and 3.0%), linseed oil (1.5% and 3.0%), and FineXNV1810 (20 g) on the carcass, meat quality, fatty acid profile, and genes (peroxisome proliferator-activated receptor-α, stearoyl-CoA desaturase, acetyl-CoA carboxylase, hydroxy-3-methylglutaryl coenzyme A, and leptin) of Barbari goats. The goat kids (n = 18) were divided into three groups, namely, group A: basal diet; group B: basal diet + oil blend level 1; and group C: basal diet + oil blend level 2, and subjected to the feeding trial for 120 days followed by slaughter and meat quality studies. No treatment effect was recorded in carcass characteristics, pH, water holding capacity, and proximate composition of meat. However, a significant (p < 0.05) treatment effect was observed in cooking loss, lightness, yellowness, and shear force values of meat. There were significant differences (p < 0.05) in linoleic acid, α-linolenic acids, conjugated linoleic acid (CLA), polyunsaturated fatty acids (PUFA), n − 3 and n − 6 PUFA, PUFA/saturated fatty acids and n − 6/n − 3 ratios, and thrombogenic index among groups. An upregulation of the studied genes in the supplemented groups was observed. There were upregulations in the studied genes in the supplemented groups. Practical applications: Goat meat is in great demand the world over, especially in tropical countries, including India, and does not carry any social or religious prohibition. Although goat meat has relatively less fat, consumers express their concern over the presence of undesirable fatty acids. The present study shows that the fatty acid configuration of goat meat can be improved by a dietary supplementation of an oil blend rich in omega fatty acids. The amount of n − 3 PUFA, n − 6 PUFA, and CLA in goat meat was significantly increased due to the dietary oil blend making it healthy for the consumers. Moreover, the dietary oil blend at the studied levels did not significantly affect the growth and meat quality parameters of the goats. Thus, the studied approach can be successfully followed to produce healthier goat meat.     

Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria

Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.     

Expression and Characterization of a New Self-Sufficient P450 Monooxygenase (P450 AZC1) from Azorhizobium caulinodans

Oxyfunctionalization of non-activated carbon bonds by P450 monooxygenases has drawn great industrial attraction. Self-sufficient P450s containing catalytic heme and reductase domains in a single polypeptide chain offer many advantages since they do not require external electron transfer partners. Here, we report the first P450 enzyme identified and expressed from Azorhizobium caulinodans. Firstly, expression conditions of P450 AZC1 were optimized for enhanced expression in E.coli. The highest P450 content was obtained in E.coli Rosetta DE3 plysS when it was incubated in TB media supplemented with 0.75 mM IPTG, 0.5 mM ALA, and 0.75 mM FeCl₃ at 25 °C for 24 hours. Subsequently, the purified enzyme showed a broad substrate spectrum including fatty acids, linear and cyclic alkanes, aromatics, and pharmaceuticals. Finally, P450 AZC1 showed optimal activity at pH 6.0 and 40 °C and a broad pH and temperature profile, making it a promising candidate for industrial applications.     

A developed ant colony algorithm for cancer molecular subtype classification to reveal the predictive biomarker in the renal cell carcinoma

Background: Recently, researchers have been attracted in identifying the crucial genes related to cancer, whichplays important role in cancer diagnosis and treatment. However, in performing the cancer molecular subtypeclassification task from cancer gene expression data, it is challenging to obtain those significant genes due to the highdimensionality and high noise of data. Moreover, the existing methods always suffer from some issues such aspremature convergence. Methods: To address those problems, we propose a new ant colony optimization (ACO)algorithm called DACO to classify the cancer gene expression datasets, identifying the essential genes of differentdiseases. In DACO, first, we propose the initial pheromone concentration based on the weight ranking vector toaccelerate the convergence speed; then, a dynamic pheromone volatility factor is designed to prevent the algorithmfrom getting stuck in the local optimal solution; finally, the pheromone update rule in the Ant Colony System isemployed to update the pheromone globally and locally. To demonstrate the performance of the proposed algorithmin classification, different existing approaches are compared with the proposed algorithm on eight high-dimensionalcancer gene expression datasets. Results: The experiment results show that the proposed algorithm performs betterthan other effective methods in terms of classification accuracy and the number of feature sets. It can be used toaddress the classification problem effectively. Moreover, a renal cell carcinoma dataset is employed to reveal thebiological significance of the proposed algorithm from a number of biological analyses. Conclusion: The resultsdemonstrate that CAPS may play a crucial role in the occurrence and development of renal clear cell carcinoma.     

Differential gene expression of the healthy conjunctiva during the day

PurposeTo determine if there is diurnal variation in gene expression in normal healthy conjunctival cells.MethodsBulbar conjunctival swab samples were collected from four healthy subjects in the morning and evening of the same day. The two swab samples were taken from one eye of each participant, with a minimum of five hours gap between the two samples. RNA was extracted and analysed using RNA sequencing (RNA-Seq).ResultsA total of 121 genes were differentially expressed between the morning and the evening conjunctival samples, of which 94 genes were upregulated in the morning, and 27 genes were upregulated in the evening. Many of the genes that were upregulated in the morning were involved in defence, cell turnover and regulation of gene expression, while the genes upregulated in the evening were involved in signalling and mucin production.ConclusionsThis study has identified several genes whose expression changes over the course of the day. Knowledge of diurnal variations of conjunctival gene expression provides an insight into the regulatory status of the healthy eye and provides a baseline for examining changes during ocular surface disease.     

从蚕的生命到艺术：中国古代生命观的哲学表达

中国考古出土的蚕业实物及蚕的艺术形象比较丰富,蚕的艺术形象如蚕纹、陶蚕蛹、牙雕蚕、玉石蚕、铜蚕、金蚕等,可统称为蚕的模拟形态。对蚕的模拟形态的功用,已有的诸多解释都有待完善。研究表明,蚕的模拟形态或艺术形象表达的功用或为饰品,或为装饰图案,或有待进一步考究。但无论哪种功用,用蚕这一形象都蕴含了特有的用意。通过对中国古代生命观的考察,文章认为蚕的艺术形象折射出相应的中国古代哲学生命观,即中国古人追求的死而复生、生生不息、羽化成仙、长乐无极等观念。