Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model

Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm, iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting protein stability change, especially when one requires more understandable knowledge.     

Dietary lipid sources affect cold tolerance of Nile tilapia (Oreochromis niloticus)

This study was carried out to evaluate the effects of dietary lipid sources on growth performance, fatty acids composition and cold tolerance of Nile tilapia (Oreochromis niloticus) fingerlings (7.00 ± 0.50 g/fish). The fish were fed four isonitrogenous (28% crude protein), isocaloric (500 kcal/100 g) diets containing four lipid sources; fish oil (FO), corn oil (CO), coconut oil (COCO) or fish oil/ corn oil mixture (1:1 ratio) (oil mix). The diets were offered to the fish at a daily rate of 3% of their body weights (BW), twice a day for two months. After the feeding trial, the fish were exposed to decreasing water temperature from 25 °C until the appearance of death symptoms. The results revealed that FO-based diets (FO and oil mix) produced the best growth rates and feed efficiency, followed by corn oil diet, while COCO resulted in the lowest performance. Fish fed on CO and oil mix showed higher body unsaturated fatty acids (UFA) and lower lethal temperature than those fed on FO- or COCO-based diets. These results indicate that cold shock can modify the lipid metabolism in Nile tilapia by lowering total body saturated fatty acids and raising n-6 and n-3 UFA. This finding suggests that the inclusion of high levels of plant oils in Nile tilapia feeds can enhance their cold tolerance.     

Vibrational spectroscopy-based quantification of liver steatosis

The liver plays a central role in lipid metabolism, and abnormal lipid accumulation in the liver is a key feature of Non-Alcoholic Fatty Liver Disease. In experimental studies, quantification of liver steatosis is commonly based on lipids staining or biochemical analysis. Here, we present a spectroscopic approach for quantitative analysis of the lipid content in the freeze-dried liver. The method is based on vibrational spectroscopy (Raman and infrared) measurements applied for Partial Least Squares (PLS) regression modeling. The obtained PLS models show a good correlation of the spectroscopic data with the reference histological evaluation of steatosis based on Oil Red O (ORO)-stained images of liver cross sections. Vibrational spectroscopy with PLS-based modeling described here represents a useful approach for the fast assessment of the liver steatosis in a small sample of freeze-dried liver tissue. In conclusion, our work demonstrates the easy-to-use method that can be applied in laboratory routine as a beneficial alternative to the established ORO staining.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Prediction of GPCR-G protein coupling specificity using features of sequences and biological functions

Understanding the coupling specificity between G protein-coupled receptors （GPCRs） and specific classes of G proteins is important for further elucidation of receptor functions within a cell. Increasing information on GPCR sequences and the G protein family would facilitate prediction of the coupling properties of GPCRs. In this study, we describe a novel approach for predicting the coupling specificity between GPCRs and G proteins. This method uses not only GPCR sequences but also the functional knowledge generated by natural language processing, and can achieve 92.2% prediction accuracy by using the C4.5 algorithm. Furthermore, rules related to GPCR-G protein coupling are generated. The combination of sequence analysis and text mining improves the prediction accuracy for GPCR-G protein coupling specificity, and also provides clues for understanding GPCR signaling.     

原生质体融合技术构建棕榈油酸高产酵母菌株

采用原生质体融合技术进行产棕榈油酸酵母Saccharomy cescerevisiaeNo.12.926和产脂酵母RhodotorulaNo.12.908的融合研究,获得了棕榈油酸高产酵母工程菌株。实验结果表明,原生质体形成的最佳条件为:对数期酵母No.12.926和No.12.908用2%蜗牛酶于30℃分别酶解1.5和2h。在最佳条件下,酵母No.12.926和No.12.908原生质体形成率分别为94%和80%,再生率分别为75%和60%。原生质体融合由聚乙二醇诱导。将得到的融合子进行多次传代培养优选,获得了遗传性状稳定的融合菌株。融合子的生物量为亲株的两倍多,其细胞形态和菌落颜色与亲株有差别。产脂和产棕榈油酸分析表明,融合子的产脂量为菌体干重的48.53%,其中棕榈油酸占油脂总量的47.29%,为菌体干重的22.95%。     

放线菌来源的羊毛硫肽研究进展

羊毛硫肽(lanthipeptide)是一类由核糖体合成并经翻译后修饰的含羊毛硫氨酸或β-甲基羊毛硫氨酸的多肽。近年来,放线菌来源的羊毛硫肽因其突出的抗菌活性和罕见的生物活性而备受关注。本文重点对放线菌来源的不同类型的羊毛硫肽的结构特征及其特性进行了综述,讨论了生物或化学方法修饰天然羊毛硫肽和基因组挖掘发现结构新颖的羊毛硫肽在开发符合实际应用需求的放线菌来源的羊毛硫肽中的应用,并对放线菌来源的羊毛硫肽的应用潜力进行了总结和展望。     

Growth performance,haematological assessment and chemical composition of Nile tilapia,Oreochromis niloticus (Linnaeus, 1758) fed different levels of Aloe vera extract as feed additives in a closed aquaculture system

A 105-day experimental trial was conducted to assess different levels of dietary Aleo vera extract supplementation on water quality parameters, proximate composition, growth performance and haematological parameters of fry Oreochromis niloticus. Four different percentages of dietary leaf extract powder of Aleo vera (ALE) with a basal feed, designated as, i.e., T0 (Control group; without ALE), T1 (1% ALE), T2 (2% ALE), and T3 (3% ALE). Fish fry was reared in concrete tanks (7.0 m, 1.6 m, 1.0: L, W, H; water volume 11.2 m3/tank), with an average initial weight 4.04 ± 0.03 g/ fry, and each treatment was triplicated. Fry was randomly distributed at a stocking rate of 450 individuals/ tanks. The water quality parameters revealed that temperature, pH, salinity, dissolved oxygen (DO) and nitrates were found in a promising range as given by FAO/WHO limits. However, the record values obtained for Electric Conductivity (EC), Total dissolved solids (TDS), and alkalinities were not found in all tanks' suitable range according to FAO/WHO limits. The results revealed a significant impact of different percentages of dietary ALE supplementation on fry's body composition and haematological parameters. Moreover, the final body weight, final body length, average daily weight gain (g), net weight gain (g) and specific growth rate (%) were significantly higher (p < 0.05) in T1 and T2 compared with T0 and T3 treatments. The poorest feed conversion ratio was recorded in the T2 group compared with other treatments. Thus, the current study provides information about the nutritional quality of Nile tilapia culturing in Pakistan.     

Oil red-O stains non-adipogenic cells: a precautionary note

Bovine adipofibroblasts, 3T3-L1 cells, L-6 myogenic cells, and sheep satellite cells were allowed to proliferate for 48 h. Oil red-O (ORO) was dissolved in three different solvents isopropanol, propylene glycol and triethyl phosphate. At 48 h, the proliferative cultures were stained with the three stains. ORO stain prepared in both propylene glycol and triethyl phosphate resulted in bright red droplets appearing in all cultures, whereas ORO dissolved in isopropanol was not taken up by any of the cells. These data suggest that certain preparations of ORO may stain cells in non-adipogenic lineages as well as undifferentiated pre-adipocytes. Caution must be exercised when choosing solvents for ORO in differentiation studies using cells of the fat/adipose lineage.     

Microbial cycling of iron and sulfur in sediments of acidic and pH-neutral mining lakes in Lusatia (Brandenburg, Germany)

A vast number of lakes developed in the abandoned opencast lignite mines of Lusatia (East Germany) contain acidic waters (mmolSm^–2a^–). Potential Fe(III) reduction measured by the accumulation of Fe(II) during anoxic incubation yielded similar rates in both types of sediments, however, the responses towards the supplementation of Fe(III) and organic carbon were different. Sulfate reduction rates estimated with ³⁵S-radiotracer were much lower in the slightly acidic sediment than in the pH-neutral sediment (156 v.s. 738mmolSO₄ ^2–m^–2a^–1). However, sulfate reduction rates were increased by the addition of organic carbon. Severe limitation of sulfate-reducing bacteria under acidic conditions was also reflected by low most probable numbers (MPN). High MPN of acidophilic iron- and sulfur-oxidizing bacteria in acidic sediments indicated a high reoxidation potential. The results show that potentials for reductive processes are present in acidic sediments and that these are determined mainly by the availability of oxidants and organic matter.