Protein Hypersaline Adaptation: Insight from Amino Acids with Machine Learning Algorithms

Traditional bioinformatics methods performed systematic comparison between the halophilic proteins and their non-halophilic homologues, to investigate the features related to hypersaline adaptation. Therefore, proposing some quantitative models to explain the sequence-characteristic relationship of halophilic proteins might shed new light on haloadaptation and help to design new biocatalysts adapt to high salt concentration. Five machine learning algorithm, including three linear and two non-linear methods were used to discriminate halophilic and their non-halophilic counterparts and the prediction accuracy was encouraging. The best prediction reliability for halophilic proteins was achieved by artificial neural network and support vector machine and reached 80 %, for non-halophilic proteins, it was achieved by linear regression and reached 100 %. Besides, the linear models have captured some clues for protein halo-stability. Among them, lower frequency of Ser in halophilic protein has not been report before.     

Electronic structure and optical properties of Cu-doping and Zn vacancy impurities in ZnTe

The geometric structures of perfect ZnTe, that with Zn vacancy (Zn_0.875Te), and Cu-doped ZnTe (Zn_0.875Cu_0.125Te) were optimized using the pseudopotential plane wave (PP-PW) method based on the density functional theory (DFT) within generalized gradient approximation (GGA). The cohesive energy, band structure, density of states, and Mulliken populations were calculated and discussed in detail. On the other hand, an accurate calculation of linear optical functions (the dielectric function, refraction index, reflectivity, conductivity function, and energy-loss spectrum) was performed. The results demonstrated that compared to the perfect ZnTe, the lattice parameters of Zn_0.875Te and Zn_0.875Cu_0.125Te were changed and the cell volumes decreased to some extent due to the vacancy and introduction of impurity. A vacancy acceptor level and an acceptor impurity level were produced in Zn_0.875Te and Zn_0.875Cu_0.125Te, respectively. By comparison, Cu doping in the ZnTe system is relatively stable while the monovacancy system is not.     

Platelet-derived growth factor A (pdgf-a) expression during zebrafish embryonic development

Zebrafish pdgf-a gene was cloned and its expression pattern studied during zebrafish embryogenesis. Zebrafish pdgf-a mRNA was present at high levels in fertilized eggs as well as in all embryonic cells up to the end of gastrulation. Spatially restricted expression started after the onset of segmentation and was mainly localized in the developing pharyngeal arches. Transient expression was also detected in Kupffer's vesicle, a teleost-specific structure, and in lateral trunk and tail regions surrounding the neural keel, as well as areas of the developing pronephros.     

Bioinformatic prediction and analysis of glucolipid metabolic regulation by miR-34a in <Emphasis Type="Italic">Megalobrama amblycephala</Emphasis>

The objective of this study was to analyze the target genes and regulatory function of miR-34a in Megalobrama amblycephala using second-generation high-throughput sequencing and bioinformatic tools. Functional enrichment analysis was performed by gene ontology. MiR-34a and target gene expression levels were measured in M. amblycephala fed normal and high-carbohydrate diets. The results revealed that miR-34a was highly conserved in several species, and miR-34a of M. amblycephala has a close evolutionary relationship to that of zebrafish and common carp. miRanda, TargetScan, RNAhybrid predicted 5,185, 6,282 and 2,168 target genes, respectively, and 645 target genes were in common. According to annotation information, the target genes were enriched in phosphate metabolism, glycerophospholipid metabolism, Golgi vesicle transport, cell division, and other biological processes (P?<?0.05). Pathway enrichment analysis revealed that these target genes were mainly enriched in alpha-linolenic acid and linoleic acid metabolism, ether lipid metabolism, VEGF signaling pathway, Fc epsilon RI signaling pathway, GnRH signaling pathway, and MAPK signaling pathway (P?<?0.05). The regulatory role of miR-34a was more significant in the liver than in the brain of M. amblycephala. MiR-34a regulates glucose lipid homeostasis induced by high glucose diets by upregulating hepatic PI3K/Akt, FOXO, and TOR signaling pathways.     

The permeability of SPION over an artificial three-layer membrane is enhanced by external magnetic field

Background  

Sensorineural hearing loss, a subset of all clinical hearing loss, may be correctable through the use of gene therapy. We are testing a delivery system of therapeutics through a 3 cell-layer round window membrane model (RWM model) that may provide an entry of drugs or genes to the inner ear. We designed an in vitro RWM model similar to the RWM (will be referred to throughout the paper as RWM model) to determine the feasibility of using superparamagnetic iron oxide (Fe₃O₄) nanoparticles (SPION) for targeted delivery of therapeutics to the inner ear.     

工业蛋白质理性设计与应用

作为合成生物学与绿色生物制造等领域的底层核心技术,蛋白理性设计可有效解决天然功能元件性能不足等共性挑战,创制高性能人工酶元件。值此天津工业生物研究所(Tianjin Institute of Industrial Biotechnology, TIB)创立10周年之际,文中回顾了研究所在工业蛋白理性设计领域的系列重要工作进展。从酶设计方法学研究、新酶反应设计到生物催化应用等方面进行了分析讨论,并展望了本领域未来发展方向。望借此搭建学术界和产业界与酶理性设计的桥梁,促进新技术、新策略的开发应用,加速融合人工酶的基础研究与产业应用,推动我国生物制造领域的科技创新升级。     

重复基因的进化－－回顾与进展

基因重复是普遍存在的生物学现象, 是基因组和遗传系统多样化的重要推动力量, 在生物进化过程中发挥着极其重要的作用。基因重复有何利弊, 基因发生重复后, 2个重复子拷贝的保留在基因功能方面是否存在偏好性, 子拷贝在表达和进化速率上如何分化, 以及重复基因为什么会被保留下来一直是进化生物学领域研究的热点问题之一。该文对以上重复基因研究的热点问题进行了介绍, 并对重复基因的进化机制和理论模型及其近年来的一些主要研究进展进行了综述。     

Distribution, metabolism and excretion of a synthetic androgen 7alpha-methyl-19-nortestosterone, a potential male-contraceptive

A synthetic androgen 7α-Methyl-19-nortestosterone (MENT) has a potential for therapeutic use in ‘androgen replacement therapy’ for hypogonadal men or as a hormonal male-contraceptive in normal men. Its tissue distribution, excretion and metabolic enzyme(s) have not been reported. Therefore, the present study tested the distribution and excretion of MENT in Sprague-Dawley rats castrated 24 h prior to the injection of tritium-labeled MENT (³H-MENT). Rats were euthanized at different time intervals after dosing, and the amount of radioactivity in various tissues/organs was measured following combustion in a Packard oxidizer. The radioactivity (% injected dose) was highest in the duodenal contents in the first 30 min of injection. Specific uptake of the steroid was observed in target tissues such as ventral prostate and seminal vesicles at 6 h, while in other tissues radioactivity equilibrated with blood. Liver and duodenum maintained high radioactivity throughout, as these organs were actively involved in the metabolism and excretion of most drugs. The excretion of ³H-MENT was investigated after subcutaneous injection of ³H-MENT into male rats housed in metabolic cages. Urine and feces were collected at different time intervals (up to 72 h) following injection. Results showed that the radioactivity was excreted via feces and urine in equal amounts by 30 h.Aiming to identify enzyme(s) involved in the MENT metabolism, we performed in vitro metabolism of ³H-MENT using rat and human liver microsomes, cytosol and recombinant cytochrome P₄₅₀ (CYP) isozymes. The metabolites were separated by thin-layer chromatography (TLC). Three putative metabolites (in accordance with the report of Agarwal and Monder [Agarwal AK, Monder C. In vitro metabolism of 7α-methyl-19-nortestosterone by rat liver, prostate, and epididymis. Endocrinology 1988;123:2187-93]), [i] 3-hydroxylated MENT by both rat and human liver cytosol; [ii] 16α-hydroxylated MENT (a polar metabolite) by both rat and human hepatic microsomes; and [iii] 7α-methyl-19-norandrostenedione (a non-polar metabolite) by human hepatic microsomes, were obtained. By employing chemical inhibitors and specific anti-CYP antibodies, ³H-MENT was found to be metabolized specifically by rat CYP 2C11 and 3-hydroxysteroid dehydrogenase (3-HSD) enzymes whereas in humans it was accomplished by CYP 3A4, 17β-hydroxysteroid dehydrogenase (17β-HSD) and 3-HSD enzymes.     

The key residues of active sites on the catalytic fragment for paclitaxel interacting with poly (ADP-ribose) polymerase

Poly(ADP-ribose) polymerase (PARP) is regarded as a target protein for paclitaxel (PTX) to bind. An important issue is to identify the key residues as active sites for PTX interacting with PARP, which will help to understand the potential drug activity of PTX against cancer cells. Using docking method and MD simulation, we have constructed a refined structure of PTX docked on the catalytic function domain of PARP (PDB code: 1A26). The residues Glu327(988), Tyr246(907), Lys242(903), His165(826), Asp105(766), Gln102(763) and Gln98(759) in PARP are identified as potential sites involved in interaction with PTX according to binding energy (E(b)) between PTX and single residue calculated with B3LYP/6-31G(d,p). These residues form an active binding pocket located on the surface of the catalytic fragment, possibly interacting with the required groups of PTX leading to its activity against cancer cells. It is noted that most of the active sites make conatct with the "southern hemisphere" of PTX except for one residue, Tyr246(907), which interacts with the "northern hemisphere" of PTX. The conformation of PTX in complex with the catalytic fragment is observed as being T-shaped, similar to that complexed with β-tubulin. The total Eb of -269.9 kJ/mol represents the potent interaction between PTX and the catalytic fragment, implying that PTX can readily bind to the active pocket. The tight association of PTX with the catalytic fragment would inhibit PARP activation, suggesting a potential application of PTX as an effective antineoplastic agent.