黄粉虫抗菌肽在大肠杆菌中表达条件优化及活性分析

为了提高黄粉虫抗菌肽基因tmAMP1m在大肠杆菌中的表达量,研究了培养温度、诱导时间及IPTG浓度等不同条件对HIS-TmAMP1m融合蛋白表达量和活性的影响。通过Tricine-SDS-PAGE分析确定最佳表达条件,同时,通过琼脂孔穴扩散法检测其抑菌活性。结果表明,含有重组质粒的大肠杆菌在37℃,使用终浓度为0.1 mmol/L IPTG培养4 h时,融合蛋白表达量较高,可占细菌总蛋白40%以上,抗菌活性最好。用Ni2+亲和层析纯化获得较纯的融合蛋白,Western blotting分析表明其能与His单克隆抗体起特异性反应。诱导表达的融合蛋白对宿主菌生长产生一定程度抑制。融合蛋白经100℃煮沸10 h,在20℃反复冻融10次,与强酸强碱缓冲液、不同的有机溶剂和蛋白酶混合后都具有极强的稳定性,仍然表现出良好的抗菌活性。此外,最小抑菌浓度(MIC)测定结果表明,融合蛋白对5种菌具有良好的抗菌活性。研究结果为昆虫抗菌肽推广应用和进一步研究奠定了基础。     

密码子优化提高aiiaB546毕赤酵母表达活性

N-酰基高丝氨酸内酯酶是一类特异性降解N-酰基高丝氨酸内酯类信号分子(AHLs)的蛋白水解酶,通过水解AHLs生成酰基高丝氨酸,使AHLs失去活性,从而阻断病原菌的群体感应路径,使病原菌失去致病能力,其广泛存在于多种微生物中[1,2]。近年来N-酰基高丝氨酸内酯酶作为一种新型抗菌策略(群体感应淬灭策略)的工具酶而成为水产养殖防治细菌性疾病研究的热点[3—5]。     

不同林龄胡桃楸林下植物多样性的差异

以黑龙江省帽儿山地区不同林龄胡桃楸(Juglans mandshurica)人工林为对象,在考虑化感物质影响的基础上,研究了不同林龄林分植物多样性的差异.结果表明:随着胡桃楸林龄的增加,林下灌木丰富度指数(IMa)、多样性指数(Isw)及Pielou均匀度指数(J)均呈现递增趋势;林下草本,除均匀度指数外,其他2个指数随着林龄的增长呈递减趋势;随着胡桃楸年龄的增加,草本种类由14种逐渐减少到10种;16年生的胡桃楸林分重要值较大的物种有蔷薇科的山楂叶悬钩子,菊科的一年蓬、蒲公英和蔷薇科的蛇莓委陵菜;23年生胡桃楸林分重要值较大的灌木物种有榆科的春榆和木犀科的暴马丁香,草本植物有禾本科的龙常草和蕨类植物;51年生胡桃楸林分中重要值较大的灌木物种为木犀科的暴马丁香,重要值较大的草本物种为木贼科的木贼和紫草科的山茄子;胡桃楸林植物多样性受胡桃醌的影响较小,土壤有效磷、速效钾对灌木的多样性指数影响较大;灌木与草本植物对pH值的适应范围明显不同;其他土壤指标,如容重、含水率、有机质、全氮等对灌木及草本多样性指数的影响均表现出相反的作用.     

Determination of an Angiotensin II-regulated Proteome in Primary Human Kidney Cells by Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC)

Angiotensin II (AngII), the major effector of the renin-angiotensin system, mediates kidney disease progression by signaling through the AT-1 receptor (AT-1R), but there are no specific measures of renal AngII activity. Accordingly, we sought to define an AngII-regulated proteome in primary human proximal tubular cells (PTEC) to identify potential AngII activity markers in the kidney. We utilized stable isotope labeling with amino acids (SILAC) in PTECs to compare proteomes of AngII-treated and control cells. Of the 4618 quantified proteins, 83 were differentially regulated. SILAC ratios for 18 candidates were confirmed by a different mass spectrometry technique called selected reaction monitoring. Both SILAC and selected reaction monitoring revealed heme oxygenase-1 (HO-1) as the most significantly up-regulated protein in response to AngII stimulation. AngII-dependent regulation of the HO-1 gene and protein was further verified in PTECs. To extend these in vitro observations, we overlaid a network of significantly enriched gene ontology terms from our AngII-regulated proteins with a dataset of differentially expressed kidney genes from AngII-treated wild type mice and AT-1R knock-out mice. Five gene ontology terms were enriched in both datasets and included HO-1. Furthermore, HO-1 kidney expression and urinary excretion were reduced in AngII-treated mice with PTEC-specific AT-1R deletion compared with AngII-treated wild-type mice, thus confirming AT-1R-mediated regulation of HO-1. Our in vitro approach identified novel molecular markers of AngII activity, and the animal studies demonstrated that these markers are relevant in vivo. These interesting proteins hold promise as specific markers of renal AngII activity in patients and in experimental models.     

Optimal stomatal conductance in relation to photosynthesis in climatically contrasting Eucalyptus species under drought

Models of stomatal conductance (g_s) are based on coupling between g_s and CO₂ assimilation (A_net), and it is often assumed that the slope of this relationship (‘g₁’) is constant across species. However, if different plant species have adapted to different access costs of water, then there will be differences in g₁ among species. We hypothesized that g₁ should vary among species adapted to different climates, and tested the theory and its linkage to plant hydraulics using four Eucalyptus species from different climatic origins in a common garden. Optimal stomatal theory predicts that species from sub‐humid zones have a lower marginal water cost of C gain, hence lower g₁ than humid‐zone species. In agreement with the theory that g₁ is related to tissue carbon costs for water supply, we found a relationship between wood density and g₁ across Eucalyptus species of contrasting climatic origins. There were significant reductions in the parameter g₁ during drought in humid but not sub‐humid species, with the latter group maintaining g₁ in drought. There are strong differences in stomatal behaviour among related tree species in agreement with optimal stomatal theory, and these differences are consistent with the economics involved in water uptake and transport for carbon gain.     

High production of cold-tolerant chitinases on shrimp wastes in bench-top bioreactor by the Antarctic fungus Lecanicillium muscarium CCFEE 5003: Bioprocess optimization and characterization of two main enzymes

The Antarctic fungus Lecanicillium muscarium CCFEE-5003 was preliminary cultivated in shaken flasks to check its chitinase production on rough shrimp and crab wastes. Production on shrimp shells was much higher than that on crab shells (104.6 ± 9.3 and 48.6 ± 3.1 U/L, respectively). For possible industrial applications, bioprocess optimization was studied on shrimp shells in bioreactor using RSM to state best conditions of pH and substrate concentration. Optimization improved the production by 137% (243.6 ± 17.3). Two chitinolytic enzymes (CHI1 and CHI2) were purified and characterized. CHI1 (MW ca. 61 kDa) showed optima at pH 5.5 and 45 °C while CHI2 (MW ca. 25 kDa) optima were at pH 4.5 and 40 °C. Both enzymes maintained high activity levels at 5 °C and were inhibited by Fe⁺⁺, Hg⁺⁺ and Cu⁺⁺. CHI2 was strongly allosamidin-sensitive. Both proteins were N-acetyl-hexosaminidases (E.C. 3.2.1.52) but showed different roles in chitin hydrolysis: CHI1 could be defined as “chitobiase” while CHI2 revealed a main “eso-chitinase” activity.     

BetaDock: Shape-Priority Docking Method Based on Beta-Complex

Abstract

This paper presents an approach and a software, BetaDock, to the docking problem by putting the priority on shape complementarity between a receptor and a ligand. The approach is based on the theory of the β-complex. Given the Voronoi diagram of the receptor whose topology is stored in the quasi-triangulation, the β-complex corresponding to water molecule is computed. Then, the boundary of the β-complex defines the β-shape which has the complete proximity information among all atoms on the receptor boundary. From the β-shape, we first compute pockets where the ligand may bind. Then, we quickly place the ligand within each pocket by solving the singular value decomposition problem and the assignment problem. Using the conformations of the ligands within the pockets as the initial solutions, we run the genetic algorithm to find the optimal solution for the docking problem. The performance of the proposed algorithm was verified through a benchmark test and showed that BetaDock is superior to a popular docking software AutoDock 4.     

Effects and statistical optimization of fermentation conditions on growth and poly (vinyl alcohol)-degrading enzyme production of Streptomyces venezuelae GY1

The effects of environmental conditions, including temperature, pH and dissolved oxygen, on growth and production of polyvinyl alcohol (PVA)-degrading enzymes of the newly-isolated strain Streptomyces venezuelae GY1 were investigated. The medium composition for strain GY1 was studied first by single factorial design and then optimized using a central composite design. PVA with high saponification is better for growth of, and PVA-degrading enzyme production by S. venezuelae GY1 compared with PVA with low saponification, in contrast with the characteristics of other bacteria producing PVA-degrading enzymes. The optimal temperature and initial pH for production of PVA-degrading enzyme by strain GY1 was 30°C and 7.0, respectively. The optimal medium composition for PVA-degrading enzyme production is: 1.01 g L^?1 of PVA1799, 0.307 g L^?1 of NaNO₃ and 0.512 g L^?1 of MgSO₄?7H₂O.     

Bone Load Estimation for the Proximal Femur Using Single Energy Quantitative CT Data

A density-based load estimation method was applied to determine femoral load patterns. Two-dimensional finite element models were constructed using single energy quantitative computed tomography (QCT) data from two femora. basic load cases included parabolic pressure joint loads and constant tractions on the greater trochanter. An optimization procedure adjusted magnitudes of the basic load cases, such that the applied mechanical stimulus approached the ideal stimulus throughout each model. Dominant estimated load directions were generally consistent with published experimental data for gait. Other estimated loads suggested that loads at extreme joint orientations may be important to maintenance of bone structure. Remodeling simulations with the estimated loads produced density distributions qualitatively similar to the QCT data sets. Average nodal density errors between QCT data and predictions were 0·24 g/cm³ and 0·28 g/cm³. The results indicate that density-based load estimation could improve understanding of loading patterns on bones.     

A combined steepest descent and genetic algorithm (SD/GA) approach for the optimization of solvation parameters

An accurate solvation model is essential for computer modeling of protein folding and other biomolecular self-assembly processes. Compared to explicit solvent models, implicit solvent models, such as the Poisson-Boltzmann (PB) with solvent accessible surface area model (PB/SA), offer a much faster speed—the most compelling reason for the popularity of these implicit solvent models. Since these implicit solvent models typically use empirical parameters, such as atomic radii and the surface tensions, an optimal fit of these parameters is crucial for the final accuracy of properties such as solvation free energy and folding free energy. In this paper, we proposed a combined approach, namely SD/GA, which takes the advantage of both local optimization with the steepest descent (SD), and global optimization with the genetic algorithm (GA), for parameters optimization in multi-dimensional space. The SD/GA method is then applied to the optimization of solvation parameters in the non-polar cavity term of the PB/SA model. The results show that the newly optimized parameters from SD/GA not only increase the accuracy in the solvation free energies for ～200 organic molecules, but also significantly improve the free energy landscape of a β-hairpin folding. The current SD/GA method can be readily applied to other multi-dimensional parameter space optimization as well.