Structural and physicochemical properties of polar lipids from thermophilic archaea

The essential general features required for lipid membranes of extremophilic archaea to fulfill biological functions are that they are in the liquid crystalline phase and have extremely low permeability of solutes that is much less temperature sensitive due to a lack of lipid-phase transition and highly branched isoprenoid chains. Many accumulated data indicate that the organism’s response to extremely low pH is the opposite of that to high temperature. The high temperature adaptation does not require the tetraether lipids, while the adaptation of thermophiles to acidic environment requires the tetraether polar lipids. The presence of cyclopentane rings and the role of polar heads are not so straightforward regarding the correlations between fluidity and permeability of the lipid membrane. Due to the unique lipid structures and properties of archaeal lipids, they are a valuable resource in the development of novel biotechnological processes. This microreview focuses primarily on structural and physicochemical properties of polar lipids of (hyper)thermophilic archaea.     

New starches: Physicochemical properties of sweetsop (Annona squamosa) and soursop (Anonna muricata) starches

Starch from the fruits of sweetsop (Anonna squamosa) and soursop (Anonna muricata) were isolated and purified and the fat, ash, phosphorus and protein contents measured. The amount of amylose present was determined spectrophotometrically and found to be very similar (19%) for both starches. Scanning electron microscopy showed very small indented and spherical granules from both with an average granule size of 4.84 μm and 4.72 μm, respectively. The physicochemical properties, namely the swelling power, solubility, pasting characteristics, paste clarity and freeze–thaw stability were studied to assess the functionality of the starch pastes as hydrocolloids. The sweetsop starch showed higher swelling power and solubility compared to soursop starch and had a lower gelatinization temperature indicating a weaker granular structure. Sweetsop starch exhibited a lower pasting temperature, higher viscosity peak, higher viscosity breakdown and lower setback, higher paste clarity and freeze–thaw stability compared to soursop starch. The low gelatinization temperature and high freeze thaw stability of sweetsop starch are comparable to that of waxy corn. The properties of sweetsop indicate that it has potential for application as a thickener in frozen foods.     

Improving Compound Quality through in vitro and in silico Physicochemical Profiling

Many compounds entering clinical studies do not survive the numerous hurdles for a good pharmacological lead to a drug on the market. The reasons for attrition have been widely studied which resulted in more early attention to compound quality related to physical chemistry, drug metabolism and pharmacokinetics (DMPK), and toxicology/safety. This paper will briefly review current physicochemical in vitro assays and in silico predictions to support compound and library design through to lead optimization. The most important physicochemical properties include lipophilicity (log P/D), pK_a, solubility, and permeability. These drive key ADMET properties such as absorption, cell penetration, access to the brain, volume of distribution, plasma protein binding, metabolism, and toxicity, as well as biopharmaceutical behavior. Much data are now available from medium‐ to high‐throughput physchem and ADMET in vitro assays, either in the public domain (see, e.g., PubChem, PubMed) or in drug companies' in‐house databases. Such data are increasingly being computer‐modelled and used in predictive chemistry. New pipelining technology makes it easier to build and update QSAR models so that such models can use the latest available data to produce robust local and global predictive in silico ADMET models.     

三峡水库及香溪河库湾理化特征的比较研究

根据2003年6月三峡水库初期蓄水后对香溪河库湾的常规监测,对该水域的理化特征及其动态进行了分析,并与三峡水库库首的数据进行了比较研究。结果显示库湾TN、NO3-N浓度要显著低于库首,前者两周年平均值为1.29mg/L,0.88mg/L,后者两周年平均值为1.62mg/L,1.22mg/L。而PO4-P则是库湾显著高于库首,并且在7—9月库首的TP/PO4-P有显著提高。结果同时表明库首的水土流失较严重,而库湾则有较好的水土保持。最后对TSIM的计算结果表明,由于TP、TN都处于高水平,库首呈现中营养化(TSIM>37),而库湾则呈现严重富营养化(TSIM>53)。     

Protein molecular function influences mutation rates in human genetic diseases with allelic heterogeneity

Molecular epidemiology studies have used the counts of different mutational types like transitions, transversions, etc. to identify putative mutagens, with little reference to gene organization and structure–function of the translated product. Moreover, geographical variation in the mutational spectrum is not limited to the mutational types at the nucleotide level but also have a bearing at the functional level. Here, we developed a novel measure to estimate the rate of spontaneous detrimental mutations called “mutation index” for comparing the mutational spectra consisting of all single base, missense, and non-missense changes. We have analyzed 1609 mutations occurring in 38 exons in 24 populations in three diseases viz. hemophilia B (F9 gene – 420 mutations in 9 populations across 8 exons), hemophilia A (F8 gene – 650, 8 and 26, respectively) and ovarian carcinoma (TP53 gene – 539, 7 and 4, respectively). We considered exons as units of evolution instead of the entire gene and observed feeble differences among populations implying lack of a mutagen-specific effect and the possibility of mutation causing endogenous factors. In all the three genes we observed elevated rates of detrimental mutations in exons encoding regions of significance for the molecular function of the protein. We propose that this can be extended to the entire exome with implications in exon-shuffling and complex human diseases.     

The extraction process optimization and physicochemical properties of polysaccharides from the roots of Euphorbia fischeriana

Response surface methodology (RSM) was used to determine the optimum extraction conditions for polysaccharides (EFP) from the roots of Euphorbia fischeriana. A Box-Behnken design (BBD) with four independent variables was investigated, such as extraction temperature (°C), water/solid ratio, extraction number (n), and extraction time (h). The results indicated optimum extraction conditions were extraction temperature of 97 °C, water/solid ratio of 9:1, extraction number of 2 and extraction time of 2.4 h, respectively. Under these conditions, the experimental value was 24.6 ± 0.62, which was well in close agreement with value predicted by the model. The preliminary chemical analysis of EFP revealed the EFP contained 25.43% polysaccharides, 20.42% uronic acids, 2.54% sulfate radical and 23.41% proteins. And the neutral polysaccharides were mainly composed of glucose, arabinose, rhamnose, galactose, xylose, mannose in the ratio of 21:8:5:3:1:1.     

AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties

Some creatures living in extremely low temperatures can produce some special materials called “antifreeze proteins” (AFPs), which can prevent the cell and body fluids from freezing. AFPs are present in vertebrates, invertebrates, plants, bacteria, fungi, etc. Although AFPs have a common function, they show a high degree of diversity in sequences and structures. Therefore, sequence similarity based search methods often fails to predict AFPs from sequence databases. In this work, we report a random forest approach “AFP-Pred” for the prediction of antifreeze proteins from protein sequence. AFP-Pred was trained on the dataset containing 300 AFPs and 300 non-AFPs and tested on the dataset containing 181 AFPs and 9193 non-AFPs. AFP-Pred achieved 81.33% accuracy from training and 83.38% from testing. The performance of AFP-Pred was compared with BLAST and HMM. High prediction accuracy and successful of prediction of hypothetical proteins suggests that AFP-Pred can be a useful approach to identify antifreeze proteins from sequence information, irrespective of their sequence similarity.     

Investigation of physicochemical form of uranium in sediment of brackish Lake Obuchi using sequential extraction procedure

The physicochemical form of uranium (²³⁸U) in the sediment of brackish Lake Obuchi was investigated using the standard procedures of sequential extraction. Approximately 60% to 70% of ²³⁸U was composed of the form bound to carbonates and iron (Fe)-manganese (Mn) oxides in silty sediments, whereas more than 50% of ²³⁸U existed in the minerals of sandy sediments. The proportions of ²³⁸U bound to carbonates in the sediments of brackish Lake Obuchi were larger than those in fresh-water lake sediments. Most of the uranium in the brackish lake sediment was considered to be mainly influenced by UO₂(CO₃)₃ ⁴⁻ in seawater, judging from the fact that the ²³⁴U/ ²³⁸U activity ratios (1.13 to 1.16) of silty sediments were very close to that of seawater (1.14). The high correlation found between the ²³⁸U concentration in the sediment and the amount of organic matter demonstrated that organic matter acts as a scavenger for ²³⁸U accumulation on the lake bottom. Received: July 2, 1999 / Accepted: May 25, 2000     

Structural and functional characterization of polyethylene terephthalate hydrolase from Ideonella sakaiensis

Polyethylene terephthalate (PET) hydrolase from Ideonella sakaiensis (IsPETase) can be used to degrade PET. In order to use IsPETase in industry, we studied the enzymatic activity of IsPETase in different conditions containing environmental and physicochemical factors commonly found in nature. We observed that salts and glycerol enhanced the enzymatic activity, while detergents and organic solvents reduced the enzymatic activity. IsPETase hydrolyzed p-nitrophenyl (p-NP) esters instead of naphthyl esters. To make IsPETase an enzyme capable of hydrolyzing naphthyl esters, site-directed mutagenesis was carried out based on the structural information provided by the crystal structure. We found that the IsPETase^S93M, IsPETase^W159F, and IsPETase^N241F mutants can hydrolyze naphthyl esters. IsPETase engineering can direct researchers to use this α/β-hydrolase protein scaffold to design enzymes that can hydrolyze a variety of polyesters.     

河西走廊春季不同盐碱土壤中微生物数量、酶活性与理化因子的关系

【目的】揭示盐碱土壤微生物量与土壤因子间的关系。【方法】选择河西走廊不同盐碱程度的11个样点在春季进行采样,研究了土壤的微生物数量、酶活和理化性质,并对其进行方差分析、简单相关分析、逐步回归分析和主成分分析。【结果】河西地区原生盐碱地、次生盐碱地与农田土在土壤理化性质和土壤微生物数量等方面均有差异;河西地区土壤较贫瘠,土壤微生物数量较低,且分布有规律性,即原生盐碱土<次生盐碱土<农田土;放线菌、真菌、碱性磷酸酶、脲酶和有效磷5个因子是引起土壤微生物数量、酶活性与理化因子之间相关性的主要因素。【结论】结果证实河西地区盐碱土壤中磷的循环很大程度上影响着土壤微生物数量。