Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins?

Intrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of IDPs. In spite of active research in past few decades, what induces structural disorder in IDPs and how is still elusive. Many studies testify that sequential and spatial neighbours often play important roles in determining structural and functional behaviour of proteins. Considering this fact, we assessed sequence neighbours of intrinsically disordered regions (IDRs) to understand if they have any role to play in inducing structural flexibility in IDPs. Our analysis includes 97% eukaryotic IDPs and 3% from bacteria and viruses. Physicochemical and structural parameters including amino acid propensity, hydrophobicity, secondary structure propensity, relative solvent accessibility, B-factor and atomic packing density are used to characterise the neighbouring residues of IDRs (NRIs). We show that NRIs exhibit a unique nature, which makes them stand out from both ordered and disordered residues. They show correlative occurrences of residue pairs like Ser-Thr and Gln-Asn, indicating their tendency to avoid strong biases of order or disorder promoting amino acids. We also find differential preferences of amino acids between N- and C-terminal neighbours, which might indicate a plausible directional effect on the dynamics of adjacent IDRs. We designed an efficient prediction tool using Random Forest to distinguish the NRIs from the ordered residues. Our findings will contribute to understand the behaviour of IDPs, and may provide potential lead in deciphering the role of IDRs in protein folding and assembly.     

A new method for quantifying residue conservation and its applications to the protein folding nucleus

The conservation of residues in columns of a multiple sequence alignment (MSA) reflects the importance of these residues for maintaining the structure and function of a protein. To date, many scores have been suggested for quantifying residue conservation, but none has achieved the full rigor both in biology and statistics. In this paper, we present a new approach for measuring the evolutionary conservation at aligned positions. Our conservation measure is related to the logarithmic probabilities for aligned positions, and combines the physicochemical properties and the frequencies of amino acids. Such a measure is both biologically and statistically meaningful. For testing the relationship between an amino acid's evolutionary conservation and its role in the Phi-value defined protein folding kinetics, our results indicate that the folding nucleus residues may not be significantly more conserved than other residues by using the biological-relevance weighted statistical scoring method suggested in this paper as an alternative to entropy-based procedures.     

南水北调中线干渠异味物质时空动态及其影响因素

为认识南水北调中线干渠异味物质的时空动态,于2018年9月至2019年8月对干渠沿线9个样点开展了6种异味物质、藻类群落及理化因子的逐月同步调查;结果显示:二甲基异莰醇含量平均值为(7.431±9.631)ng/L,夏季略超出嗅阈值;β-环柠檬醛和β-紫罗兰酮平均值分别为(12.371±12.800)和(11.973±...     

Physicochemical properties and in vitro digestibility of flour and starch from pea (Pisum sativum L.) cultivars

Flours and isolated starches from three different cultivars (1544-8, 1658-11 and 1760-8) of pea grown under identical environmental conditions were evaluated for their physicochemical properties and in vitro digestibility. The protein content, total starch content and apparent amylose content of pea flour ranged from 24.4 to 26.3%, 48.8 to 50.2%, and 13.9 to 16.7%, respectively. In pea starches, the 1760-8 showed higher apparent amylose content and total starch content than the other cultivars. Pea starch granules were irregularly shaped, ranging from oval to round with a smooth surface. All pea starches showed C-type X-ray diffraction pattern with relative crystallinity ranging between 23.7 and 24.7%. Pea starch had only a single endothermic transition (12.1-14.2 J/g) in the DSC thermogram, whereas pea flour showed two separate endothermic transitions corresponding to starch gelatinization (4.54-4.71 J/g) and disruption of the amylose-lipid complex (0.36-0.78 J/g). In pea cultivars, the 1760-8 had significantly higher setback and final viscosity than the other cultivars in both pea flour (672 and 1170 cP, respectively) and isolated starch (2901 and 4811 cP). The average branch chain length of pea starches ranged from 20.1 to 20.3. The 1760-8 displayed a larger proportion of short branch chains, DP (degree of polymerization) 6-12 (21.1%), and a smaller proportion of long branch chains, DP ≥ 37 (8.4%). The RDS, SDS and RS contents of pea flour ranged from 23.7 to 24.1%, 11.3 to 12.8%, and 13.2 to 14.8%, respectively. In pea starches, the 1760-8 showed a lower RDS content but higher SDS and RS contents. The expected glycemic index (eGI), based on the hydrolysis index, ranged from 36.9 to 37.7 and 69.8 to 70.7 for pea flour and isolated pea starch, respectively.     

Effect of available burrow densities of plateau pika (Ochotona curzoniae) on soil physicochemical property of the bare land and vegetation land in the Qinghai-Tibetan Plateau

The available burrow densities of plateau pika (Ochotona curzoniae) regulate the soil physicochemical property in alpine meadow. A field survey was conducted to investigate the effect of available burrow densities of plateau pika on soil physicochemical property of bare land (bare patch produced by burrowing behavior of plateau pika) and vegetation land (land covered with vegetation). This study indicated that the increase in available burrow of plateau pika caused the soil water content at 0–10 cm layer of bare land and that at 10–20 cm of vegetation land to reduce, and caused the soil water content at 10– 20 cm layer of bare land and that at 0–10 cm layer of vegetation land to firstly increase and then decline. In the increasing process of available burrow of plateau pika, the soil silt content firstly increased and then decreased, and soil sand content firstly decreased and then increased. With the increase of available burrow of plateau pika, the soil porosity at 0–10 cm layer of bare land and that at 10–20 cm layer of vegetation land decreased, while the soil porosity at 10–20 cm layer of bare land and that at 0–10 cm of vegetation land firstly increased and then decreased. Soil pH value, soil organic matter, total nitrogen and total phosphorus content firstly increased and then decreased, peaking at 14 available burrows per 625 m², while total soil potassium content did not respond to available burrow densities of plateau pika. This study suggested that the proper available burrows existing in the alpine meadow increased soil permeability, accelerated soil moisture to penetrate deeply, increased the proportion of soil silt, and improved the soil nutrient; however, this beneficial effect was strongly influenced by the available burrow density of plateau pika, implying that plateau pika did not benefit soil structure when its available burrow was over 34 number/625 m².     

Physicochemical properties of exopolysaccharide produced by Lactobacillus kefiranofaciens ZW3 isolated from Tibet kefir

An exopolysaccharide (EPS) producing strain, ZW3, was isolated from Tibet kefir grain and was identified as Lactobacillus kefiranofaciens. FT-IR spectroscopy revealed the presence of carboxyl, hydroxyl, and amide groups, which correspond to a typical heteropolymeric polysaccharide. The GC analysis of ZW3 EPS revealed that it was glucogalactan in nature. Exopolymer showed similar flocculation stability like xanthan gum but better than guar gum with a melting point of 93.38 degrees C which is lower than xanthan gum (153.4 degrees C) and guar gum (490.11 degrees C). Compared with other commercially available hydrocolloids like xanthan gum, guar gum and locust gum ZW3 EPS showed much better emulsifying capability.     

Physicochemical,Antioxidant, and Cytotoxic Properties of Xao Tam Phan (Paramignya trimera) Root Extract and Its Fractions

Xao tam phan (Paramignya trimera (Oliv .) Guillaum ) has been used as a medicinal plant for cancer prevention and treatment in recent years. The objective of this study was to determine the physicochemical, antioxidant, and cytotoxic properties of crude P. trimera root (PTR) extract and its fractions using MeOH as a solvent and microwave‐assisted extraction as an advanced technique for preparation of the PTR extract. The results showed that the PTR extract had high contents of saponins, phenolics, flavonoids, and proanthocyanidins (7731.05 mg escin equiv. (EE), 238.13 mg gallic acid equiv. (GAE), 81.49 mg rutin equiv., and 58.08 mg catechin equiv. (CE)/g dried extract, resp.). Antioxidant activity of PTR extract was significantly higher (P < 0.05) than those of four its fractions and ostruthin, a key bioactive compound in the P. trimera, while potent cytotoxic capacity of PTR extract on various cancer cell lines in terms of MiaPaCa‐2 (pancreas), HT29 (colon), A2780 (ovarian), H460 (lung), A431 (skin), Du145 (prostate), BE2‐C (neuroblastoma), MCF‐7 (breast), MCF‐10A (normal breast), and U87, SJ‐G2, SMA (glioblastoma) was observed with GI₅₀ values ranging from 15 to 32 μg/ml. Cytotoxic potential on pancreatic cancer cells of PTR extract (100 – 200 μg/ml) was significantly higher (P < 0.05) than those of its four fractions (50 μg/ml), ostruthin (20 μg/ml) and gemcitabine (50 nm ), and being comparable to a saponin‐enriched extract from quillajia bark, a commercial product. Based on the results achieved, we can conclude that the PTR extract is a potential source for application of in the nutraceutical, medical, and pharmaceutical industries.     

Chemical structure, surface properties and biological activities of the biosurfactant produced by Pseudomonas aeruginosa LBI from soapstock

Pseudomonas aeruginosa LBI isolated from petroleum-contaminated soil produced rhamnolipids (RL(LBI)) when cultivated on soapstock as the sole carbon source. HPLC-MS analysis of the purified culture supernatant identified 6 RL homologues (%): R(2) C(10) C(10) 28.9; R(2) C(10) C(12:1) 23.0; R(1) C(10) C(10) 23.4; R(2) C(10) C(12) 11.3; R(2) C(10) C(12) 7.9; R(2) C(10) C(12) 5.5. To assess the potential antimicrobial activity of the new rhamnolipid product, RL(LBI), its physicochemical properties were studied. RL(LBI) had a surface tension of 24 mN m(-1) and an interfacial tension of 1.31 mN m(-1); the cmc was 120 mg l(-1). RL(LBI) produced stable emulsions with hydrocarbons and vegetable oils. This product showed good antimicrobial behaviour against bacteria: MIC for Bacillus subtilis, Staphylococcus aureus and Proteus vulgaris was 8 mg l(-1), for Streptococcus faecalis 4 mg l(-1), and for Pseudomonas aeruginosa 32 mg l(-1). RL(LBI) was active against phytopathogenic fungal species, MIC values of 32 mg l(-1) being found against Penicillium, Alternaria, Gliocadium virens and Chaetonium globosum. Due to its physicochemical properties and antimicrobial behaviour, RL(LBI) could be used in bioremediation treatment and in the food, cosmetic and pharmaceutical industries.     

Cladocera Diversity,Abundance and Habitat in a Western Thailand Stream

Longitudinal and temporal distribution was determined for 40 species of cladocerans at sites between the headwaters and mouth of Khayeng Stream, a relatively pristine waterway in western Thailand. Cladocerans were confined mostly to lentic areas and abundance between April and September was highest in September, largely a consequence of a floodplain that developed near the mouth. Species richness was related directly to cladoceran abundance. Cladocerans were dominated numerically by three species, Ceriodaphnia cornuta, Diaphanosoma excisum, and D. sarsi. Most species were accommodated within four assemblages. Conductivity, water velocity, pH and temperature were important to species distribution, particularly velocity and conductivity. The most common assemblage was also the most speciose and occurred in moderate total abundance. The second assemblage was also speciose but low in total abundance. Species abundance in groups 1 and 2 tended to be positively related to conductivity and negatively, but weakly, related to pH and temperature. The third assemblage consisted of a single species and occurred in water of low conductivity while the fourth assemblage contained few species and low in overall abundance.     

In Vivo Gene Transfer to the Mouse Nasal Cavity Mucosa Using a Stable Cationic Lipid Emulsion

We evaluate a new cationic emulsion as a mucosal gene carrier and elucidate the relationship between the transfection efficiency and the stability of the carrier/DNA complex. A cationic lipid emulsion was formulated with soybean oil and 1,2-dioleoyl-sn-glycero-3-trimethylammonium-propane (DOTAP) as major components and was used to transfer genes to the epithelial cells of the mouse nasal cavity via intranasal instillation. Correlation between the transfection efficiency and the stability of the carrier/DNA complex was investigated by measuring the carrier size changes and by observing the degree of DNA protection against DNase I digestion in the presence of heparin. The cationic emulsion showed at least 3 times better transfection activity than the liposomal carriers in nasal mucosae. The cationic emulsion was stable in the presence of heparin whereas the liposomal carriers became very unstable. Unlike DNA in liposome/DNA complexes, DNA in the emulsion/DNA complex was resistant to heparin exchange and DNase I digestion. The cationic emulsion was more effective in delivering DNA to nasal mucosae than commercially available liposomal carriers. The transfection activities of the lipid carriers in nasal cavity mucosae are in agreement with the stability of the lipid carriers and their complexes with DNA.