Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: a new vista in engineering enzymes

The engineering of thermostable enzymes is receiving increased attention. The paper, detergent, and biofuel industries, in particular, seek to use environmentally friendly enzymes instead of toxic chlorine chemicals. Enzymes typically function at temperatures below 60°C and denature if exposed to higher temperatures. In contrast, a small portion of enzymes can withstand higher temperatures as a result of various structural adaptations. Understanding the protein attributes that are involved in this adaptation is the first step toward engineering thermostable enzymes. We employed various supervised and unsupervised machine learning algorithms as well as attribute weighting approaches to find amino acid composition attributes that contribute to enzyme thermostability. Specifically, we compared two groups of enzymes: mesostable and thermostable enzymes. Furthermore, a combination of attribute weighting with supervised and unsupervised clustering algorithms was used for prediction and modelling of protein thermostability from amino acid composition properties. Mining a large number of protein sequences (2090) through a variety of machine learning algorithms, which were based on the analysis of more than 800 amino acid attributes, increased the accuracy of this study. Moreover, these models were successful in predicting thermostability from the primary structure of proteins. The results showed that expectation maximization clustering in combination with uncertainly and correlation attribute weighting algorithms can effectively (100%) classify thermostable and mesostable proteins. Seventy per cent of the weighting methods selected Gln content and frequency of hydrophilic residues as the most important protein attributes. On the dipeptide level, the frequency of Asn-Glu was the key factor in distinguishing mesostable from thermostable enzymes. This study demonstrates the feasibility of predicting thermostability irrespective of sequence similarity and will serve as a basis for engineering thermostable enzymes in the laboratory.     

Genetic and chemical characterization of an EMS induced mutation in Cucumis melo CRTISO gene

In order to broaden the available genetic variation of melon, we developed an ethyl methanesulfonate mutation library in an orange-flesh ‘Charentais’ type melon line that accumulates β-carotene. One mutagenized M₂ family segregated for a novel recessive trait, a yellow–orange fruit flesh (‘yofI’). HPLC analysis revealed that ‘yofI’ accumulates pro-lycopene (tetra-cis-lycopene) as its major fruit pigment. The altered carotenoid composition of ‘yofI’ is associated with a significant change of the fruit aroma since cleavage of β-carotene yields different apocarotenoids than the cleavage of pro-lycopene. Normally, pro-lycopene is further isomerized by CRTISO (carotenoid isomerase) to yield all-trans-lycopene, which is further cyclized to β-carotene in melon fruit. Cloning and sequencing of ‘yofI’ CRTISO identified two mRNA sequences which lead to truncated forms of CRTISO. Sequencing of the genomic CRTISO identified an A–T transversion in ‘yofI’ which leads to a premature STOP codon. The early carotenoid pathway genes were up regulated in yofI fruit causing accumulation of other intermediates such as phytoene and ζ-carotene. Total carotenoid levels are only slightly increased in the mutant. Mutants accumulating pro-lycopene have been reported in both tomato and watermelon fruits, however, this is the first report of a non-lycopene accumulating fruit showing this phenomenon.     

Effect of growing region on quality characteristics and phenolic compounds of chemlali extra-virgin olive oils

The present work aims at the characterizing chemlali extra-virgin olive oils from different locations in northern, central and southern Tunisia in terms of their quality indices, fatty acids, sterol content, phenolic composition and sensory profiles to show the classification of oil samples according to the geographical area. The majority of the analytical parameters have presented statistically significant differences (p < 0.05). The main sterols found in all chemlali olive oils were β-sitosterol, ?-5-avenasterol, campesterol and stigmasterol. The phenolic compounds present in five olive oil samples were analysed by high-performance liquid chromatography (HPLC) method, thus identifying 16 phenolic compounds belonging to different phenolic types. The results have shown no qualitative differences in the phenolic fractions among extra-virgin olive oils from different geographical regions. However, the quantitative differences were observed in a wide number of phenolic compounds. In all studied olive oil samples, secoiridoids were the most abundant, followed by lignans, phenolic alcohols and flavonoids, respectively. Although there is no significant influence on the sensory scores of oils, some slight changes in sensorial profiles were noted: slightly higher intensities of sensory characteristics that are pungent, fruity and bitter in chemlali olive oil from Hammamet and Gafsa.     

New ethnic and national questions in Scotland: post-British identities among Glasgow Pakistani teenagers

The problematic relationship between 'Britishness' and the identities of UK ethnic minorities is further complicated in Scotland by the increasing salience of the Scottish dimension. This article discusses the relationship between reformulations of 'post-British' national identities, and the position of Scottish Pakistani-Muslims. The study focuses on the preferred identities of young Pakistani-Scots in West Central Scotland, reporting chiefly on the results of the modified Twenty Statement Test [TST] as administered to sixty-three Scottish-Pakistani teenagers aged between fourteen and seventeen years, estimated as a significant percentage of the Glasgow Pakistani population in this age range. Religious, ethnic and nationality labels are all adopted by these respondents. Where there are no constraints on their identity labels, religious (Muslim) statements predominate, and where a choice of labels is provided, dual ethnicity labels are preferred. The results are theorized in relation to present deficiencies in the acceptance of plural or 'hyphenate' identities within the United Kingdom.     

Selenium (Se) Seed Priming Induced Growth and Biochemical Changes in Wheat Under Water Deficit Conditions

Insufficient stand establishment at early growth stages in wheat (Triticum aestivum L.) due to drought stress is a major problem that limits overall efficiency and yield of crop. Priming of seed is an effective method for raising seed performance and improving tolerance of crops to abiotic stresses especially drought. The seeds of two local wheat cultivars (Kohistan-97 and Pasban-90) were soaked in distilled water or sodium selenate solutions of 25, 50, 75, and 100 μM for 1/2 or 1 h at 25 °C and later re-dried to their original moisture levels before sowing. One-hour priming significantly increased root length stress tolerance index, dry matter stress tolerance index, and total biomass of seedlings; however, no significant effect of changing duration of Se seed priming was observed on plant height stress tolerance index and shoot/root ratio. Among cultivars, Kohistan-97 was found to be more responsive to Se seed treatment as 1 h priming at 100 μM significantly increased its total biomass by 43 % as compared to control treatment. Although biomass of seedlings was not affected with Se seed priming under normal conditions, but it increased significantly with increase in rates of Se under drought stress conditions. One-hour priming at 75 μM increased the total sugar content and total free amino acids in both wheat cultivars. A more significant decrease in soluble proteins of seedlings was observed by 1 h priming than 1/2 h priming under drought stress conditions.     

Influence of Different Amounts and Sources of Selenium Supplementation on Performance, Some Blood Parameters, and Nutrient Digestibility in Lambs

Two trials were conducted in a 2?×?2?+?1 factorial arrangement based on a completely randomized design to evaluate the effects of different sources of selenium (Se) on performance, blood metabolites, and nutrient digestibility in male lambs on a barley-based diet. The first trial lasted for 70 days and consisted of 30 lambs (35.6?±?2.6 kg mean body weight, about 4–5 months of age) which were randomly allotted to five treatments including: (1) basal diet (containing 0.06 mg Se/kg DM; control) without supplementary Se, (2) basal diet?+?0.20 mg/kg Se as sodium selenite (SeS 0.20), (3) basal diet?+?0.40 mg/kg Se as sodium selenite (SeS 0.40), (4) basal diet?+?0.20 mg/kg Se as selenium yeast (SeY 0.20), and (5) basal diet?+?0.40 mg/kg Se as selenium yeast (SeY 0.40). For the second trial, four lambs from each group of experiment 1 were randomly allocated to individual metabolic cages for 14 days to measure the effects of dietary Se on nutrient digestibility. The results revealed that there were no significant differences for average daily gain, average daily feed intake, feed/gain ratio, hematological parameters (packed cell volume, red blood cell, white blood cell, and hemoglobin values), serum total protein, albumin, globulin, aspartate amino transferase, alkaline phosphatase, and creatine phosphokinase due to supplementation of different amounts and sources of Se in lambs. Dietary Se supplementation significantly improved (P?<?0.001) glutathione peroxidase activity in blood. Furthermore, at the end of the trial, serum tri-iodothyronine (T3) amount also increased (P?<?0.05), while serum thyroxine (T4) amount decreased (P?<?0.05). Digestibility of dry matter, organic matter, crude protein, neutral detergent fiber, and acid detergent fiber increased (P?<?0.05) by Se yeast supplementation. It may be concluded that supplementation of Se in lambs had no significant effect on performance and blood hematology, but increased blood glutathione peroxidase activity and serum T3 amount and decreased serum T4 amount as compared to non-supplemented control lambs. Furthermore, Se yeast improved nutrient digestibility in lambs.     

A reliable and efficient protocol for inducing hairy roots in Papaver bracteatum

An efficient and reliable transformation system for a very important medicinal plant Papaver bracteatum was developed through optimization of several factors that affect the rate of effective A. rhizogenes-mediated transformation and growth rate of hairy root. Five bacterial strains, A4, ATCC15834, LBA9402, MSU440 and A13, and three explants types, hypocotyls, leaves and excised shoots were examined. The highest frequency of transformation was achieved using LBA9402 strain in the excised shoots. Several inoculation and co-cultivation media and different concentration of arginine were evaluated using LBA9402 strain and the excised shoots as explant. Interestingly, a drastic increase in the frequency of transformation (47.3 %) was observed when Murashige and Skoog medium containing 1 mM arginine and lacking NH₄NO₃ KH₂PO₄, KNO₃ and CaCl₂ was used. The effect of sucrose concentration and the ratio of NH₄ ⁺: NO₃ ^? on hairy root biomass was examined. Maximum biomass was obtained in 30 g/l sucrose and 20:10 mM ratio of NH₄ ⁺ to NO₃ ^? on MS medium. Transgenic hairy root lines were confirmed by polymerase chain reaction (PCR) and Southern hybridization.     

Veronaea botryosa: Molecular Identification with Amplified Fragment Length Polymorphism (AFLP) and In vitro Antifungal Susceptibility

Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated infection in apparently healthy individuals have been reported worldwide. All tested strains of V. botryosa, identified on the basis of sequencing and phenotypic and physiological criteria prior to our study, were confirmed by AFLP analysis, yielding a clear separation of V. botryosa as a rather homogeneous group from related species. In vitro antifungal susceptibility testing resulted in MIC₉₀s across all strains in increasing order posaconazole (0.25 μg/ml), itraconazole (1 μg/ml), voriconazole (4 μg/ml), terbinafine (4 μg/ml), caspofungin (8 μg/ml), anidulafungin (8 μg/ml), isavuconazole (16 μg/ml), amphotericin B (16 μg/ml), and fluconazole (32 μg/ml). Overall, the isolates showed a uniform pattern of low MICs of itraconazole and posaconazole, but high MICs for remaining agents. The echinocandins (caspofungin and anidulafungin) had no activity against V. botryosa. There was no statistically significant difference between susceptibilities of environmental (n = 11) and clinical (n = 7) isolates of V. botryosa (P > 0.05).     

Increasing the complexity of chromatin: functionally distinct roles for replication-dependent histone H2A isoforms in cell proliferation and carcinogenesis

Replication-dependent histones are encoded by multigene families found in several large clusters in the human genome and are thought to be functionally redundant. However, the abundance of specific replication-dependent isoforms of histone H2A is altered in patients with chronic lymphocytic leukemia. Similar changes in the abundance of H2A isoforms are also associated with the proliferation and tumorigenicity of bladder cancer cells. To determine whether these H2A isoforms can perform distinct functions, expression of several H2A isoforms was reduced by siRNA knockdown. Reduced expression of the HIST1H2AC locus leads to increased rates of cell proliferation and tumorigenicity. We also observe that regulation of replication-dependent histone H2A expression can occur on a gene-specific level. Specific replication-dependent histone H2A genes are either up- or downregulated in chronic lymphocytic leukemia tumor tissue samples. In addition, discreet elements are identified in the 5′ untranslated region of the HIST1H2AC locus that confer translational repression. Taken together, these results indicate that replication-dependent histone isoforms can possess distinct cellular functions and that regulation of these isoforms may play a role in carcinogenesis.