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.     

Identification of a novel missense mutation of PEX7 gene in an Iranian patient with rhizomelic chondrodysplasia punctata type 1

Deficiency in the PTS2 protein import pathway due to mutations in PEX7 gene results in the rhizomelic chondrodysplasia punctata (RCDP) type 1. In the present study, we have reported a novel missense mutation, W75R, in the PEX7 gene in an Iranian patient with the RCDP type 1. The inability of PEX7 protein to transport PTS2 containing proteins including peroxisomal 3-ketoacyl-CoA thiolase and PTS2-EGFP protein to the surface of the peroxisomes showed that the W75R mutation in PEX7 gene severely impaired the function of PEX7 protein and was responsible for RCDP type 1 in this patient.     

A comparative study on the allergenicity, structure, and ultrastructure of two Acacia pollen grains in guinea pigs

Acacia saligna and Acacia victoria are native to Australia brought to and grown in Southern Iran. They have since had a widespread distribution and become native in Iran. As people of the region are exposed to the pollen grains from these plants during a 5 months period, this study aimed at investigating the allergenicity of their mature pollen grains. In addition, the structural and ultrastructural as well as the total protein content of the mature pollen grains were analyzed. Pollen grains of A. saligna and A. victoria were collected from the suburbs of Ahvaz, Iran. Pollen extracts (15 % concentration) were prepared in PBS (pH 7.2), and 4- to 6-week-old male guinea pigs (Hartly) were used for allergenicity tests. Skin tests showed a significant increase in flare diameter. Clinical tests also showed a significant change in the levels of eosinophils, neutrophils, and IgE. Comparative analysis of the allergenicity of A. saligna and A. victoria pollen grains revealed a higher IgE level in the latter. Comparative analysis of pollen characteristics was performed using both light and electron microscopy for sporoderm structure and ultrastructure, respectively. Twelve percent PAGE analysis of the total protein content of mature pollen grains showed a greater number of bands in A. victoria, while four bands were common in both species. In conclusion, this study demonstrates that both A. saligna and A. victoria pollen grains are allergenic, with a greater allergenicity of A. victoria pollen grains. In addition, the structural and ultrastructural as well as the total protein content of the mature pollen grains are revealed, and a potential protein allergen is proposed.     

Analytical Approach to the Surface Plasmon Resonance Characteristic of Metal Nanoparticle Dimer in Dipole-Dipole Approximation

This theoretical study deals with the effect of bi-particle interaction on the surface plasmon resonance (SPR) in a dimer which includes two identical metal nanoparticles (NPs). Considering the dipole-dipole interaction in a Drude-like model, an appropriate equation is derived for the permittivity of each NP. The restoration force related to the classical confinement originating from the finite size of NPs is considered, and an appropriate adjustment coefficient is considered for this term through analyzing experimental data. Two different polarizations are considered for the laser beam electric field, and it is shown that the orientation of the electric field has an essential role in the linear optical properties of a dimer. Numerical investigation is accomplished for a dimer of gold NPs with two different diameters of 4 nm and 20 nm. For the parallel polarization, dipole-dipole interaction leads to the redshift of SPR wavelength and increase in its peak value, while for the perpendicular polarization, the absolute opposite results are derived. For all cases, it is shown that SPR wavelength functionality with respect to the geometric factor a/d (NP radius to the separation) can be presented by a cubic equation that fits better than an exponential one suggested by the earlier studies which demonstrates the dipole-dipole characteristic of the interaction. Qualitatively, our results are in good agreement with the other experimental studies.

     

Rhinovirus 3C Protease Facilitates Specific Nucleoporin Cleavage and Mislocalisation of Nuclear Proteins in Infected Host Cells

Human Rhinovirus (HRV) infection results in shut down of essential cellular processes, in part through disruption of nucleocytoplasmic transport by cleavage of the nucleoporin proteins (Nups) that make up the host cell nuclear pore. Although the HRV genome encodes two proteases (2A and 3C) able to cleave host proteins such as Nup62, little is known regarding the specific contribution of each. Here we use transfected as well as HRV-infected cells to establish for the first time that 3C protease is most likely the mediator of cleavage of Nup153 during HRV infection, while Nup62 and Nup98 are likely to be targets of HRV2A protease. HRV16 3C protease was also able to elicit changes in the appearance and distribution of the nuclear speckle protein SC35 in transfected cells, implicating it as a key mediator of the mislocalisation of SC35 in HRV16-infected cells. In addition, 3C protease activity led to the redistribution of the nucleolin protein out of the nucleolus, but did not affect nuclear localisation of hnRNP proteins, implying that complete disruption of nucleocytoplasmic transport leading to relocalisation of hnRNP proteins from the nucleus to the cytoplasm in HRV-infected cells almost certainly requires 2A in addition to 3C protease. Thus, a specific role for HRV 3C protease in cleavage and mislocalisation of host cell nuclear proteins, in concert with 2A, is implicated for the first time in HRV pathogenesis.     

Virus-induced CRISPR-Cas9 system improved resistance against tomato yellow leaf curl virus

Molecular Biology Reports - Plant viruses are the most significant factors associated with massive economical losses in agricultural industries worldwide. Accordingly, many studies are dedicated to...     

A critical view on social performance assessment at company level: social life cycle analysis of an algae case

The International Journal of Life Cycle Assessment - Social indicators are not easy to be quantitatively analyzed, although at the local scale, the social impacts might be relevant and important....     

Overexpression of a Rice Monosaccharide Transporter Gene (OsMST6) Confers Enhanced Tolerance to Drought and Salinity Stress in Arabidopsis thaliana

Plant Molecular Biology Reporter - Monosaccharide transporter (MSTs) is a large family of integral membrane proteins that plays a crucial role in cell-to-cell and long-distance distribution of...     

Phytotoxicity and antifungal properties of the essential oil from the Juniperus polycarpos var. turcomanica (B. Fedsch.) R.P. Adams leaves

This study was performed to investigate the constituents, in vitro antifungal activity and phytotoxicity potential of the essential oil from Juniperus polycarpos var. turcomanica leaves. The essential oil was analyzed by GC–FID, and GC/MS, which predominantly contains α-pinene (51.21%), germacrene–B (4.80%), and ∆-cadinene (2.56%). The antifungal activity of the essential oil against some phytopathogenic fungi, including Alternaria alternata, Colletotrichum trichellum, Curvularia fallax, Cytospora sacchari, Fusarium oxysporum, and Macrophomina phaseolina was performed through disk diffusion and agar dilution assays. The essential oil of J. polycarpos var. turcomanica had high antifungal activity against tested phytopathogenic fungi. The most susceptible fungi to the essential oil were C. trichellum in agar dilution and M. phaseolina and C. fallax in disk diffusion methods, whereas, the most resistant fungus to the essential oil was obtained from A. alternata in both assays. Screening methods had an influence on antifungal activity of the essential oil as most of the tested fungi in this study were shown to be more resistant in disc diffusion methods. According to the phytotoxic assay results, the essential oil from J. polycarpos var. turcomanica had high phytotoxicity against three species of weeds, including P. oleracea L., A. retroflexus L., and D. stramonium L. The results of this research suggest that the herbicidal and antifungal activities of the essential oil from J. polycarpos var. turcomanica can be attributed to its major group of constituents, monoterpenes hydrocarbons.