Geometrical comparison of two protein structures using Wigner‐D functions

In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root‐mean‐square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner‐D functions to define a new criterion, which is called a “similarity value.” We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner‐D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. Proteins 2014; 82:2756–2769. © 2014 Wiley Periodicals, Inc.     

Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii

The efficiency of gene expression in all organisms depends on the nucleotide composition of the coding region. GC content and codon usage are the two key sequence features known to influence gene expression, but the underlying molecular mechanisms are not entirely clear. Here we have determined the relative contributions of GC content and codon usage to the efficiency of nuclear gene expression in the unicellular green alga Chlamydomonas reinhardtii. By comparing gene variants that encode an identical amino acid sequence but differ in their GC content and/or codon usage, we show that codon usage is the key factor determining translational efficiency and, surprisingly, also mRNA stability. By contrast, unfavorable GC content affects gene expression at the level of the chromatin structure by triggering heterochromatinization. We further show that mutant algal strains that permit high‐level transgene expression are less susceptible to epigenetic transgene suppression and do not establish a repressive chromatin structure at the transgenic locus. Our data disentangle the relationship between GC content and codon usage, and suggest simple strategies to overcome the transgene expression problem in Chlamydomonas.     

A new method for demonstrating argyrophil cells of the pancreas and intestines

A new method for demonstrating argyrophil cells of the pancreas and intestinal tract using a combined silver and reducing solution in sections of formaldehyde fixed tissue is described. Impregnating sections in a 60 C water bath, the procedure takes about 25 min. A microwave version that takes about 5 min is also given. Results are similar to those obtained with the Grimelius method for argyrophil cells.     

Free transfer of expanded parascapular, latissimus dorsi, and expander "capsule" flap for coverage of large lower-extremity soft-tissue defect

The coverage of large soft-tissue defects usually requires a large flap transfer, especially in a combination and expanded form. However, some large soft-tissue defects still cannot be covered by such flaps. In this article, we present a case of a civil war injury in a patient from Afghanistan who had severe trauma to the right knee, lower thigh, and upper leg and a marked soft-tissue defect. This large soft-tissue defect was covered with a large combined free flap of the expanded parascapular and latissimus dorsi muscle, including a large retrograde hinge flap of the tissue expander capsule and a complementary skin graft. The defect was covered completely, and the final result was excellent.     

Cold-induced physiological and biochemical responses of three grapevine cultivars differing in cold tolerance

In this study the cold tolerance potential of three Vitis vinifera cultivars including ‘Red Sultana’, ‘White Sultana,’ and ‘Flame Seedless’ was evaluated under greenhouse condition. After 15 leaves stage in average, the grapevine plants were subjected to cold stress regimes (4, 0 and ? 4 °C) and compared with control plants (24 °C). A clear increase in leaf electrolyte leakage (EL), thiobarbituric acid reactive substances (TBARS), and H₂O₂ concentrations was observed with decreasing temperature from 4 to ? 4 °C in all grapevine cultivars. Chilled plants showed marked increases in their abscisic acid (ABA), soluble sugars, and proline contents in compared to control vines. Upon exposure to cold stress, the EL, TBARS, H₂O₂, and relative water content of ‘Red Sultana’ were found to be lower compared to ‘White Sultana’ and ‘Flame Seedless’. Under 0 °C condition, ‘Red Sultana’ had the highest superoxide dismutase, guaiacol peroxidase and catalase activities, which was approximately twofold higher than those of all other cultivars. Soluble sugars such as glucose, fructose, and sucrose increased from 4 to ? 4 °C. These increments were higher in ‘Red Sultana’ compared to other cultivars which was concomitant with higher accumulation of endogenous ABA concentration in this cultivar. Higher accumulation of ABA and soluble sugars in ‘Red Sultana’ confirmed the key roles of these compounds in cold tolerance which could be applied as a cold tolerance marker for early selection of grapevine cultivars with the aim to establish vineyards in cold winter regions.     

Identification of selective neuropeptide Y2 peptide agonists

Activation of the NPY2 receptor to reduce appetite while avoiding stimulation of the NPY1 and NPY5 receptors that induce feeding provides a pharmaceutical approach to modulate food intake. The naturally occurring peptide PYY(3-36) is a nonselective NPY1, NPY2, and NPY5 agonist. N-terminal truncation of PYY to abrogate affinity for the NPY1 and NPY5 receptors and subsequent N-terminal modification with aminobenzoic analogs to restore NPY2 receptor potency results in a series of highly selective NPY2 receptor peptide agonists.     

Steroid 21-hydroxylase gene mutational spectrum in 50 Tunisian patients: Characterization of three novel polymorphisms

Congenital adrenal hyperplasia (CAH) is an autosomal recessive disease of steroid biosynthesis in humans. More than 90% of all CAH cases are caused by mutations of the 21-hydroxylase gene (CYP21A2), and approximately 75% of the defective CYP21A2 genes are generated through an intergenic recombination with the neighboring CYP21A1P pseudogene. In this study, the CYP21A2 gene was genotyped in 50 patients in Tunisia with the clinical diagnosis of 21-hydroxylase deficiency. CYP21A2 mutations were identified in 87% of the alleles. The most common point mutation in our population was the pseudogene specific variant p.Q318X (26%). Three novel single nucleotide polymorphism (SNP) loci were identified in the CYP21A2 gene which seems to be specific for the Tunisian population. The overall concordance between genotype and phenotype was 98%. With this study the molecular basis of CAH has been characterized, providing useful results for clinicians in terms of prediction of disease severity, genetic and prenatal counseling.     

Evaluation of inhibitory effect and apoptosis induction of Zyzyphus Jujube on tumor cell lines,an in vitro preliminary study

In the present study, water extract of dried fruit of Zyzyphus Jujube was tested for its possible anticancer effect and induction of apoptosis on human tumor cell lines, HEp-2, HeLa and Jurkat cell lines. The inhibitory effect of water extract of this fruit on cell proliferation was assessed by MTT colorimetric assay. The induction of apoptosis of this extract was analyzed by DNA fragmentation analysis. Zyzyphus Jujube extract showed inhibitory effects on mentioned cell lines. Jurkat leukemic line was found the most sensitive cells with IC50 of 0.1 μg mL⁻¹. Our study also showed a typical DNA laddering in this cell line. The present study showed cytotoxic activity of Zyzyphus Jujube on tumor cells. Although Zyzyphus Jujube has useful compounds for medical applications.