Structure of Haze Forming Proteins in White Wines: Vitis vinifera Thaumatin-Like Proteins

Grape thaumatin-like proteins (TLPs) play roles in plant-pathogen interactions and can cause protein haze in white wine unless removed prior to bottling. Different isoforms of TLPs have different hazing potential and aggregation behavior. Here we present the elucidation of the molecular structures of three grape TLPs that display different hazing potential. The three TLPs have very similar structures despite belonging to two different classes (F2/4JRU is a thaumatin-like protein while I/4L5H and H2/4MBT are VVTL1), and having different unfolding temperatures (56 vs. 62°C), with protein F2/4JRU being heat unstable and forming haze, while I/4L5H does not. These differences in properties are attributable to the conformation of a single loop and the amino acid composition of its flanking regions.     

Morpho-functional aspects of the hypothalanus-pituitary-gonadal axis of elasmobranch fishes

Synopsis The tetrapod hypothalamus-pars distalis axis contains a blood portal system. Contrarily, elasmobranchs appear to lack a direct vascular supply from the hypothalamus to the ventral lobe of the pituitary where gonadotropic activity resides. The hypothalamus contains GnRH immunoreactivity and GnRH causes an increase in plasma gonadal steroids, perhaps via ventral lobe stimulation. Therefore, the question arises as to how GnRH reaches the pituitary. We suggest that the general circulation route might be practicable. Indeed, in the plasma of the electric ray,Torpedo marmorata, a major early eluting form has been detected using high performance liquid chromatography coupled with region specific radioimmunoassay. The presence of GnRH in the blood may allow the molecule to reach the gonads and to act there by direct mechanisms. Intragonadal levels of steroids may have a paracrine and/or autocrine role in the regulation of steroidogenesis in the testis and in the development f specific germinal cell stages. Particularly, the zonated morphology of the testis supports the concept of a diverse environment for different spermatogenic stages. Finally, gonadal steroids may feed back to affect pituitary activity.     

Effects of Sirolimus treatment on patients with β-Thalassemia: Lymphocyte immunophenotype and biological activity of memory CD4+ and CD8+ T cells

Inhibitors of the mammalian target of rapamycin (mTOR) have been proposed to improve vaccine responses, especially in the elderly. Accordingly, testing mTOR inhibitors (such as Sirolimus) and other geroprotective drugs might be considered a key strategy to improve overall health resilience of aged populations. In this respect, Sirolimus (also known as rapamycin) is of great interest, in consideration of the fact that it is extensively used in routine therapy and in clinical studies for the treatment of several diseases. Recently, Sirolimus has been considered in laboratory and clinical studies aimed to find novel protocols for the therapy of hemoglobinopathies (e.g. β-Thalassemia). The objective of the present study was to analyse the activity of CD4⁺ and CD8⁺ T cells in β-Thalassemia patients treated with Sirolimus, taking advantages from the availability of cellular samples of the NCT03877809 clinical trial. The approach was to verify IFN-γ releases following stimulation of peripheral blood mononuclear cells (PBMCs) to stimulatory CEF and CEFTA peptide pools, stimulatory for CD4⁺ and CD8⁺ T cells, respectively. The main results of the present study are that treatment of β-Thalassemia patients with Sirolimus has a positive impact on the biological activity and number of memory CD4⁺ and CD8⁺ T cells releasing IFN-γ following stimulation with antigenic stimuli present in immunological memory. These data are to our knowledge novel and in our opinion of interest, in consideration of the fact that β-Thalassemia patients are considered prone to immune deficiency.     

RosettaDDGPrediction for high-throughput mutational scans: From stability to binding

Reliable prediction of free energy changes upon amino acid substitutions (ΔΔGs) is crucial to investigate their impact on protein stability and protein–protein interaction. Advances in experimental mutational scans allow high-throughput studies thanks to multiplex techniques. On the other hand, genomics initiatives provide a large amount of data on disease-related variants that can benefit from analyses with structure-based methods. Therefore, the computational field should keep the same pace and provide new tools for fast and accurate high-throughput ΔΔG calculations. In this context, the Rosetta modeling suite implements effective approaches to predict folding/unfolding ΔΔGs in a protein monomer upon amino acid substitutions and calculate the changes in binding free energy in protein complexes. However, their application can be challenging to users without extensive experience with Rosetta. Furthermore, Rosetta protocols for ΔΔG prediction are designed considering one variant at a time, making the setup of high-throughput screenings cumbersome. For these reasons, we devised RosettaDDGPrediction, a customizable Python wrapper designed to run free energy calculations on a set of amino acid substitutions using Rosetta protocols with little intervention from the user. Moreover, RosettaDDGPrediction assists with checking completed runs and aggregates raw data for multiple variants, as well as generates publication-ready graphics. We showed the potential of the tool in four case studies, including variants of uncertain significance in childhood cancer, proteins with known experimental unfolding ΔΔGs values, interactions between target proteins and disordered motifs, and phosphomimetics. RosettaDDGPrediction is available, free of charge and under GNU General Public License v3.0, at https://github.com/ELELAB/RosettaDDGPrediction .     

Computer simulation of antibody binding specificity

A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives⁸) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley-Liss, Inc.     

ROOT PROFILES AND COMPETITION BETWEEN THE INVASIVE,EXOTIC PERENNIAL,CARPOBROTUS EDULIS,AND TWO NATIVE SHRUB SPECIES IN CALIFORNIA COASTAL SCRUB

The mat-forming succulent, Carpobrotus edulis (Aizoaceae), surrounds and grows over many native plant species in California coastal communities. Two shrub species, Haplopappus ericoides and H. venetus var. sedoides, were found to have shallow root systems that occupied the same soil depths as those of C. edulis. In the presence of C. edulis, the normal rooting profiles of the shrubs were displaced downward, although partial overlap with C. edulis remained. Removal of C. edulis from around individuals of both shrub species resulted in higher predawn xylem pressure potentials in shrubs from the removal treatments as compared to controls, suggesting that the surrounding C. edulis was utilizing water that would otherwise have been available to these shrubs. In H. ericoides, predawn xylem pressure potentials of removal treatment shrubs remained higher than those of the controls throughout the remainder of the dry season even though these shrubs showed a marked increase in canopy area after removal of surrounding C. edulis. Removal of C. edulis from around H. venetus also initially led to higher predawn xylem pressure potentials in the removal shrubs as compared to the controls and increased production of new leaves. After this initial period the predawn xylem pressure potentials of the removal shrubs were not significantly different from those of controls, suggesting that the demand for water by the increased leaf areas eventually matched the enhanced water availability resulting from C. edulis removal. Also, the morphology of H. venetus shrubs changed to that more typical of unaffected individuals. Thus, C. edulis significantly affected not only the water relations of these two shrub species but also their shoot sizes and overall morphologies.     

Genomic changes associated with antigenic variation of visna virus. II. Common nucleotide sequence changes detected in variants from independent isolations

Naturally occurring antigenic variants of visna virus isolated from two persistently infected sheep have been compared using RNAase T₁ fingerprint analysis of the viral RNAs. All the viruses examined have oligonucleotide changes in the 3′-terminal region of the viral genome and many of the alterations are common among the variants of both sheep. There is progressive accumulation of point mutations in the 3′-terminal region of antigenically altered viruses isolated from persistently infected animals. In addition, antigenic variants isolated independently from another sheep contain the same altered oligonucleotides; the nucleotide sequences of these oligonucleotides are identical. These data strongly suggest that the alterations observed in the nucleotide sequence of the variants are related to the change in their antigenic character.     

Effect of temperature on the stability and activity of crystalline ox liver nuclear and mitochondrial glutamate dehydrogenases

A study on the response of the stability and activity of crystalline ox liver nuclear and mitochondrial glutamate dehydrogenases to temperature variations has been carried out. The thermodynamic properties of the heat inactivation process and of the reaction with the substrates glutamate and α-ketoglutarate have been investigated. The heat inactivation of nuclear glutamate dehydrogenase proceeds at a faster rate than that of the mitochondrial enzyme in the temperature range 40–51 °C; the enthalpy of activation of the inactivation process is higher and the entropy is almost double, compared to the values of mitochondrial glutamate dehydrogenase. The effect of temperature on the maximal velocity shows that, with both glutamate and α-ketoglutarate, the enthalpy of activation with nuclear glutamate dehydrogenase is double and the decrease in entropy almost half of the values of the mitochondrial enzyme. The variation of the apparent K_m with temperature shows a decrease of the affinity of both enzymes for glutamate, with no major difference in the thermodynamic properties of the reaction. With α-ketoglutarate, on the other hand, the affinity of nuclear glutamate dehydrogenase decreased, whereas that of the mitochondrial enzyme increased with temperature. The process is therefore exothermic with the former enzyme, endothermic with the latter; furthermore, it occurs with a decrease in enthropy with nuclear glutamate dehydrogenase, but with a large increase with the mitochondrial enzyme. The studies on the effect of temperature on the activity were carried out in the range 20–44 °C.