Yield quantitative trait loci from wild tomato are predominately expressed by the shoot

Plant yield is the integrated outcome of processes taking place above and below ground. To explore genetic, environmental and developmental aspects of fruit yield in tomato, we phenotyped an introgression line (IL) population derived from a cross between the cultivated tomato (Solanum lycopersicum) and a wild species (Solanum pennellii). Both homozygous and heterozygous ILs were grown in irrigated and non-irrigated fields and evaluated for six yield components. Thirteen lines displayed transgressive segregation that increased agronomic yield consistently over 2 years and defined at least 11 independent yield-improving QTL. To determine if these QTL were expressed in the shoots or the roots of the plants, we conducted field trials of reciprocally grafted ILs; out of 13 lines with an effect on yield, 10 QTL were active in the shoot and only IL8-3 showed a consistent root effect. To further examine this unusual case, we evaluated the metabolic profiles of fruits from both the homo- and heterozygous lines for IL8-3 and compared these to those obtained from the fruit of their equivalent genotypes in the root effect population. We observed that several of these metabolic QTL, like the yield QTL, were root determined; however, further studies will be required to delineate the exact mechanism mediating this effect in this specific line. The results presented here suggest that genetic variation for root traits, in comparison to that present in the shoot, represents only a minor component in the determination of tomato fruit yield

Production and partial characterization of chitinase from a halotolerant Planococcus rifitoensis strain M2-26

peer reviewedThis paper is the first to investigate the production and partial characterization of the chitinase enzyme from a moderately halophilic bacterium Planococcus rifitoensis strain M2-26, earlier isolated from a shallow salt lake in Tunisia. The impact of salt, salinity concentration, pH, carbon and nitrogen sources on chitinase production and activity have been determined. This is the first report on a high salt-tolerant chitinase from P. rifitoensis, since it was active at high salinity (from 5 to 30% NaCl) as well as in the absence of salt. This enzyme showed optimal activity at 70 C and retained up to 82 and 66% of its original activity at 80 or 90 C, respectively. The activity of the enzyme was also shown over a wide pH range (from 5 to 11). For characterization of the enzyme activity, the chitinase secreted in the culture supernatant was partially purified. The preliminary study of the concentrated dialysed supernatant on native PAGE showed at least three chitinases produced by strain M2-26, with highest activity approximately at 65 kDa. Thus, the thermo-tolerant and high salt-tolerant chitinases produced by P. rifitoensis strain M2-26 could be useful for application in diverse areas such as biotechnology and agro-industry

Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein

Overexpression of the xenotoxin transporter P-glycoprotein (P-gp) represents one major reason for the development of multidrug resistance (MDR), leading to the failure of antibiotic and cancer therapies. Inhibitors of P-gp have thus been advocated as promising candidates for overcoming the problem of MDR. However, due to lack of a high-resolution structure the concrete mode of interaction of both substrates and inhibitors is still not known. Therefore, structure-based design studies have to rely on protein homology models. In order to identify binding hypotheses for propafenone-type P-gp inhibitors, five different propafenone derivatives with known structure-activity relationship (SAR) pattern were docked into homology models of the apo and the nucleotide-bound conformation of the transporter. To circumvent the uncertainty of scoring functions, we exhaustively sampled the pose space and analyzed the poses by combining information retrieved from SAR studies with common scaffold clustering. The results suggest propafenone binding at the transmembrane helices 5, 6, 7 and 8 in both models, with the amino acid residue Y307 playing a crucial role. The identified binding site in the non-energized state is overlapping with, but not identical to, known binding areas of cyclic P-gp inhibitors and verapamil. These findings support the idea of several small binding sites forming one large binding cavity. Furthermore, the binding hypotheses for both catalytic states were analyzed and showed only small differences in their protein-ligand interaction fingerprints, which indicates only small movements of the ligand during the catalytic cycle

Prediction of Promiscuous P-Glycoprotein Inhibition Using a Novel Machine Learning Scheme

BACKGROUND: P-glycoprotein (P-gp) is an ATP-dependent membrane transporter that plays a pivotal role in eliminating xenobiotics by active extrusion of xenobiotics from the cell. Multidrug resistance (MDR) is highly associated with the over-expression of P-gp by cells, resulting in increased efflux of chemotherapeutical agents and reduction of intracellular drug accumulation. It is of clinical importance to develop a P-gp inhibition predictive model in the process of drug discovery and development. METHODOLOGY/PRINCIPAL FINDINGS: An in silico model was derived to predict the inhibition of P-gp using the newly invented pharmacophore ensemble/support vector machine (PhE/SVM) scheme based on the data compiled from the literature. The predictions by the PhE/SVM model were found to be in good agreement with the observed values for those structurally diverse molecules in the training set (n = 31, r(2) = 0.89, q(2) = 0.86, RMSE = 0.40, s = 0.28), the test set (n = 88, r(2) = 0.87, RMSE = 0.39, s = 0.25) and the outlier set (n = 11, r(2) = 0.96, RMSE = 0.10, s = 0.05). The generated PhE/SVM model also showed high accuracy when subjected to those validation criteria generally adopted to gauge the predictivity of a theoretical model. CONCLUSIONS/SIGNIFICANCE: This accurate, fast and robust PhE/SVM model that can take into account the promiscuous nature of P-gp can be applied to predict the P-gp inhibition of structurally diverse compounds that otherwise cannot be done by any other methods in a high-throughput fashion to facilitate drug discovery and development by designing drug candidates with better metabolism profile

Privaros: A Framework for Privacy-Compliant Delivery Drones

We present Privaros, a framework to enforce privacy policies on drones. Privaros is designed for commercial delivery drones, such as the ones that will likely be used by Amazon Prime Air. Such drones visit a number of host airspaces, each of which may have different privacy requirements. Privaros provides an information flow control framework to enforce the policies of these hosts on the guest delivery drones. The mechanisms in Privaros are built on top of ROS, a middleware popular in many drone platforms. This paper presents the design and implementation of these mechanisms, describes how policies are specified, and shows that Privaros's policy specification can be integrated with India's Digital Sky portal. Our evaluation shows that a drone running Privaros can robustly enforce various privacy policies specified by hosts, and that its core mechanisms only marginally increase communication latency and power consumption

An Autotetraploid Linkage Map of Rose (Rosa hybrida) Validated Using the Strawberry (Fragaria vesca) Genome Sequence

Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map

Utjecaj desflurana i sevoflurana na razine oksidativnog stresa u tkivima štakora

General anaesthetics are often used in patients who are under oxidative stress due to a critical illness or surgical trauma. Some anaesthetics may worsen oxidative stress and some may act as antioxidants. The aim of this study was to evaluate liver, brain, kidney, and lung tissue oxidative stress in rats exposed to desflurane and sevoflurane and in unexposed rats. The animals were divided in three groups: control (received only air); sevoflurane (8 %), and desflurane (4 %). After four hours of exposure, we evaluated the levels of malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), Cu, and Zn. Exposure to either of the anaesthetics significantly increased lung MDA levels compared to control (Mann-Whitney U test; P<0.05), probably because it is the tissue directly exposed to anaesthetic gases. Oxidative stress and antioxidant activity in other tissues varied between the desflurane and sevoflurane groups. Our results suggest that anaesthesiologist should not only be aware of the oxidative or antioxidative potential of anaesthetics they use, but should also base their choices on organs which are the most affected by their oxidative actionkisikovih radikala tako i zbog smanjene aktivnosti obrambenih sustava koji se mogu oduprijeti njihovu djelovanju. Stoga su saznanja o antioksidativnom kapacitetu anestetika koji se primjenjuju prije nekoga kirurškog zahvata vrlo važna i od velikog su kliničkog značenja. Sevofl uran i desfl uran su inhalacijski anestetici koji se učestalo rabe u svrhu uvođenja bolesnika u anesteziju. Cilj ovog istraživanja bio je utvrditi razine oksidativnog stresa u različitim tkivima štakora i usporediti razlike u odgovoru tkiva na izlaganje navedenim anesteticima. U tu svrhu razine oksidativnog stresa izmjerili smo u jetri, mozgu, bubrezima i plućima štakora podijeljenih u tri eksperimentalne skupine. Kontrolna skupina udisala je samo zrak, dok su druge dvije skupine izložene 8 %-tnomu sevofl uranu te 4 %-tnomu desfl uranu tijekom 4 h. Nakon završetka obrade životinje su žrtvovane i uzimani su im uzorci tkiva za biokemijske analize. Mjerena je razina malondialdehida (MDA), aktivnst enzima superoksid dismutaze (SOD) i glutation peroksidaze (GSH-Px) te razine bakra i cinka. Izloženost anesteticima izazvala je oksidativni stres u plućima, na što upućuje značajno povišena razina MDA (Mann-Whitney U-test P<0.05) izmjerena u plućnom tkivu štakora obiju izloženih skupina u odnosu na kontrolu. Plućno je tkivo u odnosu na ostala tkiva podložnije štetnim utjecajima reaktivnih kisikovih radikala vjerojatno stoga što je ono prvo izloženo plinovitim anesteticima nakon njihova ulaska u organizam. Razine oksidativnog stresa i antioksidativne aktivnosti koje smo izmjerili u ostalim tkivima bile su različite te su ovisile o primijenjenom anestetiku. Na osnovi dobivenih rezultata možemo zaključiti da bi se zbog različitog odgovora tkiva izbor anestetika trebao provoditi na individualnoj osnovi