Conformation of cyclic dipeptides from empirical energy calculations

Empirical energy calculations on cyclo-Gly-X with X- Phe, Tyr, Val, and Leu as a function of the side-chain torsion angles χ indicate that the conformation of minimum energy are characterized by χ₁ = 60°, χ² = 90° for Phe and Try, χ¹ = ?60° for Val and χ¹ = ?60°, χ² = 180° and χ¹ = 60° and χ² = 150° for Leu. The minimum energy conformation of cyclo-Gly-Phe and cyclo-Gly-Val have the side chains of Phe and Val stacked over the poperazinedione ring as suggested by NMR and found for cyclo-Gly-Tyr crystal structure. In contrast, the Leu side chain is expected to exist in an extended or a quasi-folded form.     

Copper and nickel binding to canine serum albumin. A circular dichroism study

The binding of copper and nickel to canine serum albumin has been studied using circular dichroism. In the 320-700 nm region, only a single positive extremum was observed at about 664-667.5 nm for copper bound to canine serum albumin. The intensity of this extremum was found to increase until a Cu2+/albumin molar ratio of 3 was reached. Further addition of Cu2+ led to a decrease in ellipticity. The absence of any extrema in the 560-570 and 480-510 nm regions showed that histidines were not involved in copper binding to canine albumin. In the case of nickel, initial binding was found to take place at the N-terminal tripeptide. At higher nickel to albumin molar ratios, circular dichroism spectra indicated the presence sulfur containing ligands but showed no evidence for the involvement of histidines. Canine serum albumin was found to bind six or more Cu2+ and Ni2+ ions with affinities that are lower than for human or bovine serum albumin.     

Regulation of the oxidative phosphorylation rate in the intact cell

The mechanisms that underlie the balance between the consumption and oxidative generation of ATP in the intact cell are not well-defined. Cytosolic inorganic phosphate (Pi) and ADP levels, the cytosolic ATP/ADP ratio, and the cytosolic phosphorylation potential (PP) have all been proposed as major regulatory variables, the latter as a component of a "near-equilibrium" thermodynamic regulatory scheme. Therefore, the potential regulatory roles of these variables in the intact cell were evaluated with 31P NMR and Langendorff perfused rat hearts; in this preparation, the tissue oxygen consumption rate (MVO2) can be varied over a wide range. When the exogenous carbon source was varied, none of the proposed regulatory parameters, i.e., the ATP/ADP ratio, PP, or cytosolic ADP level, were found to be uniquely related to MVO2. Rather, ADP levels at a given MVO2 decreased progressively for the exogenous carbon sources in the following order: glucose, glucose + insulin, palmitate + glucose, lactate, pyruvate + glucose, and octanoate + glucose. In the octanoate and pyruvate groups, MVO2(-1) was linearly dependent upon [ADP]-1 with apparent Km values being in the range previously observed in isolated mitochondria. A similar trend was observed in the MVO2-[Pi] relationship. The present findings suggest that exogenous carbon sources which effectuate deregulation of intramitochondrial NADH generation lower cytosolic ADP and Pi to levels which are limiting to the rate of oxidative phosphorylation. For other carbon sources, the processes controlling the rate of NADH generation also participate in determining the rate of oxidative ATP synthesis. However, this control must be exerted kinetically rather than through a near-equilibrium thermodynamic mechanism as indicated by the present data and prior kinetic studies of the ATP synthetic process in both isolated mitochondria and intact myocardium [La Noue, K. F., et al. (1986) Biochemistry 25, 7667-7675; Kingsley-Hickman, P., et al. (1987) Biochemistry 26, 7501-7510].     

L<Subscript>2</Subscript>-norm multiple kernel learning and its application to biomedical data fusion

Background  

This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L _∞, L ₁, and L ₂ MKL. In particular, L ₂ MKL is a novel method that leads to non-sparse optimal kernel coefficients, which is different from the sparse kernel coefficients optimized by the existing L _∞ MKL method. In real biomedical applications, L ₂ MKL may have more advantages over sparse integration method for thoroughly combining complementary information in heterogeneous data sources.     

Comparative analysis of DNA polymorphisms and phylogenetic relationships among Syzygium cumini Skeels based on phenotypic characters and RAPD technique

The Indian black berry (Syzygium cumini Skeels) has a great nutraceutical and medicinal properties. As in other fruit crops, the fruit characteristics are important attributes for differentiation were also determined for different accessions of S. cumini. The fruit weight, length, breadth, length: breadth ratio, pulp weight, pulp content, seed weight and pulp: seed ratio significantly varied in different accessions. Molecular characterization was carried out using PCR based RAPD technique. Out of 80 RAPD primers, only 18 primers produced stable polymorphisms that were used to examine the phylogenetic relationship. A sum of 207 loci were generated out of which 201 loci found polymorphic. The average genetic dissimilarity was 97 per cent among jamun accessions. The phylogenetic relationship was also determined by principal coordinates analysis (PCoA) that explained 46.95 per cent cumulative variance. The two-dimensional PCoA analysis showed grouping of the different accessions that were plotted into four sub-plots, representing clustering of accessions. The UPGMA (r = 0.967) and NJ (r = 0.987) dendrogram constructed based on the dissimilarity matrix revealed a good degree of fit with the cophenetic correlation value. The dendrogram grouped the accessions into three main clusters according to their eco-geographical regions which given useful insight into their phylogenetic relationships.     

不同耕作措施对冬小麦-夏玉米复种连作系统土壤有机碳和水分利用效率的影响

在连续8年田间定位试验的基础上,分析了关中平原冬小麦 夏玉米复种连作系统2008—2009年连续两个生长季期间不同耕作措施(结合秸秆还田和不还田)对土壤有机碳和水分利用率的影响.结果表明: 相对于传统耕作,保护性耕作有利于土壤有机碳、水分利用效率和作物产量的提高,其中在“深松+秸秆还田”耕作模式下的增幅最高,土壤有机碳含量在0～30 cm土层增幅达到19.5%,水分利用效率和作物产量提高了16.9%和20.5%,而免耕模式则有效提高了0～10 cm土层有机碳含量.在该地区土壤和气候条件下,深松结合秸秆粉碎还田是最理想的耕作模式,最有利于土壤有机碳累积,并提高水分利用效率和作物产量.