EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

Background  

We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment.     

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.     

Vertical distribution of female adults and larval offspring of the white grub <Emphasis Type="Italic">Dasylepida ishigakiensis</Emphasis> (Coleoptera: Scarabaeidae) in the soil of a sugarcane field on Miyako Island,Okinawa

To determine the depth of soil at which mated females of the white grub beetle Dasylepida ishigakiensis Niijima et Kinoshita oviposited and their larval offspring stayed in the soil in different seasons, 847 mated female and male adults were released into a caged sugarcane field on Miyako Island. We then excavated this field systematically to collect adults and their larval offspring in the soil once or twice per month from 24 April 2002 to 31 March 2003. Dead females were found between 10 and 50 cm deep in the soil (N = 91), but most frequently in the layer 30–40 cm deep (N = 42; 46.2%). They were recovered more frequently in the soil at the plant foot (N = 73; 80.2%) than in the furrows (N = 18; 19.8%). On the other hand, no male carcass was discovered either in the soil or on the ground surface. The number of larvae discovered in the soil per row was large on 30 April (N = 52.5) and on 5 June (N = 58.3), when they were at the first instar. It decreased rapidly thereafter until 21 August (N = 9.5), when they molted to the second instar, and remained at similar levels through to the following 31 March (N = 8.0), during which they were mostly at the third instar. The larvae were found at various soil depths ranging from 0 to 70 cm, but the majority were found between 10 and 30 cm deep. The last sampling on 31 March indicated that mature larvae moved to a deeper layer for estivation. These results suggested that physical control through rotary tillage before they move to the deeper layer may be effective.     

Genetic suppression analysis in novel vacuolar processing enzymes reveals their roles in controlling sugar accumulation in tomato fruits

In plant cells, many vacuolar proteins are synthesized as precursors in the endoplasmic reticulum and are subsequently transported to the vacuole. These precursors are subject to post-translational modifications to allow the active mature forms to be produced. Vacuolar processing enzyme (VPE) has been identified as a family of cysteine proteases involved in protein maturation in the vacuole. In this study, novel VPE genes were isolated from tomato (Solanum lycopersicum), and they were designated SlVPE1-SlVPE5. Phylogenic analysis suggested that SlVPE1 and SlVPE2 were categorized as the seed coat type, SlVPE4 was categorized as the seed type, and both SlVPE3 and SlVPE5 were categorized as the vegetative type. Expression analysis demonstrated that these genes were expressed during fruit development, and that their expression profiles agreed with this classification. High VPE enzyme activity was observed during tomato fruit development; the enzyme activity was correlated with the SlVPE mRNA levels, indicating that the SlVPE encoded active VPE proteins. The total sugar content was higher in RNA interference (RNAi) lines compared with the control plants, suggesting negative roles for SlVPE in sugar accumulation. The quantitative expression analysis of each SlVPE gene in the RNAi lines suggested that the suppression of SlVPE5 probably had the strongest effect on the sugar accumulation observed. The suppression of SlVPE did not influence the total amino acid content, suggesting that the molecular targets of SlVPE were mainly involved in sugar accumulation.     

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.     

Immunohistochemical identification of aquaporin 2 in the kidneys of young beef cattle

Aquaporin 2 (AQP2) is a small, integral tetrameric plasma membrane protein that is expressed in mammalian kidneys. The specific constitution of this protein and its selective permeability to water means that AQP2 plays an important role in hypertonic urine production. Immunolocalization of AQP2 has been studied in humans, monkeys, sheep, dogs, rabbits, rats, mice and adult cattle. We analyzed the expression of AQP2 in kidneys of 7-month-old Polish-Friesian var. black and white male calves. AQP2 was localized in the principal cells of collecting ducts in medullary rays penetrating the renal cortex and in the collecting ducts of renal medulla. AQP2 was expressed most strongly in the apical plasma membrane, but expression was observed also in the intracellular vesicles and basolateral plasma membrane. Our study provides new information concerning the immunolocalization of AQP2 in calf kidneys.     

Efficacy of agar-plate culture in detection of Strongyloides stercoralis infection

Agar-plate culture of feces using a modified petri dish proved to be highly efficient in the detection of Strongyloides stercoralis infection. Furrows left by S. stercoralis on the agar plate were distinguished readily in size from those left by Necator americanus.     

Identification of the N-terminal residue of the heavy chain of both native and recombinant human hepatocyte growth factor.

The N-terminal amino acid of the heavy chain of native (purified from human plasma) and recombinant human hepatocyte growth factor (hHGF) was determined by analyses of amino acid composition and sequence of peptide fragments derived by enzymatic cleavage, peptide mapping, and fast atom bombardment mass spectrometry. Our results indicate that the N-terminal amino acid of the heavy chain of hHGF, both native and recombinant, is pyroglutamate, derived from glutamine at the 32nd residue from the initiation methionine.