Amino acid encoding schemes from protein structure alignments: multi-dimensional vectors to describe residue types

Bioinformatic software has used various numerical encoding schemes to describe amino acid sequences. Orthogonal encoding, employing 20 numbers to describe the amino acid type of one protein residue, is often used with artificial neural network (ANN) models. However, this can increase the model complexity, thus leading to difficulty in implementation and poor performance. Here, we use ANNs to derive encoding schemes for the amino acid types from protein three-dimensional structure alignments. Each of the 20 amino acid types is characterized with a few real numbers. Our schemes are tested on the simulation of amino acid substitution matrices. These simplified schemes outperform the orthogonal encoding on small data sets. Using one of these encoding schemes, we generate a colouring scheme for the amino acids in which comparable amino acids are in similar colours. We expect it to be useful for visual inspection and manual editing of protein multiple sequence alignments.     

Reserve nutrient substance accumulation in Brassica rapa L. seeds in microgravity conditions (STS-87)

The results of study of Brassica embryo differentiation and reserve nutrient substance accumulation in the seeds were represented. Near resemblance of the spaceflight and around control embryo development was revealed. Different character of the reserve substance accumulation was noted, despite of the morphologic similarity in seeds produced in spaceflight and on the ground. It allows to consider spaceflight embryos morphologically more younger compared to the ground control.     

Photosynthetic characteristics and tolerance to photo-oxidation of transgenic rice expressing C4 photosynthesis enzymes

The photosynthetic characteristics of four transgenic rice lines over-expressing rice NADP-malic enzyme (ME), and maize phosphoenolpyruvate carboxylase (PC), pyruvate,orthophosphate dikinase (PK), and PC+PK (CK) were investigated using outdoor-grown plants. Relative to untransformed wild-type (WT) rice, PC transgenic rice exhibited high PC activity (25-fold increase) and enhanced activity of carbonic anhydrase (more than two-fold increase), while the activity of ribulose-bisphosphate carboxylase/oxygenase (Rubisco) and its kinetic property were not significantly altered. The PC transgenic plants also showed a higher light intensity for saturation of photosynthesis, higher photosynthetic CO₂ uptake rate and carboxylation efficiency, and slightly reduced CO₂ compensation point. In addition, chlorophyll a fluorescence analysis indicates that PC transgenic plants are more tolerant to photo-oxidative stress, due to a higher capacity to quench excess light energy via photochemical and non-photochemical means. Furthermore, PC and CK transgenic rice produced 22–24% more grains than WT plants. Taken together, these results suggest that expression of maize C₄ photosynthesis enzymes in rice, a C₃ plant, can improve its photosynthetic capacity with enhanced tolerance to photo-oxidation. This revised version was published online in June 2006 with corrections to the Cover Date.     

Conserved codon composition of ribosomal protein coding genes in Escherichia coli,Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics

Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of limited data from related species and widely divergent sequences with no known homologs. Here, we demonstrate that codon composition, a fusion of codon usage bias and amino acid composition signals, can accurately discriminate, in the absence of sequence homology information, cytoplasmic ribosomal protein genes from all other genes of known function in Saccharomyces cerevisiae, Escherichia coli and Mycobacterium tuberculosis using an implementation of support vector machines, SVM(light). Analysis of these codon composition signals is instructive in determining features that confer individuality to ribosomal protein genes. Each of the sets of positively charged, negatively charged and small hydrophobic residues, as well as codon bias, contribute to their distinctive codon composition profile. The representation of all these signals is sensitively detected, combined and augmented by the SVMs to perform an accurate classification. Of special mention is an obvious outlier, yeast gene RPL22B, highly homologous to RPL22A but employing very different codon usage, perhaps indicating a non-ribosomal function. Finally, we propose that codon composition be used in combination with other attributes in gene/protein classification by supervised machine learning algorithms.     

Proteomics approach to identify wound-response related proteins from rice leaf sheath

In order to avoid the complex conditions of the intact plant for simple analysis of proteins in wound-response stress, we used the detached rice leaf sheath which is a very active part of the rice seedling. Proteins were extracted from rice leaf sheath at 0, 12, 24, 48 h after cutting and separated by two-dimensional (2-D) polyacrylamide gel electrophoresis. Changes in differentially displayed proteins were found in leaf sheaths after cutting in the 0-48 h time course. Ten proteins were up-regulated, while 19 proteins were down-regulated compared with those on the four 2-D gels. Among them, 14 proteins were analyzed by N-terminal, or internal amino acid sequence. The clear functions of nine proteins could be identified. Six proteins did not yield amino acid sequence information due to their blocked N-termini. Furthermore, 11 proteins were determined by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, and identified protein database matching. It was shown that the down-regulated proteins were calreticulin (nos. 5, 6), histone H1 (no. 15) and hemoglobin (no. 17), putative peroxidase (no. 19); the up-regulated proteins were Bowman-Birk trypsin inhibitor (no. 23), putative receptor-like protein kinase (nos. 24, 25), calmodulin-related protein (no. 26), small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (no. 27), mannose-binding rice lectin (nos. 28, 29). Among all the above proteins, four (nos. 23, 24, 25, 26) have been confirmed to be wound-response proteins. The others cannot be excluded as also being related to wound-responses, such as the signal transduction-related proteins (nos. 5, 6), photosynthesis-related protein (no. 27), and stress-response proteins (nos. 19, 28, 29). This is the first time protein changes in response to wounding in rice leaf sheath have been shown.     

Photosystem II photochemistry and photosynthetic pigment composition in salt-adapted halophyte Artimisia anethifolia grown under outdoor conditions

The effects of high salinity (0-400 mmol/L NaCl) on photosystem II (PSII) photochemistry and photosynthetic pigment composition were investigated in the halophyte Artimisia anethifolia grown under outdoor conditions and exposed to full sunlight. High salinity resulted in an inhibition in plant growth and a significant accumulation of sodium and chloride in leaves. However, high salinity induced no effects on the actual PSII efficiency, the efficiency of excitation energy capture by open PSII reaction centres, photochemical quenching, and non-photochemical quenching at midday. High salinity also induced neither changes in the maximum efficiency of PSII photochemistry, the efficiency with which a trapped exciton can move an electron into the electron transport chain further than QA and the quantum yield of electron transport beyond QA, nor changes in absorption, trapping and electron transport fluxes per PSII reaction centre. No significant changes were observed in the levels of neoxanthin, lutein, beta-carotene, violaxanthin, antheraxanthin, and zeaxanthin expressed on a total chlorophyll basis in salt-adapted plants. Our results suggest that Artimisia anethifolia showed high resistance not only to high salinity, but also to photoinhibition even if it was treated with high salinity as high as 400 mmol/L NaCl and exposed to full sunlight. The results indicate that tolerance of PSII to high salinity and photoinhibition can be viewed as an important strategy for Artimisia anethifolia, a halophyte plant, to grow in very high saline soil.     

Strong-light photoinhibition treatment accelerates the changes of protein secondary structures in triton-treated photosystem I and photosystem II complexes

Changes in the protein secondary structure and electron transport activity of the Triton X-100-treated photosystem I (PSI) and photosystem II (PSII) complexes after strong illumination treatment were studied using Fourier transform-infrared (FT-IR) spectroscopy and an oxygen electrode. Short periods of photoinhibitory treatment led to obvious decreases in the rates of PSI-mediated electron transport activity and PSII-mediated oxygen evolution in the native or Triton-treated PSI and PSII complexes. In the native PSI and PSII complexes, the protein secondary structures had little changes after the photoinhibitory treatment. However, in both Triton-treated PSI and PSII complexes, short photoinhibition times caused significant loss of -helical content and increase of -sheet structure, similar to the conformational changes in samples of Triton-treated PSI and PSII complexes after long periods of dark incubation. Our results demonstrate that strong-light treatment to the Triton-treated PSI and PSII complexes accelerates destruction of the transmembrane structure of proteins in the two photosynthetic membranes.     

Utilization of the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold in the design of potent inhibitors of serine proteases: SAR studies using carboxylates

A series of carboxylate derivatives based on the 1,2,5-thiadiazolidin-3-one 1,1 dioxide and isothiazolidin-3-one 1,1 dioxide scaffolds has been synthesized and the inhibitory profile of these compounds toward human leukocyte elastase (HLE), cathepsin G (Cat G) and proteinase 3 (PR 3) was then determined. Most of the compounds were found to be potent, time-dependent inhibitors of elastase, with some of the compounds exhibiting k(inact)/K1 values as high as 4,928,300 M(-1) s(-1). The inhibitory potency of carboxylate derivatives based on the 1,2,5-thiadiazolidin-3-one 1,1 dioxide platform was found to be influenced by both the pKa and the inherent structure of the leaving group. Proper selection of the primary specificity group (R(I)) was found to lead to selective inhibition of HLE over Cat G, however, those compounds that inhibited HLE also inhibited PR 3, albeit less efficiently. The predictable mode of binding of these compounds suggests that, among closely-related serine proteases, highly selective inhibitors of a particular serine protease can be fashioned by exploiting subtle differences in their S' subsites. This study has also demonstrated that the degradative action of elastase on elastin can be abrogated in the presence of inhibitor 17.     

一株猴泡沫病毒野毒Pol基因的cDNA的直接测序

A 377 Kunming cell line of Rhesus Monkey Kidney (RMK) from Centre for Medical Pr imates was amplified the cDNA fragments of the pol gene by Nested-PCR,which of a natured infected SFV showed typical CPE after cultured for three weeks,sequence s of products position(nt 5989-6343)were determined directly.The result indicate d that the nucleotid sequences in the region had 48 nucleotids difference(10.78% ) between SFV infected cell and SFV-1 in GENE BANK,and there was 45 nucleotides difference(10.11%) compared with SFVmac in the region, the test with VspⅠ showe d aligment.