Lida Zhang

Prediction of protein structural class with Rough Sets

BackgroundA new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects.ResultsIn this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729–738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches.ConclusionThe results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics.

AaORA, a trichome‐specific AP2/ERF transcription factor of Artemisia annua, is a positive regulator in the artemisinin biosynthetic pathway and in disease resistance to Botrytis cinerea

· Six transcription factors of APETALA2/ethylene-response factor (AP2/ERF) family were cloned and analyzed in Artemisia annua. Real-time quantitative polymerase chain reaction (RT-Q-PCR) showed that AaORA exhibited similar expression patterns to those of amorpha-4,11-diene synthase gene (ADS), cytochrome P450-dependent hydroxylase gene (CYP71AV1) and double bond reductase 2 gene (DBR2) in different tissues of A. annua. · AaORA is a trichome-specific transcription factor, which is expressed in both glandular secretory trichomes (GSTs) and nonglandular T-shaped trichomes (TSTs) of A. annua. The result of subcellular localization shows that AaORA is targeted to the nuclei and the cytoplasm. · Overexpression and RNA interference (RNAi) of AaORA in A. annua regulated, positively and significantly, the expression levels of ADS, CYP71AV1, DBR2 and AaERF1. The up-regulated or down-regulated expression levels of these genes resulted in a significant increase or decrease in artemisinin and dihydroartemisinic acid. The results demonstrate that AaORA is a positive regulator in the biosynthesis of artemisinin. · Overexpression of AaORA in Arabidopsis thaliana increased greatly the transcript levels of the defense marker genes PLANT DEFENSIN1.2 (PDF1.2), HEVEIN-LIKE PROTEIN (HEL) and BASIC CHITINASE (B-CHI). After inoculation with Botrytis cinerea, the phenotypes of AaORA overexpression in A. thaliana and AaORA RNAi in A. annua demonstrate that AaORA is a positive regulator of disease resistance to B. cinerea.

Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.

An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development

Transcription factors play key roles in plant development through their interaction with cis-elements and/or other transcription factors. A HD-Zip IV family transcription factor, Gossypium barbadense Meristem Layer 1 (GbML1) has been identified and characterized here. GbML1 specifically bound to the L1 box and the promoters of GbML1 and GbRDL1. GbML1 physically interacted with a key regulator of cotton fibre development, GbMYB25. Truncated and point mutation assays indicated the START–SAD domain was required for the binding to the C terminal domain (CTD) of GbMYB25. GbML1 overexpression in Arabidopsis increased the number of trichomes on stems and leaves and increased the accumulation of anthocyanin in leaves. Taken together, the L1 box binding protein, GbML1 was identified as the first partner for GbMYB25 and the role of START domain was discovered to be a protein binding domain in plants. Our findings will help the improvement of cotton fibre production and the understanding of the key role of HD-Zip family and MYB family in plants.

A Cotton Annexin Protein AnxGb6 Regulates Fiber Elongation through Its Interaction with Actin 1

Annexins are assumed to be involved in regulating cotton fiber elongation, but direct evidence remains to be presented. Here we cloned six Annexin genes (AnxGb) abundantly expressed in fiber from sea-island cotton (G. barbadense). qRT-PCR results indicated that all six G. barbadense annexin genes were expressed in elongating cotton fibers, while only the expression of AnxGb6 was cotton fiber-specific. Yeast two hybridization and BiFC analysis revealed that AnxGb6 homodimer interacted with a cotton fiber specific actin GbAct1. Ectopic-expressed AnxGb6 in Arabidopsis enhanced its root elongation without increasing the root cell number. Ectopic AnxGb6 expression resulted in more F-actin accumulation in the basal part of the root cell elongation zone. Analysis of AnxGb6 expression in three cotton genotypes with different fiber length confirmed that AnxGb6 expression was correlated to cotton fiber length, especially fiber elongation rate. Our results demonstrated that AnxGb6 was important for fiber elongation by potentially providing a domain for F-actin organization.

Molecular evolution of the E8 promoter in tomato and some of its relative wild species

The E8 gene is related to ethylene biosynthesis in plants. To explore the effect of the expression pattern of the E8 gene on different E8 promoters, the molecular evolution of E8 promoters was investigated. A total of 16 E8 promoters were cloned from 16 accessions of seven tomato species, and were further analysed. The results from 19 E8 promoters including three previously cloned E8 promoters (X13437, DQ317599 and AF515784) showed that the size of the E8 promoters varied from 2101 bp (LA2150) to 2256 bp (LA2192); their sequences shared 69.9% homology and the average A/T content was 74.9%. Slide-window analysis divided E8 promoters into three regions — A, B and C — and the sequence identity in these regions was 72.5%, 41.2% and 70.8%, respectively. By searching the cis-elements of E8 promoters in the PLACE database, mutant nucleotides were found in some functional elements, and deletions or insertions were also found in regions responsible for ethylene biosysnthesis (−1702 to −1274) and the negative effect region (−1253 to −936). Our results indicate that the size of the functional region for ethylene biosynthesis in the E8 promoter could be shortened from 429 bp to 113 bp (−1612 to −1500). The results of molecular evolution analysis showed that the 19 E8 promoters could be classified into four clade groups, which is basically consistent with evolution of the tomato genome. Southern blot analysis results showed that the copy number of E8 promoters in tomato and some other wild species changed from 1 to 4. Taken together, our study provides important information for further elucidating the E8 gene expression pattern in tomato, analysing functional elements in the E8 promoter and reconstructing the potent E8 promoter.

SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides

UNLABELLED SORTALLER is an online allergen classifier based on allergen family featured peptide (AFFP) dataset and normalized BLAST E-values, which establish the featured vectors for support vector machine (SVM). AFFPs are allergen-specific peptides panned from irredundant allergens and harbor perfect information with noise fragments eliminated because of their similarity to non-allergens. SORTALLER performed significantly better than other existing software and reached a perfect balance with high specificity (98.4%) and sensitivity (98.6%) for discriminating allergenic proteins from several independent datasets of protein sequences of diverse sources, also highlighting with the Matthews correlation coefficient (MCC) as high as 0.970, fast running speed and rapidly predicting a batch of amino acid sequences with a single click. AVAILABILITY AND IMPLEMENTATION http://sortaller.gzhmc.edu.cn/.

Effect of wounding on gene expression involved in artemisinin biosynthesis and artemisinin production in Artemisia annua

Abstract-Effects of mechanical wounding on gene expression involved in artemisinin biosynthesis and artemisinin production in Artemisia annua leaves were investigated. HPLC-ELSD analysis indicated that there was a remarkable enhancement of the artemisinin content in 2 h after wounding treatment, and the content reached the maximum value at 4 h (nearly 50% higher than that in the control plants). The expression profile analysis showed that many important genes (HMGR, ADS, CPR, and CYP71AV1) involved in the artemisinin biosynthetic pathway were induced in a short time after wounding treatment. This study indicates that the artemisinin biosynthesis is affected by mechanical wounding. The possible mechanism of the control of gene expression during wounding is discussed.

Effects of Al doping on the thermoelectric performance of CoSi single crystal

Thermoelectric transport properties of CoSi1−xAlx single crystals have been measured over the temperature range from 300to973K to investigate the effects of Al substitution on the electrical resistivity, Seebeck coefficient, and thermal conductivity. The solubility limit of Al substitution for Si in CoSi is found to be in the range of 0.2⩽x<0.3. The electrical resistivity increases with increasing Al substitution x and reaches a maximum at x=0.08. When x is further increased, there is a drop in the electrical reisitivity between 300 and 550K and there is almost no change at higher temperatures. The Seebeck coefficients of CoSi1−xAlx single crystals shift towards the positive direction compared to that of the binary crystal over the entire measured temperature range. The Seebeck coefficient decreases as a function of temperature. The thermal conductivity and the figure of merit decrease significantly with increasing Al content. The decrease in thermal conductivity is mainly attributed to the additional sca...

Identification of Putative Artemisia annua ABCG Transporter Unigenes Related to Artemisinin Yield Following Expression Analysis in Different Plant Tissues and in Response to Methyl Jasmonate and Abscisic Acid Treatments

Artemisinin has attracted interest due to its medicinal value in treating malaria and its potential for use against certain cancers and viral diseases. Trichome density and capacity determine artemisinin content in Artemisia annua plants. Thus, the ATP-binding cassette transporter G (ABCG) subfamily involved in trichome cuticle development may also influence artemisinin accumulation. In this study, putative A. annua ABC transporter unigenes were identified and classified from the unigene sequences up to date in the National Center for Biotechnology Information database, and nine putative A. annua ABCG transporter unigenes that may be involved in cuticle development were selected for expression analyses. Two of them, AaABCG6 and AaABCG7, showed parallel expression pattern as two artemisinin biosynthesis-specific genes (amorpha-4, 11-diene synthase and a cytochrome P450-dependent hydroxylase, CYP71AV1) in different tissues and different leaf development stages and also showed similar induction in the plants after methyl jasmonate or abscisic acid treatments. Identification of these putative A. annua ABCG transporter unigenes could provide the basis for cloning of the full-length genes and further functional investigation to find the artemisinin relevant transporters, which could be used for improving artemisinin yield in both A. annua plants and heterologous systems using transgenic technology.