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Cheng Lu

Publications and source records attributed to Cheng Lu.

31 records · Page 2Linked to original sources
PubMed2005

SilkDB: a knowledgebase for silkworm biology and genomics.

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a approximately 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

Animals↗
PubMed2005

Analysis of cytochrome P450 genes in silkworm genome (Bombyx mori).

We have searched the Bombyx mori genome for members of the major enzyme family, the Cytochrome P450s, which carry out multiple reactions to enable organisms to rid themselves of foreign compounds. As a result, 86 putative P450s were discovered in silkworm genome, which are thought to belong to 32 subfamilies. A comparative genomic analysis with Drosophila melanogaster reveals that the two insects have some similar P450 distribution patterns but still have some obvious differences. Especially, the diverse distribution exists in 7 p450 subfamilies, which are CYP4A, CYP4C, CYP4D, CYP6A, CYP6AE, CYP6B and CYP9A. Furthermore, we collected expression sequence tag (EST) evidence for 49 putative P450s genes, which are expressed at the transcriptional level and more likely to be true P450s.

Animals↗
PubMed2005

[Pridiction of the Sex-effects of the Cocoon Quality Characters in Silkworm.].

In this paper , the sex-effects of the cocoon quality characters in silkworm was predicted with Mixed linear model úThe fact that the probability of effect variance and predictability of random gender of whole cocoon weight, cocoon shell weight, ratio of cocoon shell and pupa weight reached a level of extreme significance showed that the gender effect of the four traits was extremely significant, which matched with the reality completely. The predictive values of gender effect of the four traits of female(male) were 0.248g (-0.247g), 2.423cg(-2.394)cg, -1.976%(1.992%) and 0.224g(-0.223g) respectively. Each trait showed single peak distribution after adjusting by sex-effects, which fitted for the request that quantitative traits should show continuously normal standard distribution if QTL analysis was taken.

Animals↗
PubMed2005

[Study on location of QTLs controlling cocoon traits in silkworm].

On the basis of the molecular linkage map, mapmaker software QTLMapper 2.0 was used to analyze the QTLs effect of the whole cocoon weight,cocoon shell weight, ratio of cocoon shell and pupa weight of domestic silkworm. For these four cocoon quantitative traits, 7, 6, 2 and 8 effective QTLs were detected and mapped to 7, 5, 2 and 7 linkage groups, respectively. Complicated epistatic effects were found involved in the genetic variation of the whole cocoon weight and cocoon shell weight. For the whole cocoon weight, there were three pairs of QTLs with significant additive by additive interactions, in which, one pair had significant additive by dominance and dominance by dominance interactions. Whereas significant dominance were detected for three QTLs and significant additive effects one QTL had. For the cocoon shell weight, significant genetic effects, including epistatic effects were found for one pair of QTLs, significant dominance by dominance interaction for another pair of QTLs; one QTL had significant dominance and another QTL had additive by additive interaction. The ratio of cocoon shell and the pupa weight were controlled mainly by additive or dominance effects. No interaction between QTL was found for the ratio of cocoon. Most QTLs, associated with the pupa weight, had negative dominance effects. Only significant additive by additive interaction was found between one pair of QTLs. The 2nd, 3rd, 4th, 11th, 13th, 24th, 34th, 37th, and 40th linkage groups are the common chromosomal regions harboring QTLs of two or more cocoon quantitative traits. There are identical QTL or chromosomal region for the whole cocoon weight and cocoon shell weight, indicating they can be simultaneously improved by utilizing epistatic effects in breeding.

Animals↗
PubMed2005

[Antioxidant and anti-inflammatory effects of cyanidin from cherries on rat adjuvant-induced arthritis].

OBJECTIVE: To assess the possible antioxidant and anti-inflammatory activity of cyanidin from cherries on adjuvant induced arthritis (AA) in SD rats. METHOD: Arthritis was induced by the complete Freud's adjuvant in male Sprague Dauley rats and assessed based on paw swelling. Rats were randomly divided into normal group (NM), adjuvant arthritis group (AA) and three cyanidin-treated groups in high dosage (HA), middle dosage (MA), and low dosage (LA). The morphological changes in the hind limbs were conducted under a light microscope. We detected glutathione (GSH) in whole blood and malonaldehyde (MDA), superoxide dismutase (SOD), total antioxidative capacity (T-AOC) activity in serum by special kits to assess the antioxidant effects of cyanidin on AA. Moreover, the prostaglandin E2 (PGE2) levels in paw tissues were determined by radioimmunoassay and TNF-alpha levels in serum were determined using ELISA kits specific for rat. RESULT: The cyanidin could protect against the paws swelling in AA rats. From the day 14 after AA induction, the swellings of the cyanidin treated groups at high dosage and low dosage were significantly reduced compared with the model group (P < 0.05, 0.01). Histological examination of sections through the hind limbs revealed alleviation of inflammatory reaction in the joint after the treatment. The cyanidin at high and low dosage could increase the GSH, SOD activity and T-AOC levels in whole blood or serums and decrease MDA in AA rats (P < 0.01). The cyanidin could decrease the PGE2 levels in paw tissues and the TNF-alpha levels in serum at high and low dosages (P < 0.01). CONCLUSION: The cyanidin could protect against the paws swelling in AA rats, and alleviate the inflammatory reaction in the joint, and the mechanism might be via the increase activity of GSH, SOD and T-AOC that improve the total antioxidative capacity and scavenge the free radicals, perhaps as a result of that the levels of the PGE2 in paw tissues and TNF-alpha contents in serum were decreased. The results suggest that the cyanidin from cherries could be one of the potential candidates for the alleviation of arthritis.

Animals↗
PubMed2004

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

Algorithms↗
PubMed2004

Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes.

Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mouse, 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%-76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.

Animals↗
PubMed2004

QTL mapping of economically important traits in silkworm (Bombyx mori).

A backcrossed population (BC1) was derived from a cross between C100 and Dazao. AFLP technique was employed for mapping the QTLs. The QTLs for the whole cocoon weight, cocoon shell weight, ratio of cocoon shell, weight of pupae etc. were analyzed and 11 QTLs were detected based on the constructed linkage map. Two QTLs for whole cocoon weight were localized on linkage group 6 and 19; three QTLs for cocoon shell weight were localized on linkage group 3, 14 and 19; three QTLs for ratio of cocoon shell were localized on the linkage group 2, 11 and 15, and three QTLs for the weight of pupae were localized on linkage 2, 14 and 19. All these have laid an important base for the marker assisted breeding of the silkworm.

Animals↗
PubMed2004

[Construction of AFLP molecular markers linkage map and localization of green cocoon gene in silkworm (Bombyx mori)].

Based on an improved method of AFLP, AFLP markers were employed for construction of a linkage map and localization of Gc gene used a set of 44 backcross lines( BC1) of silkworm ( Bombyx mori) as a mapping population. In this work, all together 3 956 bands were obtained by 28 pairs of primers and 141.3 bands each primer pair on average. Among them 2 836 bands were in good agreement with the segregation pattern. A total of 1 018 (25.7%) polymorphic AFLP markers were detected. The 693 (68.1%) of polymorphic markers with 1:1 segregation ratio ( P < or = 0.05) were obtained. Furthermore,The analytical model was based on the backcross type and the parameters were set as following: LOD = 3.0, maximum recombination value of 0. 20 and use the command ' group', 'compare', 'try', 'map' and 'ripple' to construct the linkage maps. 407 of the 693 loci were chi2 tested in agreement with 1:1 segregation were divided into 33 linkages by Mapmaker/Exp(Version 3.0), with a total map distance of 3 676.7 cM and a mean distance of 9.1 cM between markers. The morphological gene Gc was located between L-P4T6-107 and L-PT6T4-84 on linkage group 22. In addition, 286 markers were not included in the linkage groups. The efficiency of loci mapping was 58.7%. Among the 33 linkage groups, the morphological marker Gc classically localized on linkage group 15 was relocated on linkage group 22 on the map, suggesting that this molecular linkage group corresponds to linkage group 15 on the linkage map based on morphological characters. All these have laid an important base for the marker assisted breeding of the silkworm.

Animals↗
PubMed2004

Analysis of microsatellites derived from bee Ests.

To accelerate the molecular analysis of genetics,evolution and behavior, etc. in the honey bee (Apis), the frequency and density of simple sequence repeats (SSRs) have been analyzed from the bee EST (expressed sequence tag) database comprising 15 869 sequences amounting to 7.9 Mb. Results showed that the frequency of SSRs was 1/0.52 kb in bee ESTs, and hexanucleotide repeats (45.0%) motifs appeared to be the most abundant type in bee,the dinucleotide, mononucleotide, trinucleotide, tetranucleotide and pentanucleotide repeats are 17.9%, 14.1%, 11.6%, 9.2% and 2.2%, respectively. Meanwhile, the A-rich repeats are predominant in each type of SSRs, such as A, AT, AG, AC, AAT, AAG, AAC, AAAT, AAAG, AAAAG, AAAAT, AATAT, AAAAAG and AAAAAT repeats, whereas G-rich repeats are rare in the coding regions. The further analysis suggests that, apart from minor deviations, there is no significant difference in the distribution and density of microsatellites in the redundant and non-redundant set of bee ESTs. Furthermore, the availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in bee.

Animals↗
PubMed2002

[Heat shock activated Rac-MEKK-JNK pathway and hsp90 beta gene expression].

OBJECTIVE: To study the effect of Rac-MEKK-JNK (Rac-mitogen activated protein kinase kinase kinase-C-jun N-terminal protein kinase) signal pathway on heat shock-induced hsp90 beta gene expression and the impact of Hsp90 on the regulation of the pathway. METHODS: DN-Rac, DN-MEKK or DN-JNK were cotransfected with hsp90 beta CAT reporter plasmid beta 3.1 into Jurkat or LETPa-2 cells individually, the CAT mRNA expression was then determined quantitatively by competitive RT-PCR based system. Western blot was carried out to detect the expression level and phosphorylation of c-Jun in Jurkat and LETPa-2 cells that were transfected with DN-Rac, DN-MEKK or DN-JNK. By in vitro kinase activity assay and Western blot, the effect of geldnamycin (GA) on heat induced JNK activity were evaluated. RESULTS: In Jurkat cell transfected with DN-Rac, DN-MEKK or DN-JNK, heat shock induced relative CAT mRNA expression level was decreased to (72.8 +/- 5)%, (60 +/- 13.2)% and (47.7 +/- 12.1)% of the control respectively; while in LETPa-2 cell hsp90 beta 3.1 reporter gene expression was accordingly suppressed to (16.17 +/- 5.1)%, (50.2 +/- 8.7)% and (47.5 +/- 10)% of control. C-Jun expression and phosphorylation were inhibited by the transfection of either one of DN-Rac, DN-MEKK or DN-JNK. With GA treatment, heat shock induced JNK activity was repressed, while the expression level of JNK or c-Jun was not obviously changed. CONCLUSIONS: Rac-MEKK-JNK pathway promotes heat shock induced hsp90 beta gene expression and hsp90 may participate in the regulation of heat shock activated Rac-MEKK-JNK signal pathway in both Jurkat and LETPa-2 cells.

Benzoquinones↗