Biomedical subjects

Dapeng Zhang

Publications and source records attributed to Dapeng Zhang.

11 recordsLinked to original sources

PubMed2025

A chromosome-level genome assembly of Coffea arabica L. var. 'Kona Typica'.

Coffea arabica L. var. 'Kona Typica' is renowned for its premium cup quality, but its vulnerability to pests and diseases limits production. To accelerate cultivar improvement, we generated a chromosome-level genome assembly of 'Kona Typica' using PacBio HiFi sequencing and Hi-C scaffolding technology. The final assembly spans 1.13 Gb, with a scaffold N50 of 50.50 Mb, organized into 22 chromosomes. BUSCO assessment indicated a high completeness at 99.1%. We annotated 65,458 protein-coding genes and identified 1,073,545 interspersed repeats, accounting for 65.16% of the genome. Analysis of transposon insertion ages revealed that most long terminal repeat retrotransposons proliferated after the polyploidization event. This high-quality genome assembly of 'Kona Typica' provides a valuable resource for exploring coffee genomic evolution and genetic mechanisms of complex traits, facilitating genomics studies and the development of improved coffee cultivars with enhanced disease resistance and quality traits.

Coffea↗

PubMed2006

Estimating the population of female sex workers in two Chinese cities on the basis of the HIV/AIDS behavioural surveillance approach combined with a multiplier method.

OBJECTIVE: To estimate the size of the population of female sex workers (FSWs) on the basis of the HIV/AIDS behavioural surveillance approach in two Chinese cities, using a multiplier method. METHOD: Relevant questions were inserted into the questionnaires given to two behavioural surveillance groups-female attendees of sexually transmitted disease (STD) clinics and FSWs. The size of the FSW population was derived by multiplying the number of FSWs in selected STD clinics during the study period by the proportion of FSW population who reported having attended the selected STD clinics during the same period. RESULTS: The size of the FSW population in the urban area of Xingyi, China, was estimated to be about 2500 (95% CI 2000 to 3400). This accounted for 3.6% of the total urban adult female population. There were an estimated 17,500 FSWs in the urban area of Guiyang, China (95% CI 10,300 to 31,900) or about 3.4% of its total urban adult female population (rounded to the nearest 100). CONCLUSIONS: The multiplier method could be a useful and cost-effective approach to estimate the FSW population, especially suitable in countries where HIV behavioural surveillance has been established in high-risk populations.

Adult↗

PubMed2006

Preparation and characterization of recombinant protein ScFv(CD11c)-TRP2 for tumor therapy from inclusion bodies in Escherichia coli.

Dendritic cells (DCs)-based immunotherapy represents an approach to the prevention and treatment of cancers. Targeting antigens to receptors on DCs can be expected to enhance immune response. We have constructed an expression vector pET32a(+)-ScFv(CD11c)-TRP2 based on a single-chain antibody fragment (ScFv) that targets the high affinity receptor CD11c which is expressed on murine DCs. The 3'-terminal end of the ScFv was ligated to the gene for MHC class I molecule-recognized peptide from mouse tyrosine-related protein 2 (TRP2). Using this vector, we have expressed and purified ScFv(CD11c)-TRP2, a fusion protein that could target TRP2 peptide to CD11c on DCs in vivo to elicit anti-tumor responses. This fusion protein was expressed in inclusion bodies in Escherichia coli BL21(DE3) and was refolded and purified on-column effectively by immobilized metal affinity chromatography using His-tag. Flow cytometry assays showed the specific binding ability of ScFv(CD11c)-TRP2 to DCs, which could be blocked by a hamster anti-mouse CD11c produced by N418 hybridoma. Further studies demonstrated that ScFv(CD11c)-targeted TRP2 peptide processed by DCs was capable of stimulating T cells proliferation. Thus, this fusion protein provides a basis for further research in cancer therapy in vivo.

Animals↗

PubMed2006

SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation.

Since packaging of DNA in the chromatin structure restricts the accessibility for regulatory factors, chromatin remodeling is required to facilitate nuclear processes such as gene transcription, replication, and genome recombination. Many conserved non-enzymatic protein domains have been identified that contribute to the activities of multiprotein remodeling complexes. Here we identified a novel conserved protein domain in Eukaryota whose putative function may be in regulating chromatin remodeling. Since this domain is associated with a known SANT domain in several vertebrate proteins, we named it the SANTA (SANT Associated) domain. Sequence analysis showed that the SANTA domain is approximately a 90 amino acid module and likely composed of four central beta-sheets and three flanking alpha-helices. Many hydrophobic residues exhibited high conservation along the domain, implying a possible function in protein-protein interactions. The SANTA domain was identified in mammals, chicken, frog, fish, sea squirt, sea urchin, worms and plants. Furthermore, a phylogenetic tree of SANTA domains showed that one plant-specific duplication event happened in the Viridiplantae lineage.

Amino Acid Sequence↗

PubMed2006

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

BACKGROUND AND AIMS: Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS: Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS: Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS: These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

Cacao↗

PubMed2006

Integration of membrane and nuclear estrogen receptor signaling.

The classical mechanism of estradiol (E2) action is mediated by the nuclear estrogen receptors ERalpha and ERbeta, which function as ligand-dependent transcription factors that regulate transcription of target genes containing the consensus estrogen response element (ERE) in their promoter regions. However, accumulating evidence indicates that E2 can also exert its actions through a unique membrane estrogen receptor (mER). Upon activation of the mER, various signaling pathways (i.e. Ca(2+), cAMP, protein kinase cascades) are rapidly activated and ultimately influence downstream transcription factors. Some target genes of the mER pathway may be activated independently of the nuclear estrogen receptor (nER). Additionally, it has been shown that classical nER action can be modulated by mER-initiated signaling through phosphorylation of nER and its coactivators, and by induction of third messengers (i.e. cyclin D1 and c-fos). Based on current evidence, we propose a model for E2 action integrating distinct membrane receptor and nuclear receptor signaling. This membrane receptor-nuclear receptor interaction is likely to exist for other hormones. Steroid hormones and other hormones acting through hormone receptors in the steroid receptor superfamily (i.e. thyroid hormones) also activate many of the same intracellular signaling cascades, which provides the basis for extensive crosstalk networks between hormones. The model proposed serves as a framework to investigate the diverse actions of hormones and endocrine disrupting chemicals (EDCs).

Animals↗

PubMed2005

Inter- and intra-specific variation among five Erythroxylum taxa assessed by AFLP.

BACKGROUND: and Aims The four cultivated Erythroxylum taxa (E. coca var. coca, E. novogranatense var. novogranatense, E. coca var. ipadu and E. novogranatense var. truxillense) are indigenous to the Andean region of South America and have been cultivated for folk-medicine and, within the last century, for illicit cocaine production. The objective of this research was to assess the structure of genetic diversity within and among the four cultivated alkaloid-bearing taxa of Erythroxylum in the living collection at Beltsville Agricultural Research Center. METHODS: Amplified fragment length polymorphism (AFLP) fingerprinting was performed in 86 Erythroxylum accessions using a capillary genotyping system. Cluster analysis, multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) were used to assess the pattern and level of genetic variation among and within the taxa. KEY RESULTS: A clear distinction was revealed between E. coca and E. novogranatense. At the intra-specific level, significant differentiation was observed between E. c. var. coca and E. c. var. ipadu, but the differentiation between E. n. var. novogranatense and E. n. var. truxillense was negligible. Erythroxylum c. var. ipadu had a significantly lower amount of diversity than the E. c. var. coca and is genetically different from the E. c. var. ipadu currently under cultivation in Colombia, South America. CONCLUSIONS: There is a heterogeneous genetic structure among the cultivated Erythroxylum taxa where E. coca and E. novogranatense are two independent species. Erythroxylum coca var. coca is most likely the ancestral taxon of E. c. var. ipadu and a founder effect may have occurred as E. c. var. ipadu moved from the eastern Andes in Peru and Bolivia into the lowland Amazonian basin. There is an indication of artificial hybridization in coca grown in Colombia.

Coca↗

PubMed2005

A study on methods of estimating the population size of men who have sex with men in Southwest China.

OBJECTIVE: To ascertain practical methods of estimating the population size of men who have sex with men (MSM) by field application. METHODS: Nine public places were selected, where men who have sex with men (MSM) frequented. Capture-recapture method and multiplier method were used to count the number of men who have sex with men (MSM) in the assigned places in 10 days. RESULTS: The population size estimated using multiplier method counted 877. Three estimates produced by capture-recapture method were 1408 (95% CI: 1116-1908), 1207 (95% CI: 932-1712) and 949 (95% CI: 757-1272), respectively. CONCLUSIONS: Multiplier method was easy and smooth in practice and produced highly reliable results, which yet was expensive. The application of capture-recapture method cost less in both time and funds, and the three results produced could verify each other, which was fit for the estimation.

China↗

PubMed2005

Construction and characterization of a humanized anti-human CD3 monoclonal antibody 12F6 with effective immunoregulation functions.

12F6 is a murine anti-human CD3 monoclonal antibody, which competes with OKT3 for binding to human T cells and possesses more effective T-cell suppression and activation properties compared to OKT3. It thus exhibits the potential to be developed as an immunoregulation agent for manipulating T-cell functions and preventing acute allograft rejection. In an attempt to minimize the immunogenicity of murine 12F6 (m12F6) for potential clinical application, a humanized version of 12F6, denoted as hu12F6, was successfully constructed by complementary determining region (CDR) grafting and shown to maintain both T-cell activation and suppression activities similar to m12F6. Furthermore, in order to reduce the first dose reaction syndrome caused by T-cell activation following the first administration of anti-CD3 antibodies, two amino acid mutations were introduced into the Fc region of hu12F6, resulting in the Fc-mutated 12F6 humanized antibody (hu12F6mu). This Fc-mutated version displayed a similar antigen-binding affinity and specificity compared with hu12F6 and m12F6 but with much weaker FcR binding activity. hu12F6mu was shown to be much less potent in the induction of T-cell proliferation, cytokine release (tumour necrosis factor-alpha, interferon-gamma and interleukin-10) and early activation marker expression on the cell surface (CD69 and CD25) than parental 12F6 and OKT3 did. In contrast, hu12F6mu was effective in modulating T-cell receptor/CD3 and inhibiting mixed lymphocyte reaction with a similarity as compared to m12F6 and OKT3. In conclusion, the resultant hu12F6mu was much less mitogenic to T cells but retained potent immunosuppression, suggesting it might be an alternative to OKT3 as an immunosuppressive drug with less immunogenicity and toxicity for clinical application.

Amino Acid Sequence↗

PubMed2004

FADD and its phosphorylation.

The adaptor protein FADD is essential for apoptosis induced by 'death receptors', mediating aggregation and autocatalytic activation of caspase-8. Surprisingly, FADD is also involved in regulating T and B cell development. Accumulating evidences now suggest that FADD and its phosphorylation have additional roles in controlling pathways of cellular activation and proliferation, while the kinase modifying FADD phosphorylation is still unidentified. The cellular localization of FADD may also contribute to define FADD's role in apoptosis or proliferation. FADD may be a pivotal molecule which coupling the opposite cell processes of proliferation and apoptosis. FADD, probably modulated by phosphorylation, may function as a 'cell renewal set point' co-regulating proliferation and apoptosis in parallel.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Gene expression activity and pathway selection for sucrose metabolism in developing storage root of sweet potato.

Development of sweet potato (Ipomoea batatas) storage root coincides with starch accumulation made using cleaved products of imported photoassimilate sucrose. The genes and pathways are predominantly active for sucrose metabolism in developing storage root were unknown. In this study, we used both an expressed sequence tag (EST) approach and a reverse transcription-polymerase chain reaction (RT-PCR) approach to answer this question. Sucrose synthase (SuSy) was found to be significantly more frequent in storage root ESTs than in fibrous root ESTs. SuSy was the most abundant carbohydrate-metabolism gene in the storage-root ESTs. RT-PCR results confirmed this by showing that invertase was active in fibrous roots but rapidly decreased to an undetectable level during storage root development while SuSy became predominant. Invertase expression was also detectable in young immature storage root and shoot tips, suggesting an involvement in cell formation. SuSy expression pattern showed considerable similarity to that of ADP-glucose pyrophosphorylase, an essential enzyme for starch synthesis. The results indicated that (i). SuSy was the most actively expressed enzyme in sucrose metabolism in developing storage root and was correlated with sink strength, and (ii). whereas invertase was active at cell formation stages, SuSy pathway was predominant for sucrose cleavage related to starch-accumulation.

Base Sequence↗