A5073888497- Genomics and Phylogenetic Studies
- Glycosylation and Glycoproteins Research
- Carbohydrate Chemistry and Synthesis
- Galectins and Cancer Biology
- Genetic diversity and population structure
- Forest Ecology and Biodiversity Studies
- Proteoglycans and glycosaminoglycans research
- Botany and Plant Ecology Studies
- Photosynthetic Processes and Mechanisms
- Forest Insect Ecology and Management
- Plant Gene Expression Analysis
- Plant Disease Resistance and Genetics
- Plant and Fungal Species Descriptions
- Chromosomal and Genetic Variations
- Yeasts and Rust Fungi Studies
- Protein Kinase Regulation and GTPase Signaling
- Plant nutrient uptake and metabolism
- Protist diversity and phylogeny
- Lichen and fungal ecology
- Plant and animal studies
- Genetic and phenotypic traits in livestock
- Cocoa and Sweet Potato Agronomy
- Protein Tyrosine Phosphatases
- Legume Nitrogen Fixing Symbiosis
- Genetic Mapping and Diversity in Plants and Animals
Jinan University
2018-2022
UMR BIOdiversity, GEnes & Communities
2010-2018
Centre d'Études Scientifiques et Techniques d'Aquitaine
2012-2018
Xishuangbanna Tropical Botanical Garden
2012-2016
Chinese Academy of Sciences
2014-2016
University of Gothenburg
2004-2016
Université de Bordeaux
2012-2015
Mucins are proteins that cover and protect epithelial cells characterized by domains rich in proline, threonine, serine heavily glycosylated (PTS or mucin domains). Because of their sequence polymorphism, these cannot be used for evolutionary analysis. Instead, we have made use the von Willebrand D (VWD) SEA domains, typical mucins. A number animal genomes were examined to identify homologues, resulting phylogenetic studies. The frog Xenopus tropicalis stands out because gel-forming mucins...
The gel-forming mucins are large glycosylated proteins that essential components of the mucus layers covering epithelial cells. Using novel methods identifying based on profile hidden Markov models, we have found a number such in Metazoa, aiding their classification and allowing evolutionary studies. Most vertebrates 5–6 mucin genes genomic arrangement these is well conserved throughout vertebrates. An exception frog Xenopus tropicalis with an expanded repertoire at least 26 this type....
Abstract Loci considered to be under selection are generally avoided in attempts infer past demographic processes as they do not fit neutral model assumptions. However, opportunities better reconstruct some aspects of demography might thus missed. Here we examined genetic differentiation between two sympatric E uropean oak species with contrasting ecological dynamics ( Q uercus robur and petraea ) both outlier (i.e. loci possibly affected by divergent or hitchhiking effects genomic regions...
The KNOX (KNOTTED1-like homeobox) transcription factors play a pivotal role in leaf and meristem development. majority of these proteins are characterized by the KNOX1, KNOX2, ELK homeobox domains whereas KNATM family contain only domains. We carried out an extensive inventory here report on total 394 from 48 species. land plant fall into two classes (I II) as previously shown where class I seems to be most closely related green algae homologs. restricted Eudicots some species have multiple...
Abstract Background Mucins are large glycoproteins that cover epithelial surfaces of the body. All mucins contain at least one PTS domain, a region rich in proline, threonine and serine. also characterized by von Willebrand D (VWD) domains or SEA domains. We have developed computational methods to identify mucin genes proteins based on these properties proteins. Using such we able characterize different organisms where genome sequence is available with respect their repertoire. Results here...
An Illumina Infinium SNP genotyping array was constructed for European white oaks. Six individuals of Quercus petraea and Q. robur were considered discovery using both previously obtained Sanger sequences across 676 gene regions (1371 in vitro SNPs) Roche 454 technology from 5112 contigs (6542 putative silico SNPs). The 7913 SNPs genotyped the six parental individuals, full-sib progenies (one within each species two interspecific crosses between robur) three natural populations south-western...
Mucins are large glycoproteins characterized by mucin domains that show little sequence conservation and rich in the amino acids Ser, Thr, Pro. To effectively predict mucins from genomic protein sequences obtained genome projects, we developed a strategy based on acid compositional bias characteristic of domains. This is combined with an analysis other features commonly found mucins. Our method has now been used to puffer fish Fugu rubripes were previously not identified or annotated. At...
The DNA sequence of the two human mucin genes MUC2 and MUC6 have not been completely resolved due to repetitive nature their central exon coding for Proline, Threonine Serine rich sequences. exact nucleotide these exons has remained unknown a long time limitations in traditional sequencing techniques. These are still very poorly covered new whole genome projects with corresponding protein sequences partly missing. We used BAC clone containing both third generation technology, SMRT...
The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need evaluate impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. In this study, analysed transcriptome four tropical species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae Myristicaceae). We sequenced...
Using next-generation sequencing, we developed the first whole-genome resources for two hybridizing Nothofagus species of Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control optimization putative chloroplast gene map yielded ~32,000 contigs from 43% reads produced. With 12.5% assembled reads, covered ~96% genome ~70% mitochondrial content, providing functional structural annotations 112...
The Src homology-2 domain containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders act as oncogenic drivers hematologic cancers. activated by phosphopeptide binding to the N-SH2 domain, triggering release from catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening cleft serves key “allosteric switch” driving activation. To...
Predicting protein domains is essential for understanding a protein’s function at the molecular level. However, up till now, there has been no direct and straightforward method predicting in species without reference genome sequence. In this study, we developed functionality with set of programs that can predict directly from genomic sequence data genome. Using whole data, programming mainly comprised DNA assembly combination next-generation sequencing (NGS) methods traditional methods,...
Human tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to the formation selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins distinct group that attached epithelial cell where they create dense glycocalyx facing extracellular environment. All mucin carry long stretches tandemly repeated sequences undergo extensive O-linked glycosylation form linear domains. However,...
Abstract Mucins are large glycoproteins that cover and protect epithelial surface of the body. Mucin domains gel-forming mucins rich in proline, threonine, serine heavily glycosylated. These show great complexity with tandem repeats, thus make it difficult to study sequences. With coming single molecule real-time (SMRT) sequencing technologies, we manage present sequence structure mucin via SMRT long reads for MUC2, MUC5AC, MUC5B MUC6. Our shows different individuals, nucleotide...
Obtaining chloroplast (cp) genome sequence is necessary for studying physiological roles in plants. However, it difficult to use traditional sequencing methods get cp sequences because of the complex procedures preparing templates. With advent next-generation technology, massive can be produced. Thus, a good pipeline assemble reads with optimized k-mer length essential whole sequences. Moreover, adjustment other parameters also very important, especially assembly genome. In this study, we...
Abstract Background. Gel-forming mucin domains of genes show great complexity with tandem repeats (TRs), thus make it difficult to study the sequences. Methods. With coming single molecule real-time (SMRT) sequencing technologies, we manage present sequence structure via SMRT long reads for MUC2, MUC5AC, MUC5B and MUC6. Results. Our shows that different individuals, nucleotide polymorphisms (SNPs) could be found in MUC6, while number MUC2 Conclusions. This information will provided new...
Abstract Human tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to formation selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins distinct group that attached epithelial cell where they create dense glycocalyx facing the extracellular environment. All mucin carry long stretches tandemly repeated sequences undergo extensive O-linked glycosylation form linear domains....
Abstract Mucins are large glycoproteins that cover and protect epithelial surface of the body. Gel-forming mucin domains genes rich in proline, threonine, serine heavily glycosylate. These show great complexity with tandem repeats (TRs), thus make it difficult to study sequences. With coming single molecule real-time (SMRT) sequencing technologies, we manage present sequence structure via SMRT long reads for gel-forming mucins MUC2, MUC5AC, MUC5B MUC6. Our shows different individuals,...