Chin-Fu Chen

The Rat Genome Database (RGD): developments towards a phenome database

The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGDs development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.

Decreased tryptophan metabolism in patients with autism spectrum disorders

BackgroundAutism spectrum disorders (ASDs) are relatively common neurodevelopmental conditions whose biological basis has been incompletely determined. Several biochemical markers have been associated with ASDs, but there is still no laboratory test for these conditions.MethodsWe analyzed the metabolic profile of lymphoblastoid cell lines from 137 patients with neurodevelopmental disorders with or without ASDs and 78 normal individuals, using Biolog Phenotype MicroArrays.ResultsMetabolic profiling of lymphoblastoid cells revealed that the 87 patients with ASD as a clinical feature, as compared to the 78 controls, exhibited on average reduced generation of NADH when tryptophan was the sole energy source. The results correlated with the behavioral traits associated with either syndromal or non-syndromal autism, independent of the genetic background of the individual. The low level of NADH generation in the presence of tryptophan was not observed in cell lines from non-ASD patients with intellectual disability, schizophrenia or conditions exhibiting several similarities with syndromal autism except for the behavioral traits. Analysis of a previous small gene expression study found abnormal levels for some genes involved in tryptophan metabolic pathways in 10 patients.ConclusionsTryptophan is a precursor of important compounds, such as serotonin, quinolinic acid, and kynurenic acid, which are involved in neurodevelopment and synaptogenesis. In addition, quinolinic acid is the structural precursor of NAD+, a critical energy carrier in mitochondria. Also, the serotonin branch of the tryptophan metabolic pathway generates NADH. Lastly, the levels of quinolinic and kynurenic acid are strongly influenced by the activity of the immune system. Therefore, decreased tryptophan metabolism may alter brain development, neuroimmune activity and mitochondrial function. Our finding of decreased tryptophan metabolism appears to provide a unifying biochemical basis for ASDs and perhaps an initial step in the development of a diagnostic assay for ASDs.

Phylogenetics of rat inbred strains

Laboratory rats (Rattus norvegicus) have played animportant role in biomedical research for over 100years with more than 200 strains bred as physiologi-cal models of human disease (Lindsey 1979; Steenet al. 1999; Kwitek-Black and Jacob 2001). Unlikemouse inbred strains, little is known about rela-tionships among rat strains (Festing 1979). TheAllele Characterization Project (ACP; lgr.mcw-edu/research/lgr_acp.html) was initiated to guide theidentification of individual strains, ensure purity ofstrains used for specific research purposes, and pro-vide a means of mapping genes based on linkage(Jacob et al. 1995; Brown et al. 1998; Steen et al.1999). The ACP genotyped 48 commonly used ratinbred strains by using over 4800 microsatellitemarkers with known genomic locations. The mi-crosatellite markers are spread relatively evenlyacross the rat genome and have been integrated intothe rat radiation hybrid (RH) map (Steen et al. 1999).Using the ACP microsatellite data and a limitednumber of isozymes, Canzian (1997) conducted agenealogic study of inbred rat strains to better un-derstand relationships among strains and to providea basis for the selection of rat strains for biomedicalresearch. Similar research of mouse inbred strainshas been significant for studies of evolution anddisease (Fitch and Atchley 1985; Beck et al. 2000).The Canzian (1997) study used a simple distancemodel (Fitch and Margoliash 1967) with percentagesof genotype differences. The results of this studyhave been cited by other authors to justify the use ofparticular rat strains for the study of a disease (Rapp2000) and to support the phylogenetic hypothesisthat a given strain of interest is ancestral to otherstrains (D’Cruz et al. 2000; Lorincz et al. 2001).Evolutionary models of microsatellite changehave been shown to more accurately reconstructdivergence patterns involving this type of marker,and there is a rich tradition in the evolutionary bi-ology literature of these models. These models havebeen used to measure population subdivision (Slat-kin 1995), investigate human evolution (Goldsteinet al. 1995b; Perez-Lezaun et al. 1997), map disease-related traits (Fishman et al. 2001), and understandmutations (Colson and Goldstein 1999). Models in-corporating specific hypotheses about mutationalmechanisms of microsatellite markers can clearly besuperior to simple percentage difference models thatpose no hypotheses about how markers mutate. Es-timates of mutation rates for microsatellite markersare approximately 10

Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei

BackgroundThe zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically.ResultsHere, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed.ConclusionsThe genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.

Progress in Detecting Genetic Alterations and Their Association with Human Disease

The completion of the Human Genome Project provided a reference sequence to which researchers could compare sequences from individual patients in the hope of identifying disease-causing mutations. However, this still necessitated candidate gene testing or a very limited screen of multiple genes using Sanger sequencing. With the advent of high-throughput Sanger sequencing, it became possible to screen hundreds of patients for alterations in hundreds of genes. This process was time consuming and limited to a few locations/institutions that had the space to house tens of sequencing equipment. The development of next generation sequencing revolutionized the process. It is now feasible to sequence the entire exome of multiple individuals in about 10 days. However, this meant that a massive amount of data needed to be filtered to identify the relevant alteration. This is presently the rate-limiting step in providing a convincing association between a genetic alteration and a human disorder.

Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide

Key messageOur study has identified pathways and gene candidates that may be associated with the greater flexibility and digestibility of the poplar cell walls.AbstractWith the goal of facilitating lignin removal during the utilization of woody biomass as a biofuel feedstock, we previously transformed a hybrid poplar clone with a partial cDNA sequence encoding a tyrosine- and hydroxyproline-rich glycoprotein from parsley. A number of the transgenic lines released more polysaccharides following protease digestion and were more flexible than wild-type plants, but otherwise normal in phenotype. Here, we report that overexpression of the tyrosine-rich peptide encoding sequence in these transgenic poplar plants did not significantly alter total lignin quantity or quality (S/G lignin ratio), five- and six-carbon sugar contents, growth rate, or susceptibility to a major poplar fungal pathogen, Septoria musiva. Whole-genome microarray analysis revealed a total of 411 differentially expressed transcripts in transgenic lines, all with decreased transcript abundance relative to wild-type plants. Their corresponding genes were overrepresented in functional categories such as secondary metabolism, amino acid metabolism, and energy metabolism. Transcript abundance was decreased primarily for five types of genes encoding proteins involved in cell-wall organization and in lignin biosynthesis. The expression of a subset of 19 of the differentially regulated genes by qRT-PCR validated the microarray results. Our study has identified pathways and gene candidates that may be the underlying cause for the enhanced flexibility and digestibility of the stems of poplar plants expressing the TYR transgene.

MICO: A meta-tool for prediction of the effects of non-synonymous mutations.

The Next Generation Sequencing (NGS) is a state-of-the-art technology that produces high throughput data with high resolution mutation information in the genome. Numerous methods with different efficiencies have been developed to predict mutational effects in the genome. The challenge is to present the results in a balanced manner for better biological insights and interpretation. Hence, we describe a meta-tool named Mutation Information Collector (MICO) for automatically querying and collecting related information from multiple biology/bioinformatics enabled web servers with prediction capabilities. The predicted mutational results for the proteins of interest are returned and presented as an easy-to-read summary table in this service. MICO also allows for navigating the result from each website for further analysis. Availability http: //mico.ggc.org /MICO