Protein Subcellular Localization Prediction and Genomic Polymorphism Analysis of the SARS Coronavirus

The cause of severe acute respiratory syndrome (SARS) has been identified as a new coronavi-rus (CoV). Several sequences of the complete genome of SARS-CoV have been determined. The subcellu-lar localization (SubLocation) of annotated open-reading frames of the SARS-CoV genome was predicted using a support vector machine. Several gene products were predicted to locate in the Golgi body and cell nucleus. The SubLocation information was combined with predicted transmembrane information to develop a model of the viral life cycle. The results show that this information can be used to predict the functions of genes and even the virus pathogenesis. In addition, the entire SARS viral genome sequences currently available in GenBank were compared to identify the sequence variations among different isolates. Some variations in the Hong Kong strains may be related to the special clinical manifestations and provide clues for understanding the relationship between gene functions and evolution. These variations reflect the evolu-tion of the SARS virus in human populations and may help development of a vaccine.

Genomic polymorphism in consecutive generation rice plants from seeds on board a spaceship and their relationship with space HZE particles

Dry rice seeds(Oryza sativa,subspecies indica)were sandwiched between nuclear track detectors,aboard the Chinese spaceship Shenzhou-3 for seven days.The seeds were recovered and the genomic polymorphism in 201 plants developed from these seeds was studied using random amplified polymorphism DNA analysis.When compared with plants from ground-based control seeds,the genomic polymorphic bands were amplified in 30.2%of the plants from the seeds exposed in space.The results for sequencing and SNP analyses of the polymorphic bands verified the single nucleotide variations in these plants.Genomic poly-morphisms in the consecutive generations of individual plants of the seeds from space were also discovered.Seven seeds receiving hits of HZE(high atomic number and high energy)particles from space were selected for further analyses and variable genomic polymorphisms were detected in all plants that developed from these seeds.Among them,the embryos of three seeds were hit at least once,and mutants with significant changes in agronomic traits were only found in later generations of these seeds.This result implies that the HZE particles of space are effective in inducing the changes of plant genome of inherited phenotypes.

Isolation of Microsatellite DNA and Preliminary Genomic Analysis of Mud Carp (Cirrhina molitorella)

In order to determine the applicability of microsatellite primers developed from common carp （ Cyprinuscario ） for genomic analysis in mud carp （ Cirrhina molitorella ）, 24 primer pairs from common carp were designed to amplify microsatellite loci in the mud carp containing CA, GA, AT and GGGA sequences. Thirteen primers （54%） successfully amplified specific products in the mud carp and 11 primers （48%） showed high polymorphism in the mud carp population. The results indicated that the average number of alleles per locus in the mud carp stocks was 5.2. Average heterozygosity （Ho）, unbiased expected heterozygosity （He） and polymorphism information content （PIC） in the wild population were 0.61 ± 0.2, 0.8 ± 0.09 and 0.72 ± 0.1 respectively. Several Hardy-Weinberg departure value were significandy departed from Hardy-Weinberg equilibrium. The study showed that microsatellite primers from a species of Cyprinidae can be used for mud carp genetic analysis without much cost or time input.

Genome Polymorphisms Between Indica and Japonica Revealed by RFLP

Revealing the genome polymorphisms between indica and japonica subspecies; RFLP markers, which are located across 12 chromosomes of rice, were used to analyze indica-japonica differentiation in different rice varieties. At the same time, genome sequence variations of screened loci were analyzed by bioinformatics method. Twenty-eight RFLP probes, which can classify indica-japonica rice, were confirmed. Subspecies genome polymorphisms of screened loci were found by analyzing the publication of the genome sequences data of rice. The study indicated that these screened markers can be used for classifying indica-japonica subspecies. With the publication of the genome sequences of rice, marker polymorphisms between indica and japonica subspecies can be revealed by genome differentiation.

Genes and genetics in eye diseases: a genomic medicine approach for investigating hereditary and inflammatory ocular disorders

Past 25 y have witnessed an exponential increase in knowledge and understanding of ocular diseases and their respective genetic underpinnings. As a result, scientists have mapped many genes and their variants that can influence vision and health of our eyes. Based on these findings, it is becoming clear that an early diagnosis employing genetic testing can help evaluate patients＇ conditions for instituting treatment plan（s） and follow-up care to avoid vision complications later. For example, knowing family history becomes crucial for inherited eye diseases as it can benefit members in family who may have similar eye diseases or predispositions. Therefore, gathering information from an elaborate examination along with complete assessment of past medical illness by ophthalmologists followed by consultation with geneticists can help create a roadmap for making diagnosis and treatment precise and beneficial. In this review, we present an update on ocular genomic medicine that we believe has tremendous potential towards unraveling genetic implications in ocular diseases and patients＇ susceptibilities. We also discuss translational aspects of genetic ophthalmology and genome engineering that may help advance molecular diagnostics and therapeutics.

Diversity Suppression-Subtractive Hybridization Array for Profiling Genomic DNA Polymorphisms

Genomlc DNA polymorphlsms are very useful for tracing genetic traits end studying biological diversity among species. Here, we present a method we call the ＂diversity suppresslon-subtractlve hybridization array＂ for effectively profiling genomlc DNA polymorphisms. The method first obtains the subtracted gDNA fragments between any two species by suppression subtraction hybridization （SSH） to establish e subtracted gDNA library, from which diversity SSH arrays are created with the selected subtracted clones. The diversity SSH array hybridizes with the DIG-labeled genomlc DNA of the organism to be assayed. Six closely related Dendrobium species were studied as model samples. Four Dendrobium species as testers were used to perform SSH. A total of 617 subtracted positive clones were obtained from four Dendrobium species, and the average ratio of positive clones was 80.3%. We demonstrated that the average percentage of polymorphlc fragments of palrwlse comparisons of four Dendrobium species was up to 42.4%. A dendrogram of the relatedness of six Dendrobium species was produced according to their polymorphic profiles. The results revealed that the diversity SSH array Is a highly effective platform for profiling genomlc DNA polymorphlsms and dendrograms.