Tzen-Yuh Chiang

Bio: Tzen-Yuh Chiang is an academic researcher from National Cheng Kung University. The author has contributed to research in topics: Microsatellite & Population. The author has an hindex of 17, co-authored 32 publications receiving 1595 citations. Previous affiliations of Tzen-Yuh Chiang include South China Normal University.

Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa

Abstract: Cultivated rice, Oryza sativa L., represents the world's most important staple food crop, feeding more than half of the human population. Despite this essential role in world agriculture, the history of cultivated rice's domestication from its wild ancestor, Oryza rufipogon, remains unclear. In this study, DNA sequence variation in three gene regions is examined in a phylogeographic approach to investigate the domestication of cultivated rice. Results indicate that India and Indochina may represent the ancestral center of diversity for O. rufipogon. Additionally, the data suggest that cultivated rice was domesticated at least twice from different O. rufipogon populations and that the products of these two independent domestication events are the two major rice varieties, Oryza sativa indica and Oryza sativa japonica. Based on this geographical analysis, O. sativa indica was domesticated within a region south of the Himalaya mountain range, likely eastern India, Myanmar, and Thailand, whereas O. sativa japonica was domesticated from wild rice in southern China.

Spread of hepatitis E virus among different-aged pigs: two-year survey in Taiwan

Abstract: Swine are reservoirs of hepatitis E virus (HEV). In this study, a 2-year survey of HEV in feces and sera of swine was conducted to determine if: 1) HEV has circulated among pigs for some time in Taiwan; 2) the spread of HEV among different-aged pigs; and 3) there exists HEV strains possibly imported through trading. From 1998-2000, 521 serum samples and 54 fecal specimens from pigs were examined by reverse transcription polymerase chain reaction. None of the 11 pigs in suckling stage (< 2 months) were serum HEV RNA positive. The highest viremia rate (4.5%) was in pigs of 2 months age, followed by 1.2% and 1.8% in pigs of growing (3-4 months) and finishing stages (5-6 months), and none in pigs older than 6 months. Viremia showed little variation in different years and areas. None of the 20 fecal samples from pigs in suckling stage were HEV RNA positive, whereas 9% of the 34 samples from pigs in growing or finishing stages were positive. Most swine HEV isolates in Taiwan clustered within the genotype 4, whereas the three HEV isolates cloned from pigs imported recently from the U.S. belonged to the genotype 3 HEV in the U.S. The results suggest that HEV may infect pigs at an early growing stage and spread unnoticed among pigs and possibly across countries through trading.

Characterization and phylogenetic analysis of a novel hepatitis D virus strain discovered by restriction fragment length polymorphism analysis.

Abstract: The hepatitis D virus (HDV) genotypes in 46 HDV-infected patients and 12 prostitutes were screened with Xhol restriction fragment length polymorphism (RFLP) analysis of reverse transcription PCR products of viral genomes and verified by phylogenetic analysis. The amplificates of three (6.5%) patients and two (17%) prostitutes showed a novel RFLP pattern different from those of the three known genotypes. Complete HDV genomic sequence identities between isolates with a novel RFLP and the HDV genotypes I, II and III were 72.3, 77.2 and 63.0%, respectively. Importantly, divergence was mostly seen in various regions related to replication or packaging. The novel isolates formed a monophyletic group (P < 0.05) and were most closely related to genotype II.

Clinical and epidemiological implications of swine hepatitis E virus infection.

Abstract: In nonendemic areas, most patients with acute hepatitis E were infected through traveling to endemic areas. However, some patients did not have a history of foreign travel before infection. Furthermore, high seroprevalence rates of antibody to hepatitis E virus (anti-HEV) were found in the general adult population in some countries without any recorded outbreak of hepatitis E. The significance of anti-HEV assay in these subjects remains obscure. To study if swine might be a source of HEV infection, HEV was tested in sera of 235 pigs in Taiwan, and from 5 patients with acute HEV infection who either denied or did not provide any foreign travel history. Three (1.3%) pigs had detectable swine HEV RNA. The swine and human HEV strains from Taiwan formed a monophyletic group, distinct from three previously reported groups: the United States human and swine HEV strains, the Mexico strain, and the largest group composed of the Asian and the African strains. The identity of nucleotide sequences was 84-95% between swine and human HEV strains in Taiwan, and 72-79% between Taiwan strains and those from different areas. The predicted amino acid sequence of a Taiwan swine HEV strain within the peptide 3-2 used in commercial anti-HEV assay showed a high identity (91-94%) with those of other human and swine HEV strains. Swine may be a reservoir of HEV and subclinical swine HEV infection may occur. Cross-reactivity of current anti-HEV assay may account for the high prevalence rate of anti-HEV in the general population in nonendemic areas.

Phylogeography of plants in Taiwan and the Ryukyu archipelago

Abstract: Taiwan and Ryukyus constitute an archipelago lying on the western rim of the Pacific Ocean. In contrast to volcanic islands that often arise sequentially, these continental islands emerged almost simultaneously as the Luzon arc collided with the Eurasian margin some 9 million years ago (Mya). Taiwan and Ryukyus attained their modern features and their current flora and fauna from the adjacent mainland and from tropical Asia only 5-6 Mya. Quaternary glaciation led to a drop in sea level of the South China Sea and a land bridge that connected the Taiwan-Ryukyu Archipelago to the mainland, which allowed plants and animals to migrate across what was previously ocean. These islands provided refugia for northern species that migrated south during glacial periods, as indicated by unanticipated high levels of genetic diversity in island populations of plants like Cunninghamia and Pinus. For most insect-pollinated species, allozymes and nuclear DNA markers indicate significant genetic differentiation between populations and between geographical regions of the archipelago. In contrast, organelle based DNA markers suggest a migrant-pool model, where colonists are recruited from a random sample of source populations. Consistent with this model, low elevation species have high genetic heterogeneity within populations and low levels of genetic differentiation between populations. In contrast, colonization of alpine species appeared to follow a phalanx model due to the limited availability of high elevation habitats. Genetic differentiation was detected between fragmented populations of the alpine species. A scenario of stepwise colonization from the mainland to near and then distant islands remains to be tested, although several studies indicate no such pattern. These conflicting results challenge the ability to define clear conservation criteria for the rare plant species of the archipelago.

Diversity of life

Abstract: It is clear that the above can lead to confusion when scientists of different countries are trying to communicate with each other. Another example is the burrowing rodent called a gopher found throughout the western United States. In the southeastern United States the term gopher refers to a burrowing turtle very similar to the desert tortoise found in the American southwest. One final example; two North American mammals known as the elk and the caribou are known in Europe as the reindeer and the elk. We never sing “Rudolph the Red-nosed elk”! Confused? This was the reason for creating an internationally recognized system of naming organisms. To avoid confusion, living organisms are assigned a scientific name based on Latin or Latinized words. The English sparrow is Passer domesticus or Passer domesticus (italics or underlining these two names is the official written representation of a scientific name). Using a uniform naming system allows scientists from all over the world to recognize exactly which life form a scientist is referring to. The naming process is called the binomial system of nomenclature. Passer is comparable to a surname and is called the genus, while domesticus is the specific or species name (like your given name) of the English sparrow. Now scientists can give all sparrow-like birds the genus Passer but the species name will vary. All similar genera (plural for genus) can be grouped into another, “higher” category (see below). Study the following for a more through understanding of taxonomy. Taxonomy Analogy Kingdom: Animalia Country

A map of rice genome variation reveals the origin of cultivated rice

Abstract: Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.

A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide.

Abstract: We describe a modification of the DNA extraction method, in which cetyltrimethylammonium bromide (CTAB) is used to extract nucleic acids from plant tissues. In contrast to the original method, the modified CTAB procedure is faster, omits the selective precipitation and CsCl gradient steps, uses less expensive and toxic reagents, requires only inexpensive laboratory equipment and is more readily adapted to high-throughput DNA extraction. This protocol yields approximately 5-30 microg of total DNA from 200 mg of tissue fresh weight, depending on plant species and tissue source. It can be completed in as little as 5-6 h.