Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era

Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.

A Search for Korean Origins through Genetic and Comparative Linguistic Methods

In exploring the origins of the Korean language, there are three windows through which we may penetrate the mysteries of this difficult question: archaeological, genetic/ genomic, and linguistic. In this paper I will try to answer this question by looking mainly through the latter two windows. As many linguists have attempted to place the Korean language into the proper language family according to linguistic affinity, I also want to classify the Korean language with linguistically related languages, mainly the Altaic languages. The so-called Altaic linguistics is very unstable compared with the more rigorously documented Indo-European linguistics. The lack of sufficient evidence, such as a common indigenous lexicon, has made it difficult to ascertain the genetic relationships and origins of languages such as Korean, Japanese, Manchu-Tungusic (Man, Gold(i), Oroqen, Ewenke, Lamut, Nanay, etc.), Mongolian (Khalkha, Chakhar, Urat, Khorchin, Ordos, Buriat, Oirat, Kalmyk, Da(g)ur, Monguor, Yellow Uighur. etc.) and Turkish (Turkish, Turkmen(ian), Azerbaidjani, Uighur, Uzbek, Kumyk, Tatar, Kazakh, Kirg(h)iz, Yakut, Altai, and Chuvash, etc.), which are typically classified as Altaic. Recently Starostin (1991) claimed that Proto-Altaic had disappeared around the sixth century B.c. Other measures are needed to evaluate this hypothesis, though, since the intra-linguistic debate has not provided any clear evidence or breakthroughs. That is why we turn to genetics as an approach and incorporate the results to shed new light on the origins of the Korean language. It has been shown that analysis of mitochondrial DNA, transmitted through maternal lineage, can be used to test this kind of hypothesis. After collecting data from such ethnic groups as Korean, Japanese, Ewenke, Nanay, Khalkha, Buriat, and Turkish, we have investigated information on mtDNA (mitochondrial DNA). While we do not use the popular STR markers on Y chromosomes (namely, DYS19, DYS389I, etc.) in this study, we will type a number of Korean, Tungusic and Mongolian populations on Y chromosomes, and other nuclear markers such as the gene encoding cytochrome B will be isolated by the polymerase chain reaction, as in the next study,. In reality, it was rather difficult to extract genes from hair-roots and saliva, especially when there were not many samples available for serious study. Yet, we could fill the void for Koreans in the map that shows the mitochondrial DNA types in Africans, Australian Aborigines, Caucasians, East Asians, Native Americans, and New Guineans. The nucleotide sequences were determined through phylogenetic analysis. If we can position the sequences from Koreans in the currently available genealogical tree based on mitochondrial DNA, we may be able to reassess the existing hypotheses on linguistic genealogy. However, because primordial remains or ancient fragments of linguistic evidence are not readily available in Korea due to special geo-political situations, the position of the Korean language has been left unattested in the genealogical tree based on languages. Nonetheless, there are some examples similar to the Altaic languages that are estimated to have been used in Korea, and using these we may draw the linguistic tree shown below

적변삼으로부터 분리한 내생세균의 동정 및 적변 유발

While the rusty-colored root is common in ginsengs culture and, often results in a severe economic loss, the major factors have not been found. This study was focused on the determination of a potential relationship between rusty root and endophytic bacteria. The number of endophytes was 9.6 × 101~1.5 × 102 cfu/g fw in normal ginseng roots compared to 3.7 × 106~5.1 × 107 cfu/g fw in rusty ones. Of 31 isolates from rusty ginseng roots, twenty-four isolates repeatedly induced severe to moderate rust on root while seven isolates induced slight rust. The bacteria responsible for rusty ginseng roots were mainly Gram negative aerobic. Rust inducing bacteria were identified as Agrobacterium tumefaciens, A. rhizogenes, Burkholderia phenazinium, Ensifer adharens, Lysobacter gummosus, Microbacterium luteolum, M. oxydans, Pseudomonas marginalis, P. veronii, Pseudomonas sp., Rhizobium leguminosarum, R. tropica, Rhodococcus erythropolis, Rh. globerulus, Variovorax paradoxus on the basis of bacteriological characters and 16S rDNA sequences analysis. The results in this study strongly suggested that the rusty ginseng roots were produced by infection and growth of endophytic bacteria.