Uncultured microorganisms comprise the majority of the planet's biological diversity. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Recently, new techniques for studying microbial communities, collectively called metagenomics, have been developed to overcome the limitations of culturing. This review assesses the potential of metagenomic techniques to analyze the relative abundance of microbial species under varying human environmental conditions and to discover infectious causes of unexplained human diseases.
Biodiversity ; Communicable Diseases ; Genetic Variation ; Humans ; Metagenome ; Metagenomics

In the second report in our series on the historical investigation on the introduction of western psychiatry into Korea, authors deal with the status of psychiatric education during the Japanese forced annexation of Korea. The first lecture on psychiatry in Korea under the title "Mental Diseases" was held in Dae-han-eui-won around 1910. In 1913, the Department of Psychiatry branched off from the Department of Internal Medicine of Chosen-sotoku-fu-iing, the Colonial Governmental Clinic, the successor of Dae-han-eui-won. The chairman, Professor Suiju Sinji; and the Korean assistant Sim Ho-seop administered the psychiatric ward with 35 beds. Since 1913, an Australian missionary psychiatrist, Dr. McLaren began to teach neurology and psychiatry at Severance Union Medical College and established a Department of Psychiatry in 1923. Dr. McLaren was a faithful Christian and open minded toward Oriental religious thought such as in Buddhism and Taoism. He devoted himself to the humanitarian care of mentally ill patients and served there until 1937 when he had to leave the land due to Japanese persecution. His disciple, Dr. Lee Jung Cheol succeeded the chair of the Psychiatric Department of Severance Medical College and served until 1939. In 1916, Keijo(Seoul) Medical College was established and in 1928, Keijo Teikoku Daigaku(Imperial University). From 1929 to 1941, the Department of Neurology and Psychiatry of Keijo Imperial University grew under the chairmanship of Professor Kubo Kioji followed by Professor Watanabe until 1945. Many assistants including a few Koreans were gathered to the Department for training and research. The main textbook used for the psychiatric education for medical students in Korea was on Kraepelinian German Psychiatry translated and edited by Japanese psychiatrists. Lectures and clerkships for Neurology and Psychiatry were allocated generally in the curriculum for senior students for weekly 1-3 hours. Postgraduate professional training for the psychiatrists was carried out according to the tutorial system under the supervision of professors and staff. In regard to a wide range of references discovered in the library of the Department of Neurology and Psychiatry, Keijo Imperial University the trainees seem to have had opportunity to contact with diverse subspecialties of psychiatry and also to exercise specific laboratory examinations in the setting of the German "Klinik". Comparisons of psychiatry in Korea and Japan during Japanese occupation suggest the following conclusions: 1. Extreme discrimination against Korean trainees in their academic careersprobably due to colonial policy. After 35 years of Japanese occupation of Korea only ten Korean neuro-psychiatrists and neurologists were left; 2. Somewhat narrow academic interests of psychiatrists in Korea in research fields focusing on neuropathology and opium addiction etc and the lackness of the interest in social psychiatric issues: for example, the rights of the mentally ill patient or non-restraining care systems as seen in Japanese psychiatry in Japan. 3. Extremely limited number of psychiatry teaching staffs in Korea. For a long time Keijo Imperial University's Department of Neurology and Psychiatry was the only center for training psychiatrists in Korea.
Western World/history ; Schools, Medical/history ; Psychiatry/education/*history ; Korea ; Japan ; Humans ; History, 20th Century ; Colonialism/*history

The MinION(TM) is a miniature nanopore-based analysis device in which the characteristics of an analyte, as it passes through the nanopore, cause changes in the flow of ions through the pore, which are measured, as current flow, by a low noise amplifier and analogue-to-digital converter. Potentially any molecular analyte capable of passing through the nanopore may modify the flow of ions and generate a signal which might be diagnostic. In practice the current device is focussed on DNA sequencing, directly sequencing RNA is a likely development. With the MinION Access Program making the MinION(TM) widely available a flood of applications exploiting its real time, long read capabilities have been published. We review the background to the technology and compare it to current next generation sequencing.
Ions ; Nanopores ; Noise ; RNA ; Sequence Analysis, DNA

The rotavirus nonstructural glycoprotein, NSP4, has been identified as the first viral enterotoxin capable of inducing diarrhea. To investigate the biological function of NSP4 in the inflammatory process, a cDNA from human rotavirus (Wa strain) RNA segment 10 was amplified by RT-PCR, cloned into TA vector, and subsequently subcloned into pET23b expression plasmid. The expression of NSP4 protein was determined by SDS-PAGE and Western blotting, then, the protein was purified by affinity chromatography on Ni-NTA-agarose column. The inflammatory effects of NSP4, namely, production of nitric oxide (NO), pro-inflammatory cytokines (IL-1β, IL-6, IL-10, and TNF-α), and prostaglandin E2 (PGE₂), was evaluated using NSP4-stimulated RAW 264.7 murine macrophages and compared with those observed after stimulation with lipopolysaccharide (LPS). The levels of IL-1β, IL-6, and TNF-α were significantly increased, and those of NO and PGE₂ also increased in NSP4-stimulated RAW 264.7 cells. These findings indicate that NSP4 plays an important role in the inflammatory response observed during rotavirus infection.
Blotting, Western ; Chromatography, Affinity ; Clone Cells ; Cytokines ; Diarrhea ; Dinoprostone ; DNA, Complementary ; Electrophoresis, Polyacrylamide Gel ; Enterotoxins* ; Glycoproteins ; Humans ; Inflammation ; Interleukin-10 ; Interleukin-6 ; Macrophages* ; Nitric Oxide ; Plasmids ; RAW 264.7 Cells* ; RNA ; Rotavirus Infections ; Rotavirus*

The epidemiology of human group A rotavirus was analyzed by examining genotypic data acquired from 1989 to 2009 in South Korea. This information was derived from all the available published articles on rotavirus studies in South Korea, retrieved from both the PubMed and KoreaMed databases. Four common G types (G1, G2, G3, and G4) and three common P types (P[8], P[4], and P[6]) accounted for approximately 93% and 99% of the rotavirus reports, respectively. The G9 type was frequently detected after 2000, and because of this prevalence, it is considered to be the fifth most important G type rotavirus after the G1.G4 genotypes. Less common G types of the virus such as G12, G11, and G10 were detected in some geographic settings, and it is important to consider the context of these subtypes and their epidemiological significance. The P[9] virus genotype was observed in the study and has been discussed in many other studies; however, the P[3], P[10] and P[25] genotypes were rarely detected in the epidemiological research. In general, the distributions of the G and P genotypes showed temporal and geographical fluctuations, and a nationwide rotavirus vaccine program that targeted these genotypes demonstrated effectiveness in protecting against the circulating rotavirus strains. However, further analysis is needed to determine the true long-term effectiveness of these vaccines; the analysis should also consider the unexpected effects of vaccinations, such as vaccine-induced diseases, herd immunity, and changes in host susceptibilities.
Epidemiology ; Genotype* ; Humans ; Immunity, Herd ; Prevalence* ; Republic of Korea* ; Rotavirus* ; Vaccination ; Vaccines ; Viruses

BACKGROUND: The aims of this study were to compare the suitability of repetitive-PCR genomic fingerprinting procedures to investigate genetic relatedness of the genus Vibrio and its applicability for the molecular identification of Vibrio vulnificus. METHODS: Forty-eight Vibrio strains were included for this study. REP-, ERIC-, BOX- and SERE-PCR were compared with 13 members of the genus Vibrio. RESULTS: REP-, BOX- and SERE-PCR showed V. vulnificus strains could not be separated well from other Vibrio species. However, approximately 320 bp of highly discriminatory specific fragments was recovered from V. vulnificus strains by ERIC-PCR. CONCLUSIONS: ERIC-PCR could be used as rapid classification and identification methods of V. vulnificus from other members of the genus Vibrio.
Classification* ; Dermatoglyphics* ; Vibrio vulnificus ; Vibrio*

The nonstructural protein 4 (NSP4) of rotavirus encoded by gene 10, plays an important role in rotavirus pathogenicity. In this study, NSP4 gene sequences of human rotaviruses circulating in Seoul, Korea between March 2004 and April 2005 were determined. The nucleotide sequence data indicated that the NSP4 genes of human rotavirus Korean isolates were 750 or 751 bases in length and encoded one open reading frame of 175 amino acids with two glycosylation sites. The NSP4 of Korean isolates exhibited amino acid sequence homologies between 59.4% and 98.9%. The NSP4 of CAU4 and CAU15 showed a high degree of amino acid sequence homologies with NSP4 genotype A viruses, but the NSP4 of CAU5, CAU6, CAU11, CAU14, CAU16 and CAU22 exhibited a high degree of amino acid sequence homologies with NSP4 genotype B viruses. Interestingly, CAU3 and CAU7 showed low degree of amino acid sequence homology with those of currently described NSP4 genotypes A to D and belonged a distinct lineage on the phylogenetic tree. These findings suggests that distinct NSP4 type was circulating among human rotavirus strains in the local community of Seoul and raising intriguing questions regarding possible explanations for new genotype.
Amino Acid Sequence ; Amino Acids ; Base Sequence ; Genetic Variation* ; Genotype ; Glycosylation ; Herpesvirus 1, Cercopithecine ; Humans* ; Korea ; Open Reading Frames ; Rotavirus* ; Seoul* ; Sequence Homology, Amino Acid ; Virulence

Functional defects in mitochondria are involved in the induction of cell death in cancer cells. We assessed the toxic effect of camptothecin against the human cervical and uterine tumor cell line SiHa with respect to the mitochondria-mediated cell death process, and examined the combined effect of camptothecin and anticancer drugs. Camptothecin caused apoptosis in SiHa cells by inducing mitochondrial membrane permeability changes that lead to the loss of mitochondrial membrane potential, decreased Bcl-2 levels, cytochrome c release, caspase-3 activation, formation of reactive oxygen species and depletion of GSH. Combination of camptothecin with other anticancer drugs (carboplatin, paclitaxel, doxorubicin and mitomycin c) or signaling inhibitors (farnesyltransferase inhibitor and ERK inhibitor) did not enhance the camptothecin-induced cell death and caspase-3 activation. These results suggest that camptothecin may cause cell death in SiHa cells by inducing changes in mitochondrial membrane permeability, which leads to cytochrome c release and activation of caspase-3. This effect is also associated with increased formation of reactive oxygen species and depletion of GSH. Combination with other anticancer drugs (or signaling inhibitors) does not appear to increase the anti-tumor effect of camptothecin against SiHa cells, but rather may reduce it. Combination of camptothecin with other anticancer drugs does not seem to provide a benefit in the treatment of cervical and uterine cancer compared with camptothecin monotherapy.
Apoptosis ; Camptothecin ; Carcinoma, Squamous Cell ; Caspase 3 ; Cell Death ; Cell Line ; Cell Line, Tumor ; Cytochromes c ; Doxorubicin ; Humans ; Membrane Potential, Mitochondrial ; Mitochondria ; Mitochondrial Membranes ; Mitomycin ; Paclitaxel ; Permeability ; Reactive Oxygen Species ; Uterine Neoplasms

Although viruses are the most common cause of acute gastroenteritis (AGE) in humans, details about the causative viruses in AGE are largely unknown because many causative viruses are unable to be cultured by current culture techniques. In our study, fecal samples from 10 children under five years of age with unexplained AGE and 10 healthy children were investigated for RNA viruses using random priming (RP)-mediated sequence-independent single primer amplification (SISPA). The causative viruses in cases of cryptogenic diarrhea were then assessed for their potential diagnostic value. Of the 1,129 viral clones identified, rotavirus was most commonly associated with AGE (125 sequences, 22.4%). In contrast, bacteriophage was most common (43 sequences, 13.6%) in healthy children. The remaining 515 viral clones were unidentifiable. These findings suggest that investigation of cases or outbreaks of unexplained diarrhea using a metaviromic strategy is a new avenue for diagnosis.
Bacteriophages ; Child ; Clone Cells ; Culture Techniques ; Diagnosis ; Diarrhea ; Disease Outbreaks ; Feces* ; Gastroenteritis* ; Humans ; Parechovirus ; RNA Viruses ; Rotavirus

Bronchial asthma can be triggered by microbial agents in the oropharynx. This study was designed to identify the differences in microbiota of oropharynx of bronchial asthmatic patients in contrast to normal controls. In order to resolve the qualitative and quantitative diversity of the 16S rRNA gene present in the oropharynx microbiota of 4 patients and 4 controls, we compared microbial communities using Sanger sequencing and 376 sequences of 16S rRNA gene were analyzed. Of the total microbial diversity detected in the oropharynx in asthmatic patients 45.6% comprised members of the Firmicutes. In contrast, Proteobacteria (44.0%) dominated the oropharyngeal microbiota in the normal control group. Members of the Bacteroidetes, Fusobacteria, Actinobacteria, TM7, Cyanobacteria and unclassified bacteria were present in both groups. In conclusion, the difference in the microbiota of the oropharynx between patients and normal individuals could trigger symptomatic attacks in bronchial asthma.
Actinobacteria ; Asthma* ; Bacteria ; Bacteroidetes ; Cyanobacteria ; Fusobacteria ; Genes, rRNA ; Humans ; Metagenome ; Microbiota* ; Oropharynx ; Proteobacteria