Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA.

Unno, Tatsuya,Di, Doris Y W,Jang, Jeonghwan,Suh, Yae Seul,Sadowsky, Michael J,Hur, Hor-Gil American Chemical Society 2012 Environmental science & technology Vol.46 No.1

<P>Genotypic microbial source tracking (MST) methods are now routinely used to determine sources of fecal contamination impacting waterways. We previously reported the development of a pyrosequencing-based MST method that assigns contamination sources based on shared operational taxonomic units (OTUs) between fecal and environmental bacterial communities. Despite decreasing sequencing costs, pyrosequencing-based MST approaches are not used in routine water quality monitoring studies due in large part to difficulties in handling massive data sets and difficulties in determining sources of fecal contamination. In the studies presented here we describe the development of an online MST tool, PyroMiST ( http://env1.gist.ac.kr/aeml/MST.html) that uses total bacterial or Bacteroidetes 16S rDNA pyrosequencing reads to determine fecal contamination of waterways. The program cd-hit was used for OTU assignment and a Perl script was used to calculate the number of shared OTUs. The analyses require only a small number of pyrosequencing reads from environmental samples. Our results indicate that PyroMiST provides a user-friendly web interface for pyrosequence data that significantly reduces analysis time required to determine potential sources of fecal contamination in the environment.</P>

A class I histone deacetylase HDA-2 is essential for embryonic development and size regulation of fertilized eggs in Caenorhabditis elegans

Unno Takuma,Takatsuka Hisashi,Ohnishi Yuto,Ito Masahiro,Kubota Yukihiko 한국유전학회 2022 Genes & Genomics Vol.44 No.3

Background: Caenorhabditis elegans encodes three class I histone deacetylases (HDACs), HDA-1, HDA-2, and HDA-3. Although HDA-1 is known to be involved in embryogenesis, the regulatory roles of HDA-2 and HDA-3 in embryonic development remain unexplored. Objective: To elucidate the functional roles of the three class I HDACs in C. elegans embryonic development. Methods: The roles of Class I HDACs, HDA-1, HDA-2, and HDA-3 in Caenorhabditis elegans during embryogenesis were investigated through the analysis of embryonic lethality via gene knockdown or deletion mutants. Additionally, the size of these knockdown and mutant eggs was observed using a differential interference contrast microscope. Finally, expression pattern and tissue-specific role of hda-2 and transcriptome of the hda-2 mutant were analyzed. Results: Here, we report that HDA-1 and HDA-2, but not HDA-3, play essential roles in Caenorhabditis elegans embryonic development. Our observations of the fertilized egg size variance demonstrated that HDA-2 is involved in regulating the size of fertilized eggs. Combined analysis of expression patterns and sheath cell-specific rescue experiments indicated that the transgenerational role of HDA-2 is involved in the viability of embryonic development and fertilized egg size regulation. Furthermore, transcriptome analysis of hda-2 mutant embryos implies that HDA-2 is involved in epigenetic regulation of embryonic biological processes by downregulating and upregulating the gene expression. Conclusion: Our finding suggests that HDA-2 regulates the embryonic development in Caenorhabditis elegans by controling a specific subset of genes, and this function might be mediated by transgenerational epigenetic effect.

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis

Unno, Tatsuya The Korean Society for Microbiology and Biotechnol 2015 Journal of microbiology and biotechnology Vol.25 No.6

Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (<uri>http://biotech.jejunu.ac.kr/ ~abl/16s/</uri>) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.

Pulpal Regeneration Following Allogenic Tooth Transplantation into Mouse Maxilla

Unno, Hideki,Suzuki, Hironobu,Nakakura-Ohshima, Kuniko,Jung, Han-Sung,Ohshima, Hayato Wiley (John WileySons) 2009 The anatomical record Vol.292 No.4

<P>Autogenic tooth transplantation is now a common procedure in dentistry for replacing a missing tooth. However, there are many difficulties in clinical application of allogenic tooth transplantation because of immunological rejection. This study aims to clarify pulpal regeneration following allogenic tooth transplantation into the mouse maxilla by immunohistochemistry for 5-bromo-2'-deoxyuridine (BrdU) and nestin, and by the histochemistry for tartrate-resistant acid phosphatase (TRAP). The upper right first molar (M1) of 2-week-old mice was extracted and allografted in the original socket in both the littermate and non-littermate after the extraction of M1. Tooth transplantation weakened the nestin-positive reactions in the pulp tissue that had shown immunoreactivity for nestin before operation. On postoperative Days 5-7, tertiary dentin formation commenced next to the preexisting dentin where nestin-positive odontoblast-like cells were arranged in all cases of the littermate group until Day 14, except for one case showing immunological rejection in the pulp chamber. In the non-littermate group, bone-like tissue formation occurred in the pulp chamber in addition to tertiary dentin formation until Day 14. The rate of tertiary dentin was 38%, and the rate of the mixed form of dentin and bone-like tissue formation was 23% (the remainder was immunological rejection). Interestingly, the periodontal tissue recovered even in the case of immunological rejection in which the pulp chamber was replaced by sparse connective tissue. These results suggest that the selection of littermate or non-littermate is decisive for the survival of odontoblast-lineage cells and that the immunological rejection does not influence the periodontal regeneration.</P>

Professor Yi’s Article “Annexation of Korea Failed to Come Into Being” Reexamined

Unno Fukuju 서울대학교 규장각한국학연구원 2005 Seoul journal of Korean studies Vol.18 No.-

Fecal pollution: new trends and challenges in microbial source tracking using next‐generation sequencing

Unno, Tatsuya,Staley, Christopher,Brown, Clairessa M.,Han, Dukki,Sadowsky, Michael J.,Hur, Hor‐,Gil BLACKWELL SCIENCE 2018 ENVIRONMENTAL MICROBIOLOGY Vol.20 No.9

<P>In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.</P>

Changes in human gut microbiota influenced by probiotic fermented milk ingestion

Unno, T.,Choi, J.H.,Hur, H.G.,Sadowsky, M.J.,Ahn, Y.T.,Huh, C.S.,Kim, G.B.,Cha, C.J. American Dairy Science Association 2015 Journal of dairy science Vol.98 No.6

We investigated the effect of consuming probiotic fermented milk (PFM) on the microbial community structure in the human intestinal tract by using high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings of PFM daily for 3wk, and their fecal microbiota were analyzed before and after 3wk of PFM ingestion period and for another 3wk following the termination of PFM ingestion (the noningestion period). Fecal microbial communities were characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA gene. All subjects showed a similar pattern of microbiota at the phylum level, where the relative abundance of Bacteriodetes species increased during the PFM ingestion period and decreased during the noningestion period. The increase in Bacteroidetes was found to be due to an increase in members of the families Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the phylum level, the taxonomic composition at the genus level showed a considerable alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis of operational taxonomic units (OTU), the numbers of shared OTU were low among the 3 different treatments (before, during, and after PFM ingestion), but the abundance of the shared OTU was relatively high, indicating that the majority (>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion and after its termination. Our results suggest that PFM consumption could alter microbial community structure in the gastrointestinal tract of adult humans while maintaining the stability of microbiota.

Genotypic and Phenotypic Trends in Antibiotic Resistant Pathogenic <i>Escherichia coli</i> Isolated from Humans and Farm Animals in South Korea

Unno, Tatsuya,Han, Dukki,Jang, Jeonghwan,Widmer, Kenneth,Ko, GwangPyo,Sadowsky, Michael J.,Hur, Hor-Gil Japanese Society of Microbial Ecology · The Japane 2011 Microbes and environments Vol.26 No.3

<P>South Korea uses more antibiotics for animal production than any other member of the OECD. The excessive use could potentially lead to a greater incidence of antibiotic resistant microorganisms, some of which may be pathogenic. In this study, we examined potential diarrheagenic and extraintestinal pathogenic <I>E. coli</I> (ExPEC) isolates using virulence gene profiling (<I>eaeA</I>, <I>est</I>, <I>elt</I>, <I>ipaH</I>, <I>stx1</I> and <I>stx2</I> as diarrheagenic and <I>afa/dra</I>, <I>iutA</I>, <I>kpsMT II</I>, <I>papA/C</I>, and <I>sfa/foc</I> as extraintestinal pathogenic virulence genes). A cluster analysis of DNA fingerprint data indicated that certain genotypes of chicken <I>E. coli</I> isolates are likely ExPEC. Moreover, our results showed 38 of the 60 potential diarrheagenic and ExPEC isolates obtained from animals and humans were also resistant to antibiotics, mostly to tetracycline groups, penicillin groups, and folate pathway inhibitors. Our results suggest that the use of antibiotics in agriculture should be controlled due to potential impacts on human health.</P>

COSMOLOGY, EPISTEMOLOGY AND CHAOS

Unno, Wasaburo The Korean Astronomical Society 1992 天文學論叢 Vol.7 No.1

We may consider the following three fundamental epistemological questions concerning cosmology. Can cosmology at last understand the origin of the universe? Can computers at last create? Can life be formed at last synthetically? These questions are in some sense related to the liar paradox containing the self-reference and, therefore. may not be answered by recursive processes in finite time. There are, however. various implications such that the chaos may break the trap of the self-reference paradox. In other words, Goedel's incompleteness theorem would not apply to chaos, even if the chaos can be generated by recursive processes. Internal relations among cosmology, epistemology and chaos must be investigated in greater detail.

Absence of Escherichia coli Phylogenetic Group B2 Strains in Humans and Domesticated Animals from Jeonnam Province, Republic of Korea

Unno, Tatsuya,Han, Dukki,Jang, Jeonghwan,Lee, Sun-Nim,Ko, GwangPyo,Choi, Ha Young,Kim, Joon Ha,Sadowsky, Michael J.,Hur, Hor-Gil American Society for Microbiology 2009 Applied and environmental microbiology Vol.75 No.17

<B>ABSTRACT</B><P>Multiplex PCR analyses of DNAs from genotypically unique <I>Escherichia coli</I> strains isolated from the feces of 138 humans and 376 domesticated animals from Jeonnam Province, South Korea, performed using primers specific for the <I>chuA</I> and <I>yjaA</I> genes and an unknown DNA fragment, TSPE4.C2, indicated that none of the strains belonged to <I>E. coli</I> phylogenetic group B2. In contrast, phylogenetic group B2 strains were detected in about 17% (8 of 48) of isolates from feces of 24 wild geese and in 3% (3 of 96) of isolates obtained from the Yeongsan River in Jeonnam Province, South Korea. The distribution of <I>E. coli</I> strains in phylogenetic groups A, B1, and D varied depending on the host examined, and there was no apparent seasonal variation in the distribution of strains in phylogenetic groups among the Yeongsan River isolates. The distribution of four virulence genes (<I>eaeA</I>, <I>hlyA</I>, <I>stx</I>1, and <I>stx</I>2) in isolates was also examined by using multiplex PCR. Virulence genes were detected in about 5% (38 of 707) of the total group of unique strains examined, with 24, 13, 13, and 9 strains containing <I>hlyA</I>, <I>eaeA</I>, <I>stx</I>2, and <I>stx</I>1, respectively. The virulence genes were most frequently present in phylogenetic group B1 strains isolated from beef cattle. Taken together, results of these studies indicate that <I>E. coli</I> strains in phylogenetic group B2 were rarely found in humans and domesticated animals in Jeonnam Province, South Korea, and that the majority of strains containing virulence genes belonged to phylogenetic group B1 and were isolated from beef cattle. Results of this study also suggest that the relationship between the presence and types of virulence genes and phylogenetic groupings may differ among geographically distinct <I>E. coli</I> populations.</P>