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Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Chun, Jongsik,Oren, Aharon,Ventosa, Antonio,Christensen, Henrik,Arahal, David Ruiz,da Costa, Milton S.,Rooney, Alejandro P.,Yi, Hana,Xu, Xue-Wei,De Meyer, Sofie,Trujillo, Martha E. Microbiology Society 2018 International journal of systematic and evolutiona Vol.68 No.1
Flores-Fernandez, Carol N.,Chavez-Hidalgo, Elizabeth,Santos, Marco,Zavaleta, Amparo I.,Arahal, David R. The Korean Society for Microbiology and Biotechnol 2019 한국미생물·생명공학회지 Vol.47 No.3
All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, $tRNA^{Ile(GAT)}$ and $tRNA^{Ala(TGC)}$, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the $tRNA^{Ala}$ gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.
( Carol N. Flores-fernandez ),( Elizabeth Chavez-hidalgo ),( Marco Santos ),( Amparo I. Zavaleta ),( David R. Arahal ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 한국미생물·생명공학회지 Vol.47 No.3
All Idiomarina species are isolated from saline environments; microorganisms in such extreme habitats develop metabolic adaptations and can produce compounds such as proteases with an industrial potential. ARDRA and 16S rRNA gene sequencing are established methods for performing phylogenetic analysis and taxonomic identification. However, 16S-23S ITS is more variable than the 16S rRNA gene within a genus, and is therefore, used as a marker to achieve a more precise identification. In this study, ten protease producing Idiomarina strains isolated from the Peruvian salterns were characterized using biochemical and molecular methods to determine their bacterial diversity and industrial potential. In addition, comparison between the length and nucleotide sequences of a 16S-23S ITS region allowed us to assess the inter and intraspecies variability. Based on the 16S rRNA gene, two species of Idiomarina were identified (I. zobellii and I. fontislapidosi). However, biochemical tests revealed that there were differences between the strains of the same species. Moreover, it was found that the ITS contains two tRNA genes, tRNA<sup>Ile (GAT)</sup> and tRNA<sup>Ala (TGC)</sup>, which are separated by an ISR of a variable size between strains of I. zobellii. In one strain of I. zobellii (PM21), we found nonconserved nucleotides that were previously not reported in the tRNA<sup>Ala</sup> gene sequences of Idiomarina spp. Thus, based on the biochemical and molecular characteristics, we can conclude that protease producing Idiomarina strains have industrial potential; only two I. zobellii strains (PM48 and PM72) exhibited the same properties. The differences between the other strains could be explained by the presence of subspecies.
Validation Study of Peripheral Blood Diagnostic Test for Acute Rejection in Kidney Transplantation
Lee, Arah,Jeong, Jong-Cheol,Choi, Young-Wook,Seok, Hwa-Young,Kim, Yang-Gyun,Jeong, Kyung-Hwan,Moon, Ju-Young,Lee, Tae-Won,Ihm, Chun-Gyoo,Jeon, Hee Jung,Koo, Tai-Yeon,Ahn, Curie,Lim, Sung-Jig,Yang, Jae by Lippincott Williams Wilkins 2014 Transplantation Vol.98 No.7
BACKGROUND: Diagnosing acute rejection (AR) in kidney transplant recipients typically requires an invasive kidney biopsy. A previous study has suggested that expression of five genes in peripheral blood can indicate the presence of AR in American pediatric kidney transplant recipients. This study aims to validate if these five genes are also useful to diagnose AR in Korean adult kidney transplant patients. METHODS: Blood samples were collected from 143 patients (39 biopsy-proven AR, 84 stable patients, and 20 other graft injuries) at an average of 9 months posttransplantation and performed real-time PCR for five-gene biomarkers (DUSP1, NKTR, MAPK9, PSEN1, and PBEF1). RESULTS: Patients with acute cellular rejection (ACR) had a significantly decreased level of MAPK9 and a significantly increased level of PSEN1 when compared with controls and also with patients with other graft injury (OGI). In multivariate logistic regression analysis, for discrimination between ACR and OGI, an excellent diagnostic accuracy was observed in the gene sets but five-gene set generated a higher AUC than two-gene set. With clinical variables combined to these gene sets, the diagnostic accuracy increased in both five-gene set and two-gene set. CONCLUSIONS: These results support the validity of 5 gene-set for the prediction of AR in Asian adult kidney transplant recipients and suggest the promising role of the peripheral blood gene test in the diagnosis of AR in kidney transplantation.
Mix-and-Match Assembly of Block Copolymer Blends in Solution
Cho, Arah,La, Yunju,Jeoung, Sungeun,Moon, Hoi Ri,Ryu, Ja-Hyoung,Shin, Tae Joo,Kim, Kyoung Taek American Chemical Society 2017 Macromolecules Vol.50 No.8
<P>The chemical structure of a block copolymer (BC?) dictates the size, shape, and function of its self-assembled structure in solution. This direct correspondence demands precision synthesis of a specific BCP with optimized structural parameters to obtain the desired nanostructures with structural and functional complexity by solution self-assembly. Here we show that the binary blends of BCPs self-assemble into the desired nanostructure in solution by adjusting the composition of the blend. By modifying the structural parameters of a binary BCP blend through control of the composition, two BCPs sharing the repeating units in both polymer blocks coassemble into the desired structures, which range from spherical micelles to inverse cubic and hexagonal mesophases. These BCP blends not only allow the direct creation of complex periodic mesoporous structures of the desired periodicity and pore size but also provide nanostructures of unprecedented morphology by simple solution self-assembly without relying on the synthesis of correspondingly designed BCPs.</P>
Cho, Arah,La, Yunju,Shin, Tae Joo,Park, Chiyoung,Kim, Kyoung Taek American Chemical Society 2016 Macromolecules Vol.49 No.12
<P>Inverse bicontinuous cubic (IBC) structures consisting of triply periodic minimal surfaces of block copolymers (BCPs) are emerging as materials of interest owing to their structural characteristics, which resemble those of their biological counterparts constructed from lipids. Solution self-assembly of amphiphilic BCPs with nonlinear architectures has recently been shown to form colloidal particles (polymer cubosomes) and macroscopic monoliths having mesoporous networks of water channels embedded in the periodic minimal surfaces of the BCP bilayers. Here we report that BCP architectures play a crucial role in controlling the packing parameter (P) of BCPs; a value greater than unity is a prerequisite for preferential self-assembly into IBC mesophases in solution. We show that the branched architecture of the polymer blocks constituting the BCP critically influences the structural parameters, such as the molecular area and, in particular, the critical length of the hydrophobic domain. Adjusting these structural parameters not only increases the P value of the BCP without depending on the asymmetry of the volume ratio of two polymer blocks (block ratio) but also dictates the lattice and periodicity of the resulting minimal surfaces of the BCPs. Our results could provide a rationale to design and synthesize amphiphilic block copolymers to directly self-assemble into periodic porous structures in solution, which could be promising materials having highly ordered mesopore networks.</P>
An, Tae Hyun,La, Yunju,Cho, Arah,Jeong, Moon Gon,Shin, Tae Joo,Park, Chiyoung,Kim, Kyoung Taek American Chemical Society 2015 ACS NANO Vol.9 No.3
<P>Solution self-assembly of amphiphilic block copolymers into inverse bicontinuous cubic mesophases is an emerging strategy for directly creating highly ordered triply periodic porous polymer nanostructures with large pore networks and desired surface functionalities. Although there have been recent reports on the formation of highly ordered triply periodic minimal surfaces of self-assembled block copolymer bilayers, the structural requirements for block copolymers in order to facilitate the preferential formation of such inverse mesophases in solution have not been fully investigated. In this study, we synthesized a series of model block copolymers, namely, branched poly(ethylene glycol)-<I>block</I>-polystyrene (bPEG-PS), to investigate the effect of the architecture of the block copolymers on their solution self-assembly into inverse mesophases consisting of the block copolymer bilayer. On the basis of the results, we suggest that the branched architecture of the hydrophilic block is a crucial structural requirement for the preferential self-assembly of the resulting block copolymers into inverse bicontinuous cubic phases. The internal crystalline lattice of the inverse bicontinuous cubic structure can be controlled <I>via</I> coassembly of branched and linear block copolymers. The results presented here provide design criteria for amphiphilic block copolymers to allow the formation of inverse bicontinuous cubic mesophases in solution. This may contribute to the direct synthesis of well-defined porous polymers with desired crystalline order in the porous networks and surface functionalities.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancac3/2015/ancac3.2015.9.issue-3/nn507338s/production/images/medium/nn-2014-07338s_0013.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nn507338s'>ACS Electronic Supporting Info</A></P>