• BMB Reports
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• v.57 no.1
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• pp.40-49
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• 2024

Prokaryotes encode clustered regularly interspaced short palindromic repeat (CRISPR) arrays and CRISPR-associated (Cas) genes as an adaptive immune machinery. CRISPR-Cas systems effectively protect hosts from the invasion of foreign enemies, such as bacteriophages and plasmids. During a process called 'adaptation', non-self-nucleic acid fragments are acquired as spacers between repeats in the host CRISPR array, to establish immunological memory. The highly conserved Cas1-Cas2 complexes function as molecular recorders to integrate spacers in a time course manner, which can subsequently be expressed as crRNAs complexed with Cas effector proteins for the RNA-guided interference pathways. In some of the RNA-targeting type III systems, Cas1 proteins are fused with reverse transcriptase (RT), indicating that RT-Cas1-Cas2 complexes can acquire RNA transcripts for spacer acquisition. In this review, we summarize current studies that focus on the molecular structure and function of the RT-fused Cas1-Cas2 integrase, and its potential applications as a directional RNA-recording tool in cells. Furthermore, we highlight outstanding questions for RT-Cas1-Cas2 studies and future directions for RNA-recording CRISPR technologies.

• The Plant Pathology Journal
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• v.38 no.1
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• pp.12-24
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• 2022

In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2005.06a
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• pp.1045-1049
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• 2005

In this paper, the dynamic crawling of a five-bar planar mechanism is investigated. One complete cycle of the crawling selected in this study consists of four different steps, i) sliding at one contact point between the mechanism and the ground, ii) changing its configuration without sliding at two contact points, iii) sliding at the other contact point, and iv) again changing its configuration without sliding at two contact points. In this type of crawling, the crawling mechanism maintains the shape of the parallel structure throughout a complete crawling cycle. The modeling algorithm for serial manipulators proposed by M. Thomas and et al.[1] is employed by introducing imaginary joints and links which represent the contact interfaces between the one end of the mechanism and the ground, while the other end of the mechanism is regarded as an end-effector of the imaginary serial manipulator which treats the reaction force and torque at the contact point as external forces. Then, a complete cycle of dynamic crawling of the mechanism is investigated through various computer simulations. The simulation result show that the stable crawling characteristics of the mechanism could be secured when the proper configurations depending on specified frictional constraints are met.

• Korean Journal of Microbiology
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• v.50 no.3
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• pp.245-248
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• 2014

Pseudomonas syringae pv. actinidiae is the causal agent of bacterial canker in kiwifruit (genus Actinidia). Multilocus sequence analysis of seven housekeeping and 11 type III effector genes differentiated the virulent P. syringae pv. actinidiae isolates worldwide into three groups designated as Psa1-Psa3. In this work, a total of 12 P. syringae pv. Actinidiae strains, including three Psa1, three Psa2, three Psa3 strains isolated from Korea and three Psa3 strains from Italy, were compared based on their phenotypic properties. Strains with different geographic origins had unique growth patterns as demonstrated by growth rate at several temperatures; all tested strains exhibited maximum growth at temperatures below $22^{\circ}C$, while the growth of Psa3 strains was completely inhibited above $30^{\circ}C$. Psa3 strains isolated from Korea had longer lag phases than the Psa3 strains from Italy. The Psa2 strains were different from Psa1 and Psa3 strains in the API 20NE test, in which the Psa2 strains could not utilize potassium gluconate, capric acid and trisodium citrate. Psa3 strains isolated from Korea could hydrolyze esculin. The API ZYM test showed that ${\beta}$-glucosidase activity was detected only from Psa3 strains. The strains belonging to the three Psa groups differed with regard to their susceptibility to ampicillin, novobiocin, and oleandomycin.