• Journal of Microbiology and Biotechnology
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• 제30권10호
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• pp.1583-1591
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• 2020

CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-base-mutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various target-mismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate single-mismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.

• The Journal of Advanced Prosthodontics
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• 제11권6호
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• pp.341-349
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• 2019

PURPOSE. A novel retentive type of implant prosthesis that does not require the use of cement or screw holes has been introduced; however, there are few reports examining the biomechanical aspects of this novel implant. This study aimed to evaluate the biomechanical features of cementless fixation (CLF) implant prostheses. MATERIALS AND METHODS. The test groups of three variations of CLF implant prostheses and a control group of conventional cement-retained (CR) prosthesis were designed three-dimensionally for finite element analysis. The test groups were divided according to the abutment shape and the relining strategy on the inner surface of the implant crown as follows; resin-air hole-full (RAF), resin-air hole (RA), and resin-no air hole (RNA). The von Mises stress and principal stress were used to evaluate the stress values and distributions of the implant components. Contact open values were calculated to analyze the gap formation of the contact surfaces at the abutment-resin and abutment-implant interfaces. The micro-strain values were evaluated for the surrounding bone. RESULTS. Values reflecting the maximum stress on the abutment were as follows (in MPa): RAF, 25.6; RA, 23.4; RNA, 20.0; and CR, 15.8. The value of gap formation was measured from 0.88 to 1.19 ㎛ at the abutment-resin interface and 24.4 to 24.7 ㎛ at the abutment-implant interface. The strain distribution was similar in all cases. CONCLUSION. CLF had no disadvantages in terms of the biomechanical features compared with conventional CR implant prosthesis and could be successfully applied for implant prosthesis.

• Molecules and Cells
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• 제46권10호
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• pp.611-626
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• 2023

Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.

• The Plant Pathology Journal
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• 제26권2호
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• pp.139-148
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• 2010

A virus causing stunt, yellowing, severe mosaic, malformation symptoms on leaves and uneven development and malformation on fruits of zucchini was prevalent around Goseong, Gyeongsangnam-do, Korea. A survey conducted (2004) in the Goseong area revealed about 20% virus infection rate. The disease causative identified as Cucumber mosaic virus (CMV-Z1) was further characterized. The isolate induces mosaic symptoms on Cucumis sativus, while severe mosaic, stunt and malformation on C. pepo. Thin section analyses have shown that virus inclusions are formed in the cuticle layers as well as epidermal, parenchyma and collenchymas cells in virus-infected Nicotiana tabacum. CMV-Z1 isolate induced specific cytoplasmic inclusion bodies such as irregular clumps (IC), crystal (Cr) and irregular chloroplasts (ICh). IC was made up of virus particles interspersed with a darkly stained amorphous material and found both in the cytoplasm and vacuoles, whereas ICh and Cr were rarely found in the vacuoles. The genome of CMV-Z1 RNA-1 consists of 3359 nucleotide (nt) encoding 1a protein of 993 amino acids (aa). The CMV-Z1 RNA-2 was 3050 nt in length containing 2a (857 aa) and 2b (110 aa), while RNA-3 encoding 3a movement protein (279 aa) and coat protein (218 aa) was 2215 nt in length. Phylogenetic analyses of nucleotide sequences of CMV-Z1 isolate appeared it is more closely related to subgroup IA than to subgroup IB or II.

• 동의생리병리학회지
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• 제23권6호
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• pp.1449-1459
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• 2009

Coptidis rhizoma (huanglian) is an herb that is widely used in traditional Chinese medicine that has recently been shown to possess anticancer activity. However, the molecular mechanism underlying the anticancer effects of this herb is poorly understood. In this study, we investigated the anticancer activity of a combination of CR extract and arsenic trioxide, as well as the apoptotic pathway associated with its mechanism of action in human lung cancer H157 cells. Combined treatment of H157 cells with CR extract and arsenic trioxide resulted in significant apoptotic death. In addition, combined treatment with CR extract and arsenic trioxide acted in concert to induce a loss of mitochondrial membrane potential (${\Delta}{\Psi}$), the release of cytochrome c from mitochondria, and an increase in the expression of pro-apoptotic p53 and Bax protein, which resulted in activation of caspases and apoptosis. CR extract combined with arsenic trioxide also increased the lipid peroxidation, mRNA expression of DR4 and DR5 and caspase-8 activity. These data indicate that combined treatment with CR extract and arsenic trioxide enhanced apoptotic cell death in H157 cells through diverse pathways, including mitochondrial dysfunction and death receptors, particularly DR4 and DR5. Thus, this treatment may be an effective from of chemotherapy.

• 대한본초학회지
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• 제24권1호
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• pp.179-189
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• 2009

Objectives : Coptidis Rhizoma (Coptis japonica MAKINO; CR) is a well known crude drug as antimicrobial, antibacterial, anti-inflammatory, antioxidant activity. However, there is no study of the effect of CR on brain infarction and it's mechanism. The aim of this study was to investigate the effects on ischemic stroke induced by photothrombotic infarction by evaluating the functional & neuronal recovery after brain infarction. Materials & Methods : Male Sprague-Dawley rats (250-300 g) were induced photothrombotic brain infarction on sensorimotor cortex, and brain infarction volume by image J software (NIH, USA) after Nissl stain, also single pellet reaching task as a functional motor recovery were observed. After orally pretreated by CR (500 mg/kg) or normal saline as a sham control before 7 days from the time of photothrombotic infarction, rats were sacrificed. After then we analysed anti-inflammatory cytokines (TNF-$\alpha$, IL-6, IL-1$\beta$), by RT-PCR and ELISA method, and immunohistochemistry (GFAP, connexin-43) as a marker of neural plasticity. Results : CR (100, 250, 500 mg/kg) decreased the infarction volume dose-dependently, however the effect of 500mg/kg of CR (CR 500) showed the best (P=0.051). Also, CR 500 decreased the infarction volume time-dependently, the most effective time was 3-7 days after stroke. Photothrombosis increased inflammatory cytokines after infarction, CR 500 suppressed significantly mRNA expression of IL-1$\beta$, IL-6 and TNF-$\alpha$. In serum, CR 500 decreased the amount of IL-1$\beta$, 12h, 24h and 48h respectively (p < 0.05), also decreased that of IL-6 and TNF-$\alpha$, 12h respectively (p < 0.05) after infarction. The more astrocytes were observed and neural plasticity was facilitated in the rat brain of CR 500 than that of sham control in immunohistochemistry. Conclusions : This results suggest that CR decrease infarction volume and improve functional motor recovery in acute stage in photothrombotic ischemic infarction model in the mechanism of anti-inflammation and promoting neural plasticity.

• 대한치매학회지
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• 제17권4호
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• pp.131-136
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• 2018

Alzheimer's disease (AD) related genes have been elucidated by advanced genetic techniques. Familial autosomal dominant AD genes founded by linkage analyses are APP, PSEN1, PSEN2, ABCA7, and SORL1. Genome-wide association studies have found risk genes such as ABCA7, BIN1, CASS4, CD33, CD2AP, CELF1, CLU, CR1, DSG2, EPHA1, FERMT2, HLA-DRB5-HLA-DRB1, INPP5D, MEF2C, MS4A6A/MS4A4E, NME8, PICALM, PTK2B, SLC24A4, SORL1, and ZCWPW1. ABCA7, SORL1, TREM2, and APOE are proved to have high odds ratio (>2) in risk of AD using next generation sequencing studies. Thanks to the promising genetic techniques such as CRISPR-CAS9 and single-cell RNA sequencing opened a new era in genetics. CRISPR-CAS9 can directly link genetic knowledge to future treatment. Single-cell RNA sequencing are providing useful information on cell biology and pathogenesis of diverse diseases.

• 한국자기공명학회논문지
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• 제22권3호
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• pp.71-75
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• 2018

The CRISPR-Cas system is the adaptive immune system in bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, an endonuclease Cas9 cleaves DNA targets of phages as directed by guide RNA comprising crRNA and tracrRNA. To avoid targeting and destruction by Cas9, phages employ anti-CRISPR (Acr) proteins that act against host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of AcrIIA4 that inhibits endonuclease activity of type II-A Listeria monocytogenes Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The secondary structures of AcrIIA4 predicted by the backbone chemical shifts show an ${\alpha}{\beta}{\beta}{\beta}{\alpha}{\alpha}$ fold, which is used to determine the solution structure.

• 한국발생생물학회지:발생과생식
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• 제22권2호
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• pp.175-182
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• 2018

In order to examine the effects of four different light spectra (white, red, green, and blue) on the oocyte maturation, the change of reproductive parameters, via brain-pituitary-gonad (BPG) axis in grass puffer, were investigated. After exposure four different light spectra for 7 weeks, the abundance of gonadotropin-releasing hormone (GnRH) mRNA which is a type of seabream (sbGnRH) and two different subunit of gonadotropin hormones mRNAs, follicle-stimulating hormone ($fsh{\beta}$) mRNA and luteinizing hormone ($lh{\beta}$) mRNA, were analyzed in the brain and pituitary. Histological analysis showed that the mature oocyte ratio in the green spectrum was higher than other light spectra-exposed groups. Gonadosomatic index (GSI) and oocyte developmental stage were also investigated in the gonad based on histological observations. GSI value with the presence of yolk stage oocytes was significantly increased in the green spectrum-exposed group when compared to that of the other light-exposed groups (white, red, and blue) (p<0.05). The abundances of sbGnRH mRNA and $fsh{\beta}$ mRNA in the green spectrum-exposed group were also significant higher than those of the other light spectra-exposed groups (p<0.05). These results indicate that the maturation of oocyte in grass puffer can be accelerated by exposure to the spectrum of green. To better understand the molecular mechanism for the maturation of oocyte in grass puffer, further study examining the relationship between oocyte development and its related genes is required.

• Asian-Australasian Journal of Animal Sciences
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• 제32권6호
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• pp.834-841
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• 2019

Objective: This study was conducted to investigate the effects of in ovo feeding (IOF) of creatine pyruvate (CrPyr) on the energy metabolism in thigh muscle of embryos and neonatal broilers. Methods: A total of 960 eggs were randomly assigned to three treatments: i) non-injected control group, ii) saline group injected with 0.6 mL of physiological saline (0.75%), and iii) CrPyr group injected with 0.6 mL of physiologi-cal saline (0.75%) containing 12 mg CrPyr/egg on 17.5 d of incubation. After hatching, 120 male chicks (close to the average body weight of the pooled group) in each group were randomly assigned to eight replications. The feeding experiment lasted 7 days. Results: The results showed that IOF of CrPyr increased glucose concentrations in the thigh muscle of broilers on 2 d after injection (p<0.05). Compared with the control and saline groups, the concentration of creatine in CrPyr group was increased on 2 d after injection and the day of hatch (p<0.05). Moreover, IOF of CrPyr increased the creatine kinase activity at hatch and increased the activities of hexokinase and pyruvate kinase on 2 d after injection and the day of hatch (p<0.05). Chicks in CrPyr group showed higher mRNA expressions of glucose transporter 3 (GLUT3) and GLUT8 on the day of hatch (p<0.05). Conclusion: These results demonstrated that IOF of CrPyr was beneficial to enhance muscle energy reserves of em-bryos and hatchlings.