• Title/Summary/Keyword: library 3.0

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Cloning and Characterization of Cellulase Gene (cel5C) from Cow Rumen Metagenomic Library (소 반추위 메타게놈에서 새로운 섬유소분해효소 유전자(cel5C) 클로닝 및 유전산물의 특성)

  • Kim, Min-Keun;Barman, Dhirendra Nath;Kang, Tae-Ho;Kim, Jung-Ho;Kim, Hoon;Yun, Han-Dae
    • Journal of Life Science
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    • v.22 no.4
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    • pp.437-446
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    • 2012
  • A metagenomic library of cow rumen in the pCC1FOS phage vector was screened in $E.$ $coli$ EPI300 for cellulase activity on carboxymethyl cellulose agar plates. One clone was partially digested with $Sau$3AI, ligated into the $Bam$HI site of the pBluescript II SK+ vector, and transformed into $E.$ $coli$ $DH5{\alpha}$. We obtained a 1.5 kb insert DNA, designated $cel$5C, which hydrolyzes carboxymethyl cellulose. The cel5C gene has an open reading frame (ORF) of 1,125 bp encoding 374 amino acids. It belongs to the glycosyl hydrolase family 5 with the conserved domain LIMEGFNEIN. The molecular mass of the Cel5C protein induced from $E.$ $coli$ $DH5{\alpha}$, as analyzed by CMC SDS-PAGE, appeared to be approximately 42 kDa. The enzyme showed optimum cellulase activity at pH 4.0, and $50^{\circ}C$. We examined whether the $cel$5C gene comes from the 49 identified cow rumen bacteria using PCR. No PCR bands were identified, suggesting that the $cel$5C gene came from the unidentified cow rumen bacteria.

Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing

  • Lee, Minho;Choi, Shin-Jung;Han, Sangjo;Nam, Miyoung;Kim, Dongsup;Kim, Dong-Uk;Hoe, Kwang-Lae
    • Genomics & Informatics
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    • v.16 no.2
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    • pp.22-29
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    • 2018
  • Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

Analyzing Vomit of Platalea minor (Black-faced Spoonbill) to Identify Food Components using Next-Generation Sequencing and Microscopy (차세대염기서열 및 현미경 분석을 통한 저어새의 토사물 내 먹이생물 분석)

  • Kim, Hyun-Jung;Lee, Taek-Kyun;Jung, Seung Won;Kwon, In-Ki;Yoo, Jae-Won
    • Korean Journal of Environmental Biology
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    • v.36 no.2
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    • pp.165-173
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    • 2018
  • We sampled vomit of black-faced spoonbills(Platalea minor) during the brood-rearing season (from June 2011 to June 2014) at the Namdong reservoir in Incheon and analyzed the food components in the vomit using microscopy and next-generation sequencing (NGS). Microscopic observations primarily helped in identifying osteichthyes (bony fishes), crustaceans, and polychaetes. In particular, species belonging to the families Mugilidae and Gobiidae among the fish, and Macrophthalmus japonicas among the crustaceans, were observed at high frequency. Results of NGS analysis revealed the predominant presence of bony fish (42.58% of total reads) and crustaceans (40.75% of total reads), whereas others, such as polychaetes (12.66%), insects (0.24%), and unidentified species (3.78%), occurred in lower proportions. At the species level, results of NGS analysis revealed that Macrophthalmus abbreviates and Macrobrachium sp. among the crustaceans, and Acanthogobius hasta, Tridentiger obscurus, and Pterogobius zacalles among the bony fish, made up a high proportion of the total reads. These food species are frequently found at tidal flats in the Songdo and Sihwa lakes, emphasizing the importance of these areas as potential feeding sites of the black-faced spoonbill. Feed composition of the black-faced spoonbill, as evaluated by analyzing its vomit, differed when the evaluations were done by microscopic observation or by NGS analysis. Evaluation by microscopic observation is difficult and not error free, owing to the degradation of the samples to be analyzed; however, NGS analysis is more accurate, because it makes use of genetic information. Therefore, accurately analyzing food components from morphologically indistinguishable samples is possible by using genetic analysis.

Effect of luteal phase support with vaginal progesterone on pregnancy outcomes in natural frozen embryo transfer cycles: A meta-analysis

  • Seol, Aeran;Shim, Yoo Jin;Kim, Sung Woo;Kim, Seul Ki;Lee, Jung Ryeol;Jee, Byung Chul;Suh, Chang Suk;Kim, Seok Hyun
    • Clinical and Experimental Reproductive Medicine
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    • v.47 no.2
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    • pp.147-152
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    • 2020
  • Objective: The purpose of this study was to determine the effect of vaginal progesterone for luteal phase support (LPS) on the clinical pregnancy rate (CPR) in natural frozen embryo transfer (FET) cycles via a meta-analysis. Methods: We performed a meta-analysis of randomized controlled trials (RCTs) and retrospective studies that met our selection criteria. Four online databases (PubMed, Embase, Medline, and the Cochrane Library) were searched between January 2017 and May 2017. Studies were selected according to predefined inclusion criteria and meta-analyzed using R software version 2.14.2. The main outcome measure was CPR. Results: A total of 18 studies were reviewed and assessed for eligibility. One RCT (n = 435) and three retrospective studies (n = 3,033) met the selection criteria. In a meta-analysis of the selected studies, we found no significant difference in the CPR (odds ratio [OR], 0.96; 95% confidence interval [CI], 0.60-1.55) between the vaginal progesterone and control groups. An analysis of the two retrospective cohort studies that reported the live birth rate (LBR) following FET showed a significantly higher LBR in the vaginal progesterone group (OR, 1.72; 95% CI, 1.21-2.46). A subgroup meta-analysis of FET conducted 5 days after injection of human chorionic gonadotropin showed no significant differences between the two groups with regard to the CPR (OR, 1.18; 95% CI, 0.90-1.55) or miscarriage rate (OR, 0.73; 95% CI, 0.36-1.47). Conclusion: The results of this meta-analysis of the currently available literature suggest that LPS with vaginal progesterone in natural FET cycles does not improve the CPR.

Efficacy of alpha-lipoic acid in patients with burning mouth syndrome compared to that of placebo or other interventions: a systematic review with meta-analyses

  • Christy, Jessica;Noorani, Salman;Sy, Frank;Al-Eryani, Kamal;Enciso, Reyes
    • Journal of Dental Anesthesia and Pain Medicine
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    • v.22 no.5
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    • pp.323-338
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    • 2022
  • Burning mouth syndrome (BMS) is a chronic oral disorder of unknown etiology which presents therapeutic challenges. Alpha-lipoic acid (ALA) has been studied as a potential treatment for BMS. The objective of this systematic review and meta-analysis was to evaluate the effectiveness of ALA compared to that of placebo or other interventions in individuals with BMS. Randomized controlled trials (RCT) using ALA to treat BMS were identified from MEDLINE, Cochrane Library, EMBASE, and Web of Science up to February 3, 2021. The assessment of the risk of bias in the included studies was based on the Cochrane guidelines. The primary outcome evaluated was the visual analog scale (VAS) pain intensity. ALA was compared with placebo, clonazepam, gabapentin, pregabalin, ALA plus gabapentin, capsaicin, Biotène®, and laser therapy. Altogether, 137 records were scanned for inclusion/exclusion, and nine RCTs (two unclear and seven at high risk of bias) were included in the qualitative and quantitative analyses, with a total of 594 patients with BMS included in this review. All studies reported an improvement in VAS pain scores ranging from -0.72 to -2.77. Meta-analysis results showed a non-significant reduction in pain intensity for ALA (P = 0.616) compared to that of placebo on a VAS of 0-10. Patients taking ALA were 1.923 times more likely to show an improvement in self-reported BMS symptoms (P = 0.031) than those in the placebo group. Clonazepam and pregabalin showed a significant VAS pain reduction of 4.08 and 4.68 (P < 0.001), respectively, compared to that with ALA. Although ALA intervention provided a non-significant improvement in the pain score and was more likely to produce a reduction in BMS symptoms, the evidence was of low quality. Further research is needed to establish clear guidelines for the use of ALA for BMS treatment.

Molecular Cloning and Expression of the $\beta$-Xylosidase Gene (xylB) of Bacillus stearothermophilus in Escherichia coli

  • Suh, Jung-Han;Eom, Soo-Jung;Cho, Ssang-Goo;Choi, Yong-Jin
    • Journal of Microbiology and Biotechnology
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    • v.6 no.5
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    • pp.331-335
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    • 1996
  • The second $\beta$-Xylosidase gene (xylB) from Bacillus stearothermophilus was isolated from the genomic library, cloned into pBR322, and subsequently transferred into Escherichia coli HB101. Six out of 10, 000 transformants were selected from the selective LB medium supplemented with p-nitrophenyl-$\alpha$-L-arabinofuranoside (pNPAf) and ampicillin ($50\mu g$/ml) based on their ability to form a yellow ring around the colony. One of the clones was found to harbor the recombinant plasmid with 5.0 kb foreign DNA, which was identical to the $\alpha$-L-arabinofuranosidase gene (arfI) previously cloned in this lab, while the other five had 3.5 kb of the foreign DNA. Southern blotting experiments confirmed that the 3.5 kb insert DNA was from B. stearothermophilus chromosomal DNA. A zymogram with 4-methylumbelliferyl-$\alpha$-L-arabinofuranoside as the enzyme substrate revealed that the cloned gene product was one of the mutiple $\alpha$-L-arabinofuranosidases produced by B. stearothermophilus. Unlike the arfI gene product, the product of the gene on the insert DNA (xylB) showed an activity not only on pNPAf but also on oNPX suggesting that the cloned gene product could be a bifunctional enzyme having both $\alpha$-L-arabinofuranosidase and $\beta$-xylosidase activities.

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Molecular Cloning and Characterization of a Bile Salt Hydrolase from Lactobacillus acidophilus PF01

  • Oh, Hae-Keun;Lee, Ji-Yoon;Lim, Soo-Jin;Kim, Min-Jeong;Kim, Geun-Bae;Kim, Jung-Hoan;Hong, Soon-Kwang;Kang, Dae-Kyung
    • Journal of Microbiology and Biotechnology
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    • v.18 no.3
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    • pp.449-456
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    • 2008
  • Phenotypic screening for bile salt hydrolase (BSH) activity was performed on Lactobacillus acidophilus PF01 isolated from piglet feces. A gene encoding BSH was identified and cloned from the genomic library of L. acidophilus PF01. The bsh gene and surrounding regions were characterized by nucleotide sequence analysis and were found to contain a single open reading frame (ORF) of 951 nucleotides encoding a 316 amino acid protein. The potential bsh promoter region was located upstream of the start codon. The protein deduced from the complete ORF had high similarity with other BSHs, and four amino acid motifs located around the active site, FGRNXD, AGLNF, VLTNXP, and GXGXGXXGXPGD, were highly conserved. The bsh gene was cloned into the pET21b expression vector and expressed in Escherichia coli BLR(DE3) by induction with 0.1mM of isopropylthiogalactopyranoside. The BSH enzyme was purified with apparent homogeneity using a $Ni^{2+}$-NTA agarose column and characterized. The overexpressed recombinant BSH enzyme of L. acidophilus PF01 exhibited hydrolase activity against tauroconjugated bile salts, but not glycoconjugated bile salts. It showed the highest activity against taurocholic acid. The maximum BSH activity occurred at approximately $40^{\circ}C$. The enzyme maintained approximately 70% of its maximum activity even at $60^{\circ}C$, whereas its activity rapidly decreased at below $37^{\circ}C$. The optimum pH was 6, and BSH activity was rapidly inactivated below pH 5 and above pH 7.

Home exercise program adherence strategies in vestibular rehabilitation: a systematic review

  • Gaikwad, Shilpa B.;Mukherjee, Tatri;Shah, Parita V.;Ambode, Oluwaseun I.;Johnsonb, Eric G.;Daher, Noha S.
    • Physical Therapy Rehabilitation Science
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    • v.5 no.2
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    • pp.53-62
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    • 2016
  • Objective: The aim of this systematic review was to investigate for effective strategies to improve home exercise program (HEP) adherence in vestibular rehabilitation (VR). Design: Systematic review. Methods: A systematic review was conducted to identify effective strategies used to improve HEP adherence of patients in VR. Six databases, Academic Search Premier, Cochrane Library, CINAHL, PUBMED, PsycINFO, and Web of Science were searched from their inception to December 31, 2015. The keywords used for search were 'home program', 'home intervention', 'compliance', 'adherence', 'vestibular rehabilitation', 'motion sickness', and 'motion sensitivity'. Results: A total of eight studies were selected to be included in the review. There was 95.2% agreement between the two reviewers who reviewed the studies using a quality assessment tool. The overall inter-rater agreement (${\kappa}$=0.73) showed good agreement between the reviewers. Strong evidence was identified for 3 major categories of effective HEP adherence strategies, 1) providing patient with written summary of HEP; 2) asking patient to maintain a record of HEP and symptoms; and 3) providing tele-rehabilitation in form of email and/or telephone support along with in person treatment sessions. Also, based on strong evidence, computerized technology was not found to be superior to other strategies for improving patients' HEP adherence in VR. Conclusions: The effective strategies for improving HEP in VR include written summary of exercise, maintenance of log of HEP and symptoms and tele-rehabilitation along with in person treatment sessions.

Structure-Based Virtual Screening and Biological Evaluation of Non-Azole Antifungal Agent

  • Lee, Joo-Youn;Nam, Ky-Youb;Min, Yong-Ki;Park, Chan-Koo;Lee, Hyun-Gul;Kim, Bum-Tae;No, Kyoung-Tai
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2005.09a
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    • pp.139-143
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    • 2005
  • Cytochrome P450 14${\alpha}$-sterol demethylase enzyme (CYP51) is the target a of azole type antifungals. The azole blocks the ergosterol synthesis and thereby inhibits fungal growth. A three-dimensional (3D) homology model of CYP51 from Candida albicans was constructed based on the X-ray crystal structure of CYP51 from Mycobacterium tuberculosis. Using this model, the binding modes for the substrate (24-methylene-24, 25-dihydrolanosterol) and the known inhibitors (fluconazole, voriconazole, oxiconazole, miconazole) were predicted from docking. Virtual screening was performed employing Structure Based Focusing (SBF). In this procedure, the pharmacophore models for database search were generated from the protein-ligands interactions each other. The initial structure-based virtual screening selected 15 compounds from a commercial available 3D database of approximately 50,000 molecule library, Being evaluated by a cell-based assay, 5 compounds were further identified as the potent inhibitors of Candida albicans CYP51 (CACYP51) with low minimal inhibitory concentration (MIC) range. BMD-09-01${\sim}$BMD-09-04 MIC range was 0.5 ${\mu}$g/ml and BMD-09-05 was 1 ${\mu}$g/ml. These new inhibitors provide a basis for some non-azole antifungal rational design of new, and more efficacious antifungal agents.

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Design of General Peripheral Interface Using Serial Link (직렬 링크 방식의 주변 장치 통합 인터페이스 설계)

  • Kim, Do-Seok;Chung, Hoon-Ju;Lee, Yong-Hwan
    • The Journal of Korea Institute of Information, Electronics, and Communication Technology
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    • v.4 no.1
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    • pp.68-75
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    • 2011
  • The performance of peripheral devices is improving rapidly to meet the needs of users for multimedia data. Therefore, the peripheral interface with wide bandwidth and high transmission rate becomes necessary to handle large amounts of data in real time for multiple high-performance devices. PCI Express is a fast serial interface with the use of packets that are compatible with previous PCI and PCI-X. In this paper, we design and verify general peripheral interface using serial link. It includes two kinds of traffic class (TC) labels which are mapped to virtual channels (VC). The design adopts TC/VC mapping and the scheme of arbitration by priority. The design uses a packet which can be transmitted through up to four transmission lanes. The design of general peripheral interface is described in Verilog HDL and verified using ModelSim. For FPGA verification, Xilinx ISE and SPARTAN XC3S400 are used.We used Synopsys Design Compiler as a synthesis tool and the used library was MagnaChip 0.35um technology.