• Title/Summary/Keyword: molecular data

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Structural Characteristics of Low Molecular Weight Laminarin Prepared by Ionizing Irradiation (이온화 방사선 조사에 의해 얻어진 저분자 laminarin의 분자구조 특성)

  • Choi, Jong-Il
    • Korean Chemical Engineering Research
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    • v.51 no.6
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    • pp.780-783
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    • 2013
  • Recently, it has been reported that low molecular weight laminarin had the enhanced biological activities. In this study, molecular structure of low molecular weight laminarin prepared by ionizing irradiation was studied. Low molecular weight laminarin samples of 13.5, 8.5, 7, and 6 kDa were obtained from 15 kDa laminarin by irradiation. From gel permeation chromatography data, low molecular weight laminarin was shown to have low polydispersity. To define the changes of functional groups in laminarin with different molecular weights, Fourier-transform infrared analysis was carried out. There was found no significant changes of functional groups in low molecular weight laminarin, except the increase of carbonyl group. The granular fissures from scanning electron microscopy showed the breakage of glycosidic bond in low molecular weight laminarin. These results could be utilized for the investigation of the enhanced biological activities of low molecular weight polysaccharides including laminarin.

Expression profiling of cultured podocytes exposed to nephrotic plasma reveals intrinsic molecular signatures of nephrotic syndrome

  • Panigrahi, Stuti;Pardeshi, Varsha Chhotusing;Chandrasekaran, Karthikeyan;Neelakandan, Karthik;PS, Hari;Vasudevan, Anil
    • Clinical and Experimental Pediatrics
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    • v.64 no.7
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    • pp.355-363
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    • 2021
  • Background: Nephrotic syndrome (NS) is a common renal disorder in children attributed to podocyte injury. However, children with the same diagnosis have markedly variable treatment responses, clinical courses, and outcomes, suggesting molecular heterogeneity. Purpose: This study aimed to explore the molecular responses of podocytes to nephrotic plasma to identify specific genes and signaling pathways differentiating various clinical NS groups as well as biological processes that drive injury in normal podocytes. Methods: Transcriptome profiles from immortalized human podocyte cell line exposed to the plasma of 8 subjects (steroid-sensitive nephrotic syndrome [SSNS], n=4; steroid-resistant nephrotic syndrome [SRNS], n=2; and healthy adult individuals [control], n=2) were generated using microarray analysis. Results: Unsupervised hierarchical clustering of global gene expression data was broadly correlated with the clinical classification of NS. Differential gene expression (DGE) analysis of diseased groups (SSNS or SRNS) versus healthy controls identified 105 genes (58 up-regulated, 47 down-regulated) in SSNS and 139 genes (78 up-regulated, 61 down-regulated) in SRNS with 55 common to SSNS and SRNS, while the rest were unique (50 in SSNS, 84 genes in SRNS). Pathway analysis of the significant (P≤0.05, -1≤ log2 FC ≥1) differentially expressed genes identified the transforming growth factor-β and Janus kinase-signal transducer and activator of transcription pathways to be involved in both SSNS and SRNS. DGE analysis of SSNS versus SRNS identified 2,350 genes with values of P≤0.05, and a heatmap of corresponding expression values of these genes in each subject showed clear differences in SSNS and SRNS. Conclusion: Our study observations indicate that, although podocyte injury follows similar pathways in different clinical subgroups, the pathways are modulated differently as evidenced by the heatmap. Such transcriptome profiling with a larger cohort can stratify patients into intrinsic subtypes and provide insight into the molecular mechanisms of podocyte injury.

List-event Data Resampling for Quantitative Improvement of PET Image (PET 영상의 정량적 개선을 위한 리스트-이벤트 데이터 재추출)

  • Woo, Sang-Keun;Ju, Jung Woo;Kim, Ji Min;Kang, Joo Hyun;Lim, Sang Moo;Kim, Kyeong Min
    • Progress in Medical Physics
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    • v.23 no.4
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    • pp.309-316
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    • 2012
  • Multimodal-imaging technique has been rapidly developed for improvement of diagnosis and evaluation of therapeutic effects. In despite of integrated hardware, registration accuracy was decreased due to a discrepancy between multimodal image and insufficiency of count in accordance with different acquisition method of each modality. The purpose of this study was to improve the PET image by event data resampling through analysis of data format, noise and statistical properties of small animal PET list data. Inveon PET listmode data was acquired as static data for 10 min after 60 min of 37 MBq/0.1 ml $^{18}F$-FDG injection via tail vein. Listmode data format was consist of packet containing 48 bit in which divided 8 bit header and 40 bit payload space. Realigned sinogram was generated from resampled event data of original listmode by using adjustment of LOR location, simple event magnification and nonparametric bootstrap. Sinogram was reconstructed for imaging using OSEM 2D algorithm with 16 subset and 4 iterations. Prompt coincidence was 13,940,707 count measured from PET data header and 13,936,687 count measured from analysis of list-event data. In simple event magnification of PET data, maximum was improved from 1.336 to 1.743, but noise was also increased. Resampling efficiency of PET data was assessed from de-noised and improved image by shift operation of payload value of sequential packet. Bootstrap resampling technique provides the PET image which noise and statistical properties was improved. List-event data resampling method would be aid to improve registration accuracy and early diagnosis efficiency.

Taxonomic status of Goodyera rosulacea (Orchidaceae): molecular evidence based on ITS and trnL sequences (로젯사철란(Goodyera rosulacea: Orchidaceae)의 분류학적 위치: ITS와 trnL 염기서열에 의한 분자적 증거)

  • Lee, Chang Shook;Eom, Sang Mi;Lee, Nam Sook
    • Korean Journal of Plant Taxonomy
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    • v.36 no.3
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    • pp.189-207
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    • 2006
  • Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

The temperature and density distribution of molecular gas in a galaxy undergoing strong ram pressure: a case study of NGC 4402

  • Lee, Bumhyun;Chung, Aeree
    • The Bulletin of The Korean Astronomical Society
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    • v.40 no.1
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    • pp.77.2-77.2
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    • 2015
  • Galaxies are known to evolve passively in the cluster environment. Indeed, much evidence for HI stripping has been found in cluster galaxies to date, which is likely to be connected to their low star formation rate. What is still puzzling however, is that the molecular gas, which is believed to be more directly related to star formation, shows no significant difference in its fraction between the cluster population and the field galaxies. Therefore, HI stripping alone does not seem to be enough to fully understand how galaxies become passive in galaxy clusters. Intriguingly, our recent high resolution CO study of a subsample of Virgo spirals which are undergoing strong ICM pressure has revealed a highly disturbed molecular gas morphology and kinematics. The morphological and kinematical peculiarities in their CO data have many properties in common with those of HI gas in the sample, indicating that strong ICM pressure in fact can have impacts on dense gas deep inside of a galaxy. This implies that it is the molecular gas conditions rather than the molecular gas stripping which is more responsible for quenching of star formation in cluster galaxies. In this study, using multi transitions of 12CO and 13CO, we investigate the density and temperature distributions of CO gas of a Virgo spiral galaxy, NGC 4402 to probe the physical and chemical properties of molecular gas and their relations to star formation activities.

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Hydrogen Bonds in GlcNAc( β1,3)Gal( β)OMe in DMSO Studied by NMR Spectroscopy and Molecular Dynamics Simulations

  • Shim, Gyu-Chang;Shin, Jae-Min;Kim, Yang-Mee
    • Bulletin of the Korean Chemical Society
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    • v.25 no.2
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    • pp.198-202
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    • 2004
  • Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

Comparison of Ectopic Gene Expression Methods in Rat Neural Stem Cells

  • Kim, Woosuk;Kim, Ji Hyeon;Kong, Sun-Young;Park, Min-Hye;Sohn, Uy Dong;Kim, Hyun-Jung
    • The Korean Journal of Physiology and Pharmacology
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    • v.17 no.1
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    • pp.23-30
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    • 2013
  • Neural stem cells (NSCs) have the ability to proliferate and differentiate into various types of cells that compose the nervous system. To study functions of genes in stem cell biology, genes or siRNAs need to be transfected. However, it is difficult to transfect ectopic genes into NSCs. Thus to identify the suitable method to achieve high transfection efficiency, we compared lipid transfection, electroporation, nucleofection and retroviral transduction. Among the methods that we tested, we found that nucleofection and retroviral transduction showed significantly increased transfection efficiency. In addition, with retroviral transduction of Ngn2 that is known to induce neurogenesis in various types of cells, we observed facilitated final cell division in rat NSCs. These data suggest that nucleofection and retroviral transduction provide high efficiency of gene delivery system to study functions of genes in rat NSCs.

Molecular Modeling and its Experimental Verification for the Catalytic Mechanism of Candida antarctica Lipase B

  • Kwon, Cheong-Hoon;Shin, Dae-Young;Lee, Jong-Ho;Kim, Seung-Wook;Kang, Jeong-Won
    • Journal of Microbiology and Biotechnology
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    • v.17 no.7
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    • pp.1098-1105
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    • 2007
  • Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

'Drawing' a Molecular Portrait of CIN and Cervical Cancer: a Review of Genome-Wide Molecular Profiling Data

  • Kurmyshkina, Olga V;Kovchur, Pavel I;Volkova, Tatyana O
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.11
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    • pp.4477-4487
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    • 2015
  • In this review we summarize the results of studies employing high-throughput methods of profiling of HPV-associated cervical intraepithelial neoplasia (CIN) and squamous cell cervical cancers at key intracellular regulatory levels to demonstrate the unique identity of the landscape of molecular changes underlying this oncopathology, and to show how these changes are related to the 'natural history' of cervical cancer progression and the formation of clinically significant properties of tumors. A step-wise character of cervical cancer progression is a morphologically well-described fact and, as evidenced by genome-wide screenings, it is indeed the consistent change of the molecular profiles of HPV-infected epithelial cells through which they progressively acquire the phenotypic hallmarks of cancerous cells. In this sense, CIN/cervical cancer is a unique model for studying the driving forces and mechanisms of carcinogenesis. Recent research has allowed definition of the whole-genome spectrum of both random and regular molecular alterations, as well as changes either common to processes of carcinogenesis or specific for cervical cancer. Despite the existence of questions that are still to be investigated, these findings are of great value for the future development of approaches for the diagnostics and treatment of cervical neoplasms.

Identification of Lactic Acid Bacteria from Meat by Low Molecular Weight(LMW) RNA Profiles (Low Molecular Weight(LMW) RNA Profiles에 의한 젖산균의 동정)

  • Cha, Woen-Suep
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.21 no.6
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    • pp.681-685
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    • 1992
  • Low molecular weight RNA(LMW RNA : 5S rRNA and tRNAs, <150 nucleotides) profiles of several bacteriocin production lactic acid bacteria from pig meats and reference lactic acid bacteria were generated on 10% denaturing polyacrylamide gel electrophoresis. Data evaluation including three molecular weight markers enabled the calculation of relative nucleotide units(RNU) for every band. Gels profiles and RNU evaluations were effective for identification of lactic acid bacteria species. LMW RNA profiles of lactic acid bacteria showed no variation in dependence on APT(All Purpose Tryptone Broth), TSB(Tryptic Soy Broth), MRS(Lactobacilli MRS Broth) different cultural medium.

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