• Title/Summary/Keyword: biodesign

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Crystal structure of unphosphorylated Spo0F from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier

  • Lee, Chang Woo;Park, Sun-Ha;Jeong, Chang Sook;Lee, Chang Sup;Hong, Jong Wook;Park, Hyun Ho;Park, Hyun;Park, HaJeung;Lee, Jun Hyuck
    • Biodesign
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    • v.6 no.4
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    • pp.84-91
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    • 2018
  • Spo0F is a response regulator that modulates sporulation, undergoes phosphorylation for phosphorelay signal transduction, and interacts with various regulatory proteins; however, the mechanisms through which phosphorylation induces structural changes and regulates interactions with binding partners remain unclear. Here, we determined the unphosphorylated crystal structure of Spo0F from the psychrophilic bacterium Paenisporosarcina sp. TG-14 (PaSpo0F) and established a phosphorylation-state structural model. We found that PaSpo0F underwent structural changes (Lys54 and Lys102) by phosphorylation and generated new interactions (Lys102/Gln10 and Lys54/Glu84) to stabilize the ${\beta}4/{\alpha}4$ and ${\beta}1/{\alpha}1$ loop structures, which are important target-protein binding sites. Analysis of Bacillus subtilis Spo0 variants revealed movement by BsSpo0F Thr82 and Tyr84 residues following interaction with BsSpo0B, providing insight into the movement of corresponding residues in PaSpo0F (Thr80 and Tyr82), with further analysis of BsSpo0F/BsRapH interaction revealing alterations in the ${\beta}4/{\alpha}4$ loop region. These results suggest that phosphorylation-induced structural rearrangement might be essential for PaSpo0F activation and expand the understanding of Spo0F-specific activation mechanisms during sporulation.

Development of Intelligent Severity of Atopic Dermatitis Diagnosis Model using Convolutional Neural Network (합성곱 신경망(Convolutional Neural Network)을 활용한 지능형 아토피피부염 중증도 진단 모델 개발)

  • Yoon, Jae-Woong;Chun, Jae-Heon;Bang, Chul-Hwan;Park, Young-Min;Kim, Young-Joo;Oh, Sung-Min;Jung, Joon-Ho;Lee, Suk-Jun;Lee, Ji-Hyun
    • Management & Information Systems Review
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    • v.36 no.4
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    • pp.33-51
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    • 2017
  • With the advent of 'The Forth Industrial Revolution' and the growing demand for quality of life due to economic growth, needs for the quality of medical services are increasing. Artificial intelligence has been introduced in the medical field, but it is rarely used in chronic skin diseases that directly affect the quality of life. Also, atopic dermatitis, a representative disease among chronic skin diseases, has a disadvantage in that it is difficult to make an objective diagnosis of the severity of lesions. The aim of this study is to establish an intelligent severity recognition model of atopic dermatitis for improving the quality of patient's life. For this, the following steps were performed. First, image data of patients with atopic dermatitis were collected from the Catholic University of Korea Seoul Saint Mary's Hospital. Refinement and labeling were performed on the collected image data to obtain training and verification data that suitable for the objective intelligent atopic dermatitis severity recognition model. Second, learning and verification of various CNN algorithms are performed to select an image recognition algorithm that suitable for the objective intelligent atopic dermatitis severity recognition model. Experimental results showed that 'ResNet V1 101' and 'ResNet V2 50' were measured the highest performance with Erythema and Excoriation over 90% accuracy, and 'VGG-NET' was measured 89% accuracy lower than the two lesions due to lack of training data. The proposed methodology demonstrates that the image recognition algorithm has high performance not only in the field of object recognition but also in the medical field requiring expert knowledge. In addition, this study is expected to be highly applicable in the field of atopic dermatitis due to it uses image data of actual atopic dermatitis patients.

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Application of Statistical Analysis for Optimization of Organic Wastes Acidogenesis (유기성 폐기물의 산발효 최적화를 위한 통계학적 분석 방안의 적용)

  • Jeong, Emma;Kim, Hyun-Woo;Nam, Joo-Youn;Oh, Sae-Eun;Hong, Seung-Mo;Shin, Hang-Sik
    • Journal of Korean Society of Environmental Engineers
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    • v.30 no.8
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    • pp.781-788
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    • 2008
  • This study shows how to find out optimum co-substrate conditions and continuous operating parameters for maximum acidification of three different organic wastes - livestock wastewater, sewage sludge and food waste. Design of experiments and statistical analysis were revealed as appropriate optimization schemes in this study. Analyses of data obtained from batch tests demonstrated the optimum substrate mixing ratio, which was determined by maximum total volatile fatty acids(TVFA) increase and soluble chemical oxygen demand(SCOD) increase simultaneously. Suggested optimum mixing ratio of livestock wastewater, sewage sludge and food waste was 0.4 : 1.0 : 1.1 based on COD, respectively. Response surface methodology(RSM) contributed to find out optimum operating parameter - hydraulic retention time(HRT) and substrate concentration - for the semi-continuous acidogenic fermentation of mixed organic wastes. The optimum condition for maximum TVFA increase was 2 days of HRT and 29,237 mg COD/L. Empirical equations obtained through regression analysis could predict that TVFA increase would be 73%. To confirm the validity of the statistical experimental strategies, a confirmation experiment was conducted under the obtained optimum conditions, and relative error between theoretical and experimental results was within 4%. This result reflects that using statistical and RSM technique can be effectively used for the optimization of real waste treatment processes.

Identification and Characterization of Genes Involved in Cysteine Auxotrophy in Salmonella typhi (Salmonella typhi의 시스테인 영양요구성에 관여하는 유전자의 동정 및 특성 연구)

  • Lee, Sang-Ho;Kim, Sam-Woong;Yu, Jong-Earn;Yoo, Ah-Young;Kim, Young-Hee;Oh, Jeong-Il;Baek, Chang-Ho;Kang, Ho-Young
    • Journal of Life Science
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    • v.18 no.11
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    • pp.1507-1512
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    • 2008
  • In spite of long research period for Salmonella typhi, little information is known about the pathogenesis mechanism of human typhoid fever caused by S. typhi due to lack of infection model in animals. A wild-type of S. typhi Ty2 strain requires cysteine to grow on minimal media. We hypothesized that this cysteine requirement may restrict colonization of S. typhi in animals during infection process. Among the S. typhi strains carrying Salmonella typhimurium genomic library, we have isolated three S. typhi transformants growing on minimal media without cysteine. Although there were three ORFs in DNA of pBP71, the STM1490 ORF complemented cysteine auxotrophy of S. typhi. Analysis of the deduced amino acid sequence of the STM1490 homolog in S. typhi revealed that there are differences in two amino acids. Plasmids containing amino acid substitutions in STM1490 supported S. typhi growth on minimal media without cysteine, indicating irrelevance of these two amino acids to STM1490 function. These results tells us that there are other factors or systems involved in cysteine requirement of S. typhi.

Regulation of an Outer Membrane Protein, OmpW, Expression and Its Biological Function in Salmonell typhimurium (Salmonella typhimurium 외막 단백질 OmpW의 발현조절 및 기능에 관한 연구)

  • Yoo, Ah-Young;Yu, Jong-Earn;Yang, Ji-Seon;Kim, Young-Hee;Bae, Chang-Ho;Oh, Jeong-Il;Kang, Ho-Young
    • Journal of Life Science
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    • v.18 no.11
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    • pp.1606-1611
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    • 2008
  • Outer membrane proteins (OMPs) expressed in the Gram negative bacteria such as Salmonella play multiple functions including material transports, adhesive factors and reception of external signals. This study has been focused on an OmpW protein known as a protein required to form a hydrophobic porin in outer membrane. We have constructed a S. typhimurium CK10 mutant deleting an ompW gene on chromosome. The CK10 strain was more tolerant to SDS than the wild-type strain did. As increase of salt concentration in the culture media, significantly decreased amount of OmpW protein in cells were detected. The maximum OmpW protein was expressed in the absence of salt supplement. However, the growth of CK10 strain was indistinguishable compared to that of the wild-type strain at the variable osmotic conditions. The biological role of differential OmpW expression in response to osmotic conditions remains to be investigated.

HISTOLOGICAL CHANGES IN THE ELONGATED BONE AFFECTED BY OSTEODISTRACTION OF THE MANDIBLE IN THE DOG (성견 하악골 절단 후 기계적 골 견인에 의해 형성된 골 신장부에 대한 시기별 조직학적 변화)

  • Baek, Sun-Ho;Ahn, Byoung-Keun;Park, Young-Ju;Park, Hee-Geon;Park, Jun-Woo;Rhee, Gun-Joo;Lee, Yong-Chan;Cho, Byoung-Ouck
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.27 no.5
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    • pp.404-416
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    • 2001
  • Purpose : Traditionally, the treatement of choice has been a bone grafting procedure to increase the length of bone in case of actual length discrepancy. But, bone grafting procedure has many disadvantages, for example, graft resorption, donor site morbidity, and so on. So, many trials have been performed to avert the use of autogenous bone graft via introducing new materials or methods. And, one of those trials has been realized by the development of a technique inducing bone lengthening by osteotomy (or corticotomy) and slow gradual distraction of the osteotomized segments. This new technique of bone lengthening dates back to the early 20th century. But, the majority of information concerning the biology of new bone formation during bone lengthening and technical details of the procedure were produced by extensive clinical and experimental studies performed by Ilizarov, a Russian surgeon. According to Ilizarov, with adequate blood supply, preservation of periosteum, rigid fixation of the osteotomized segments, and proper rate and rhythm of distraction, intramembranous bone rapidly develops within the distraction gap in the limb lengthening procedure. In the limb lengthening, many orthopedic surgeons try to observe the biologic and clinical principles recommended by Ilizarov. In the oral and maxillofacial region, however, not a few studies must be performed to apply this surgical technique in the clinical cases. Besides, the mechanism of bone formation in the distraction gap is not clear, yet. The purpose of this experiment was to scrutinize serially the histological changes in the elongated bone affected by osteodistraction of the mandibular body in an adult canine model. In addition, it was performed to confirm the presence of specific region(s) which was important in the bone formation in the gap through the observation of the expression pattern of osteocalcin and osteonectin with the immunohistochemical examination. Materials and Methods : The experimental and control specimens were obtained from seven adult male mongrel dogs weighing over 20kg. The distractors were custom-made linear extraoral devices and bicortical fixation screws were 2.3mm in diameter, 50mm in total length, 15mm in screw length. The distractors were devised to produce a linear gap of 0.75mm between two bony segments every $360^{\circ}$ turn of the rotation rod of the device. The mandibular body of the right side of each animal was corticotomized perpendicular to the occlusal plane and then two bony segments were separated completely by careful manipulation of the segments with bone forceps. The left side of each animal was left intact. This side was served as control. At sixth day after osteotomy and fixation of the segments were performed, distraction of the segments was commenced with a rate of 1.1mm/day and a rhythm of two/day for ensuing 7 days. The animals were euthanized at the 16th. 29th, and 44th day after the osteotomy. The bony specimens were decalcified, embedded in paraffin, sectioned $5{\mu}m$ thick and stained with H&E. The prepared specimens were examined under the light microscope. And, immunohistochemical examinations using anti-osteocalcin antibody (OC1, Biodesign, USA) and anti-osteonectin antibody (Haematologic Technologies Inc., Essex, VT) to locate the expressions of osteocalcin and osteonectin, respectively, were performed. Results : 1. New bone was observed already at the 16th. day after osteotomy. This suggests that new bone formation in osteodistraction was commenced at an early stage of the regenerative process. But, radiologically and microscopically, bony union was not completed in the distraction gap at the 44th. day after osteotomy. Therefore, rigid fixation must be maintained between the bony fragments till the complete bony union is confirmed clinically rather than one month or so after the completion of distraction.

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A study on bio-design (바이오 디자인에 관한 고찰)

  • 이재국
    • Archives of design research
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    • no.16
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    • pp.41-51
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    • 1996
  • A matter of primary concern about all design is concentrated on how to create more valuable things to allow people to live an affluent life. However, it is very difficult to achieve the goal because every design work is changed in accordance with given situatio ns. In this sense, it is significant to study on biodesign because it can be both a basic principle and a fudamantal index to show the way of new design direction. Accordingly, the main purpose of the thesis is to catch every meaning of bio-design and to close analyze its factors in order to generate more fresh ideas and put them into practice. The thesis is composed of five Chapters: Introduction, Background of bio-design, Principle of bio-design, Practice of bio-design, and Conclusion. In Introduction, the purpose and background of the study are presented. I n Chapter 2, source of design orgin, vernacular design, and design for life are researched. In Chapter 3, organic order. the survial of the fittest, and subjective & objective are considered. In Chapter 4, hi-tech & hi-touch, criteria of problem -solving, and harmony with nature are searched. In Conclusion, some suggestive words on the study are mentioned.

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