Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach

So‑Ra Han,Sung‑Min Jang,Young Min Chi,Byeollee Kim,정상희,Yung Mi Lee,Jun Uetake,Jun Hyuck Lee,Hyun Park,오태진 한국유전학회 2020 Genes & Genomics Vol.42 No.9

Background Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. Objective In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. Methods Genome sequencingwas performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI nonredundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). Results The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confrmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. Conclusion In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by fnding new genes that degradation the pectin

당의 종류를 달리한 녹차다식의 제조특성

한영숙,김소라,최원석 誠信女子大學校 生活文化硏究所 2009 生活文化硏究 Vol.24 No.1

For this study, potato starch, an easily accessible ingredient, was used to make the traditional pressed sweet, dasik, with honey, sirup and fructooligosaccharides as the binding material and green tea powder added to create“ green tea dasik.”Green tea dasik were then examined on their qualities such as sugar content, moisture, Aw, pH, color and mechanical measurements and the sensory acceptability was evaluated. To improve the texture of green tea dasik with 8% green tea powder, honey and fructooligosaccharides were respectively used in place of sirup as the binding material. As a result, the sugar content was the highest when honey was used, but it was also higher with fractooligosaccharides than with sirup. The moisture content was the highest with honey; Aw was the lowest with fractooligosaccharides; and pH was the highest with sirup. The chromaticity test results showed that the L value was the lowest with honey, revealing dark colors. Dasik with fractooligosaccharides showed the brightest colors. As for the a value, dasik using honey, sirup and oligosaccharide showed -5.93, -2.64 and -8.85, respectively. The b value for yellow chromaticity was the highest with fractooligosaccharides. The mechanical measurement test results showed that dasik with fructooligosaccharides have the highest values in elasticity, cohesiveness, chewiness and gumminess. In the sensory acceptability test, the scores for dasik with honey were high in color, sweetness and moistness while the scores for dasik with fructooligosaccharides were the highest in adhesiveness, chewiness, hardness and overall acceptability. As a result of investigating the characteristics in the making of green tea dasik, fructooligosaccharides are evaluated highly as a possible ingredient of dasik.

압궤손상을 입은 혈관에서 Ginkgo Biloba 추출물(EGb 761)이 혈관문합술후 개통율에 미치는 영향

강소라,이동진,차진한,김양우 大韓成形外科學會 1999 Archives of Plastic Surgery Vol.26 No.3

Replantation after crush amputation has a relatively low success rate. Thrombus formation due to vessel and tissue trauma is considered as the principal cause of failure. In the laboratory and clinically, we have been tried to improve the post-anastomosis patency rate in crushed microvasculature. To accomplish this, we have usually used several anticoagulant drugs. Extracts from the leaves of Ginkgo biloba (EGb) have been used therapeutically for centuries. EGb exerts a number of pharmacologic actions. Eighty rats were control group and another 80 rats were treated with EGb 761. The femoral arteries underwent crush injury with an energy of 0.4J, and the vessles in each group were divided and anastomosed by a standard microsurgical technique. Each group was comprised as follows: ① control group(A1,A2): group A1(n=40); intraluminal saline irrigation, group A2(n=40); intraluminal saline irrigation+heparin 40 u/ml(IV) ② EGb 761 treated group(B1, B2): groupB1(n=40); intraluminal saline irrigation, group B2(n=40); intraluminal saline irrigation + heparin 40 u/ml(IV). At postoperative 14 days, the patency rates were; group A1 20%, group A2 77.5%, group B1 47.5%, group B2 92.5%. These results were interpreted as follows: the patency rate was significantly increased in the EGb 761-only treated group(p<0.01), the heparin-only treated group(p<0.01), and the EGb 761 and heparin-combined at crushed microvessel surgery. However the patency rate of the EGb-only treated group was significantly lower than that of the heparin-only treated group(p<0.01). And in the EGb 761 and heparin-combined treated group compared to the heparin-only treated group, there was some patency rate increase in the combined treated group, but there was no significant difference between them(p=0.060).

임신과 연관된 유방삽입물 주의 피막 구형 구축의 변화에 대한 임상적 연구

이윤호,임동헌,윤진호,강소라,김한중,배원배 大韓成形外科學會 1997 Archives of Plastic Surgery Vol.24 No.6

It has been reported that the frequency of the development of peripheral capsuler contracture after breast augmentation surgery using silicone-gel implants amounts between 25 to 50%. Various treatments to cure or prevent the capsular contracture are mow being studied and introduced, including submuscular insertion of breast implants, steroid instillation, oral intake of Vit-E, postoperative breast massage, regional injection of antibiotics, and a saline-filled implantation without gel-bleed. This paper reports, along with the literal study, on the improvement of the softening of capsular contracture condition observed from 12 patients who have undergone pregnancy and delivery after breast augmentation surgery operated at the Plastic surgery departments of Ewha University Medical Center and Seoul National University Medical Center during 1985-1995. Conceivably, the softening of the capsular contracture is attributable to the hormonal change, immunologic and inflammatory alteration, and the masking effect resulting from mammary alveolar hypertrophy. It is believed that a study should be continued on the relationship between the pregnancy and the softening of capsular contracture condition.

Comparative Analysis of Arthrobacter spp. Provide Insight into Their Elucidating the Role of CAZyme in a Cold Environment

So-Ra HAN,Tae-Jin OH 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.9

Antimicrobial activity of various solvent extracts of <i>Auricularia auricula-judae</i> against oral bacteria

Han, So-Ra,Yu, Sang-Cheol,Lee, Joo-Ho,Jung, Sang-Hee,Lim, Kun-Ok,Oh, Tae-Jin Diva Enterprises Private Limited 2018 Indian journal of public health research & develop Vol.9 No.11

Complete Genome of the Xylan-Degrading Lichen-Associated Arctic Bacteria, Mucilaginibacter sp. PAMC 26640 and Carbohydrate Active Enzymes

So-Ra HAN,Hyun PARK,Joo-Ho LEE,Tae-Jin OH 한국생물공학회 2017 한국생물공학회 학술대회 Vol.2017 No.10

Herbal extract THI improves metabolic abnormality in mice fed a high-fat diet

Han, So-Ra,Oh, Ki-Sook,Yoon, Yoo-Sik,Park, Jeong-Su,Park, Yun-Sun,Han, Jeong-Hye,Jeong, Ae-Lee,Lee, Sun-Yi,Park, Mi-Young,Choi, Yeon-A,Lim, Jong-Seok,Yang, Young The Korean Nutrition Society 2011 Nutrition Research and Practice Vol. No.

Target herbal ingredient (THI) is an extract made from two herbs, Scutellariae Radix and Platycodi Radix. It has been developed as a treatment for metabolic diseases such as hyperlipidemia, atherosclerosis, and hypertension. One component of these two herbs has been reported to have anti-inflammatory, anti-hyperlipidemic, and anti-obesity activities. However, there have been no reports about the effects of the mixed extract of these two herbs on metabolic diseases. In this study, we investigated the metabolic effects of THI using a diet-induced obesity (DIO) mouse model. High-fat diet (HFD) mice were orally administered daily with 250 mg/kg of THI. After 10 weeks of treatment, the THI-administered HFD mice showed reduction of body weights and epididymal white adipose tissue weights as well as improved glucose tolerance. In addition, the level of total cholesterol in the serum was markedly reduced. To elucidate the molecular mechanism of the metabolic effects of THI in vitro, 3T3-L1 cells were treated with THI, after which the mRNA levels of adipogenic transcription factors, including C/$EBP{\alpha}$ and $PPAR{\gamma}$, were measured. The results show that the expression of these two transcription factors was down regulated by THI in a dose-dependent manner. We also examined the combinatorial effects of THI and swimming exercise on metabolic status. THI administration simultaneously accompanied by swimming exercise had a synergistic effect on serum cholesterol levels. These findings suggest that THI could be developed as a supplement for improving metabolic status.

Complete genome sequencing of <i>Shigella</i> sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation

Han, So-Ra,Kim, Do Wan,Kim, Byeollee,Chi, Young Min,Kang, Seunghyun,Park, Hyun,Jung, Sang-Hee,Lee, Jun Hyuck,Oh, Tae-Jin Elsevier 2019 Microbial pathogenesis Vol.137 No.-

<P><B>Abstract</B></P> <P> <I>Shigella</I> sp. PAMC 28760 (isolated from <I>Himantormia</I> sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated <I>S.</I> sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus <I>Shigella</I>, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. <I>S.</I> sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding <I>Shigella</I> survival adaptation mechanisms under extremely cold Antarctic conditions.</P> <P><B>Highlights</B></P> <P> <UL> <LI> <I>Shigella</I> sp. PAMC 28760 from an Antarctic lichen has cellulolytic, amylolytic, and glycogen metabolic pathway. </LI> <LI> The complete genome of <I>Shigella</I> sp. PAMC 28760 showing differences from pathogenic reported previously. </LI> <LI> The foundation for understanding <I>Shigella</I> adaptation mechanism to extremely conditions is provided. </LI> </UL> </P>

다양한 건조방법에 따른 블랙베리 분말의 품질 특성

최소라 ( So-ra Choi ),송은주 ( Eun-ju Song ),송영은 ( Young-eun Song ),최민경 ( Min-kyung Choi ),한현아 ( Hyun-ah Han ),이인석 ( In-sok Lee ),신소희 ( So-hee Shin ),이기권 ( Ki-kwon Lee ),김은주 ( Eun-ju Kim ) 한국식품영양학회 2017 韓國食品營養學會誌 Vol.30 No.3

This experiment was carried out to enhance the availability of blackberry. Since it is difficult to use blackberry as a fresh fruit, we investigated the quality characteristics of blackberry powder obtained by various drying methods (freeze drying and hot-air drying at 40~80℃). The L- and b-values of freeze-dried powder was higher than hot-air dried powder. The pH (3.2) was lowest and the acidity (14.4%) was highest in freeze-dried powder. In freeze drying, the brix degree was 65.7 °Bx, but it increased from 54.7 °Bx to 68.5 °Bx with increasing temperature during hot air drying. The total polyphenol and flavonoids contents were the highest in freeze-dried powder, at 9.3 and 6.2 mg/g, respectively. The levels increased as temperature increased in hot air drying. Anthocyanin content in freeze-dried powder was 8.51 mg/g, while it sharply decreased to 1.17~2.45 mg/g in hot-air drying. Vitamin C content in freeze drying (979.4 μg/g) was higher than that in hot-air drying (48.3~303.2 μg/g). The sample concentration required for 50% reduction of DPPH free radical scavenging (RC50) was 79.7 μg/mL in freeze drying, and showed high antioxidant activity. Also it decreased from 122.4 μg/mL to 87.7 μg/mL with temperature increase during hot air drying. We therefore conclude from the above results that freeze drying is more suitable for the production of blackberry powder, because this method showed high value of chromaticity, total polyphenol, flavonoid, anthocyanin content, vitamin C and antioxidant activity.