• Molecules and Cells
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• 제40권4호
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• pp.262-270
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• 2017

MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thoroughbred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miRNAs that are expressed in several tissues and are thought to have biological functions.

• 미생물학회지
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• 제44권2호
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• pp.164-167
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• 2008

PCR 방법과 더불어 최근 핵산증폭기법으로 주목받기 시작한 방법이 Rolling Circle Amplification (RCA) 기법을 응용한 것이다. 본 논문에서 RCA 기술을 활용하는 실험에 이용할 수 있는 특정 길이(N-mer)를 가진 primer의 후보 리스트를 vector 서열이나 특정 미생물 염색체 서열에서 검색할 수 있는 프로그램인 RCA-mer를 개발하였다. RCA-mer는 사용자의 염기서열을 입력으로 받아 이 서열을 대상으로 특정 길이의 N-mer에 대한 존재 유무에 대한 리스트의 후브를 웹으로 보여주는 기능을 가지고 있다. 또한 서로 다른 두 개의 염기서열들에 대해 N-mer가 공통으로 존재하는지, 한쪽 서열에만 존재하는지 확인할 수 있는 기능을 가지도록 개발하였다. 사용자는 선발된 primer 후보들로 부터 적절한 N-mer 서열을 선택하여 실제 RCA를 이용한 실험 곧바로 응용할 수 있도록 후보 primer를 선별하여 사용할 수 있도록 하였다.

• Bulletin of the Korean Chemical Society
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• 제35권9호
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• pp.2809-2812
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• 2014

The 43-residue defensin-like peptide coprisin, which is isolated from dung bettle, Copris tripartitus, is a potent antimicrobial peptide. In our previous work, we determined the tertiary structure of coprisin and found that alpha helical region of coprisin from residue 19 to residue 30 is important for its antimicrobial activities. Here, we designed cop12mer and cop9mer analogs of coprisin based on the tertiary structure of coprisin. To investigate the relationship between hydrophobicity and antimicrobial activities and develop the potent peptide antibiotics, we designed cop9mer-1 with substitution of $His^2$ with Trp in cop9mer. The results showed that cop9mer-1 has higher toxicities as well as improved antimicrobial activities compared to cop9mer. In order to reduce the toxicity of cop9mer-1, we designed cop9mer-2 and cop9mer-3 with substitution of $Cys^3$ with Lys or Ser. Substitution of $Cys^3$ with these hydrophilic amino acids results in lower cytotoxicities compared to cop9mer-1. Cop9mer-2 with substitution of $Cys^3$ with Lys in Cop9mer-1 showed high antibacterial activities against drug resistant bacteria without cytotoxicity. Antibiotic action of cop9mer-1 analog appears to involve permeabilization of the bacterial cell membrane while cop9mer-2 and cop9mer-3 may have different mechanism of action. These results imply that that optimum balance in hydrophobicity and hydrophilicity in these 9-meric peptides plays key roles in their antimicrobial activities as well as cytotoxicities.

• Journal of Microbiology and Biotechnology
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• 제20권5호
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• pp.917-924
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• 2010

The practicability of transgenic tobacco engineered to express bacterial native mercuric reductase (MerA), responsible for the transport of $Hg^{2+}$ ions into the cell and their reduction to elemental mercury ($Hg^0$), without any codon modification, for phytoremediation of mercury pollution was evaluated. Transgenic tobacco plants reduce mercury ions to the metallic form; take up metallic mercury through their roots; and evolve the less toxic elemental mercury. Transformed tobacco produced a large amount of merA protein in leaves and showed a relatively higher resistance phenotype to $HgCl_2$ than wild type. Results suggest that the integrated merA gene, encoding mercuric reductase, a key enzyme of the bacterial mer operon, was stably integrated into the tobacco genome and translated to active MerA, which catalyzes the bioconversion of toxic $Hg^{2+}$ to the least toxic elemental $Hg^0$, and suggest that MerA is capable of reducing the $Hg^{2+}$, probably via NADPH as an electron donor. The transgenic tobacco expressing merA volatilized significantly more mercury than wild-type plants. This is first time we are reporting the expression of a bacterial native merA gene via the nuclear genome of Nicotiana tabacum, and enhanced mercury volatilization from tobacco transgenics. The study clearly indicates that transgenic tobacco plants are reasonable candidates for the remediation of mercurycontaminated areas.

• 정보처리학회논문지A
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• 제8A권4호
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• pp.509-516
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• 2001

생명 과학의 발전과 많은 게놈(genome) 프로젝트의 결과로 여러 종의 게놈 서열이 밝혀지고 있다. 생물체의 서열을 분석하는 방법은 전역정렬(global alignment), 지역정렬(local alignment) 등 여러 가지 방법이 있는데, 그 중 하나가 k-mer 분석이다. k-mer는 유전자의 염기 서열내의 길이가 k인 연속된 염기 서열로서 k-mer 분석은 염기서열이 가진 k-mer들의 빈도 분포나 대칭성 등을 탐색하는 것이다. 그런데 게놈의 염기 서열은 대용량 텍스트이고 k가 클 때 기존의 온메모리 알고리즘으로는 처리가 불가능하므로 효율적인 자료구조와 알고리즘이 필요하다. 스트링 B-트리는 패턴 일치(pattern matching)에 적합하고 외부 메모리를 지원하는 좋은 자료구조이다. 본 논문에서는 스트링 B-트리(string B-tree)를 k-mer 분석에 효율적인 구조로 개선하여, C. elegans 외의 30개의 게놈 서열에 대해 분석한다. k-mer들의 빈도 분포와 대칭성을 보여주기 위해 CGR(Chaotic Game Representation)을 이용한 가시화 시스템을 제시한다. 게놈 서열과 매우 유사한 서열 상의 어떤 부분을 시그니쳐(signature)라 하고, 높은 유사도를 가지는 최소 길이의 시그니쳐를 찾는 알고리즘을 제시한다.

• Biomolecules & Therapeutics
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• 제10권3호
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• pp.156-164
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• 2002

In the present study, we tried to investigate whether polymerized basic amino acid e.g. poly-L-lysine (PLL) which has the degree of polymerization under 50mer significantly affects the physiological and stimulated mucin release from cultured hamster tracheal surface epithelial cells. Confluent primary hamster tracheal surface epithelial (HTSE) cells were metabolically radiolabeled with $^3{H}$-glucosamine for 24 hr and chased for 30 min in the presence of either PLLs or adenosine triphosphate (ATP) and PLL to assess the effects on basic or ATP-stimulated $^3{H}$-mucin release. Possible cytotoxicities of PLLs were assessed by measuring lactate dehydrogenase (LDH) release from HTSE cel1s during treatment. The results were as follows: PLLs significantly inhibited basic mucin release from cultured HTSE cells in a dose-dependent manner from the range of 46mer to 14mer; PLL 46mer significantly inhibited the stimulated mucin release by ATP from cultured HTSE cells; there was no significant release of LDH from cultured HTSE cells during treatment. We conclude that PLLs inhibit both physiological and stimulated mucin release from airway epithelial cells without significant cytotoxicity and PLL lost its activity under the range of 14mer. This finding suggests that polymer of basic amino acid like PLL might function as a regulator for hypersecretion of mucus manifested in various respiratory diseases.

• 한국정보과학회논문지:소프트웨어및응용
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• 제27권7호
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• pp.731-741
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• 2000

본 논문은 얼굴 인식 또는 표정 인식 분야에 있어서 중요한 특징인 얼굴과 얼굴의 주요소인 눈과 입, 눈썹의 영역 추출 및 그의 윤곽선 추출에 관한 방법을 제시한다. 얼굴요소의 영역 추출은 엣지정보와 이진화 영상을 병합하여 이용한 프로젝션 분석을 통하여, 얼굴 및 각 얼굴요소를 포함하는 최소포함사각형(MER: Minimum Enclosing Rectangle)을 추출한다. 윤곽선 추출은 얼굴요소 모양의 개인차가 반영되고 빠른 수렴을 할 수 있는 스네이크 모델을 정의하여 수행한다. 스네이크는 초기 윤곽선의 설정이 윤곽선 추출 결과에 큰 영향을 미치므로, 초기 윤곽선의 설정 과정이 매우 중요하다. 본 논문에서는 얼굴 및 각 얼굴요소를 포함하는 각각의 최소포함사각형(MER)을 추출하고, 추출된 MER 내에서 얼굴 및 각 얼굴요소의 일반적인 모양을 초기 윤곽선으로 설정하는 방법을 사용한다. 실험결과 눈, 입, 얼굴의 MER 추출은 성능이 모두 우수하고, 눈썹이 흐린 사람들의 경우에만 눈썹의 MER 추출 결과가 좋지 않았다. 추출된 MER을 기반으로 하여 스네이크 모델을 적용한 결과, 눈, 입, 눈썹, 얼굴의 다양한 모양을 반영한 윤곽선 추출 결과를 보였다. 특히 눈의 경우는 1차 유도 엣지 연산자에 의한 엣지와 2차 유도 연산자를 이용한 영점 교차점(Zero Crossing)과 병합한 에너지 함수를 설정하여 보다 더 나은 윤곽선 추출 결과를 얻었다. 얼굴의 윤곽선의 경우도 엣지값과 밝기값을 병합한 에너지 함수에 의해 비교적 정확한 결과를 얻을수 있었다.

• 미생물학회지
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• 제52권4호
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• pp.428-436
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• 2016

항균제에 대한 내성 증가는 국내뿐만 아니라 세계적으로도 인류 건강에 큰논란이 되고 있다. 박테리아에 의한 감염을 치료하기 위해 같은 혹은 다른 계열의 항생제에 순차적으로 노출된다. 따라서, 본 연구는 ciprofloxacin과 meropenem의 순차적 처리에 따른 폐렴간균(Klebsiella pneumoniae)의 생육, 항생제 민감성, 돌연변이 빈도, ${\beta}$-lactamase activity, 생물막 형성 및 내성 관련 유전자 발현을 평가하기 위해 설계되었다. 처리군은 대조군(control; CON), 1/2 MIC ciprofloxacin (1/2CIP), 2 MIC ciprofloxacin (2CIP), 1/2 MIC ciprofloxacin+1/2 MIC meropenem+2 MIC ciprofloxacin (1/2CIP-1/2MEM-2CIP), 1/2 MIC ciprofloxacin+1/2 MIC meropenem+2 MIC meropenem(1/2CIP-1/2MEM-2MEM), 1/2 MIC ciprofloxacin+2 MIC ciprofloxacin+2 MIC meropenem (1/2CIP-2CIP-2MEM)을 포함한다. 24시간의 배양 동안 2CIP처리군에서 K. pneumoniae의 생육이 관찰되지 않았다. 모든 처리군에서 planktonic cell의 수는 7에서 10 log CFU/ml의 유의적인 차이를 보였으나 biofilm cell의 수는 7 log CFU/ml로 비슷하였다. 돌연변이 빈도는 1/2CIP-1/2MEM-2CIP에서 가장 낮은 14%을 보였다. 대조군과 비교하여 1/2CIP-2CIP-2MEM 처리 K. pneumoniae는 piperacillin, cefotaxime, nalidixic에 대한 민감도가 감소되었다. 1/2CIP-1/2MEM-2CIPrk 가장 높은 ${\beta}$-lactamase activity(22 nmol/min/ml)을 보인 반면 1/2CIP-2CIP-2MEM은 가장 낮은 ${\beta}$-lactamase activity (6 nmol/min/ml)을 보였다. Multidrug efflux pump 관련 유전자(acrA, acrB, and ramA)의 발현은 1/2CIP-1/2MER-2MER and 1/2CIP2CIP-2MER 처리된 K. pneumoniae에서 2배 이상 증가하였다. 따라서 순차적 항생제의 처리는 K. pneumoniae의 항생제 내성 양상을 변화시킬 수 있다.

• Journal of Microbiology and Biotechnology
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• 제29권2호
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• pp.274-282
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• 2019

Mercury-resistant ($Hg^R$) bacteria were isolated from heavy metal polluted wastewater and soil collected near to tanneries of district Kasur, Pakistan. Bacterial isolates AZ-1, AZ-2 and AZ-3 showed resistance up to $40{\mu}g/ml$ against mercuric chloride ($HgCl_2$). 16S rDNA ribotyping and phylogenetic analysis were performed for the characterization of selected isolates as Bacillus sp. AZ-1 (KT270477), Bacillus cereus AZ-2 (KT270478) and Bacillus cereus AZ-3 (KT270479). Phylogenetic relationship on the basis of merA nucleotide sequence confirmed 51-100% homology with the corresponding region of the merA gene of already reported mercury-resistant Gram-positive bacteria. The merE gene involved in the transportation of elemental mercury ($Hg^0$) via cell membrane was cloned for the first time into pHLV vector and transformed in overexpressed C43(DE3) E. coli cells. The recombinant plasmid (pHLMerE) was expressed and the native MerE protein was obtained after thrombin cleavage by size exclusion chromatography (SEC). The purification of fusion/recombinant and native protein MerE by Ni-NTA column, dialysis and fast protein liquid chromatography (FPLC/SEC) involved unfolding/refolding techniques. A small-scale reservoir of wastewater containing $30{\mu}g/ml$ of $HgCl_2$ was designed to check the detoxification ability of selected strains. It resulted in 83% detoxification of mercury by B. cereus AZ-2 and B. cereus AZ-3, and 76% detoxification by Bacillus sp. AZ-1 respectively (p < 0.05).

• Asian-Australasian Journal of Animal Sciences
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• 제8권1호
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• pp.59-66
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• 1995

Energy obtained by grazing cattle in oil palm plantations is usually used for maintenance of body functions, the construction of body tissues and pregnancy, the synthesis of milk and the conversion to mechanical energy used for activities such as walking, eating and others. In this study, attempt was made to estimate metabolizable energy (ME) requirement of grazing cattle. Models of ME requirement (MER) for maintenance, gain, pregnancy, lactation and activities were developed. ME system and units were used because of wide recognition. Estimation of ME intake in grazing cattle was expressed as MEVI = $14.58{\times}VI{\times}DMD$, and under grazing condition MEVI = $MER_i$. MER was expressed as a function of net energy(NER, MJ) required for the i'th body function. Coefficient of efficiency for conversion of ME into net energy(ki) was adopted from literatures. Quantifying of ME requirement for Kedah-Kelantan cattle under grazing condition was made by using equation MERM = NEM / kn. The estimated values of MER for Kedah-Kelantan cattle is quite reasonable if compared with other estimates as reported in literatures from stall-fed animals. Dynamic MER models for grazing herd was developed in order to estimate ME requirement for maintenance and productions. These ME requirement models can be used for prediction of energy utilization pattern of the herd in the grazing systems.