• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• The Plant Pathology Journal
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• 제38권3호
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• pp.194-202
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• 2022

Erwinia amylovora and Erwinia pyrifoliae cause fire blight and black-shoot blight, respectively, in apples and pears. E. pyrifoliae is less pathogenic and has a narrower host range than that of E. amylovora. Fire blight and black-shoot blight exhibit similar symptoms, making it difficult to distinguish one bacterial disease from the other. Molecular tools that differentiate fire blight from black-shoot blight could guide in the implementation of appropriate management strategies to control both diseases. In this study, a primer set was developed to detect and distinguish E. amylovora from E. pyrifoliae by conventional polymerase chain reaction (PCR). The primers produced amplicons of different sizes that were specific to each bacterial species. PCR products from E. amylovora and E. pyrifoliae cells at concentrations of 10⁴ cfu/ml and 10⁷ cfu/ml, respectively, were amplified, which demonstrated sufficient primer detection sensitivity. This primer set provides a simple molecular tool to distinguish between two types of bacterial diseases with similar symptoms.

• Journal of Microbiology and Biotechnology
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• 제32권8호
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• pp.1011-1016
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• 2022

Bacillus subtilis is a useful bacterium in the food industry with applications as a starter strain for fermented food and as a probiotic. However, it is difficult to discriminate B. subtilis from other Bacillus species because of high phenotypic and genetic similarity. In this study, we employed five previously constructed multilocus sequence typing (MLST) methods for the discrimination of B. subtilis from other Bacillus species and all five MLST assays clearly distinguished B. subtilis. Additionally, the 17 housekeeping genes used in the five MLST assays also clearly distinguished B. subtilis. The pyruvate carboxylase (pyrA) and shikimate dehydrogenase (aroE) genes were selected for the discrimination of B. subtilis because of their high number of polymorphic sites and the fact that they displayed the lowest homology among the 17 housekeeping genes. Specific primer sets for the pyrA and aroE genes were designed and PCR products were specifically amplified from B. subtilis, demonstrating the high specificity of the two housekeeping genes for B. subtilis. This species-specific PCR method provides a quick, simple, powerful, and reliable alternative to conventional methods in the detection and identification of B. subtilis.

• Journal of Veterinary Science
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• 제24권6호
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• pp.82.1-82.12
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• 2023

Background: The current conventional serotyping based on antigen-antisera agglutination could not provide a better understanding of the potential pathogenicity of Salmonella enterica subsp. enterica serovar Brancaster. Surveillance data from Malaysian poultry farms indicated an increase in its presence over the years. Objective: This study aims to investigate the virulence determinants and antimicrobial resistance in S. Brancaster isolated from chickens in Malaysia. Methods: One hundred strains of archived S. Brancaster isolated from chicken cloacal swabs and raw chicken meat from 2017 to 2022 were studied. Two sets of multiplex polymerase chain reaction (PCR) were conducted to identify eight virulence genes associated with pathogenicity in Salmonella (invasion protein gene [invA], Salmonella invasion protein gene [sipB], Salmonella-induced filament gene [sifA], cytolethal-distending toxin B gene [cdtB], Salmonella iron transporter gene [sitC], Salmonella pathogenicity islands gene [spiA], Salmonella plasmid virulence gene [spvB], and inositol phosphate phosphatase gene [sopB]). Antimicrobial susceptibility assessment was conducted by disc diffusion method on nine selected antibiotics for the S. Brancaster isolates. S. Brancaster, with the phenotypic ACSSuT-resistance pattern (ampicillin, chloramphenicol, streptomycin, sulphonamides, and tetracycline), was subjected to PCR to detect the corresponding resistance gene(s). Results: Virulence genes detected in S. Brancaster in this study were invA, sitC, spiA, sipB, sopB, sifA, cdtB, and spvB. A total of 36 antibiogram patterns of S. Brancaster with a high level of multidrug resistance were observed, with ampicillin exhibiting the highest resistance. Over a third of the isolates displayed ACSSuT-resistance, and seven resistance genes (β-lactamase temoneira [bla_TEM], florfenicol/chloramphenicol resistance gene [floR], streptomycin resistance gene [strA], aminoglycoside nucleotidyltransferase gene [ant(3")-Ia], sulfonamides resistance gene [sul-1, sul-2], and tetracycline resistance gene [tetA]) were detected. Conclusion: Multidrug-resistant S. Brancaster from chickens harbored an array of virulence-associated genes similar to other clinically significant and invasive non-typhoidal Salmonella serovars, placing it as another significant foodborne zoonosis.

• 한국발생생물학회지:발생과생식
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• 제14권4호
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• pp.287-295
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• 2010

최근 시상하부에서 생성되는 nesfatin-1/NUCB2가 섭식과 에너지 대사를 조절한다는 사실이 새롭게 밝혀졌다. 본 연구에서는 이러한 단백질이 생쥐의 생식기관에서도 발현을 하는지, 그리고 그 수용체가 생식기관 내에 존재하는 지를 확인함으로써 nesfatin-1이 생식기능에 미칠 수 있는 가능성을 알아보고자 하였다. 암컷 생쥐에서 난소와 자궁을 획득하여 conventional PCR 방법으로 NUCB2 mRNA 발현을 조사하였고, real-time PCR 방법으로 상대적인 NUCB2 mRNA 발현량을 비교 분석하였다. 난소 내 nesfatin-1 단백질의 발현 위치를 조사하기 위하여 nesfatin-1 항체를 이용한 면역조직화학염색법을 수행하였으며, biotin conjugated nesfatin-1을 이용하여 nesfatin-1 결합 부위를 확인하였다. 또한 생식소 내 NUCB2 mRNA 발현이 성선자극호르몬에 의해 영향을 받는지 알아보기 위해 PMSG 투여 후 NUCB2 mRNA 발현량을 조사하였다. 실험 결과, 생쥐의 난소와 자궁에서 확인된 NUCB2 유전자가 시상하부에서 만큼이나 많은 양이 발현되고 있었다. 면역조직화학적 염색 결과, nesfatin-1 단백질은 협막세포와 대부분의 기질세포에서 발현되었고, 일부 황체세포에서도 발현이 확인되었다. 반면, 난포 내 과립세포에서는 발현되지 않았으나, 특정 난포 내 난자에서는 발현됨을 확인하였다. 한편, nesfatin-1 단백질의 결합 부위는 난소 백막 주위의 기질세포와 협막세포에서 관찰되었다. 또한 PMSG 투여 후 난소와 자궁에서 NUCB2 mRNA의 발현이 유의하게 증가함을 확인하였다. 이상의 결과에서 난소 내 nesfatin-1 단백질의 발현과 그 결합 부위의 존재는 nesfatin-1이 뇌에서 뿐만 아니라 생식기관에서도 국부조절인자로써 중요한 역할을 할 것으로 사료되며, 앞으로 생식기관에 미치는 nesfatin-1의 역할을규명하기위한더많은연구가필요하다고판단된다.

• Asian Pacific Journal of Cancer Prevention
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• 제17권4호
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• pp.2159-2164
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• 2016

Background: A diagnosis of chronic myeloid leukemia (CML) is made on discovery of the presence of a Philadelphia (Ph) chromosome. The success of the treatment of this form of leukemia with tyrosine kinase inhibitor (TKI) is monitored by reduction of the Ph chromosome. Objective: To compare the role of conventional cytogenetic (CC) methods with a real time quantitative polymerase chain reaction (RQ-PCR) and fluorescence in situ hybridization (FISH) for diagnosis and treatment monitoring of CML patients. The secondary outcome was to analyze the treatment responses to TKI in CML patients. Materials and Methods: This was a retrospective study of CML patients who attended the Hematology clinic at Chiang Mai University Hospital from 2005-2010. Medical records were reviewed for demographic data, risk score, treatment response and the results of CC methods, FISH and RQ-PCR. Results: One hundred and twenty three cases were included in the study, 57.7% of whom were male with a mean age of 46.9 years. Most of the patients registered as intermediate to high risk on the Sokal score. At diagnosis, 121 patients were tested using the CC method and 118 (95.9%) were identified as positive. Five patients failed to be diagnosed by CC methods but were positive for BCR-ABL1 using the FISH method. Imatinib was the first-line treatment used in 120 patients (97.6%). In most patients (108 out of 122, 88.5%), a complete cytogenetic response (CCyR) was achieved after TKI therapy and in 86 patients (70.5%) CCyR was achieved long term by the CC method. Five out of the 35 analyzed patients in which CCyR was achieved by the CC method had a positive FISH result. Out of the 76 patients in which CCyR was achieved, RQ-PCR classified patients to only CCyR in 17 patients (22.4%) with a deeper major molecular response (MMR) in 4 patients (5.3%) and complete molecular response (CMR) in 55 patients (72.4%). In the case of initial therapy, CCyR was achieved in 95 patients (79.1%) who received imatinib and in both patients who received dasatinib (100%). For the second line treatment, nilotinib were used in 30 patients and in 19 of them (63.3%) CCyR was achieved. In half of the 6 patients (50%) who received dasatinib as second line or third line treatment CCyR was also achieved. Conclusions: CML patients had a good response to TKI treatment. FISH could be useful for diagnosis in cases where CC analysis failed to detect the Ph chromosome. RQ-PCR was helpful in detecting any residual disease and determining the depth of the treatment response at levels greater than the CC methods.

• 한국정보통신학회논문지
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• 제10권12호
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• pp.2329-2334
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• 2006

본 논문에서는 기존의 conting 구성 프로그램의 단점인 단편들 간의 결합 실패를 보완하는 알고리즘을 제안하였다. 제안된 방법은 매우 긴 DNA의 염기 서열을 자동 서열 분석기로 한번에 분석 가능한 약 700개의 단편들을 한 주형으로 만들어 PCR 방법으로 클론 3을 생성 후, $600\sim700$개의 길이로 단편화하여 기준 주형과 비교하여 일치율을 계산한다. 이때 Compute Agreement 알고리즘을 이용하여 일치율을 계산하는 시간을 단축시킨다. 계산된 단편 쌍들의 중첩 정도를 기준으로 주형마다 2개의 결합 후보 단편을 추출하여 추출된 각 단편들의 일치율과 각 DNA 염기의 A,G,C,T 소속도 및 각 A,G,C,T 이 전 빈도수를 퍼지 추론 규칙을 이용하여 결합 여부를 판단한다. 본 논문에서는 결정된 최 적의 비교 단편을 결합하고, 더 이상 단편이 없을 때까지 반복하여 서열 결합을 완성한다. 실험을 위해 완성된 단백질 지놈인 'Synechocystis PCC6803'을 각각 1만개, 10만개씩 추출하여 $600{\sim}700$개의 길이를 가진 단편을 생성하였으며, 이 단편을 임 의의 mutation을 유발하여 실험한 결과, FAP 프로그램보다 속도가 줄어들었으며, conting 구성 프로그램의 단점 인 결합 실패가 발생하지 않았다.

• 대한환경공학회지
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• 제29권8호
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• pp.895-903
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• 2007

매립지를 직접 생태학적으로 모니터링하는 방법을 개발하고자, 매립지 내의 생화학적 반응에 관여하는 세균들과 효소의 양을 정량함과 동시에 지하수 수질인자와 상호 연관성을 조사하여 생태학적 인자와의 연계 이용 가능성을 평가하였다. 이를 위하여 4개의 매립 종료된 비위생 매립지(천안(C), 원주(W), 논산(N), 평택(P) 매립지)에서 계절별로 지하수 시료를 채취하였으며 동시에 16S rDNA 방법을 사용하여 미생물 다양성을 분석하였다. 이를 기반으로, 매립지에서 주로 발견되는 세균과 효소를 대표하는 유전자를 정량하기 위한 특이 프라이머 쌍을 제작하였으며 상관계수에 기초하여 수질인자와 유전자 지표 인자간의 정량적 관련성을 비교하였다. 그 결과 DSR(황환원 세균) gene과 BOD(생화학적 산소요구량)사이의 상관관계는 0.8 이상인데 반해 NSR(질산화 세균-Nitrospira sp.) gene과 질산성 질소는 0.9 이상이었다. 안정화지표(BOD/COD)와 MTOT(메탄 산화 세균), MCR(Methyl coenzyme M reductase), Dde(Dechloromonas denitrificans) gene들은 0.8 이상의 상관관계를 가졌으나 3가 철과 Fli(Ferribacterium limineticm) gene은 0.7로 낮았다. MTOT gene의 경우, BOD/COD과의 관련성이 100%에 가깝게 높았다. 또한, 혐기성 유전자들(nirS-아질산 환훤효소, MCR, Dde, DSR)과 DO 역시 0.8 이상으로 나타나 일반적인 매립지 혐기성 반응들이 DO에 크게 의존함을 보였다. 결론적으로 분자생물학적 조사와 수질인자가 높은 상호연관성이 있었으며 real-time PCR이 전통적인 모니터링 인자들과 동시에 상호 보완적으로 모니터링에 사용됨으로써 매립지안정화 및 주변 영향을 평가하는데 효율적으로 사용 될 수 있음을 알 수 있었다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권16호
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• pp.7077-7084
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• 2015

Background: Oral squamous cell carcinoma (OSCC) is the most prevalent malignancy among males in India. While tobacco and alcohol are main aetiological factors, human papilloma virus (HPV) presence has surprisingly increased in head and neck Squamous Cell Carcinoma (HNSCC) in the past two decade but its frequency in OSCCS is still uncertain. We aim to explore the frequency of HPV and its major genotypes in North Indian patients and their association with clinicopathological and histopathological features and p16 expression pattern. Materials and Methods: The study group comprised 250 histologically proven cases of OSCC. HPV was detected by real time PCR in tumor biopsy specimens and confirmed by conventional PCR with PGMY09/PGMY11 primers. Genotyping for high-risk types 16/18 was conducted by type specific PCR. p16 expression was assessed by immunohistochemsitry. Results: HPV presence was confirmed in 23/250 (9.2%) OSCC cases, of which 30.4% had HPV 16 infection, 17.4%were positive for HPV 18 and 26.1% had co-infections. HPV presence was significantly associated with male gender (p=0.02) and habit of pan masala chewing (p=0.01). HPV positive cases also had a history of tobacco consumption in 91.3% cases. p16 over expression was observed in 39.1% of HPV positive cases but this was not significantly different from negative cases (p=0.54). Conclusions: The frequency of HPV in OSCC is low in North-India and majority of cases are associated with a tobacco habit. It appears that tobacco shows a confounding effect in HPV positive cases and use of p16 protein as a reliable marker to assess the potential etiological role of HPV in OSCC in our population is not suggested.

• Fisheries and Aquatic Sciences
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• 제22권10호
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• pp.21.1-21.7
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• 2019

Background: Lactococcus garvieae is one of the most important risk factors in the rainbow trout culture. Therefore, the purpose of this study was to identify and detect strains isolated from rainbow trout suspected of having Lactococcus garvieae using biochemical characteristics and PCR and determination of the degree of severity of isolated strains. Methods: In this study, the cause of lactococcosis in selected rainbow trout farms in Kohkilooieh and Boyerahmad province was assayed. Gram-positive and catalase-negative bacterial isolates were first obtained from selected trout fish farms using conventional biochemical tests and PCR assay. The 10-day LD₅₀ method (concentration causing 50% mortality in 10 days) was used to determine the severity of the isolated bacteria. Results: One bacterial isolate was detected from all sampled fish which confirmed as Lactococcus garvieae using a specific PCR assay based on the 16S rDNA gene by producing a single band of 1107 bp. Analysis of the rate of mortality showed that the 10-day LD₅₀ was 4.6 × 10⁵ CFU/fish. The results of this study showed that isolated bacteria had high severity for rainbow trout. The presence of bacteria in internal organs of suspected fish showed a severe systemic infection in challenged fish. Antibiogram assay also indicated that the isolated Lactococcus garvieae were resistant to some mostly used antibiotics in rainbow trout. Conclusions: According to current research, it can be concluded that the condition of lactococcosis in the studied area is not suitable, and despite the presence of disease, there is no proper action to control and prevent the disease. Unfortunately, isolated bacteria from the studied area have a very high severity compared to bacteria isolated from other regions of the country or other countries. Therefore, further investigation is needed to determine the cause of this difference and possibly in the design of the vaccine.