• 제목/요약/키워드: Fragment size

검색결과 284건 처리시간 0.03초

Analysis of Genomic Structure of an Aflatoxin Biosynthesis Homologous Gene Cluster in Aspergillus oryzae RIB Strains

  • Lee, Yun-Hae;Tominaga, Mihoko;Hayashi, Risa;Sakamoto, Kazutoshi;Yamada, Osamu;Akita, Osamu
    • 한국균학회소식:학술대회논문집
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    • 한국균학회 2006년도 추계학술대회 및 정기총회
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    • pp.32-44
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    • 2006
  • To investigate non-aflatoxin-production of A. oryzae at the molecular level, an aflatoxin biosynthesis gene homolog cluster of RIB 40 was analyzed. Although most genes in the corresponding cluster exhibited from 97 to 99 % similarity to those of Aspergillus flavus, three genes shared 93 % similarity or less. In addition, although slight expression of aflR, positive transcriptional regulator gene, was detected in some A. oryzae strains having seven aflatoxin biosynthesis homologous genes, other genes related to aflatoxin production were not detected. RIB strains were mainly divided into group 1, having seven aflatoxin biosynthesis homologous genes (aflT, nor-i, aflR, norA, avnA, verB, and vbs), and group 2, having three homologous (avnA, verB, and vbs). Partial aflatoxin homologous gene cluster of RIB62 from group 2 was sequenced and compared with that of RIB40 from group 1. RIB62 showed a large deletion upstream of ver-1 with more than half of the aflatoxin homologous gene cluster missing including aflR, a positive transcriptional regulatory gene. Adjacent to the deletion of the aflatoxin homologous gene cluster, RIB62 has a unique sequence of about 8kb and a telomere. Southern analysis of A. oryzae RIB strains with four kinds of probe derived from the unique sequence of RIB62 showed that all group 2 strains have identical hybridizing signals. Polymerase chain reaction with specific primer set designed to amplify the junction between ver-1 and the unique sequence of RIB62 resulted in the same size of DNA fragment only from group 2 strains. Based on these results, we developed a useful genetic tool that distinguishes A. oryzae group 2 strains from the other groups' strains and propose that it might have differentiated from the ancestral strains due to chromosomal breakage.

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부산지역에서 분리된 Salmonella enterica serovar Typhi균에 대한 PFGE를 이용한 Molecular typing (Molecular Typing of Salmonella enterica serovar Typhi Strains Isolated in Busan by Pulsed-Field Gel Electrophoresis)

  • 민상기;이주현;박은희;김정아;김규원
    • 생명과학회지
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    • 제16권4호
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    • pp.664-671
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    • 2006
  • 1996년부터 2005년까지 부산지역에서 분리된 Salmonella enterica serovar Typhi 균주에 대한 항균제 내성 변화양상 및 Pulsed-field gel electrophoresis(PFGE)를 이용한 분리주의 분자역학적 형별을 분석하였다. 전체 424주에 대한 항균제 감수성 시험결과 multidrug-resistant (MDR) 6주(1.4%)와 nalidixic acid에만 내성을 보이는 2주를 제외한 나머지 416주(98.1%)가 시험 항균제 18종 모두에 감수성을 보였다. 부산지역 분리 장티푸스균의 유전적 이질성을 확인하고자 실시한 산발 분리 50주의 PFGE/XbaI 시험결과, 최소 32종의 다양한 패턴이 나타났다. 각 패턴별로 제한효소 절편 수는 13개에서 18개까지였고, 절편크기는 약 20 kb에서 630 kb 범위였다. 본 시험결과 부산지역의 장티푸스의 산발 또는 집단 발생시 PFGE는 유용한 역학적 지표로 사용가능함을 알 수 있었으며 또한 전국적 PulseNet 구축의 기초 자료로서 활용도가 높을 것으로 사료된다.

천연인디고 색소의 구조분석 (Structural Analysis of Natural Indigo Colorants Extracted from Polygonum tinctorium)

  • 정인모;이광길;성규병;김현복;남성희;홍인표
    • 한국잠사곤충학회지
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    • 제49권1호
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    • pp.8-13
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    • 2007
  • 쪽풀 생잎에서 우려낸 색소 액에 소석회를 첨가한 후 쪽풀 색소의 침전물을 만들어서 냉동 건조시켜 쪽풀 색소를 제조하여, 그 성분을 조사한 결과 다음과 같은 결론을 얻었다. 1. UV분광광도, TLC 정성 분석, HPLC 측정 결과 쪽 분말 용액의 2개 bend가 나타났으며, 적색색소대인 540nm 와 청색 색소대인 620nm가 존재함을 알 수 있었다. 2. FT-IR 분석으로부터 $1627cm^{-1}$에서 채, $3200{\sim}3300cm^{-1}$에서 NH의 흡수대가 나타나고, 적색 및 청색 색소의 IR spectrum이 일치하였으며, 3. EI-mass 분석 결과 청색과 적색 색소의 fragment 이온의 m/z가 일치하고, $^1H_MNR$ 분석결과로부터 두 색소는 이성질체임을 알 수 있었고, 4. 쪽 염료 성분 함량을 조사한 결과 인디고 색소 4.06%와 인디루빈 1.06%이었다.

국내 사육 꿩에서 분리된 뉴켓슬병 바이러스의 hemagglutinin-neuraminidase(HN) 유전자의 클론닝과 염기서열 분석 (Molecular cloning and nucleotide sequence of the gene encoding hemagglutinin-neuraminidase(HN) of Newcastle disease virus isolated from a diseased pheasant in Korea)

  • 장경수;곽길한;장승익;김지영;김태용;송영환;송희종;전무형
    • 한국동물위생학회지
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    • 제25권3호
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    • pp.245-257
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    • 2002
  • The gene encoding the HN protein from the CBP-1 strain, a heat stable Newcastle disease virus (NDV) isolated from diseased pheasants in Korea, was characterized by reverse transcriptase- polymerase chain reaction(RT-PCR) and the nucleotide and amino acid sequences were analyzed following cloning of the HN gene. In all of the NDV strains studied, a 1.75 kb size cDNA fragment for the HN gene was generated by RT-PCR and smaller specific band sizes harboring the internal portions of the HN gene were also detected by using four pairs of primers. The RT-PCR was sensitive enough to detect viral transcripts when the virus titer was above 25 hemagglutination units. The amplified 1.75 kb cDNA was cloned into a BamHI site of the pVL1393 Baculo transfer vector. The nucleotide sequences of the 1,758 bp HN gene from the CBP-1 strain were determined by the dye terminator cyclic sequencing method. The gene sequences were compared among the strains of CBP-1, Texas GB, Beaudette C, LaSota, B1 and Ulster. The homology of the CBP-1 HN gene to other HN variants was 97.8% to Texas GB, 98.4% to Beaudette C, 95.4% to LaSota, 95.6% to B1 and 90.2% to Ulster. As the deduced 577 amino acid sequences were compared among the strains, the homology for CBP-1 HN appeared to be 96.7% to Texas GB, 97.9% to Beaudette C, 95.5% to LaSota, 95.5% to B1 and 92.7% to Ulster. It was evident that the amino acid sequences included 5 sites for N-asparagine linked glycosylation and 12 cysteine residues. The three conserved leucine residues within the predicted transmembrane domain of the HN protein are amino acid 30, 37 and 44. The three antigenic sites on the HN protein of NDV are amino acids 347(Glu), 481(Asn) and 495(Glu). These data indicate that the genotype of the CBP-1 strain is more closely associated with the strains of Texas GB and Beaudette C than it is for the LaSota, B1 and Ulster strains.

여름느타리의 Chitin synthase 유전자 단편분리 및 발현 특성 분석 (Isolation and Characterization of a Chitin Synthase Gene Fragments from Pleurotus sajor-caju)

  • 정미정;박수철;김범기;유영복;류진창
    • 한국균학회지
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    • 제26권3호통권86호
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    • pp.354-360
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    • 1998
  • 여름 느타리 Pleurotus sajor-caju로부터 Chitin synthase(CHS) gene 특이 primer를 이용한 PCR을 통해 3개의 DNA 단편을 분리하여 cloning하였다. 분리된 DNA 단편들을 기존에 보고된 CHS 유전자들과의 염기서열을 분석한 결과, 이들 DNA 단편들 3개가 모두 CHS 유전자의 단편임을 확인하였고, 또한 이들은 각각 서로 다른 종류의 CHS 유전자들임을 알 수 있었다. 한편, RT-PCR 방법을 이용하여 분리된 유전자의 발현 실험을 실시해본 결과, 이들중 하나인 PsCHS3 유전자는 갓과 균사에서만 발현되는 기관특이 발현 특성을 보였으며, 또한 이 유전자는 상처 처리에 의해 그 발현이 증가되는 것을 확인하였다. 이러한 실험결과로 볼 때 p. sajor-caju의 경우, 다른 균류들의 경우처럼 다양한 기능을 가진 여러 종류(최소 3종류)의 CHS 유전자를 보유하고 있으며, 이들 각각은 다른 기관, 또는 다른 생육 단계에 작용하고 있을 것으로 생각되고, 특히 병 방어 기작에도 관여할 것으로 추측되어진다.

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폐 미세플라스틱(PET)의 물벼룩 만성독성 연구 (Effect of Chronic Toxicity by Waste Microplastics (PET) on Daphnia magna)

  • 한보미;박건우;유승우;김창해;정진호;나주림
    • Ecology and Resilient Infrastructure
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    • 제8권4호
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    • pp.281-289
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    • 2021
  • 상업에서 사용되는 일회용 컵은 환경으로 유입되어 파편화되어 미세플라스틱 (MP)이 될 수 있다. 또한 MP는 수생 생물에게 섭식 될 수 있으며, 다양한 부작용을 미칠 수 있다. 본 연구는 일회용 컵에서 유래된 MP 조각이 물벼룩에게 미치는 급성 및 만성 독성을 평가했다. MP 조각은 33.18 ±7.76 ㎛ 크기의 PET (Polyethylene terephthalate) MP 조각으로 확인되었으며, 3종류의 첨가제 (1- Propanone. 1-phenyl-3-[2-(phenylmethoxy)phenyl]-, p-Xylene and ethylbenzene)가 함유되어 있는 것을 확인하였다. 48시간 급성 독성은 최고 농도의 PET MP (200 mg L-1)에 노출된 물벼룩에서 20%의 유영저해 및 사망을 발견하였다. 21일 만성 독성은 5 mg L-1의 PET MP 조각에 노출된 D. magna에서 대조군과 비교하여 줄어든 생존율 (31%)과 번식 (52%)을 보여주었다. 더욱이 PET MP는 태어난 개체의 발달 이상을 (3.5%) 대조군 (0.3%)과 비교하여 유의하게 (p < 0.05) 증가시켰다. 이러한 결과는 MP 조각의 섭취에 의한 장 막힘과 더 긴 체류 시간 때문일 수 있다. 본 연구의 결과는 일회용 컵 (PET 폴리머)이 작은 크기의 MP 조각으로 단편화되면 수생 생물에 심각한 생태학적 위험을 제기할 수 있음을 시사하고 있다. 또한 MP 독성 및 첨가제에 대한 근본적인 독성 메커니즘을 확인하기 위해 추가 연구가 수행되어야 한다.

치주염 원인균에 대한 천연 식물 추출물의 항균효과 (Antimicrobial Effect of Natural Plant Extracts against Periodontopathic Bacteria)

  • 이승희;김민정
    • 한국콘텐츠학회논문지
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    • 제19권1호
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    • pp.242-255
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    • 2019
  • 이 연구는 34종의 천연 식물 추출물을 이용하여 치주염 원인균 Actinobacillus actinomycetemcomitans와 Prevotella intermedia에 대한 항균효과를 조사하였다. 이에 본 연구는 치주염 원인균에 대한 천연 식물 추출물의 항균효과를 연구하고자 유기용매 추출물을 이용하여 생육저지활성을 측정하고, 시료 추출물의 최소생육저해농도(Minimum Inhibition Concentration, MIC)를 측정한다. 1차적으로 34종의 각 천연 식물 추출물을 에탄올로 추출하여 디스크 확산법(disk diffusion method)을 이용하여 각 추출물의 생육저지환(clear zone, mm)의 크기를 측정한 결과 나복자, 목통, 백작약, 사간, 선복화, 어성초, 연교, 진교, 천련자, 황금, (천)황련, 황백, 해동피 등 13종에서 천연 식물 추출물이 치주염의 원인균인 A. actinomycetemcomitans에 대해서 생육저지 활성을 나타내었다. P. intermedia의 경우, 나복자, (일)당귀, 목통, 사간, 선복화, 어성초, 육계, 자완, 천련자, 황금, (천)황련, 황백, 해동피 등 13종에서 생육저지 활성을 나타내었다. A. actinomycetemcomitans에 대해서는 사간, 육계, 해동피, 황백, (천)황련에서 항균효과가 나타났다. (천)황련은 A. actinomycetemcomitans의 모든 유기용매 분획에서 가장 우수한 생육저지 활성을 나타내었다. P. intermedia는 사간, 육계, 천련자, 황백, 황련에서 생육저지 활성이 나타났다.

Simulation study on effects of loading rate on uniaxial compression failure of composite rock-coal layer

  • Chen, Shao J.;Yin, Da W.;Jiang, N.;Wang, F.;Guo, Wei J.
    • Geomechanics and Engineering
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    • 제17권4호
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    • pp.333-342
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    • 2019
  • Geological dynamic hazards during coal mining can be caused by the failure of a composite system consisting of roof rock and coal layers, subject to different loading rates due to different advancing velocities in the working face. In this paper, the uniaxial compression test simulations on the composite rock-coal layers were performed using $PFC^{2D}$ software and especially the effects of loading rate on the stress-strain behavior, strength characteristics and crack nucleation, propagation and coalescence in a composite layer were analyzed. In addition, considering the composite layer, the mechanisms for the advanced bore decompression in coal to prevent the geological dynamic hazards at a rapid advancing velocity of working face were explored. The uniaxial compressive strength and peak strain are found to increase with the increase of loading rate. After post-peak point, the stress-strain curve shows a steep stepped drop at a low loading rate, while the stress-strain curve exhibits a slowly progressive decrease at a high loading rate. The cracking mainly occurs within coal, and no apparent cracking is observed for rock. While at a high loading rate, the rock near the bedding plane is damaged by rapid crack propagation in coal. The cracking pattern is not a single shear zone, but exhibits as two simultaneously propagating shear zones in a "X" shape. Following this, the coal breaks into many pieces and the fragment size and number increase with loading rate. Whereas a low loading rate promotes the development of tensile crack, the failure pattern shows a V-shaped hybrid shear and tensile failure. The shear failure becomes dominant with an increasing loading rate. Meanwhile, with the increase of loading rate, the width of the main shear failure zone increases. Moreover, the advanced bore decompression changes the physical property and energy accumulation conditions of the composite layer, which increases the strain energy dissipation, and the occurrence possibility of geological dynamic hazards is reduced at a rapid advancing velocity of working face.

밀양근교에서 채집한 야생 동충하초 계통의 PCR 산물에 근거한 계통 유전학적 연구 (Phylogenetic Analysis on Wild Cordyceps Collected from Miryang Region of South Korea)

  • 박현철;이상몽;박남숙
    • 한국자원식물학회지
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    • 제34권1호
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    • pp.1-16
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    • 2021
  • 남부 지방의 밀양 근교에 자생하고 있는 야생 동충하초 균주(Cordyceps sp., Paecilomyces sp., Beauveria sp., Aranthomyces sp., Isaria sp., Himenostilbe sp.)를 채집 분리하여 rDNA 및 internal transcribed spacer (ITS) 부위의 염기서열을 비교하였다. ITS 영역에 특정적인 프라이머인 ITS1과 ITS4를 이용하여 PCR을 수행하여 증폭하였다. 다양한 균주에서 같은 크기의 PCR 생산물을 얻을 수 있었고, 이들의 서열분석을 위하여 pGEM-T easy 벡터에 클로닝하였으며, ITS1, 5.8S, ITS2 영역 부위의 염기서열들을 BLAST 수행하여 유연관계를 분석하였다. 밀양 근교에서 분리한 32개의 균주 중에 Cordyceps militaris는 서열이 등록된 유전정보 AY49191, EU825999, AY491992와 100% 일치하였으며, 몇 개의 종은 보고된 서열과 모두 일치하지는 않았다. 예를 들어 strain P17은 울주군 가지산에서 분리한 P. tenuipes로서 밀양시 조천읍 가지산에서 분리한 P. tenuipes와는 서열상에서 다른 부분들이 있었다. 결론적으로 밀양 근교의 균주들을 분리하는데 ITS영역분석이 분류와 검정에 효율적이고, 본 연구를 통하여 동충하초의 생태학적인 유전자원들을 확보할 수 있었다.

Brief Introduction of Research Progresses in Control and Biocontrol of Clubroot Disease in China

  • He, Yueqiu;Wu, Yixin;He, Pengfei;Li, Xinyu
    • 한국균학회소식:학술대회논문집
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    • 한국균학회 2015년도 춘계학술대회 및 임시총회
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    • pp.45-46
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    • 2015
  • Clubroot disease of crucifers has occurred since 1957. It has spread to the whole China, especially in the southwest and nourtheast where it causes 30-80% loss in some fields. The disease has being expanded in the recent years as seeds are imported and the floating seedling system practices. For its effective control, the Ministry of Agriculture of China set up a program in 2010 and a research team led by Dr. Yueqiu HE, Yunnan Agricultural University. The team includes 20 main reseachers of 11 universities and 5 institutions. After 5 years, the team has made a lot of progresses in disease occurrence regulation, resources collection, resistance identification and breeding, biological agent exploration, formulation, chemicals evaluation, and control strategy. About 1200 collections of local and commercial crucifers were identified in the field and by artificiall inoculation in the laboratories, 10 resistant cultivars were breeded including 7 Chinese cabbages and 3 cabbages. More than 800 antagostic strains were isolated including bacteria, stretomyces and fungi. Around 100 chemicals were evaluated in the field and greenhouse based on its control effect, among them, 6 showed high control effect, especially fluazinam and cyazofamid could control about 80% the disease. However, fluzinam has negative effect on soil microbes. Clubroot disease could not be controlled by bioagents and chemicals once when the pathogen Plasmodiophora brassicae infected its hosts and set up the parasitic relationship. We found the earlier the pathogent infected its host, the severer the disease was. Therefore, early control was the most effective. For Chinese cabbage, all controlling measures should be taken in the early 30 days because the new infection could not cause severe symptom after 30 days of seeding. For example, a biocontrol agent, Bacillus subtilis Strain XF-1 could control the disease 70%-85% averagely when it mixed with seedling substrate and was drenching 3 times after transplanting, i.e. immediately, 7 days, 14 days. XF-1 has been deeply researched in control mechanisms, its genome, and development and application of biocontrol formulate. It could produce antagonistic protein, enzyme, antibiotics and IAA, which promoted rhizogenesis and growth. Its The genome was sequenced by Illumina/Solexa Genome Analyzer to assembled into 20 scaffolds then the gaps between scaffolds were filled by long fragment PCR amplification to obtain complet genmone with 4,061,186 bp in size. The whole genome was found to have 43.8% GC, 108 tandem repeats with an average of 2.65 copies and 84 transposons. The CDSs were predicted as 3,853 in which 112 CDSs were predicted to secondary metabolite biosynthesis, transport and catabolism. Among those, five NRPS/PKS giant gene clusters being responsible for the biosynthesis of polyketide (pksABCDEFHJLMNRS in size 72.9 kb), surfactin(srfABCD, 26.148 kb, bacilysin(bacABCDE 5.903 kb), bacillibactin(dhbABCEF, 11.774 kb) and fengycin(ppsABCDE, 37.799 kb) have high homolgous to fuction confirmed biosynthesis gene in other strain. Moreover, there are many of key regulatory genes for secondary metabolites from XF-1, such as comABPQKX Z, degQ, sfp, yczE, degU, ycxABCD and ywfG. were also predicted. Therefore, XF-1 has potential of biosynthesis for secondary metabolites surfactin, fengycin, bacillibactin, bacilysin and Bacillaene. Thirty two compounds were detected from cell extracts of XF-1 by MALDI-TOF-MS, including one Macrolactin (m/z 441.06), two fusaricidin (m/z 850.493 and 968.515), one circulocin (m/z 852.509), nine surfactin (m/z 1044.656~1102.652), five iturin (m/z 1096.631~1150.57) and forty fengycin (m/z 1449.79~1543.805). The top three compositions types (contening 56.67% of total extract) are surfactin, iturin and fengycin, in which the most abundant is the surfactin type composition 30.37% of total extract and in second place is the fengycin with 23.28% content with rich diversity of chemical structure, and the smallest one is the iturin with 3.02% content. Moreover, the same main compositions were detected in Bacillus sp.355 which is also a good effects biocontol bacterial for controlling the clubroot of crucifer. Wherefore those compounds surfactin, iturin and fengycin maybe the main active compositions of XF-1 against P. brassicae. Twenty one fengycin type compounds were evaluate by LC-ESI-MS/MS with antifungal activities, including fengycin A $C_{16{\sim}C19}$, fengycin B $C_{14{\sim}C17}$, fengycin C $C_{15{\sim}C18}$, fengycin D $C_{15{\sim}C18}$ and fengycin S $C_{15{\sim}C18}$. Furthermore, one novel compound was identified as Dehydroxyfengycin $C_{17}$ according its MS, 1D and 2D NMR spectral data, which molecular weight is 1488.8480 Da and formula $C_{75}H_{116}N_{12}O_{19}$. The fengycin type compounds (FTCPs $250{\mu}g/mL$) were used to treat the resting spores of P. brassicae ($10^7/mL$) by detecting leakage of the cytoplasm components and cell destruction. After 12 h treatment, the absorbencies at 260 nm (A260) and at 280 nm (A280) increased gradually to approaching the maximum of absorbance, accompanying the collapse of P. brassicae resting spores, and nearly no complete cells were observed at 24 h treatment. The results suggested that the cells could be lyzed by the FTCPs of XF-1, and the diversity of FTCPs was mainly attributed to a mechanism of clubroot disease biocontrol. In the five selected medium MOLP, PSA, LB, Landy and LD, the most suitable for growth of strain medium is MOLP, and the least for strains longevity is the Landy sucrose medium. However, the lipopeptide highest yield is in Landy sucrose medium. The lipopeptides in five medium were analyzed with HPLC, and the results showed that lipopeptides component were same, while their contents from B. subtilis XF-1 fermented in five medium were different. We found that it is the lipopeptides content but ingredients of XF-1 could be impacted by medium and lacking of nutrition seems promoting lipopeptides secretion from XF-1. The volatile components with inhibition fungal Cylindrocarpon spp. activity which were collect in sealed vesel were detected with metheds of HS-SPME-GC-MS in eight biocontrol Bacillus species and four positive mutant strains of XF-1 mutagenized with chemical mutagens, respectively. They have same main volatile components including pyrazine, aldehydes, oxazolidinone and sulfide which are composed of 91.62% in XF-1, in which, the most abundant is the pyrazine type composition with 47.03%, and in second place is the aldehydes with 23.84%, and the third place is oxazolidinone with 15.68%, and the smallest ones is the sulfide with 5.07%.

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