JPH05103700A - Oligonucleotide probe and detection of bacterium with the same - Google Patents

Oligonucleotide probe and detection of bacterium with the same

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Publication number
JPH05103700A
JPH05103700A JP26574891A JP26574891A JPH05103700A JP H05103700 A JPH05103700 A JP H05103700A JP 26574891 A JP26574891 A JP 26574891A JP 26574891 A JP26574891 A JP 26574891A JP H05103700 A JPH05103700 A JP H05103700A
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JP
Japan
Prior art keywords
paracoccus
bacterium
detecting
bacteria
sequence
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
JP26574891A
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Japanese (ja)
Other versions
JP3052487B2 (en
Inventor
Hirotaka Minagawa
宏貴 皆川
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NEC Corp
Original Assignee
NEC Corp
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Publication of JPH05103700A publication Critical patent/JPH05103700A/en
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Abstract

PURPOSE:To detect and count bacteria belonging to the genus Paracoccuswithout culturing the bacteria in a method for detecting the bacteria. CONSTITUTION:In a method for detecting Paracoccus.kocurii, the Paracoccus.kocurii is detected and counted by the use of a fluorescent light- labeled nucleotide probe obtained by addition-reacting a fluorescent light pigment to an oligonucleotide in which a complementary sequence is disposed in the base sequence of the variable region of the 16 Sr RNA of the Paracoccus.kocurii, represented by the drawing.

Description

【発明の詳細な説明】Detailed Description of the Invention

【0001】[0001]

【産業上の利用分野】本発明はパラコッカス属に属し、
水酸化テトラメチルアンモニウム分解能を有するパラコ
ッカス・コクリを検出する方法に関するものである。
The present invention belongs to the genus Paracoccus,
The present invention relates to a method for detecting Paracoccus cocci having a tetramethylammonium hydroxide decomposing ability.

【0002】[0002]

【従来の技術】一般に自然界(土壌、河川等)から目的
の微生物を単離するためには特別な培地による選択培養
を行なうことが多い。この方法は簡便であるため広く用
いられているが、微生物の種類によっては培養が不可能
であったり困難な場合がある。このような場合には放射
性同位元素または蛍光色素でラベルした抗体を用いる方
法が知られているが、この方法は抗体を得るのに手間が
かかるという難点があった。
2. Description of the Related Art Generally, in order to isolate a desired microorganism from the natural world (soil, river, etc.), selective culturing is often carried out using a special medium. This method is widely used because it is simple, but depending on the type of microorganism, culturing may be impossible or difficult. In such a case, a method using an antibody labeled with a radioisotope or a fluorescent dye is known, but this method has a drawback that it takes time to obtain the antibody.

【0003】この方法に代わるものとして、生物種に特
異的な核酸の塩基配列を、それに相補的な配列を持つオ
リゴヌクレオチドをプローブにして検出する方法が発表
されている。特に生物に普遍的に存在するリボゾームの
構成要素である16SrRNAの塩基配列を検出するプ
ローブは特異性が高く、また高次な分類にも使用可能な
ものとして期待されている。
As an alternative to this method, a method of detecting the base sequence of a nucleic acid specific to a biological species by using an oligonucleotide having a sequence complementary thereto as a probe has been published. In particular, a probe for detecting the nucleotide sequence of 16S rRNA, which is a ribosome component that is ubiquitous in organisms, has high specificity and is expected to be usable for higher-order classification.

【0004】レーンらによると(プロシーディング・ナ
ショナル・アカデミーオブサイエンス・ユーエスーエー
(Proceeding National Acad
emy of Science USA)、82巻、6
955−6959頁 1985年)16SrRNAには
原核生物全体に保存されている領域と種あるいは属に特
異的な領域とがあり、保存されている領域を使って特異
的な領域の配列を決定することが可能である。
According to Lane et al. (Proceeding National Academy of Science USA)
emy of Science USA), Vol. 82, 6
955-6959 (1985) 16S rRNA has a region conserved in the whole prokaryotes and a region specific to the species or genus, and the sequence of the specific region should be determined using the conserved region. Is possible.

【0005】[0005]

【発明が解決しようとする課題】特定の微生物を利用し
て廃水処理を行なう場合、処理条件や生育条件を最適に
するために、その微生物の活性汚泥中での優占度や生育
状況を知る必要がある。そのためには微生物を特異的に
検出し、計数しなければならないが、いままでパラコッ
カス・コクリを検出、計数するためには水酸化テトラメ
チルアンモニウムを唯一の炭素源とする選択培地による
培養を行なわなければならなかった。
When wastewater treatment is carried out by utilizing a specific microorganism, the predominance and growth condition of the microorganism in activated sludge are known in order to optimize the treatment conditions and growth conditions. There is a need. For that purpose, it is necessary to specifically detect and count microorganisms, but until now, in order to detect and count Paracoccus cocci, culture must be performed in a selective medium using tetramethylammonium hydroxide as the only carbon source. I had to do it.

【0006】以下に従来の一例を述べると、パラコッカ
ス・コクリを検出、計数するためには細菌懸濁液をTM
ACl培地(1gテトラメチルアンモニウム,20mg
塩酸チアミン,1g硫酸アンモニウム,20ミリリット
ルHutnerの無機塩溶液,40ミリリットルNa2
HPO4 +KH2 PO4 緩衝液,15g寒天/1000
ミリリットル)上で5〜7日間37℃で培養し、出現し
たコロニーをカウントしなければならなかった。これに
は検出、計数にほぼ一週間を必要とし、活性汚泥中での
挙動をリアルタイムでモニタリングするということはで
きなかった。
A conventional example is described below. To detect and count Paracoccus cocci, a bacterial suspension is used for TM.
ACl medium (1g tetramethylammonium, 20mg
Thiamine Hydrochloride, 1 g Ammonium Sulfate, 20 ml Hutner's Inorganic Salt Solution, 40 ml Na 2
HPO 4 + KH 2 PO 4 buffer, 15g agar / 1000
The cells had to be cultured for 5 to 7 days at 37 ° C. and the colonies that appeared had to be counted. This required almost one week for detection and counting, and it was not possible to monitor the behavior in activated sludge in real time.

【0007】本発明の目的は迅速にかつ特異的にパラコ
ッカス・コクリを検出、計数する方法を提供することに
ある。
An object of the present invention is to provide a method for rapidly and specifically detecting and counting Paracoccus cocci.

【0008】[0008]

【課題を解決するための手段】本発明は、(1)パラコ
ッカス属に属する細菌の16SrRNAの可変領域に相
補的な配列をもつデオキシリボヌクレオチドまたはリボ
ヌクレオチドにおいて、塩基配列5’AACCCTCT
GTCACCACCAT3’を含むオリゴヌクレオチド
プローブと、(2)パラコッカス属に属する細菌の16
SrRNAの可変領域に相補的な配列をもつデオキシリ
ボヌクレオチドまたはリボヌクレオチドに、蛍光色素を
付加することにより得られたプローブを用いて、パラコ
ッカス属に属する細菌を特異的に検出することを特徴と
する方法とである。
The present invention provides (1) a deoxyribonucleotide or ribonucleotide having a sequence complementary to the variable region of 16S rRNA of a bacterium belonging to the genus Paracoccus, which has a base sequence of 5'AACCCTCT.
An oligonucleotide probe containing GTCACCACCAT3 ′, and (2) 16 of bacteria belonging to the genus Paracoccus
A method for specifically detecting a bacterium belonging to the genus Paracoccus using a probe obtained by adding a fluorescent dye to a deoxyribonucleotide or ribonucleotide having a sequence complementary to the variable region of SrRNA. And.

【0009】[0009]

【作用】本発明はパラコッカス・コクリ16SrRNA
の部分塩基配列を1392−1405(大腸菌16Sr
RNAのナンバーリング)の保存領域をプライマーとし
て逆転写酵素を使ったジデオキシ法によって決定し、他
の細菌の16SrRNA配列と比較することで可変領域
を探索することにより得た。図1に決定されたパラコッ
カス・コクリ16SrRNAの部分塩基配列と本発明の
オリゴヌクレオチドプローブが結合する部分を示す。図
2のA、Bにそれぞれ本発明に関わるパラコッカス・コ
クリと比較のためのエッシェリシア・コリの16SrR
NAの部分塩基配列を示す。図2Aの塩基の下の*は、
エッシェリシア・コリと同じ塩基であることを示し、図
2Bの塩基の下の数字5’末端からの塩基数を示す。図
2A、Bの比較からまた他の細菌との16SrRNA配
列の比較からも本発明の結合部分はパラコッカス・コク
リに特異的であることが確かめられた。
The present invention is based on Paracoccus cochlei 16S rRNA.
The partial base sequence of 1392-1405 (E. coli 16Sr
The conserved region of (numbering of RNA) was determined by the dideoxy method using a reverse transcriptase as a primer, and compared with the 16S rRNA sequence of another bacterium to obtain the variable region. FIG. 1 shows the determined partial base sequence of Paracoccus cochlei 16S rRNA and the portion to which the oligonucleotide probe of the present invention binds. 2A and 2B are respectively Paracoccus cochlei of the present invention and 16SrR of Escherichia coli for comparison.
The partial base sequence of NA is shown. The * under the base in Figure 2A is
It shows that it has the same base as Escherichia coli, and shows the number of bases from the number 5 ′ end under the base in FIG. 2B. Comparison of FIGS. 2A, B and comparison of 16S rRNA sequences with other bacteria confirmed that the binding moieties of the present invention are specific for Paracoccus coccoli.

【0010】[0010]

【実施例】【Example】

(実施例1)パラコッカス・コクリ(Paracocc
us Kocurii)JCM7684(インターナシ
ョナル・ジャーナル・オブ・システマティック・バクテ
リオロジー(International Journ
al of Systematic Bacterio
logy)40巻292−296頁1990年)とエッ
シェリシア・コリ(Escherichia col
i)ATCC24977を菌数が約1×107 個/ミリ
リットルになるようにリン酸緩衝液(145mMNaC
l,100mM Sodiumphosphate,p
H7.5)で希釈する。1/10ボリュームの37%ホ
ルムアルデヒドを加えて菌体を固定し、0.1%ゼラチ
ン,0.01%クロムミョウバンでコートしたスライド
グラスに30マイクロリットル滴下し風乾する。スライ
ドグラスを90%メタノール,3.7%ホルムアルデヒ
ドに室温で10分間侵して菌体を再固定した後、純水で
洗浄する。
Example 1 Paracocc
us Kocurii JCM7684 (International Journal of Systematic Bacteriology)
al of Systematic Bacterio
40) 292-296, 1990) and Escherichia coli.
i) A phosphate buffer solution (145 mM NaC) was added to ATCC24977 so that the number of bacteria was about 1 × 10 7 cells / ml.
l, 100 mM Sodium phosphate, p
Dilute with H7.5). 1/10 volume of 37% formaldehyde is added to fix the cells, and 30 microliters of the solution is dropped on a slide glass coated with 0.1% gelatin and 0.01% chrome alum and air-dried. The slide glass is immersed in 90% methanol and 3.7% formaldehyde at room temperature for 10 minutes to re-fix the cells, and then washed with pure water.

【0011】次にスライドグラスをトリス緩衝液(10
0mM Tris−HCl,pH8.0,50mM S
odium borohydride)に室温、遮光し
た状態で30分間侵す。スライドグラスを純水で洗浄後
風乾する。5’AACCCTCTGTCACCACCA
T3’の配列を持つオリゴヌクレオチドの5’末端から
2番目と3番目の塩基(AとC)の間のリン酸基にフル
オレセインイソチオシアネート(Fluorescei
n isothiocyanate)を付加した蛍光標
識プローブを1.7ng/マイクロリットルになるよう
に、ハイブリダゼイション緩衝液(750mM NaC
l,100mM Tris−HCl pH7.8,5m
M EDTA,0.2% bovine seruma
lbumin,10% dextran sulfat
e,0.01% polyadenylic aci
d)で希釈し、30マイクロリットルをスライドグラス
に滴下する。スライドグラスを気密性の容器にいれ、遮
光した状態にして37℃で5時間以上反応させる。
Next, slide the slide glass in Tris buffer (10
0 mM Tris-HCl, pH 8.0, 50 mM S
Odor borohydride) at room temperature for 30 minutes in the dark. Wash the slide glass with pure water and air dry. 5'AACCCTCTGTCACCACCA
Fluorescein isothiocyanate (Fluorescei) is added to the phosphate group between the second and third bases (A and C) from the 5'end of the oligonucleotide having the T3 'sequence.
Fluorescence-labeled probe added with niisothiocyanate was added to a hybridization buffer solution (750 mM NaC) at 1.7 ng / microliter.
1, 100 mM Tris-HCl pH 7.8, 5 m
M EDTA, 0.2% bovine seruma
lbumin, 10% dextran sulfat
e, 0.01% polyadenylic aci
Dilute with d) and add 30 microliters dropwise to a slide glass. The slide glass is put in an airtight container, and the mixture is allowed to react at 37 ° C. for 5 hours or more in a light-shielded state.

【0012】反応後、SET緩衝液(30mM NaC
l,4mM Tris−HCl pH7.8,0.2m
M EDTA)でスライドグラスを洗浄する。暗所で風
乾後、落射型蛍光顕微鏡で検鏡する。励起光源には水銀
ランプを使用し、フィルター(ZEISS 48790
9)で励起光を調整する。検鏡の結果パラコッカス・コ
クリは蛍光が認められたが、エッシェリシア・コリでは
認められなかった。またバックグラウンドの蛍光はほと
んど観測されなかった。
After the reaction, SET buffer solution (30 mM NaC
1, 4 mM Tris-HCl pH 7.8, 0.2 m
Wash slides with M EDTA). After air-drying in the dark, examine with an epi-illumination fluorescent microscope. A mercury lamp is used as an excitation light source, and a filter (ZEISS 48790 is used.
The excitation light is adjusted in 9). As a result of the microscopic examination, fluorescence was observed in Paracoccus cocci but not in Escherichia coli. Also, background fluorescence was hardly observed.

【0013】(実施例2)パラコッカス・コクリとバシ
ラス・サブチリス(Bacillus subtili
s)IFO13719について上記の実施例と同様の操
作を行なった結果パラコッカス・コクリにのみ蛍光が観
測された。
(Example 2) Paracoccus kokuri and Bacillus subtilis
s) IFO13719 was subjected to the same operation as in the above example, and as a result, fluorescence was observed only in Paracoccus cocci.

【0014】[0014]

【発明の効果】本発明の方法では従来と比較し、短期間
で迅速にかつ特異的にパラコッカス・コクリを検出、計
数することができる。
INDUSTRIAL APPLICABILITY According to the method of the present invention, Paracoccus cocci can be detected and counted rapidly and specifically in a short period of time as compared with the conventional method.

【図面の簡単な説明】[Brief description of drawings]

【図1】パラコッカス・コクリの16SrRNAの部分
塩基配列とそれに結合したオリゴヌクレオチドプローブ
を示した図である。
FIG. 1 is a view showing a partial base sequence of 16S rRNA of Paracoccus cocci and an oligonucleotide probe bound thereto.

【図2】パラコッカス・コクリとエッシェリシア・コリ
との16SrRNAの部分塩基配列を比較した図であ
る。(A)は本発明に関わるパラコッカス・コクリの1
6SrRNAの部分塩基配列で、(B)は比較のための
エッシェリシア・コリの16SrRNAの部分塩基配列
を示す
FIG. 2 is a diagram comparing the partial base sequences of 16S rRNA between Paracoccus cocci and Escherichia coli. (A) is one of Paracoccus kokuri related to the present invention
Partial base sequence of 6SrRNA, (B) shows partial base sequence of 16SrRNA of Escherichia coli for comparison.

─────────────────────────────────────────────────────
─────────────────────────────────────────────────── ───

【手続補正書】[Procedure amendment]

【提出日】平成4年12月28日[Submission date] December 28, 1992

【手続補正1】[Procedure Amendment 1]

【補正対象書類名】明細書[Document name to be amended] Statement

【補正対象項目名】0006[Correction target item name] 0006

【補正方法】変更[Correction method] Change

【補正内容】[Correction content]

【0006】以下に従来の一例を述べると、パラコッカ
ス・コクリを検出、計数するためには細菌懸濁液をTM
ACl培地(1gテトラメチルアンモニウム,20mg
塩酸チアミン,1g硫酸アンモニウム,20ミリリット
ルHutnerの無機塩溶液,40ミリリットルNa2
HPO4 +KH2 PO4 緩衡液,15g寒天/1000
ミリリットル)上で5〜7日間30℃で培養し、出現し
たコロニーをカウントしなければならなかった。これに
は検出、計数にほぼ一週間を必要とし、活性汚泥中での
挙動をリアルタイムでモニタリングするということはで
きなかった。
A conventional example is described below. To detect and count Paracoccus cocci, a bacterial suspension is used for TM.
ACl medium (1g tetramethylammonium, 20mg
Thiamine Hydrochloride, 1 g Ammonium Sulfate, 20 ml Hutner's Inorganic Salt Solution, 40 ml Na 2
HPO 4 + KH 2 PO 4 buffer solution, 15g agar / 1000
They had to be cultured for 5 to 7 days at 30 ° C. and the colonies that appeared had to be counted. This required almost one week for detection and counting, and it was not possible to monitor the behavior in activated sludge in real time.

【手続補正2】[Procedure Amendment 2]

【補正対象書類名】明細書[Document name to be amended] Statement

【補正対象項目名】0009[Correction target item name] 0009

【補正方法】追加[Correction method] Added

【補正内容】[Correction content]

【0009】[0009]

【作用】本発明はパラコッカス・コクリ16SrRNA
の部分塩基配列を1392−1405(大腸菌16Sr
RNAのナンバーリング)の保存領域をプライマーとし
て逆転写酵素を使ったジデオキシ法によって決定し、他
の細菌の16SrRNA配列と比較することで可変領域
を探索することにより得た。図1に決定されたパラコッ
カス・コクリ16SrRNAの部分塩基配列と本発明の
オリゴヌクレオチドプローブが結合する部分を示す。図
2のA、Bにそれぞれ本発明に関わるパラコッカス・コ
クリと比較のためエッシェリシア・コリの16SrRN
Aの部分塩基配列を示す。図2Aの塩基の下の*は、エ
ッシェリシア・コリと同じ塩基であることを示し、図2
Bの塩基の下の数字5’末端からの塩基数を示す。図
2A、Bの比較からまた他の細菌との16SrRNA配
列の比較からも本発明の結合部分はパラコッカス・コク
リに特異的であることが確かめられた。
The present invention is based on Paracoccus cochlei 16S rRNA.
The partial base sequence of 1392-1405 (E. coli 16Sr
The conserved region of (numbering of RNA) was determined by the dideoxy method using a reverse transcriptase as a primer, and compared with the 16S rRNA sequence of another bacterium to obtain the variable region. FIG. 1 shows the determined partial base sequence of Paracoccus cochlei 16S rRNA and the portion to which the oligonucleotide probe of the present invention binds. 2A and 2B are respectively Escherichia coli 16SrRN for comparison with Paracoccus cochleus associated with the present invention.
The partial base sequence of A is shown. The * under the base in FIG. 2A indicates that it is the same base as Escherichia coli.
Numbers below the base B is the number of bases from the 5 'end. Comparison of FIGS. 2A, B and comparison of 16S rRNA sequences with other bacteria confirmed that the binding moieties of the present invention are specific for Paracoccus coccoli.

【手続補正3】[Procedure 3]

【補正対象書類名】明細書[Document name to be amended] Statement

【補正対象項目名】0010[Correction target item name] 0010

【補正方法】変更[Correction method] Change

【補正内容】[Correction content]

【0010】[0010]

【実施例】 (実施例1)パラコッカス・コクリ(Paracocc
us ocurii)JCM7684(インターナシ
ョナル・ジャーナル・オブ・システマティック・バクテ
リオロジー(International Journ
al of Systematic Bacterio
logy)40巻292−296頁1990年)とエッ
シェリシア・コリ(Escherichia col
i)ATCC24977を菌数が約1×107 個/ミリ
リットルになるようにリン酸緩衝液(145mMNaC
l,100mM Sodiumphosphate,p
H7.5)で希釈する。1/10ボリュームの37%ホ
ルムアルデヒドを加えて菌体を固定し、0.1%ゼラチ
ン,0.01%クロムミョウバンでコートしたスライド
グラスに30マイクロリットル滴下し風乾する。スライ
ドグラスを90%メタノール,3.7ホルムアルデヒド
に室温で10分間侵して菌体を際固定した後、純水で洗
浄する。
Example 1 Example 1 Paracocc
us k ocurii) JCM7684 (International Journal of Systematic Bacteriology Biology (International Journ
al of Systematic Bacterio
40) 292-296, 1990) and Escherichia coli.
i) A phosphate buffer solution (145 mM NaC) was added to ATCC24977 so that the number of bacteria was about 1 × 10 7 cells / ml.
l, 100 mM Sodium phosphate, p
Dilute with H7.5). 1/10 volume of 37% formaldehyde is added to fix the cells, and 30 microliters of the solution is dropped on a slide glass coated with 0.1% gelatin and 0.01% chrome alum and air-dried. The slide glass is immersed in 90% methanol, 3.7 formaldehyde at room temperature for 10 minutes to immobilize the cells, and then washed with pure water.

Claims (2)

【特許請求の範囲】[Claims] 【請求項1】 パラコッカス属に属する細菌の16Sr
RNAの可変領域に相補的な配列をもつデオキシリボヌ
クレオチドまたはリボヌクレオチドにおいて、塩基配列
5’AACCCTCTGTCACCACCAT3’を有
することを特徴とするオリゴヌクレオチドプローブ。
1. 16Sr of a bacterium belonging to the genus Paracoccus
An oligonucleotide probe having a base sequence 5′AACCCTCTGTCACCACCCAT3 ′ in a deoxyribonucleotide or ribonucleotide having a sequence complementary to the variable region of RNA.
【請求項2】 パラコッカス属に属する細菌の16Sr
RNAの可変領域に相補的な配列をもつデオキシリボヌ
クレオチドまたはリボヌクレオチドに、蛍光色素を付加
することにより得られたプローブを用いて、パラコッカ
ス属に属する細菌を特異的に検出することを特徴とする
オリゴヌクレオチドプローブを用いた細菌の検出方法。
2. 16Sr of a bacterium belonging to the genus Paracoccus
An oligo characterized by specifically detecting a bacterium belonging to the genus Paracoccus using a probe obtained by adding a fluorescent dye to a deoxyribonucleotide or ribonucleotide having a sequence complementary to the variable region of RNA. A method for detecting a bacterium using a nucleotide probe.
JP26574891A 1991-10-15 1991-10-15 Oligonucleotide probes and methods for detecting bacteria using them Expired - Lifetime JP3052487B2 (en)

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000066785A3 (en) * 1999-05-03 2001-04-05 Gen Probe Inc Polynucleotide probes for detection and quantitation of bacteria in the family enterobacteriaceae
US6821770B1 (en) 1999-05-03 2004-11-23 Gen-Probe Incorporated Polynucleotide matrix-based method of identifying microorganisms

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000066785A3 (en) * 1999-05-03 2001-04-05 Gen Probe Inc Polynucleotide probes for detection and quantitation of bacteria in the family enterobacteriaceae
US6326486B1 (en) 1999-05-03 2001-12-04 Gen-Probe Incorporated Polynucleotide probes for detection and quantitation of bacteria in the family enterobacteriaceae
US6821770B1 (en) 1999-05-03 2004-11-23 Gen-Probe Incorporated Polynucleotide matrix-based method of identifying microorganisms
US7449328B2 (en) 1999-05-03 2008-11-11 Gen-Probe Incorporated Probe matrix-based device for identifying microorganisms

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