公开(公告)号：US08501408B2

公开(公告)日：2013-08-06

申请号：US11321984

申请日：2005-12-29

申请人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6895 ,  C12Q1/689

摘要： Methods and compositions useful in the detection and identification of species of Candida are disclosed. The compositions are combinations of oligonucleotides, where the forward primers of the primer pairs have identical sequences, while each reverse primer of the primer pairs has a unique sequence relative to all of the other reverse primers; or the reverse primers of the primer pairs have identical sequences, while each forward primer of the primer pairs has a unique sequence relative to all of the other forward primers. The oligonucleotides also include probes capable of detecting these amplicons, and sequencing primers for determining, in primer extension reactions, the nucleotide sequences contained within the amplicons. The detection of an amplicon indicates that the sample contains at least one isolate of Candida albicans, Candida glabrata, Candida parapsilosis, or Candida tropicalis, and the nucleotide sequence data is used to determine which of these four Candida species is present.

摘要翻译： 公开了用于检测和鉴定假丝酵母菌种的方法和组合物。 组合物是寡核苷酸的组合，其中引物对的正向引物具有相同的序列，而引物对的每个反向引物相对于所有其它反向引物具有唯一的序列; 或引物对的反向引物具有相同的序列，而引物对的每个正向引物相对于所有其它正向引物具有唯一的序列。 寡核苷酸还包括能够检测这些扩增子的探针和测序引物，用于在引物延伸反应中测定扩增子中包含的核苷酸序列。 扩增子的检测表明该样品含有至少一种白色念珠菌，光滑假丝酵母（Candida glabrata），假丝酵母​​（Candida parapsilosis）或热带假丝酵母（Candida tropicalis））的分离物，并且使用核苷酸序列数据来确定这四种假丝酵母属中存在哪一种。

公开(公告)号：US07745595B2

公开(公告)日：2010-06-29

申请号：US11502694

申请日：2006-08-10

申请人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

IPC分类号： C07H21/04 ,  C12Q1/68

CPC分类号： C12Q1/689

摘要： Disclosed are oligonucleotides useful in methods for determining whether a sample contains Atopobium vaginae or has an increased likelihood of containing Atopobium vaginae, an organism which is seen in conjunction with bacterial vaginosis or is a causative agent of bacterial vaginosis. These oligonucleotides, which have nucleotide sequences derived from a segment of the genome of Atopobium vaginae, are useful as forward and reverse primers for a polymerase chain reaction using nucleic acids from a biological sample as a template, and as probes for detecting any resultant amplicon. Detection of an amplicon indicates the sample contains Atopobium vaginae or has an increased likelihood of containing Atopobium vaginae.

摘要翻译： 公开了用于确定样品是否含有阴道弧菌的方法中的寡核苷酸或具有增加的可能性，其含有与细菌性阴道炎联合观察的生物体或阴道细菌性阴道炎的致病因子的阴道角膜的可能性增加。 这些寡核苷酸具有源自阴道角膜的基因组的片段的核苷酸序列，可用作使用来自生物样品的核酸作为模板的聚合酶链反应的正向和反向引物，以及用于检测任何所得扩增子的探针。 扩增子的检测表明样品含有阴道角膜，或具有增加阴道角化的可能性。

公开(公告)号：US09145593B2

公开(公告)日：2015-09-29

申请号：US13461122

申请日：2012-09-17

申请人： Jason Trama ,  Martin E Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E Adelson ,  Eli Mordechai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6895 ,  C12Q1/689 ,  C12Q2561/113 ,  C12Q2565/301 ,  C12Q2600/156

摘要： Methods for using oligonucleotides in the detection of Aspergillus fumigatus are disclosed. The oligonucleotides of the invention have nucleotide sequences derived from the gene encoding the cytochrome P450 14 alpha-sterol demethylase (the cyp51A protein) of Aspergillus fumigatus. The oligonucleotides include primers capable of producing amplicons specific to cyp51A in polymerase chain reactions using nucleic acids isolated from Aspergillus fumigatus as templates. The oligonucleotides also include probes capable of detecting these cyp51A-specific amplicons. The oligonucleotides of the invention also include primers for nucleotide sequencing reactions to determine whether an isolate of Aspergillus fumigatus is more tolerant than wild-type Aspergillus fumigatus to a triazole.

摘要翻译： 公开了在检测烟曲霉中使用寡核苷酸的方法。 本发明的寡核苷酸具有衍生自编码烟曲霉的细胞色素P45014α-固醇脱甲基酶（cyp51A蛋白）的基因的核苷酸序列。 寡核苷酸包括能够使用从烟曲霉分离的核酸作为模板在聚合酶链反应中产生cyp51A特异性扩增子的引物。 寡核苷酸还包括能够检测这些cyp51A特异性扩增子的探针。 本发明的寡核苷酸还包括用于核苷酸测序反应的引物，以确定烟曲霉分离物是否比野生型烟曲霉对三唑的耐受性更高。

公开(公告)号：US20080102449A1

公开(公告)日：2008-05-01

申请号：US11321984

申请日：2005-12-29

申请人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6895 ,  C12Q1/689

摘要： Methods and compositions useful in the detection and identification of species of Candida are disclosed. These species include Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis, each of which is a causative agent for vaginal candidiasis. The compositions of the invention are combinations of oligonucleotides. These oligonucleotides include pairs of forward and reverse primers for polymerase chain reactions, wherein each primer pair is capable of priming the synthesis of an amplicon specific to one of Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis, but preferably is not capable of priming the synthesis of an amplicon specific to any of the other three species. In preferred embodiments, the forward primers of the primer pairs have identical sequences, while each reverse primer of the primer pairs has a unique sequence relative to all of the other reverse primers; or the reverse primers of the primer pairs have identical sequences, while each forward primer of the primer pairs has a unique sequence relative to all of the other forward primers. These unique primer sequences account for the species specificity of the resultant amplicons. The oligonucleotides also include probes capable of detecting these amplicons, and sequencing primers for determining, in primer extension reactions, the nucleotide sequences contained within the amplicons. In preferred methods of the invention, a biological sample is tested for the presence of at least one isolate of Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis by isolating nucleic acid from the sample, attempting a polymerase chain reaction in a mixture containing this nucleic acid and a plurality of these primer pairs, ascertaining whether any amplicon is produced in the mixture using an oligonucleotide probe, and determining the sequence of any resultant amplicon using the sequencing primers. The detection of an amplicon indicates that the sample contains at least one isolate of Candida albicans, Candida glabrata, Candida parapsilosis, or Candida tropicalis, and the nucleotide sequence data is used to determine which of these four Candida species is present.

公开(公告)号：US08932832B2

公开(公告)日：2015-01-13

申请号：US13199380

申请日：2011-08-26

申请人： Martin E. Adelson ,  Melanie Feola ,  Jason Trama ,  Eli Mordechai

发明人： Martin E. Adelson ,  Melanie Feola ,  Jason Trama ,  Eli Mordechai

IPC分类号： C07H21/04 ,  C12Q1/70

CPC分类号： C12Q1/705

摘要： Methods are described herein for detecting and identifying distinct species of nucleic acids, in a single container, for example, from a certain genus of infectious agents or otherwise causative agents comprising, for example, providing a forward PCR primer common to a homologous gene region between the distinct species, and providing a reverse PCR primer common to a homologous gene region between the distinct species, to thereby define a PCR target region amongst the species, and providing a first oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a first species, providing a second oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a second species, wherein the first and second oligonucleotide probes are each detectably labeled with distinctly different detectable labels, conducting a PCR reaction in the container by means of the primers to amplify the target region amongst the species, and detecting the distinct labels, thereby identifying distinct species of nucleic acids corresponding to distinct species of infectious agents. Methods are preferred, for example, wherein the infectious agent is a member of the Herpesviridae family.

摘要翻译： 在本文中描述了用于在单个容器中，例如来自某一感染因子或其他致病因子的单个容器中检测和鉴定不同种类的核酸的方法，所述诱导剂包括例如提供在同源基因区域之间共同的正向PCR引物 并且提供与不同物种之间的同源基因区域共有的反向PCR引物，从而在物种间限定PCR靶区域，并提供对靶区域内的核酸序列特异的第一寡核苷酸探针， 提供对目标区域内具有特征的第二种类的核酸序列特异性的第二寡核苷酸探针，其中第一和第二寡核苷酸探针各自可检测地用明显不同的可检测标记物标记，进行PCR反应 在容器中通过引物扩增目标区域amo 并检测不同的标签，从而识别与不同种类的感染因子相对应的不同种类的核酸。 方法是优选的，例如，其中感染剂是疱疹病毒科家族的成员。

公开(公告)号：US20070269810A1

公开(公告)日：2007-11-22

申请号：US11436506

申请日：2006-05-18

申请人： Jason Trama ,  Eli Mordechai ,  Martin E. Adelson

发明人： Jason Trama ,  Eli Mordechai ,  Martin E. Adelson

IPC分类号： C12Q1/68 ,  C07H21/04

CPC分类号： C12Q1/689

摘要： Disclosed are methods and compositions for conducting assays of samples utilizing polymerase chain reactions (“PCRs”) in the detection of serotypes of Chlamydia trachomatis capable of causing lymphogranuloma venereum (“LGV”). These serotypes are in the L group of Chlamydia trachomatis, and include the L I, L II, and L III serotypes. These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L III serotypes. The genome of each of these three serotypes contains the nucleotide sequence of SEQ ID NO:1 and the nucleotide sequence of SEQ ID NO:2, wherein the nucleotide at the 3′ end of SEQ ID NO:1 and the nucleotide at the 5′ end of SEQ ID NO:2 are contiguous, and wherein the deletion point of the cytotoxin gene locus is located between these two nucleotides. Each of these assays employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during the PCR. Synthesis during the PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis. The amplicon can be detected during real-time PCR using a labeled oligonucleotide as a probe, or after end-point PCR by gel electrophoresis.

摘要翻译： 公开了用于在检测能引起淋巴肉芽肿（“LGV”）的沙眼衣原体血清型中使用聚合酶链反应（“PCR”）进行测定的方法和组合物。 这些血清型是L组沙眼衣原体，包括L I，L II和L III血清型。 这些测定利用在L I，L II和L III血清型特异性的细胞毒素基因位点中发生的缺失。 这三种血清型中的每一种的基因组含有SEQ ID NO：1的核苷酸序列和SEQ ID NO：2的核苷酸序列，其中SEQ ID NO：1的3'末端的核苷酸和5' SEQ ID NO：2的末端是连续的，并且其中细胞毒素基因位点的缺失点位于这两个核苷酸之间。 这些测定中的每一个采用具有位于缺失点的一侧侧翼的核苷酸序列的第一引物和具有位于缺失点另一侧侧翼的核苷酸序列的第二引物，其中第一引物和第二引物能够分别与 PCR期间沙眼衣原体基因组的正链和负链。 在含有该缺失点的序列特异性扩增子的PCR期间的合成表明样品含有对造成衣原体沙眼衣原体的导致LGV的血清型特异的核酸。 使用标记的寡核苷酸作为探针，或通过凝胶电泳进行终点PCR后，可以在实时PCR中检测扩增子。

公开(公告)号：US20130309683A1

公开(公告)日：2013-11-21

申请号：US13935599

申请日：2013-07-05

申请人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6895 ,  C12Q1/689

摘要： Methods and compositions useful in the detection and identifcation of species of Candida are disclosed. The compositions are combinations of oligonucleotides, where the forward primers of the primer pairs have identical sequences, while each reverse primer of the primer pairs has a unique sequence relative to all of the other reverse primers; or the reverse primers of the primer pairs have identical sequences, while each forward primer of the primer pairs has a unique sequence relative to all of the other forward primers. The oligonucleotides also include probes capable of detecting these amplicons, and sequencing primers for determining, in primer extension reactions, the nucleotide sequences contained within the amplicons. The detection of an amplicon indicated that the sample contains at least one isolate of Candida ablicans, Candida glabrata, Candida parapsilosis, or Candida tropicalis, and the nucleotide sequence data is used to determine which of these four Candida species is present.

摘要翻译： 公开了用于检测和鉴定假丝酵母属物种的方法和组合物。 组合物是寡核苷酸的组合，其中引物对的正向引物具有相同的序列，而引物对的每个反向引物相对于所有其它反向引物具有唯一的序列; 或引物对的反向引物具有相同的序列，而引物对的每个正向引物相对于所有其它正向引物具有唯一的序列。 寡核苷酸还包括能够检测这些扩增子的探针和测序引物，用于在引物延伸反应中测定扩增子中包含的核苷酸序列。 扩增子的检测表明样品含有至少一种假丝酵母，光滑念珠菌，热带假丝酵母或热带假丝酵母的分离物，核苷酸序列数据用于确定这四种假丝酵母属中存在哪一种。

公开(公告)号：US08394936B2

公开(公告)日：2013-03-12

申请号：US11436506

申请日：2006-05-18

申请人： Jason Trama ,  Eli Mordechai ,  Martin E. Adelson

发明人： Jason Trama ,  Eli Mordechai ,  Martin E. Adelson

IPC分类号： C07H21/04

CPC分类号： C12Q1/689

摘要： Disclosed are methods and compositions for conducting assays of samples utilizing polymerase chain reactions (“PCRs”) in the detection of serotypes of Chlamydia trachomatis capable of causing lymphogranuloma venereum (“LGV”). These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L serotypes. Each of these assays employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during the PCR. Synthesis during the PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis.

摘要翻译： 公开了用于在检测能引起淋巴肉芽肿（LGV）的沙眼衣原体的血清型中使用聚合酶链反应（PCR）进行样品测定的方法和组合物。 这些测定利用在L I，L II和L血清型特异性的细胞毒素基因座中发生的缺失。 这些测定中的每一个采用具有位于缺失点的一侧侧翼的核苷酸序列的第一引物和具有位于缺失点另一侧侧翼的核苷酸序列的第二引物，其中第一引物和第二引物能够分别与 PCR期间沙眼衣原体基因组的正链和负链。 在含有该缺失点的序列特异性扩增子的PCR期间的合成表明样品含有对造成衣原体沙眼衣原体的导致LGV的血清型特异的核酸。

公开(公告)号：US08030032B2

公开(公告)日：2011-10-04

申请号：US11246976

申请日：2005-10-07

申请人： Martin E. Adelson ,  Melanie Feola ,  Jason Trama ,  Eli Mordechai

发明人： Martin E. Adelson ,  Melanie Feola ,  Jason Trama ,  Eli Mordechai

IPC分类号： C12P19/34

CPC分类号： C12Q1/705

摘要： Methods are described herein for detecting and identifying distinct species of nucleic acids, in a single container, for example, from a certain genus of infectious agents or otherwise causative agents comprising, for example, providing a forward PCR primer common to a homologous gene region between the distinct species, and providing a reverse PCR primer common to a homologous gene region between the distinct species, to thereby define a PCR target region amongst the species, and providing a first oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a first species, providing a second oligonucleotide probe specific to a nucleic acid sequence within the target region that is characteristic of a second species, wherein the first and second oligonucleotide probes are each detectably labeled with distinctly different detectable labels, conducting a PCR reaction in the container by means of the primers to amplify the target region amongst the species, and detecting the distinct labels, thereby identifying distinct species of nucleic acids corresponding to distinct species of infectious agents. Methods are preferred, for example, wherein the infectious agent is a member of the Herpesviridae family.

摘要翻译： 在本文中描述了用于在单个容器中，例如来自某一感染因子或其他致病因子的单个容器中检测和鉴定不同种类的核酸的方法，所述诱导剂包括例如提供在同源基因区域之间共同的正向PCR引物 并且提供与不同物种之间的同源基因区域共有的反向PCR引物，从而在物种间限定PCR靶区域，并提供对靶区域内的核酸序列特异的第一寡核苷酸探针， 提供对目标区域内具有特征的第二种类的核酸序列特异性的第二寡核苷酸探针，其中第一和第二寡核苷酸探针各自可检测地用明显不同的可检测标记物标记，进行PCR反应 在容器中通过引物扩增目标区域amo 并检测不同的标签，从而识别与不同种类的感染因子相对应的不同种类的核酸。 方法是优选的，例如，其中感染剂是疱疹病毒科家族的成员。

公开(公告)号：US09267179B2

公开(公告)日：2016-02-23

申请号：US13935599

申请日：2013-07-05

申请人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

发明人： Jason Trama ,  Martin E. Adelson ,  Eli Mordechai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6895 ,  C12Q1/689

摘要： Methods and compositions useful in the detection and identification of species of Candida are disclosed. The compositions are combinations of oligonucleotides, where the forward primers of the primer pairs have identical sequences, while each reverse primer of the primer pairs has a unique sequence relative to all of the other reverse primers; or the reverse primers of the primer pairs have identical sequences, while each forward primer of the primer pairs has a unique sequence relative to all of the other forward primers. The oligonucleotides also include probes capable of detecting these amplicons, and sequencing primers for determining, in primer extension reactions, the nucleotide sequences contained within the amplicons. The detection of an amplicon indicated that the sample contains at least one isolate of Candida ablicans, Candida glabrata, Candida parapsilosis, or Candida tropicalis, and the nucleotide sequence data is used to determine which of these four Candida species is present.

摘要翻译： 公开了用于检测和鉴定假丝酵母菌种的方法和组合物。 组合物是寡核苷酸的组合，其中引物对的正向引物具有相同的序列，而引物对的每个反向引物相对于所有其它反向引物具有唯一的序列; 或引物对的反向引物具有相同的序列，而引物对的每个正向引物相对于所有其它正向引物具有唯一的序列。 寡核苷酸还包括能够检测这些扩增子的探针和测序引物，用于在引物延伸反应中测定扩增子中包含的核苷酸序列。 扩增子的检测表明样品含有至少一种假丝酵母，光滑念珠菌，热带假丝酵母或热带假丝酵母的分离物，核苷酸序列数据用于确定这四种假丝酵母属中存在哪一种。