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1. 发明申请

US20070059743A1 Method for the design of oligonucleotides for molecular biology techniques 有权
标题翻译：分子生物学技术寡核苷酸设计方法
公开(公告)号：US20070059743A1
公开(公告)日：2007-03-15
申请号：US11506089
申请日：2006-08-17
申请人： Alejandro Maass Sepulveda , Andres Aravena Duarte , Mauricio Gonzalez Canales , Servet Martinez Aguilera , Pilar Parada Valdecantos , Katia Ehrenfeld Stolzenbach
发明人： Alejandro Maass Sepulveda , Andres Aravena Duarte , Mauricio Gonzalez Canales , Servet Martinez Aguilera , Pilar Parada Valdecantos , Katia Ehrenfeld Stolzenbach
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G06F19/20
摘要： The present invention discloses a method that can be used to identify one DNA sequence or one specific group of DNA sequences from a complex biological sample. Diverse molecular biology methods require the use of short DNA sequences, called oligonucleotides, that are artificially synthesized from a description of their composing bases. The disclosed method allows the design of oligonucleotides useful for said molecular biology procedures, like probe design procedures, and is characterized by the construction of a database of reference sequences, the selection of a subset of sequences belonging to target organisms, the selection of candidate oligonucleotides from such sequences, the depuration of these candidate oligonucleotides according to hybridization specificity and thermodynamic stability criteria, and the sorting of such oligonucleotides according to their taxonomic specificity. In a second aspect, a method is disclosed to design oligonucleotides pairs or primers, which are required in certain molecular biology techniques, like polymerase chain reaction (PCR) techniques. This method is similar to the first aspect of the invention, but thermodynamically compatible oligonucleotides pairs or primers that hybridize to the same sequence at a distance which is within a given range are evaluated.
摘要翻译：本发明公开了一种可用于从复杂生物样品鉴定一个DNA序列或一个特定的DNA序列组的方法。不同的分子生物学方法需要使用称为寡核苷酸的短DNA序列，它们是从它们的组成基础的描述中人工合成的。所公开的方法允许设计可用于所述分子生物学过程的寡核苷酸，如探针设计程序，其特征在于构建参考序列数据库，选择属于靶生物的序列的子集，候选寡核苷酸的选择从这些序列中，根据杂交特异性和热力学稳定性标准，这些候选寡核苷酸的纯化，以及根据其分类学特异性对这些寡核苷酸的分选。在第二方面，公开了设计寡核苷酸对或引物的方法，其在某些分子生物学技术中是需要的，例如聚合酶链反应（PCR）技术。该方法类似于本发明的第一方面，但评价了在与给定范围内的距离处与相同序列杂交的热力学相容的寡核苷酸对或引物。

2. 发明申请

US20090054249A2 DNA FRAGMENTS ARRAY FROM BIOMINING MICROORGANISMS AND METHOD FOR DETECTION OF THEM 有权
标题翻译： DNA片段从生物微生物中分离出来并检测其方法
公开(公告)号：US20090054249A2
公开(公告)日：2009-02-26
申请号：US11601516
申请日：2006-11-17
申请人： Ricardo BADILLA OHLBAUM , Alejandro MAASS SEPULVEDA , Pilar PARADA VALDECANTOS , Andres ARAVENA DUARTE , Mauricio GONZALEZ CANALES , Servet MARTINEZ AGUILERA , Katia EHRENFELD STOLZENBACH , Pablo MORENO CORTES
发明人： Ricardo BADILLA OHLBAUM , Alejandro MAASS SEPULVEDA , Pilar PARADA VALDECANTOS , Andres ARAVENA DUARTE , Mauricio GONZALEZ CANALES , Servet MARTINEZ AGUILERA , Katia EHRENFELD STOLZENBACH , Pablo MORENO CORTES
IPC分类号： C40B30/04 , C40B40/06
CPC分类号： C22B3/18 , Y02P10/234
摘要： The present invention discloses an array of DNA fragments from biomining microorganisms and a method to identify readily and simultaneously said microorganisms in a sample. This method is a useful tool in biomining, in every circumstance where a global understanding of the present microbiological diversity is required, or simply to assess the presence of some microorganism with biomining relevance, either on the mineral, or in a bioleaching heap, in the biomining laboratory or in any other circumstance involving biomining microorganisms.
摘要翻译：本发明公开了一种来自生物微生物的DNA片段的阵列，以及容易地和同时鉴定样品中微生物的方法。这种方法是生物研究中有用的工具，在需要全球了解当前微生物多样性的每种情况下，或简单地评估在矿物质或生物浸出堆中具有生物相关性的一些微生物的存在，生物实验室或涉及生物微生物的任何其他情况。

3. 发明申请

US20070054300A1 Method for the identification and quantification of microorganisms useful in biomining processes 审中-公开
标题翻译：用于鉴定和定量生物工艺中有用的微生物的方法
公开(公告)号：US20070054300A1
公开(公告)日：2007-03-08
申请号：US11509870
申请日：2006-08-25
申请人： Pilar Parada Valdecantos , Katia Ehrenfeld Stolzenbach , Igor Pacheco Cruz , Alejandro Maass Sepulveda , Andres Aravena Duarte , Mauricio Gonzalez Canales , Servet Martinez Aguilera
发明人： Pilar Parada Valdecantos , Katia Ehrenfeld Stolzenbach , Igor Pacheco Cruz , Alejandro Maass Sepulveda , Andres Aravena Duarte , Mauricio Gonzalez Canales , Servet Martinez Aguilera
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： C12Q1/689 , C22B3/18 , Y02P10/234
摘要： The present invention discloses a method to identify and quantify environmental microorganisms useful in biomining processes. These microorganisms are basically 10, belonging to Bacteria: Acidiphilium sp., Leptospirillum sp., Sulfobacillus sp., Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans; and Archaea: Acidianus sp., Ferroplasma sp., Metallosphaera sp., Sulfolobus sp. and Thermoplasma sp. The method comprises performing a two-stage PCR known as nested PCR, where in the first stage, called primary PCR, 16S ribosomal DNA sequences (nucleotides 27 to 1492, with E. coli rDNA numbering) are amplified using universal primers for the Bacteria and Archaea kingdoms. In the second stage, these primary amplicons are used as template in qPCR reactions, called secondary PCR, in which internal universal primers for either Bacteria or Archaea kingdoms, as it corresponds, and specific primers designed in our laboratories for different taxons to be determined are used. The first PCR linearly multiplies 16S sequences from bacteria or archaea, thus increasing template abundance for the secondary PCR keeping the original microorganism proportion of the sample. This gives a higher sensitivity to the process when compared to the case of directly using taxon-specific primers on the sample. With qPCR results and other data obtained from the analyzed sample, the microorganism concentration of each analyzed taxon present in the sample is calculated using a mathematical formula.
摘要翻译：本发明公开了一种鉴定和定量生物工艺中有用的环境微生物的方法。这些微生物基本上为10，属于细菌：嗜酸菌属，钩端螺旋体属，硫磺杆菌属，氧化亚铁硫杆菌和硫氧化硫酸硫杆菌; 和古菌：Acidianus sp。，Ferroplasma sp。，Metallosphaera sp。，Sulfolobus sp。和热血浆该方法包括进行称为嵌套PCR的两阶段PCR，其中在第一阶段称为初级PCR，使用通用引物扩增16S核糖体DNA序列（具有大肠杆菌rDNA编号的核苷酸27至1492）古代王国在第二阶段，这些初级扩增子用作qPCR反应中的模板，称为二级PCR，其中细菌或古细菌王国的内部通用引物对应，以及在我们的实验室中设计的用于确定不同分类的特异性引物是用过的。第一次PCR将来自细菌或古细菌的16S序列线性相乘，从而增加二次PCR的模板丰度，保持样品的原始微生物比例。与在样品上直接使用分子标记特异性引物的情况相比，这对该过程具有更高的敏感性。使用qPCR结果和从分析样品获得的其他数据，使用数学公式计算样品中存在的每个分析的分类单元的微生物浓度。

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