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1. 发明申请

US20100112588A1 METHODS FOR SANGER SEQUENCING USING PARTICLE ASSOCIATED CLONAL AMPLICONS AND HIGHLY PARALLEL ELECTROPHORETIC SIZE-BASED SEPARATION 审中-公开
标题翻译：使用颗粒相关的克隆AMPLICONS和高度并行电泳大小分离的方法
公开(公告)号：US20100112588A1
公开(公告)日：2010-05-06
申请号：US12611528
申请日：2009-11-03
申请人： Javier Farinas , Andrea Chow , John Wallace Parce
发明人： Javier Farinas , Andrea Chow , John Wallace Parce
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q2563/149 , C12Q2535/122 , C12Q2535/101
摘要： Methods for highly parallel Sanger sequencing are discussed. In particular, provided herein are methods using particles to clonally amplify templates and to introduce the amplified nucleic acids into many parallel channels with a single template per channel. Once in the channels, the nucleic acids are separated by size using electrophoresis to produce long read length sequencing information. Methods involving optical detection of the size-separated nucleic acids and analysis of the resulting electropherograms to yield the sequences are disclosed.
摘要翻译：讨论了高度并行Sanger测序的方法。特别地，本文提供了使用颗粒克隆放大模板并将扩增的核酸引入具有每个通道的单个模板的多个并行通道的方法。一旦在通道中，核酸通过电泳被大小分离以产生长的读取长度测序信息。公开了涉及尺寸分离的核酸的光学检测和所得的电泳图的分析以产生序列的方法。

2. 发明申请

US20120220486A1 METHODS AND APPARATUS FOR BINDING ASSAYS 审中-公开
标题翻译：用于绑定测试的方法和装置
公开(公告)号：US20120220486A1
公开(公告)日：2012-08-30
申请号：US13505455
申请日：2010-10-31
申请人： Javier Farinas , Andrea Chow , John Wallace Parce
发明人： Javier Farinas , Andrea Chow , John Wallace Parce
IPC分类号： G01N33/53 , C40B30/04
CPC分类号： C12Q1/6825 , C12Q1/6834 , G01N33/54346 , C12Q2565/107 , C12Q2523/303 , C12Q2565/607
摘要： The present teachings relate to methods, systems, and apparatus for low cost label-free assay detection. The present teachings, in a variety of embodiments, employ opposing forces to detect signals which depend on the number of charges on and/or the size of a particle. The particle, which can be subjected to opposing forces, can have specific capture probes at its surface. As analytes of interest are captured by the particle, the number of charges on the particle surface and/or the size of the particle is changed. A particle parameter or kinematic property such as the position, velocity, acceleration or force of/on the particle can be measured, and results obtained relating, for example, to the present, absence, quantity, and such, of one or more analytes of interest. Various embodiments are described for efficient, high throughput assays of samples potentially including one or more analytes of interest, such as bioanalytes. As well, various embodiments are described wherein binding assays can be carried out without the need or use of extrinsic labels. A number of embodiments provide, for example, methods, systems, and apparatus for detecting analytes (such as nucleic acids, proteins, cells and other entities, particulates, and the like) in one or more samples. Also described are: detection of a single copy of a target biomolecule, such as DNA, captured onto a trapped (e.g., tethered) bead; protocols for fabricating encoded bead arrays for multiplex assays; and methods, systems and apparatus for efficient and specific capture of pathogen biomolecular markers onto bead-bound capture probes, as well as detection and measurement of such capture events.
摘要翻译：本教导涉及用于低成本无标签测定检测的方法，系统和装置。在各种实施例中，本教导使用相反的力来检测取决于粒子的数量和/或粒子尺寸的信号。可以受到相反力的颗粒在其表面可以具有特定的捕获探针。当感兴趣的分析物被颗粒俘获时，粒子表面上的电荷数和/或粒子的大小被改变。可以测量颗粒参数或运动学特性，例如颗粒上的/位置，速度，加速度或力，或者与例如当前，不存在，数量等相关的一种或多种分析物利益。描述了针对可能包括一种或多种感兴趣的分析物（例如生物分析物）的样品的有效，高通量测定的各种实施方案。同样，描述了各种实施方案，其中可以在不需要或使用外在标记的情况下进行结合测定。许多实施例提供了例如在一个或多个样品中检测分析物（例如核酸，蛋白质，细胞和其他实体，颗粒等）的方法，系统和装置。还描述了：捕获到捕获的（例如，系留的）珠粒上的目标生物分子（例如DNA）的单拷贝的检测; 用于制备用于多重测定的编码珠阵列的方案; 以及用于将有效和特异性捕获病原体生物分子标记物转移到珠束捕获探针上的方法，系统和装置，以及这些捕获事件的检测和测量。

3. 发明申请

US20110059864A1 Sequence Determination By Use Of Opposing Forces 审中-公开
标题翻译：使用反对力的序列确定
公开(公告)号：US20110059864A1
公开(公告)日：2011-03-10
申请号：US12877103
申请日：2010-09-07
申请人： Javier Farinas , Andrea Chow , John Wallace Parce
发明人： Javier Farinas , Andrea Chow , John Wallace Parce
IPC分类号： C40B30/10 , C12M1/34
CPC分类号： C12Q1/6872 , C12Q1/6874
摘要： The present teachings relate to systems, methods, and the like, for analyzing biological polymers, by use of opposing forces. Among other things, the present teachings can be used to determine sequence information, such as in genetic sequencing and genotyping applications. Various embodiments are described for efficient, high throughput sequencing of nucleic-acid molecules, such as DNA. Various embodiments are described wherein nucleic-acid sequence information is determined without the need or use of extrinsic labels. As well various embodiments of methods, systems, and the like, are described, which can provide long and accurate read lengths for low-cost nucleic acid sequencing.
摘要翻译：本教导涉及通过使用相反的力分析生物聚合物的系统，方法等。除其他之外，本教导可用于确定序列信息，例如在遗传测序和基因分型应用中。描述了用于核酸分子（例如DNA）的有效，高通量测序的各种实施方案。描述了其中确定核酸序列信息而不需要或使用外在标记的各种实施方案。还描述了方法，系统等的各种实施方案，其可以为低成本核酸测序提供长且准确的读取长度。

4. 发明申请

US20060246533A1 Method and apparatus for performing peptide digestion on a microfluidic device 有权
公开(公告)号：US20060246533A1
公开(公告)日：2006-11-02
申请号：US11397307
申请日：2006-04-03
申请人： Bahram Fathollahi , Javier Farinas , Andrea Chow , Stephane Mouradian
发明人： Bahram Fathollahi , Javier Farinas , Andrea Chow , Stephane Mouradian
IPC分类号： C12Q1/37 , G01N33/543
CPC分类号： G01N33/6842
摘要： The invention provides methods and apparatuses that allow a protein sample to undergo reduction, alkylation, and digestion in a continuous flow process carried out within a microfluidic device. Methods and apparatuses in accordance with the invention can be employed as part of an automated proteomics analysis carried out in an integrated proteomics system.

5. 发明申请

US20090211908A1 Devices and methods for detecting and quantitating nucleic acids using size-separation of amplicons 审中-公开
标题翻译：使用扩增子的大小分离来检测和定量核酸的装置和方法
公开(公告)号：US20090211908A1
公开(公告)日：2009-08-27
申请号：US12321598
申请日：2009-01-22
申请人： Javier Farinas
发明人： Javier Farinas
IPC分类号： G01N27/453 , G01N27/447
CPC分类号： B01L3/5027 , B01L3/502715 , B01L3/5082 , B01L7/52 , B01L2200/0689 , B01L2200/10 , B01L2200/141 , B01L2300/0816 , B01L2400/0421 , B01L2400/0487 , G01N27/44756
摘要： Devices and methods are described for detecting and quantifying nucleic acids using a sealed system that minimizes contamination. In particular, provided herein are devices for and methods using nucleic acid amplification that permit multiple sampling of an amplification reaction mixture and quantitation and identification of amplicons during the course of an amplification reaction. Methods involving the transfer of samples from an amplification reaction mixture into a separation network, separation of nucleic acids based on size, and identification and quantitation of nucleic acids are disclosed.
摘要翻译：描述了使用最小化污染的密封系统来检测和定量核酸的装置和方法。特别地，本文提供了使用核酸扩增的装置和方法，其允许扩增反应混合物的多次取样以及扩增反应过程中扩增子的定量和鉴定。涉及将样品从扩增反应混合物转移到分离网络中的方法，基于大小分离核酸以及核酸的鉴定和定量。

6. 发明申请

US20050221385A1 Pressure based mobility shift assays 审中-公开
标题翻译：基于压力的移动性变化测定
公开(公告)号：US20050221385A1
公开(公告)日：2005-10-06
申请号：US11051445
申请日：2005-02-03
申请人： Theo Nikiforov , Jill Baker , Sansan Lin , J. Parce , Jude Dunne , Javier Farinas , Esther Huang , Mingqing Li , Thi Trinh
发明人： Theo Nikiforov , Jill Baker , Sansan Lin , J. Parce , Jude Dunne , Javier Farinas , Esther Huang , Mingqing Li , Thi Trinh
IPC分类号： G01N30/88 , G01N33/53
CPC分类号： G01N30/88
摘要： Methods for chromatographically separating materials, including the separation of materials in kinase or phosphatase assays, in microfluidic devices under positive or negative fluid pressure. Devices and integrated systems for performing chromatographic separations are also provided.
摘要翻译：用于在正或负流体压力下在微流体装置中色谱分离材料的方法，包括在激酶或磷酸酶测定中分离材料。还提供了用于执行色谱分离的设备和集成系统。

7. 发明授权

US07045305B1 Methods and reagents for targeting organic compounds to selected cellular locations 有权
标题翻译：将有机化合物靶向选定的细胞位置的方法和试剂
公开(公告)号：US07045305B1
公开(公告)日：2006-05-16
申请号：US09403882
申请日：1999-04-08
申请人： Javier Farinas
发明人： Javier Farinas
IPC分类号： G01N33/53 , C12N15/13 , C12P21/08 , C07H21/04
CPC分类号： G01N33/84 , C07K16/00 , C07K2317/81 , C07K2319/05 , G01N33/582 , G01N33/6857
摘要： The present invention provides methods and reagents for targeting probes to selected cellular locations, through the expression of specific binding partners to that probe within the cell. In one embodiment, the probes may comprise spectroscopic probe that can be used in a method for localizing a specific binding partner within a cell, and for creating assays for post-translational activities. The invention allows the monitoring of the location of such intracellular specific binding partners over time and in response to stimuli, such as test chemicals. The spectroscopic probes can be used for screening a test chemical for activity. The present invention also includes cells and transgenic organisms comprising the intracellular specific binding partner, wherein the specific binding partner can bind with the spectroscopic probe/ligand conjugate.
摘要翻译：本发明提供通过在细胞内表达特异性结合配偶体到该探针的方法和试剂来将探针靶向选定的细胞位置。在一个实施方案中，探针可以包含可用于定位细胞内的特异性结合配偶体的方法中的光谱探针，以及用于产生翻译后活性的测定。本发明允许监测这些细胞内特异性结合配偶体随时间和响应于刺激物（例如测试化学品）的位置。光谱探针可用于筛选测试化学品的活性。本发明还包括细胞和包含细胞内特异性结合配偶体的转基因生物，其中特异性结合配偶体可以与光谱探针/配体缀合物结合。

8. 发明申请

US20060068410A1 Methods and systems for monitoring intracellular binding reactions 审中-公开
公开(公告)号：US20060068410A1
公开(公告)日：2006-03-30
申请号：US11070155
申请日：2005-03-01
申请人： H. Wada , Javier Farinas , Theo Nikiforov
发明人： H. Wada , Javier Farinas , Theo Nikiforov
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6841 , G01N21/6428 , G01N21/6445 , G01N21/6458 , G01N33/5008 , G01N33/5041 , G01N33/542 , G01N33/582 , G01N33/6872 , C12Q2561/119
摘要： Intracellular binding reactions, and particularly DNA/DNA binding protein reactions are detected in situ, using intracellular fluorescence polarization detection. The methods comprise providing a biological cell having at least a first component of a binding reaction disposed therein. The cell is contacted with a second component of the binding reaction whereby the second component is internalized within the biological cell. At least one of the first and second components has a fluorescent label. The amount of binding between the first and second components within the cell is determined by measuring a level of polarized and/or depolarized fluorescence emitted from within the biological cell.

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