Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2000-05-15
2004-09-28
Brusca, John (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C702S022000, C435S004000, C435S006120
Reexamination Certificate
active
06799119
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to the detection of biological related materials and, in particular, the detection of biological related materials that may present a health risk to a population that is or may be exposed to such materials.
BACKGROUND OF THE INVENTION
There are many types of biological related materials that pose health risks to populations (human, animal or plant) that may be exposed to such materials. Among the biological related materials that pose health risks are bacteria, viruses, and toxins (which are chemicals that are derived from biological entities). Among the more well known bacteria that present health risks to humans are
Bacillus anthracis
(anthrax),
Yersinia pestis
(plague) and
Vibrio cholerae
(cholera). Examples of viruses that pose health risks to humans are the small pox, Ebola, Marburg and Hanta viruses. Toxins that present a danger to humans include polyethers, proteins and mycotoxins.
Presently, there are a number of techniques available for detecting biological related materials (hereinafter referred to as “biological agents”). One traditional technique is to: (1) obtain a sample of the material that is suspected of containing a biological agent; (2) place the sample in an environment (such as a petrie dish with agar) in which certain biological agents, if present, can grow and multiply; and (3) after sufficient time has elapsed for any such agents to grow and replicate, visually identify (typically, with a microscope) the biological agent present in the nurturing environment.
Immuno-assay is another technique that is used to detect biological agents. In the immuno-assay technique, a sample of the material that is suspected of containing a biological agent is obtained and processed so as to place any biological agent present in the sampled material into a liquid suspension. The liquid with any biological agent suspended therein is then subjected to an immuno-assay test. In the test, an antibody that reacts with a specific biological agent (for example,
Bacillus anthracis
) is provided. If there is a biological agent present in the liquid sample and the agent is of the genus for which the antibody is present, a reaction will occur that is detectable. In one implementation, the liquid sample is applied to a glass microscope slide (also referred to as a “ticket”) that includes antibodies for at least one biological agent. If a biological agent of the genus or species that corresponds to the antibody is present in the sampled liquid, there is a reaction between the antibody and the biological agent (antigent) that results in a visible indication of the presence of the biological agent being provided.
Another technique for detecting biological agents is the polymerase chain reaction (PCR) technique, which is a DNA analysis technique. In the PCR technique, the material that is suspected of containing a biological agent is sampled and, if necessary, transferred to a liquid medium. The DNA of any biological agent that is present in the sample is then placed in an environment that, for only a particular biological agent of interest, will cause a section or vectors of its DNA to multiply or replicate. For example, if the biological agent of interest is anthrax, the environment will only promote the multiplication of a vector of anthrax DNA, if any, present in the sample. If the particular biological agent of interest is present in the sample, the increase in the number of DNA for the biological agent produced by the noted environment creates a signal that can be detected by, for example, electrophoresis or fluorescence.
Yet another method for detecting biological agents is known as the MIDI technique. In the MIDI technique, the material that is suspected of containing a biological agent is sampled and, if needed, transferred to a liquid suspension. Any biological agent present in the liquid is then transferred to a nurturing environment, such as an agar filled petrie dish, so that the agent can grow and replicate. After any biological agent present in the sample has had sufficient time to grow and replicate, the agent is harvested from the nurturing environment and the fatty acids present within the cells of the agent are subjected to a process in which the fatty acids are converted to fatty acid methyl esters. The fatty acid methyl esters are then analyzed with a gas chromatograph to produce a “fingerprint” of the fatty acid methyl esters. The “fingerprint” of the unidentified agent is then compared to the “fingerprints” for known biological agents contained in a database (which commonly has 10,000 or more “fingerprints”) to identify the biological agent in the sample. Due to the large number of “fingerprints” against which the unidentified “fingerprint” is compared, the technique identifies a number (typically, 10) of the known biological agents as having the closest “fingerprints” to the unidentified “fingerprint.”
Yet a further technique for detecting biological agents is matrix assisted laser desorption ionization (“MALDI”) mass spectrometry. As with the prior techniques, the material that is suspected of containing a biological agent is sampled and, if required, any biological agent present in the sample is transferred to a liquid suspension. The liquid containing any biological agent is then combined with an organic compound that is capable of absorbing infrared or ultraviolet light. The mixture is then dried so that any biological agent present in the sampled atmosphere is bound up in the crystalline matrix of the organic compound. The dried material is then bombarded with light from an infrared or ultraviolet laser that results in any protein associated with any biological agent present in the sample being ionized. The ionized proteins are then analyzed with a mass spectrometer to produce a mass spectrum that is compared to a data base of mass spectra of known proteins to identify the biological agent present in the sample.
SUMMARY OF THE INVENTION
The present invention provides a method for analyzing data related to the composition of an unidentified biological agent to both identify the agent and assess the reliability of the identification. In one embodiment, the method includes receiving the data related to the composition of the unidentified biological agent. Typically, the received data is type of mass spectral data (e.g., “full scan” MS, MS/MS, mix-Collision Induced Dissociation (CID) or full-CID) or chromatographic data. The received data is applied to a machine learning procedure that makes an initial identification of the unidentified biological agent. Depending upon the particular application of the method, the machine learning procedure may involve a single step or several steps. For instance, if the method is to be used to determine whether the unidentified biological agent is a bacteria, virus or toxin, it is feasible to implement the machine learning procedure in a single step. In contrast, if a detailed identification is required, such as a particular bacteria, the machine learning procedure is typically implemented in a multi-step fashion. The step or steps of the machine learning procedure are implemented using machine learning techniques, such as artificial neural networks and/or multi-variate statistical analysis. For example, in a multi-step machine learning procedure, each step utilizes a distinct artificial neural network.
Once the identification has been made, ion fragmentation analysis (e.g., MS/MS, mix-CID or full-CID) is used to assess the reliability of the identification provided by the machine learning procedure. In one embodiment, the ion fragmentation analysis is used to assess whether the initial identification of the unidentified biological agent is a false positive or a false negative. An example of a false positive would be if the unidentified biological agent is initially identified as a harmful virus and this identification is subsequently shown to be incorrect by the ion fragmentation analysis. In contrast, an example of a false negative would be if the unidentified biologic
Basile Francisco
Voorhees Kent J.
Brusca John
Colorado School of Mines
Holland & Hart LLP
Kulish, Esq. Christopher J.
Zhou Shubo
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