Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent for environmental testing thereby

• US 20030225529A1
• Filed: 12/18/2002
• Published: 12/04/2003
• Est. Priority Date: 06/26/2001
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Sampath, Rangarajan, McNeil, John, Ecker, David J., Crooke, Stanley T., Hofstadler, Steven, Griffey, Richard
• Application Number:
  US10/323,210
• Publication Number:
  US 20030225529A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/10 Nucleic acid folding
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 99/00 Subject matter not provided for in other groups of this subclass
• CPC Class Codes: G16H 50/80 for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

Claims

1. A method of identifying an unknown bioagent in an environmental sample using a database of molecular masses of known bioagents comprising:

contacting nucleic acid from said bioagent in said environmental sample with at least one pair of oligonucleotide primers that hybridize to sequences of said nucleic acid, wherein said sequences flank a variable nucleic acid sequence of said bioagent in said environmental sample;

producing an amplification product of said variable nucleic acid sequence;

determining a first molecular mass of said amplification product; and

comparing said first molecular mass to the molecular masses of known bioagents, thereby identifying the unknown bioagent in said environmental sample.

2. The method of claim 1 wherein said sequences to which said at least one pair of oligonucleotide primers hybridize are highly conserved.

3. The method of claim 1 wherein said sequences to which said at least one pair of oligonucleotide primers hybridize are highly conserved across at least two species.

4. The method of claim 1 further comprising the step of isolating a nucleic acid from said environmental sample prior to contacting said nucleic acid with said at least one pair of oligonucleotide primers, wherein the comparing step further comprises comparing a base-pair count resulting from a translation of the corresponding molecular mass, and wherein a master database of molecular masses of known bioagents further includes a translation of said molecular masses of known bioagents to corresponding base-pair counts of each known bioagent resulting from a specific primer pair set and comparing the base-pair count of said unknown bioagent against the obtained base-pair count of known bioagents for the selected primer pair set for determining the identity of said unknown bioagent in said environmental sample.

5. The method of claim 4 further comprising the step of reconciling the database of molecular masses of known bioagents with the master database of molecular masses of known bioagents.

6. The method of claim 1 wherein said bioagent is a bacterium, parasite, fungi, virus, cell or spore.

7. The method of claim 1 wherein said environmental sample is a water sample, air sample, or land sample.

8. The method of claim 7 wherein said water sample is obtained from a lake, river, ocean, stream, water treatment system, rainwater, groundwater, water table, reservoir, well, or bottled water.

9. The method of claim 7 wherein said air sample is obtained from a ventilation system, airplane cabin, school, hospital, or mass transit location.

10. The method of claim 9 wherein said mass transit location is a subway, train station, or airport.

11. The method of claim 1 wherein said amplification product is ionized by electorospray ionization, matrix assisted laser desorption or fast atom bombardment prior to molecular mass determination.

12. The method of claim 1 wherein said molecular mass is determined by mass spectrometry.

13. The method of claim 5 wherein said master database of molecular masses of known bioagents and the database of molecular masses of known bioagents are reconciled over a network.

14. The method of claim 4 wherein the identity is determined by statistically correlating the molecular mass of the unknown bioagent with at least one molecular mass of said master database.

15. A database having cell-data positional significance comprising at least a first table of a plurality of data-containing cells, said first table organized into at least a first row and a second row, each row having columns and data-containing cells;

and wherein said data-containing cells have an alignment with at least one other row for differentiating aligned from non-aligned data-containing cells, and wherein said differentiation in alignment of said data-containing cells designates a structural feature of a polymer present in an environmental sample.

16. The database according to claim 15 wherein said alignment is a vertical alignment according to base pair homology along a linear segment within each polymer.

17. The database according to claim 15 wherein said vertical alignment further aligns cell-data according to inter-species conserved regions.

18. The database according to claim 15 wherein the structural feature is a bulge or a loop.

19. The database according to claim 15 wherein the polymer is an RNA.

20. The method of claim 15 wherein said environmental sample is a water sample, air sample, or land sample.

21. The method of claim 20 wherein said water sample is obtained from a lake, river, ocean, stream, water treatment system, rainwater, groundwater, water table, reservoir, well, or bottled water.

22. The method of claim 20 wherein said air sample is obtained from a ventilation system, airplane cabin, school, hospital, or mass transit location.

23. The method of claim 22 wherein said mass transit location is a subway, train station, or airport.

24. A service providing information related to a bioagent in an environmental sample comprising:

providing a dimensional master database for storing a molecular mass, an identity and a detail corresponding to a plurality of known bioagents and, said master database storing the molecular mass, the identity and the detail for a plurality of known bioagents;

interrogating the master database with an identification request of an unknown bioagent in said environmental sample to generate a response; and

delivering said response from the master database to a requester.

25. The service according to claim 24 wherein the molecular mass is of a selected portion of the known bioagent, the identity comprises at least a geographic origin and a name for the known bioagent, and the detail comprises at least a treatment.

26. The service according to claim 24 wherein the request comprises a symptomatology and the identification comprises a recommended pair of primers for hybridizing to sequences of nucleic acid flanking a variable nucleic acid sequence of the unknown bioagent, and said pair of primers are hybridized to the sequences of nucleic acid flanking a variable nucleic acid sequence of the unknown bioagent.

27. The service according to claim 26 wherein the nucleic acid sequence of the unknown bioagent between said pair of primers defines the selected portion of both the known bioagents and the unknown bioagent.

28. The service according to claim 27 wherein the response is delivered through a network.

29. The service according to claim 27 wherein the request comprises a molecular mass of the unknown bioagent for the selected portion and where the response generated thereto comprises a set of molecular masses for analogous selected portions of know bioagents, and said set comprising at least one molecular mass from the master database.

30. The service according to claim 28 wherein the network is a local area network.

31. The service according to claim 28 wherein the network is a wide area network.

32. The service according to claim 29 wherein the network is the internet.

33. A method of determining a geographical origin of a selected bioagent in an environmental sample using a database of molecular masses of known bioagents comprising:

contacting nucleic acid from said selected bioagent in said environmental sample with at least one pair of oligonucleotide primers which hybridize to sequences of said nucleic acid, wherein said sequences flank a variable nucleic acid sequence of the bioagent in said environmental sample;

producing an amplification product of said variable nucleic acid sequence;

determining a first molecular mass of said amplification product; and

comparing said first molecular mass to the molecular masses of known bioagents for determining a geographic origin of said selected bioagent, said comparison determining an identity and a geographic origin of said selected bioagent in said environmental sample.

34. The method of claim 33 wherein said sequences to which said at least one pair of oligonucleotide primers hybridize are highly conserved.

35. The method of claim 33 wherein said sequences to which said at least one pair of oligonucleotide primers hybridize are highly conserved across species.

36. The method of claim 33 further comprising the step of isolating a nucleic acid from said selected bioagent prior to contacting said nucleic acid with said at least one pair of oligonucleotide primers, wherein the comparing step further comprises interrogating a master database of molecular masses of known bioagents for obtaining molecular masses of known bioagents and comparing the molecular mass of said selected bioagent against the obtained molecular masses of known bioagents thereby determining an origin of said selected bioagent.

37. The method of claim 36 further comprising the step of reconciling the database of molecular masses of known bioagents with the master database of molecular masses of known bioagents.

38. The method of claim 33 wherein said bioagent is a bacterium, parasite, fungi, virus, ell or spore.

39. The method of claim 33 wherein said environmental sample is a water sample, air sample, or land sample.

40. The method of claim 39 wherein said water sample is obtained from a lake, river, ocean, stream, water treatment system, rainwater, groundwater, water table, reservoir, well, or bottled water.

41. The method of claim 39 wherein said air sample is obtained from a ventilation system, airplane cabin, school, hospital, or mass transit location.

42. The method of claim 41 wherein said mass transit location is a subway, train station, or airport.

43. The method of claim 33 wherein said amplification product is ionized by electorospray ionization, matrix assisted laser desorption or fast atom bombardment prior to molecular mass determination.

44. The method of claim 33 wherein said molecular mass is determined by mass spectrometry.

45. The method of claim 36 wherein said master database of molecular masses of known bioagents and the database of molecular masses of known bioagents are reconciled over a network.

46. The method of claim 36 wherein the origin comprises a statistical group of matching molecular masses and the geographic origin corresponding thereto.