Sample processing

1. A sample processing apparatus, comprising:

a tubule, comprising:

a proximal end having an opening through which a sample is introducible;

a distal end; and

at least a first segment containing at least one substance capable of specific binding to a preselected component of a sample when the sample is added to the tubule, a second segment distal to the first segment and containing a wash reagent, and a third segment distal to the second segment and containing an amplification reagent, each of which segments is:

defined by the tubule;

fluidly isolated, at least in part by a fluid-tight seal formed by a bonding of opposed wall portions of the tubule to one another such that:

(a) the seal is broken by application of fluid pressure on a segment that is fluidly isolated in part by the seal; and

(b) the seal is capable of being clamped where the opposed wall portions of the tubule are bonded, without breaking the seal, to prevent the seal from being broken by application of fluid pressure on a segment that is fluidly isolated in part by the seal;

so expandable as to receive a volume of fluid expelled from another segment; and

so compressible as to contain substantially no fluid when so compressed;

a cap for closing the opening, the cap containing a chamber in fluid communication with the tubule, and the cap permitting free escape of gasses but retaining all liquid volumes and infectious agents in the tube;

a rigid frame to which the tubule's proximal and distal ends are held; and

an integral tubule tensioning mechanism or an attachment of the tubule to the frame that pulls the tubule sufficiently taut so as to facilitate compression and flattening of the tubule.

2. The apparatus of claim 1 , wherein at least a portion of the tubule is transparent.

3. The apparatus of claim 1 , further comprising at least one pressure gate in fluid communication with at least one segment.

4. The apparatus of claim 1 , further comprising at least one filter in the tubule.

5. The apparatus of claim 1 , wherein the preselected component is nucleic acid.

6. The apparatus of claim 5 , wherein the substance capable of specific binding to nucleic acid includes at least one of an antibody, nucleic acid, peptide nucleic acid, phosphothioate nucleic acid, silica coated surface, electrostatically charged surface, and enzyme.

7. The apparatus of claim 6 , wherein the substance capable of specific binding to nucleic acid has a preselected amino acid or base sequence.

8. The apparatus of claim 1 , wherein the substance comprises at least one of a receptor, a ligand, an antibody, an antigen, a nucleic acid probe, a peptide nucleic acid probe, a phosphothioate nucleic acid probe, a bacteriophage, silica, and an electrostatic charged surface.

9. The apparatus of claim 1 , wherein the substance is capable of specific binding to a preselected component of at least one of bacteria, virus, parasite, cells, nucleic acid, and spores.

10. The apparatus of claim 9 , wherein the substance is capable of specific binding to a preselected component of at least one of Yersinia pestis, Francisella tularensis, Listeria monocytogenes, Bacillus anthracis, Escherichia coli, Salmonella enteritidis, Campylobacter pylori, Campylobacter jejuni Clostridium perfringens, Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitides, Vibrio cholerae, Mycobacterium tuberculosis , and Mycobacterium leprae.

11. The apparatus of claim 9 , wherein the substance is capable of specific binding to a preselected component of at least one of human immunodeficiency virus 1, human immunodeficiency virus 2, influenza virus, yellow fever virus, dengue virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, Epstein Barr virus, West Nile virus, hantavirus, and small pox.

12. The apparatus of claim 9 , wherein the substance is capable of specific binding to a preselected component of at least one of Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, Plasmodium malariae, Leishmania tropica, Leishmania donovani, Leishmania infantum, Leishmania major, Leishmania mexicana, Leishmania chagasi, Leishmania brasiliensis , and Leishmania amazoniensis.

13. The apparatus of claim 1 , wherein the substance capable of specific binding to a preselected component of a sample is coupled to a solid substrate.

14. The apparatus of claim 13 , wherein the substance forms a coating on the solid substrate.

15. The apparatus of claim 13 , wherein the solid substrate comprises at least one of beads, a pad, a filter, a sheet, an electrostatic surface, and a portion of a tubule wall surface.

16. The apparatus of claim 13 , wherein the substrate comprises at least one of silica beads, magnetic beads, silica magnetic beads, glass beads, nitrocellulose colloid beads, and magnetized nitrocellulose colloid beads.

17. The apparatus of claim 13 , wherein the substance comprises silica, and the substrate comprises a filter or a sheet.

18. The apparatus of claim 13 , wherein the substrate comprises a pad formed at least in part from an absorbent material comprising at least one of paper, film, filter, foam, mesh, and fiber matrix.

19. The apparatus of claim 13 , wherein the substrate is coupled to a tubule wall.

20. The apparatus of claim 1 , further comprising a solid substrate which comprises a pad formed at least in part from an absorbent material comprising at least one of paper, film, filter, foam, mesh, and fiber matrix.

21. The apparatus of claim 1 , wherein the cap comprises a sample collection device including at least one of a swab, a stick, a scoop, an inoculation loop, a forceps, a dropper, a capillary tube, and a syringe.

22. The apparatus of claim 21 , wherein the sample collection device is so disposed in or on the cap as to transfer a sample from the device to the tubule when the cap is positioned in relation to the tubule to close the open end of the tubule.

23. The apparatus of claim 1 , wherein the cap comprises a member defining the chamber, and wherein the chamber is expandable.

24. The apparatus of claim 23 , wherein a cap wall defines a vent.

25. The apparatus of claim 1 , wherein the frame comprises an interface, the interface receiving the proximal end of the tubule.

26. The apparatus of claim 25 , wherein the interface also receives the cap, thereby sealing the proximal end of the tubule.

27. The apparatus of claim 1 , further comprising at least one of a diluent, suspension reagent, lysis reagent, neutralization reagent, elution reagent, proteolytic reagent, glycosylase, nucleic acid, nuclease, ligase, alcohol, reverse transcription reagent, and germination reagent.

28. The apparatus of claim 27 , wherein the tubule comprises an elution reagent that includes at least one of Tris buffer, water, and buffer suitable for polymerase chain reaction.

29. The apparatus of claim 27 , wherein the tubule comprises a lysis reagent that includes at least one of a guanidinium salt, a chaotropic salt, a red blood cell lysis reagent, a detergent, a chelator, a spore germination reagent, sodium hydroxide, proteinase K, DNase inhibitor, RNase, RNase inhibitor, anticoagulant, coagulant, a protease, a germinant solution, and a surfactant.

30. The apparatus of claim 27 , wherein the tubule comprises a germination reagent including heart brain infusion medium and at least one of L-alanine, inosine, L-phenylalanine, L-Serine and L-proline.

31. The apparatus of claim 1 , wherein the segments form a substantially linear array.

32. The apparatus of claim 1 , wherein the segments form a contiguous array.

33. A sample processing apparatus, comprising:

a tubule, comprising:

a plurality of segments, each of which is:

defined by the tubule;

fluidly isolated, at least in part by a fluid-tight seal formed by a bonding of opposed wall portions of the tubule to one another such that:

 (a) the seal is broken by application of fluid pressure on a segment that is fluidly isolated in part by the seal; and

 (b) the seal is capable of being clamped where the opposed wall portions of the tubule are bonded, without breaking the seal, to prevent the seal from being broken by application of fluid pressure on a segment that is fluidly isolated in part by the seal;

separated from adjacent segments only by seals;

so expandable as to receive a volume of fluid expelled from another segment; and

so compressible as to contain substantially no fluid when so compressed;

wherein:

a segment contains at least one of a lysis reagent and a diluent;

a segment contains at least a nucleic acid binding reagent;

a segment contains at least a wash reagent;

a segment contains at least a nucleic acid eluting regent; and

a segment contains at least nucleic acid amplification reagents;

a cap for closing the opening, the cap containing a chamber in fluid communication with the tubule, and the cap permitting free escape of gasses but retaining all liquid volumes and infectious agents in the tube;

a rigid frame to which the tubule's proximal and distal ends are held; and

an integral tubule tensioning mechanism or an attachment of the tubule to the frame that pulls the tubule sufficiently taut so as to facilitate compression and flattening of the tubule.

34. The apparatus of claim 1 , wherein at least one of the reagents is in a dry format.

35. The apparatus of claim 1 , wherein the segments form a contiguous and substantially linear array.

36. The apparatus of claim 1 , further comprising at least a fourth segment that (a) is distal to the second segment and (b) contains at least one of an elution reagent, second wash regent, lysis reagent, reverse transcription reagent, a nucleic acid, a nuclease, and glycosylase.

37. The apparatus of claim 1 , further comprising at least a fourth segment that (a) is proximal to the first segment and (b) contains at least one of a germination reagent, suspension reagent, lysis reagent, neutralization reagent, diluent, second wash reagent, elution reagent, nucleic acid, and proteolytic reagent.

38. The apparatus of claim 1 , further comprising at least a fourth segment that (a) is distal to the third segment and (b) contains at least one of a second amplification reagent, a nuclease, a detection reagent, and a glycosylase.

39. The apparatus of claim 1 , further comprising at least a fourth segment that (a) is distal to the first segment and (b) contains at least one of a diluent, suspension reagent, nucleic acid, lysis reagent, second wash reagent, a solid substrate, and alcohol.

40. The apparatus of claim 1 , further comprising:

a fourth segment that (a) is proximal to the first segment and (b) contains at least one of a lysis reagent and a diluent; and

a fifth segment that (a) is distal to the second segment, (b) proximal to the third segment, and (c) contains an elution reagent.

41. The apparatus of claim 1 , wherein the amplification reagent in the third segment comprises at least one of a nucleic acid polymerase and nucleotide triphosphates.

42. The apparatus of claim 1 , wherein the at least one substance capable of specific binding to a preselected component of a sample in the first segment specifically binds nucleic acid.

43. The apparatus of claim 1 , wherein the third segment contains a detection reagent.

44. The apparatus of claim 1 , wherein the opposed wall portions of the tubule are left free of projections when the seal is broken.

45. The apparatus of claim 44 , wherein the segments form a substantially linear array.

46. The apparatus of claim 45 , wherein the segments form a contiguous array.

47. The apparatus of claim 1 , wherein the cap chamber has a wall that comprises a barrier preventing liquid escape and that defines a waste cavity in fluid communication with the opening.

48. The apparatus of claim 1 , wherein the cap chamber has a wall that comprises a vent, and a member preventing liquid escape, and that defines a waste cavity in fluid communication with the opening.

49. The apparatus of claim 1 , wherein the cap chamber has a flexible membrane that prevents liquid escape, that defines a waste cavity in fluid communication with the opening, and that is deformable to increase the waste cavity volume.

50. The apparatus of claim 1 , wherein a fourth segment distal to the third segment contains a detection reagent.

51. The apparatus of claim 1 , wherein the substance capable of specific binding to a preselected component of the sample is, comprises, or is coupled to a solid phase substrate.

52. The apparatus of claim 51 , wherein the wash reagent is capable of retaining the preselected component on the solid phase substrate while allowing removal of components of the sample not bound to the substrate.

53. The apparatus of claim 52 , wherein the amplification reagent is capable of amplifying the preselected component of the sample.

54. The apparatus of claim 51 , wherein the amplification reagent is capable of amplifying the preselected component of the sample.

55. The apparatus of claim 51 , further comprising a fourth segment that (a) is distal to the second segment, (b) is proximal to the third segment, and (c) contains an elution reagent capable of eluting the preselect component from the substrate.

56. The apparatus of claim 1 , wherein the amplification reagent is capable of amplifying the preselected component of the sample.

57. The apparatus of claim 5 , wherein:

the substance capable of specific binding to the preselected component of the sample comprises silica;

the silica is coupled to magnetic beads; and

the amplification reagent comprises at least one of a primer, a nucleotide triphosphate, and an amplification enzyme.

58. The apparatus of claim 1 , wherein the segments are prepacked with their respective contents.

59. The apparatus of claim 1 , wherein the cap chamber contains a reagent.

60. The apparatus of claim 1 , wherein the apparatus comprises the integral tubule tensioning mechanism, and the mechanism comprises cantilever or leaf springs.

61. The apparatus of claim 1 , wherein the apparatus comprises the attachment of the tubule to the frame, and the attachment comprises at least one of a seal, a weld, an adhesive joint, and an insert-molding.

62. The apparatus of claim 1 , wherein the cap further comprises a filter that permits the free escape of gasses while retaining all liquid volumes and infectious agents in the tube.

63. The apparatus of claim 1 , wherein the cap further contains a waste cavity in fluid communication with the tubule.