Self-contained biological analysis

1. A method of nucleic acid extraction and multiplex PCR in a self-contained system, comprising:

(a) providing the self-contained system having, in fluid communication:

i. one or more ports, including an injector port for introducing a sample into the self-contained system, wherein the one or more ports are sealable ports that provide the only access from an exterior of the self-contained system such that when all of the one or more ports are closed, the self-contained system is a fully closed, sealed environment that prevents access from the self-contained system to surrounding atmosphere,

ii. a cell lysis zone configured for lysing cells or spores located in the sample,

iii. a nucleic acid preparation zone, the nucleic acid preparation zone configured for purifying a plurality of nucleic acids that may be in the sample, wherein the nucleic acid preparation zone is fluidly connected to the injector port through the cell lysis zone;

iv. at least one amplification zone, the amplification zone configured for amplification of the plurality of nucleic acids that may be in the sample;

(b) introducing the sample into the self-contained system via the injector port;

(c) lysing cells or spores in the cell lysis zone by impacting the cell lysis zone with rotating blades or paddles for bead-milling;

(d) preparing the plurality of nucleic acids that may be in the sample in the nucleic acid preparation zone subsequent to step (c);

(e) moving the plurality of nucleic acids that may be in the sample into the amplification zone to mix with a plurality of primer pairs in the amplification zone;

(f) thermal cycling the plurality of nucleic acids that may be in the sample in the amplification zone in the presence of PCR reaction components and the plurality of primer pairs to create an amplification mixture;

(g) detecting which of the plurality of nucleic acids are present in the amplification mixture in the amplification zone; and

(h) closing the one or more ports, wherein step (h) takes place after step (b).

2. The method of claim 1 , wherein at least one of the ports of the one or more ports is a one-way valve.

3. The method of claim 2 , wherein the amplification zone is provided with dried amplification reagents therein.

4. The method of claim 1 , wherein the amplification zone is provided with dried amplification reagents therein.

5. The method of claim 1 , wherein the detecting step includes detecting fluorescent emission from a fluorescent dye in the amplification zone.

6. The method of claim 5 , wherein the fluorescent dye is a dsDNA binding dye.

7. The method of claim 5 , wherein the fluorescent dye is incorporated in a fluorescently labeled oligonucleotide probe.

8. The method of claim 1 , wherein each of the plurality of primer pairs is configured to amplify nucleic acids from a different species.