The analyte of interest may be biological or chemical in nature, and by way of example, only may include chemical moieties (toxins, metabolites, drugs and drug residues), peptides, proteins, cellular components, viruses, and combinations thereof. The analyte of interest may be in either a fluid or a supporting medium, such as a gel. SOFIA has demonstrated its potential as a device with a wide range of applications. These include clinical applications, such as detecting diseases, discovering predispositions to pathologies, establishing a diagnosis and tracking the effectiveness of prescribed treatments, and nonclinical applications, such as preventing the entry of toxins and other pathogenic agents into products intended for human consumption: * Clinical applications – SOFIA may be used to conduct both qualitative tests (either positive or negative results) to detect or identify bacteria or viruses, and quantitative tests (measuring substances) to detect or quantify biological constants or markers, which are substances produced by the body in the presence of, for example, an infectious disease (to allow determination of viral load, for instance, in AIDS therapy, or the level of toxicity in drugs of abuse detection). * Nonclinical applications - As an<unk> , SOFIA can potentially be used on a wider scale to monitor the quality of food, pharmaceuticals, cosmetics, or water, as well as general environmental parameters and agricultural products. The ability to detect and screen bacteria and toxins for a wide range of products is a growing and more complex requirement as may be evidenced by the increase incidence of food- and animal-borne diseases, such as E. coli, Salmonella, BSE, avian influenza, etc. Ante mortem test for prion diseases SOFIA has been used to rapidly detect the abnormal form of the prion protein (PrPSc) in samples of bodily fluids, such as blood or urine. PrPSc is the marker protein used in diagnostics for transmissible spongiform encephalopathies (TSEs), examples of which include bovine spongiform encephalopathy in cattle (i.e. “mad cow” disease), scrapie in sheep, and Creutzfeldt–Jakob disease in humans. Currently, no rapid means exists for the ante mortem detection of PrPSc in the dilute quantities in which it usually appears in bodily fluids. SOFIA has the advantages of requiring little sample preparation, and allowing for electronic diagnostic equipment to be placed outside the containment area. Background TSEs, or prion diseases, are infectious neurodegenerative diseases of mammals that include bovine spongiform encephalopathy, chronic wasting disease of deer and elk, scrapie in sheep, and Creutzfeldt–Jakob disease (CJD) in humans. TSEs may be passed from host to host by ingestion of infected tissues or blood transfusions. Clinical symptoms of TSEs include loss of movement and coordination and dementia in humans. They have incubation periods of months to years, but after the appearance of clinical signs, they progress rapidly, are untreatable and invariably are fatal. Attempts at TSE risk-reduction have led to significant changes in the production and trade of agricultural goods, medicines, cosmetics, blood and tissue donations, and biotechnology products. Post mortem neuropathological examination of brain tissue from an animal or human has remained the ‘gold standard’ of TSE diagnosis and is very specific, but not as sensitive as other techniques. To improve food safety, it would be beneficial to screen all the animals for prion diseases using ante mortem, preclinical testing, i.e., testing prior to presentation of symptoms. However, PrPSc levels are very low in presymptomatic hosts. In addition, PrPScs are generally unevenly distributed in body tissues, with highest concentration consistently found in nervous system tissues and very low concentrations in easily accessible body fluids such as blood or urine. Therefore, any such test would be required to detect extremely small amounts of PrP and would have to differentiate PrPC and PrPSc. Current PrPSc detection methods are time-consuming and employ post mortem analysis after suspicious animals manifest one or more symptoms of the disease. Current diagnostic methods are based mainly on detection of physiochemical differences between PrPC and PrPSc which, to date, are the only reliable markers for TSEs. For example, the most widely used diagnostic tests exploit the relative protease resistance of PrPSc in brain samples to discriminate between PrPC and PrPSc, in combination with antibody-based detection of the PK-resistant portion of PrPSc. It has as yet not been possible to detect prion diseases by using conventional methods, such as polymerase chain reaction, serology, or cell culture assays. An agent-specific nucleic acid has not yet been identified, and the infected host does not elicit an antibody response. The conformationally altered form of PrPC is PrPSc. Some groups believe PrPSc is the infectious agent (prion agent) in TSEs, while other groups do not. PrPSc could be a neuropathological product of the disease process, a component of the infectious agent, the infectious agent itself, or something else altogether. Regardless of what its actual function in the disease state is, PrPSc is clearly specifically associated with the disease process, and detection of it indicates infection with the agent causing prion diseases. SOFIA as an ante mortem test for prion diseases SOFIA provides, among other things, methods to diagnose prion diseases by detection of PrPSc in biological samples. Samples can be brain tissue, nerve tissue, blood, urine, lymphatic fluid, cerebrospinal fluid, or a combination thereof. Absence of PrPSc indicates no infection with the infectious agent up to the detection limits of the methods. Detection of a presence of PrPSc indicates infection with the infectious agent associated with prion disease. Infection with the prion agent may be detected in both presymptomatic and symptomatic stages of disease progression. These and other improvements have been achieved with SOFIA. SOFIA's sensitivity and specificity eliminates the need for PK digestion to distinguish between the normal and abnormal PrP isoforms. Further detection of PrPSc in blood plasma has been addressed by limited protein misfolding cyclic amplification (PMCA) followed by SOFIA. Because of the sensitivity of SOFIA, PMCA cycles can be reduced, thus decreasing the chances of spontaneous PrPSc formation and the detection of false-positive samples. SOFIA meets the needs of increased sensitivity in the detection of prion diseases in both presymptomatic and symptomatic TSE infected animals, including humans, by providing methods of analysis using highly sensitive instrumentation, which requires less sample preparation than previously described methods, in combination with recently developed Mabs against PrP. The method of the present version of SOFIA provides sensitivity levels sufficient to detect PrPSc in brain tissue. When coupled with limited sPMCA, the methods of the present inventions provide sensitivity levels sufficient to detect PrPSc in blood plasma, tissue and other fluids collected antemortem. The methods combine the specificity of the Mabs for antigen capture and concentration with the sensitivity of a<unk><unk><unk>  detection technology. In contrast to previously described methods for detection of PrPSc in brain homogenates, these techniques, when used to study brain homogenates, do not use seeded polymerization, amplification, or enzymatic digestion (for example, by proteinase K, or “PK”). This is important in that previous reports have indicated the existence of PrPSc isoforms with varied PK sensitivity, which decreases reliability of the assay. The sensitivity of this assay makes it suitable as a platform for rapid prion detection assay in biological fluids. In addition to prion diseases, the method may provide a means for rapid, high-throughput testing for a wide spectrum of infections and disorders. While about 40 cycles of sPMCA combined with immunoprecipitation were found to be inadequate for PrPSc detection in plasma by ELISA or western blotting, the PrPSc has also been found to be readily measured by SOFIA methods. The limited numbers of cycles necessary for the present assay platform virtually eliminates the possibility of obtaining PMCA-related false-positive results such as those previously reported (Thorne and Terry, 2008). Other clinical applications With rapid developments in the field of biomarker research, many infections and disorders that have not been possible to diagnose via in vitro testing, are becoming increasingly possible. SOFIA is predicted to be of broader use in diagnostic assay development for infections and disorders beyond the scope of prion diseases. A major potential application is for other protein misfolding diseases, in particular Alzheimer's.
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