WO2009158682A2 - Compositions and methods for diagnosing and treating pathogenic disorders - Google Patents

Abstract

The present invention is a method of detection to identify antigen reactivity between infective agents, e.g., bacteria, viruses, parasites, bacteriophages, spirochetes, microbes and common foods, beverages, inhalants, chemical preparations, perfumes, fragrances, pollens, animal proteins and dander. As a result of the specific identification of the pathogenic agent/antigen reaction, a vaccine can be constructed to eradicate such allergic reaction. The test platform represents a series of impregnated test modules or bioelectric collections containing sample libraries of infective materials which have potential cross reactivity with a human subject's biological fluid sample or response testing using galvanic skin response testing to other methods of electromedicine techniques and reagent and/or filters when needed. Automated sequential retesting or manual biopanning for the positive reactions; allergen/bacteria, bacteria/virus, virus/bacteria, result in the underlying antigen/pathogenic agent reaction. Once such causative infective agent relationship is identified there are several options for vaccine preparation or treatment to reduce or eradicate the identified causative pathogenic agent.

Description

COMPOSITIONS AND METHODS FOR DIAGNOSING AND TREATING PATHOGENIC DISORDERS

CROSS REFERENCE TO RELATED APPLICATION

[0001] This application claims the benefit of U.S. Provisional Application No. 61/076,571, entitled "Compositions and Methods for Diagnosing and Treating Immune Disorders," filed June 27, 2008, which is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

[0002] The immune system in vertebrates provides a defense mechanism against foreign agents, including foreign macromolecules or infecting microorganisms. The immune system utilizes a common recognition system for both foreign macromolecules (e.g., proteins, polysaccharides or nucleic acids) or microbes (e.g. viruses or bacteria) through specific binding of the proteins of the host immune system to specific sites on the foreign agent, or antigen, surface, known as antigenic determinants.

[0003] The adaptive immune system, which is composed of specialized systemic cells, including T-cells, act to prevent pathogenic infestation. The adaptive immune system provides the ability to recognize and remember specific pathogens, and to initiate and generate an immune response to the pathogen. The system is adaptable to its host through the use of hypermutation and recombination processes, that allow the generation of a large number of different antigen receptors, which are then uniquely expressed on individual lymphocytes. Lymphocytes, including B-cells and T-cell lymphocytes play a large role in the immune response system. B-cells play a major role in the humoral immune response, while T-cells are intimately involved with cell-mediated immune responses, together with the helper T cell responses, including T-helper cells (Th-I and Th-2) and regulatory T-cells.

[0004] During an immune response Th-I cells respond to bacteria, virus, some parasites, some metals and vaccines. The immune response is characterized by the production of certain cytokines, including interferon-gamma(IFN-Y), and interleukins (for example, IL-2 and IL-12), which activates the bactericidal activities of macrophages, and induces B-cells to make coating antibodies, leading to cell-mediated immunity. The Th2 response, which responds largely to allergies, mold, yeast, fungus, foods and some parasites and metals, is characterized by the release of interleukin 4 (IL4), interleukin 10 (ILlO), which results in the activiation of B-cells to make neutralizing antibodies, leading to humoral immunity. Defects in the immune system's ability to govern these responses by regulatory T-cells often result in an incomplete action of the Th-I response, thus resulting in immune hypersensitivities to fragments (for example, proteins, amino acid sequences, polysaccharides and/or nucleic acids) of Th-I stimulants. These fragments continue to act as immune stimulators, resulting in both autoimmunity as well as to an allergic Th-2 immune response. The incomplete Th- 1 response results in a dominance of Th-2 cytokines or in a dominance of Th-3 regulatory cells, either of which may worsen symptoms and stimulate disease chronicity in a variety of disorders; including chronic fatigue, fibromyalgia, Lyme disease, Parkinson's disease, autoimmune disorders, skin conditions, hair loss and asthma. Other conditions that may have a link to defects or weaknesses in the immune system through this same Th-I mechanism include polycystic liver disease, polycystic kidney disease, autism, cancer and mental illness.

[0005] Mechanisms whereby immune disruption (Th-2 dominance and regulatory T-cell dysfunction) occurs may result from multiple stressors, such as repetitive or prolonged antibiotic use, use of hand sanitizers, antiseptic creams and lotions, mouth wash use, steroids, Th-2 stimulatory vaccines, environmental toxins, chronic electrical frequency exposure and/or emotional stressors. Any or all of these environmental stressors may set the stage for multiple pathogenic or microbial infections, including but not limited to bacterial or viral infections, also affect physiological systems that are not exposed or have limited exposure to the body's immune system. One non-limiting example includes microbial infestation in the oral cavity that may lead to tooth decay halitosis. Other examples include bacterial growth on the skin, in nails, on hair, scalp or on other bodily surfaces where there is limited or no appropriate immune exposure. Certain of the pathogens may even cross the blood brain barrier, which may have an impact upon neurological systems and pathways. Pathogenic or microbial growth can also occur in many non-physiological systems, including but not limited to inorganic or organic surfaces, such as kitchen or bathroom countertops, fabrics, carpet, bedding and other surfaces. In addition, pathogenic or microbial growth can affect environmental systems, including but not limited to the quality of air or water systems.

SUMMARY OF THE INVENTION

[0006] The present invention relates to the identification and treatment of microbial or pathogenic growth or infections Such growth or infections result from current and/or unresolved bacterial, microbial, pathogenic infections in a maladapted (Th-I, Th-2 or Th-3) immune system, and may be the primary cause of chronic illness, allergy, autoimmunity, odor and disease. Pathogenic or microbial growth or infections may also occur in non-physiological or environmental systems, affecting the quality of, for example, air or water systems.

[0007] One embodiment disclosed herein is the diagnosis and treatment of disorders of the immune system, including allergies, chronic illness, chronic fatigue, fibromyalgia, Lyme disease, Parkinson's disease, autoimmune disorders, skin conditions, hair loss, cancer, asthma, polycystic liver disease, polycystic kidney disease, autism and mental illness. The underlying cause may include a pathogenic or microbial infection, including but not limited to a bacterial or viral infection resulting from incomplete processing by the immune system, which induces the immunological system to mount an attack to similar structures or fragments. Although not limited to this particular concept, it is believed through the research and studies disclosed herein that nucleoproteins, glycoprotein patterning, lipoprotein patterning and structural sequences of the environmental allergens mimic the infective agents' structure and/or identifying sequences underlying the allergic reaction, which in turn perpetuates the faulty immune response related to disorders of the immune system, including allergic reactions. Also contemplated within the present embodiments are methods of treatment of individuals suffering from disorders related to the immune system, including but not limited to vaccines designed and developed with the information obtained from the diagnostic methods disclosed herein.

[0008] In some embodiments, the methods disclosed herein are used for correlating allergic or environmental agents with an underlying infectious agent, such as a bacteria or virus, to create a correlative library for determining underlying infective agents associated with an allergic or environmental agent. Accordingly, disclosed herein are methods for identifying correlative relationships between antigenic or environmental agents, e.g. environmental allergens, proteins or other agents, common foods, beverages, inhalants, chemical preparations, perfumes, fragrances, pollens, animal proteins and dander, and pathogenic agents, e.g. microbial agents, including bacteria, viruses, parasites, bacteriophages, spirochetes and other microbes, and environmental allergens, to determine the underlying cause related to immune system, including allergic reactions, or other physiological or environmental disorder in a plurality of samples from individuals afflicted with a disorder. The test platform may represent, for example, a series of impregnated test modules containing sample libraries of infective material which have potential cross reactivity with a biological or environmental sample, and a reagent when needed. Sequential testing or manual biopanning for positive reactions, e.g. allergen/bacteria, bacteria/virus, virus/bacteria, may result in identifying the underlying infective agent. Such tests may determine through an iterative process, for example, a correlative relationship between antigens or other enviornmental agents, and the underlying infectious agent, and provide information for later treatment of the underlying infectious pathway.

[0009] In other embodiments, the methods disclosed herein are used for determining underlying infectious agents that may induce an adverse reaction, including allergic reactions with antigen(s) traditionally found responsible (e.g. dust mites, pollen, etc.) for adverse physiological reactions, including allergic reactions. The test platform for determination of such underlying infectious agents, including bacterial or viral growth, represents a series of impregnated test modules containing sample libraries of infective material which have potential cross reactivity with a subject's biological fluid sample and a reagent when needed. The underlying infective agents may be identified through detection of DNA, RNA or proteins associated with the underlying infective agent, including PCR techniques. Alternatively, the test modules may be stored on bioelectrically imprinted collections or libraries containing individual resonant frequencies of known infective material. The bioelectrically imprinted collections or libraries may be screened through an individual's galvanic skin response or other bioelectric method of testing and filter-like frequency when needed. Sequential testing or manual biopanning for positive reactions, e.g. allergen/bacteria, bacteria/virus, virus/bacteria and cross-referencing results from the biopanning assay, or alternativley the cross-reactivity of resonant bioelectric finger prints to allergen/bacterial or bacterial/virus bioelectric signatures may result in the identification of the underlying allergenic/infective agent reaction. Such tests may determine through an iterative process, for example, a correlative relationship between antigens, including environmental allergen(s), and the underlying infectious agent, and provide information for later treatment of the underlying infectious pathway. Correlation of the underlying allergenic/infective agent reaction with reactivity of a subject's biological sample with known enviromental antigens or allergens allows the application of appropriate treatment regimens to ameliorate or eradicate the underlying infection to traditional immune assay results.

[0010] In other embodiments, the methods disclosed herein are used for determining underlying pathogenic or microbial agents that may affect physiological systems that are not exposed or have limited exposure to the body's immune system. The test platform represents a series of impregnated test modules containing sample libraries of infective material which have potential cross reactivity with a subject's biological sample and a reagent when needed. Alternatively, the test modules may be stored on bioelectrically imprinted collections containing individual resonant frequencies of known infective material. Similarly, the libraries may be screened through an individual's galvanic skin response or other bioelectric method of testing and filter-like frequency when needed. Sequential testing or manual biopanning for positive reactions, e.g. bacteria or virus, and cross-referencing results from the biopanning assay may result in the identification of the underlying allergenic/infective agent reaction. Such tests may provide information for treatment or elimination of the underlying pathogenic or microbial growth or infection, including bacterial or viral growth or infection.

[0011] In other embodiments, the methods disclosed herein are used for determining underlying pathogenic or microbial agents that may affect non-physiological or environmental systems described. The test platform here represents a series of impregnated test modules and/or bioelectric collections containing sample libraries of infective material which have potential cross reactivity with a sample and/or frequency fingerprint, and a reagent or filter-like frequency when needed. Sequential testing or manual biopanning for positive reactions, e.g. bacteria or virus, and cross-referencing results from the biopanning assay may result in the identification of infective agent. Such tests may provide information for treatment or elimination of the pathogenic or microbial growth or infection, including bacterial or viral growth or infection. [0012] Another embodiment disclosed herein is a means for determining the underlying infectious agent that may be responsible for an adverse reaction, including an allergic reaction. The underlying infectious agent may be tested directly from a sample, including a patients' biological sample or tested via the galvanic skin response of the patient to the electrical imprint of the infective agent, or for example identification through molecular amplification reactions of a DNA fingerprint of the infectious agent.

[0013] Methods are also described herein to treat or eliminate the underlying pathogenic or microbial infection or growth, including but not limited to viral or bacterial growth. For example, a method of treating a patient includes the steps of: 1) testing of a series of impregnated test modules containing sample libraries of infective material which have potential cross reactivity with a subject's biological sample, and a reagent when needed; 2) identifying the underlying pathogenic or microbial cross-reactivity to the patient samples, through, for example testing of collections of libraries of bioresonant imprints of infective material which have cross-reactivity with a subject via the use of bioelectric testing, such as acupuncture point testing, galvanic skin response testing or other forms of bioelectric monitoring; alternatively, the underlying infective material may be determined through the use of correlative libraries utilizing the methods and assays disclosed herein; and 3) treating said patient with a medicament or a system of bioelectric phage therapies that target specific infectious agent from the subject. Bacterial-phage and/or viral-phage therapy or any other means of reducing or eliminating the underlying infectious agent or correcting or amelioration of the related disorder in the immune system, may be used to reduce or eliminate the underlying microbial infective agent. Such treatments may also include, but are not limited to, antibiotics, including pencillins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors.

[0014] Also disclosed herein is a method of treating non-physiological systems or surfaces including the steps of: 1) testing of a series of impregnated test modules containing sample libraries of infective material which have potential cross reactivity with a sample, and a reagent when needed; 2) identifying the pathogenic or microbial infection or growth; and 3) treating the non-physiological system or surface with a medicament or system that may reduce or eliminate the infectious agent from the non-physiological system or surface.

[0015] Another embodiment disclosed herein is a method for treating or disinfecting non-physiological systems and/or surfaces to eliminate infective materials. Non-physiological systems and/or surfaces may support the growth of infective agents that may be resistant to disinfectants commonly employed for such purposes. Eradication, treatment or disinfection of the non-physiological systems or surfaces includes the use of the assays disclosed herein to identify infective agents residing on or in the non-physiological systems or surfaces. Methods to identify the infective agents include the sampling of the infective material from bioeletrically imprinted collections of libraries, which may represent a comparable sample of infective agents commonly found on similar surfaces when cultured. These infective agents can be computer-modeled and their individual bioresonance tested against samples of bioelectric bacterial phages or bioelectric viral phages and thus be tested for effectiveness in the elimination of the identified infective agent. Bacterial-phage therapy, as well as viral phage therapies may be employed to treat, disinfect or eradicate the identified infective agents; alternatively, any other means of reducing or eliminating the underlying infectious agent or correcting or amelioration of the related disorder in the immune system, may be used to reduce or eliminate the underlying microbial infective agent. Such treatments may also include, but are not limited to, antibiotics, including pencillins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors. [0016] Disclosed herein are methods of treating environmental systems including the steps of: 1) testing of a series of impregnated test modules containing sample libraries which have potential cross reactivity with an environmental sample, and a reagent when needed; 2) identifying the underlying pathogenic or microbial infection or growth; and 3) treating the environmental system to reduce or eliminate the infectious agent from the environmental system or surface. PCT analysis, such as QT-PCR, immunoassays or other any other assays may be used to identify the infective agent in the sample. Phage therapy or any other means of reducing or eliminating the underlying infectious agent or correcting or amelioration of the infection or growth may be used to reduce or eliminate the microbial or pathogenic infective agent. Such treatments may also include, but are not limited to, antibiotics, including pencillins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors. [0017] Another embodiment disclosed herein is a method for treating or disinfecting environmental systems, such as water and air systems, to eliminate infective materials. Environmental systems, such as water and air systems, are frequently disinfected with toxins which are themselves harmful to those chronically exposed to such substances, which may result in illness, allergy and hypersensitivity reactions. Treatment or disinfection of environmental systems includes the use of the assays disclosed herein to identify infective agents residing on or in the environmental systems. Methods to identify the infective agents include the sampling of the infective material from bioeletrically imprinted collections of libraries, which may represent a comparable sample of infective agents commonly found in the environmental systems when cultured. These infective agents can be computer- mo deled and their individual bioresonance tested against samples of bioelectric bacterial phages or bioelectric viral phages and thus be tested for effectiveness in the elimination of the identified infective agent. Bacterial-phage therapy, as well as viral phage therapies may be employed to treat, disinfect or eradicate the identified infective agents; alternatively, any other means of reducing or eliminating the underlying infectious agent or correcting or amelioration of the infection or growth, may be used to reduce or eliminate the microbial or pathogenic infective agent. Such treatments may also include, but are not limited to, antibiotics, including pencillins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors. [0018] Also contemplated herein is a method of formulating and treating a subject with a vaccine to lessen or eliminate an adverse reaction, such as an allergic reaction, wherein the vaccine is constructed from information obtained through the diagnostic methods disclosed above. The vaccine may be synthesized through any conventional means. Alternatively, the vaccine may be synthesized through bioelectric replication technology, for example, a product capsule.

INCORPORATION BY REFERENCE

[0019] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

DETAILED DESCRIPTION OF THE INVENTION

[0020] The present disclosure relates in part to the diagnosis and treatment of disorders of the immune system, including allergies, chronic illness, chronic fatigue, fibromyalgia, Lyme Disease, Parkinson's disease, multiple sclerosis, autoimmune disorders, skin conditions, hair loss, cancer, asthma, polycystic liver disease, polycystic kidney disease, autism and mental illness, by combining known testing methodologies, such as RAST or other tests detecting and/or quantifying the presence of immunoglobulin or other immunomodulatory molecules with complementary diagnostic tests to treat underlying causes related to disorders of the immune system, including allergic reactions. The underlying cause may include bacterial or other pathogenic or microbial infection resulting from incomplete processing by the immune system. Although not limited to this particular concept, it is believed through the research and studies disclosed herein that nucleoproteins, glycoprotein patterning, lipoprotein patterning and structural sequences of the environmental allergens mimic the infective agents underlying the allergic reaction, which in turn perpetuates the faulty response related to disorders of the immune system, including allergic reactions and autoimmunity. Also contemplated within the present embodiments disclosed herein are methods of treatment of individuals suffering from disorders related to the immune system. Optionally included is the treatment of the immune-related disorders with vaccines designed and developed with the information obtained from the diagnostic methods disclosed herein.

[0021] Accordingly, disclosed herein are methods for identifying the reactivity between infective agents, e.g. microbial or pathogenic agents, including bacteria, viruses, parasites, bacteriophages, spirochetes and other microbes, and environmental allergens, including common foods, beverages, inhalants, chemical preparations, perfumes, fragrances, pollens, animal proteins and dander, to determine the underlying cause related to disorders of the immune system, including allergic reactions. In some embodiments, the methods disclosed herein are used for determining underlying infectious agents that may induce an adverse reaction, including allergic reactions with antigen(s) traditionally found responsible (e.g. dust mites, pollen, etc.) for adverse reactions, including allergic reactions. The test platform represents a series of impregnated test modules or bioelectric collections containing sample libraries of infective material which have potential cross reactivity with a human subject's biological fluid sample. Skin tests, such as galvanic skin response, acupuncture point testing and other testing techniques known in the art of bioelectric medicine is optionally used in combination with a reagent and/or filter when needed to determine the correlative underlying infective agent responsible. Sequential testing using automated methods or manual biopanning for positive reactions, e.g. allergen/bacteria, bacteria/virus and/or virus/bacteria may result in the underlying allergenic/infective agent reaction. Such tests may determine through an iterative process, for example, a correlative relationship between antigens, including environmental allergen(s), and the underlying infectious agent, and provide information for later treatment of the underlying infectious pathway.

[0022] Also disclosed herein are methods for identifying the reactivity between microbial or pathogenic agents, including bacteria, viruses, parasites, bacteriophages, spirochetes and other microbes, and environmental agents, including proteins or molecules residing in environmental samples, such as water or air samples, or non-physiological surface or materials, including kitchen or bathroom countertops, fabrics, carpets and other samples or systems. In some embodiments, the methods disclosed herein are used for determining underlying agents that may induce a noxious smell. The test platform represents a series of impregnated test modules or bioelectric collections containing sample libraries of infective material which have potential cross reactivity with a sample, and a reagent and/or filter when needed. Automated sequential testing or manual biopanning for positive reactions, e.g. allergen/bacteria, bacteria/virus and/or virus/bacteria may result in the identification of the underlying allergenic/infective agent reaction. Such tests may determine through an iterative process, for example, a correlative relationship between environmental agents and the underlying microbial and/or pathogenic agents, and provide information for later treatment or eradication of the underlying microbial or pathogenic agent. [0023] In addition to the correlative tests provided, also disclosed herein is a method for testing a mammalian patient to determine the antigen(s) responsible for the adverse reaction related to disorders of the immune system (e.g. dust mites, pollen, etc.), and to correlate the antigenic(s) information with the underlying infectious agent that may be responsible for the adverse reaction, including allergic reactions. Such tests would incorporate results of the correlative studies that may determine the relationship between the antigen(s), including potential allergens, and underlying infectious agents. Correlative information may also be obtained through patient questionnaires regarding potential or known environmental allergens that have been previously established in said patient.

[0024] Another embodiment of the present invention is a means for determining the underlying infectious agent that may be responsible for an adverse reaction, including an allergic reaction. The underlying infectious agent may be tested directly from a patient's biological sample, for example, identification through molecular amplification reactions of a DNA fingerprint of the underlying infectious agent.

[0025] A method of treating a patient in need of such treatment is also disclosed. This method includes the steps of: 1) diagnosing the traditional antigen, e.g. allergen, responsible; 2) determining the correlative underlying infectious agent; and 3) treating said patient with a medicament or system that may reduce or eliminate the infectious agent from the patient. In addition, conventional treatment with medicaments of microbial agents are also contemplated. Such medicaments may include, but are not limited to, antibiotics, including pencil lins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors. Alternatively, phage therapy, interleukin-interferon manipulation, or any other means of reducing or eliminating the underlying infectious agent or correcting or amelioratin the related disorder in the immune system, may be used to reduce or eliminate the underlying microbial infective agent [0026] An allergy is a hypersensitive reaction to antigens in subjects, which in similar amounts and circumstances are harmless in other individuals. An allergic response to foreign agents is thought to develop when an individual's natural immune response is disturbed (atopy).

[0027] Allergy can affect many body systems, including sinus, skin, digestive, lungs, genital, urinary, nervous system and can range from minor symptoms to life threatening emergencies and even death. Allergy can also serve as the catalyst for multiple infective diseases. Conversely, a disease state can serve as a catalyst for allergy.

[0028] Multiple theories have emerged to explain the exponential rise in the number of allergic and auto immune diseases. One of the more popular explanations centers on the growth of allergies and autoimmunity within developed countries. This theory points to the increased emphasis upon hygiene as a potential cause, postulating that the present allergic epidemic is partially due to changes in life style. The lack of exposure to significant infective agents prohibits those in more industrialized nations to go without the many opportunities in which to exercise the immune response that would result in active and complete antibody formation.

[0029] Another such theory for the distinct differences in allergic populations of developed and undeveloped countries may have to do with certain stressors which cause the immune system to develope preferentially in T-cell differentiation to the T- helper (Th-2) cell. Such stressors may include Th-2 stimulating vaccines: pertussis, diptheria and tetanus. Additional stressors may include the exposure to certain industrial chemicals and plastics, which are known to have significant effects upon various signalling hormones which result in abnormal Cortisol levels and thus preferential dominance of T-helper cell 2 populations.

[0030] In addition industrialized countries with significant technological advances bring with them greater stresses upon the body which can result in the dampening of the immune response from an imbalance of the autonomic nervous system, i.e. the "flight or fight" response. Excessive sympathetic nervous system dominance and deficiency of the parasympathetic modulating affect results in a more unstable immune response. This response results in a dysregulation of the immune regulatory cells and a faulty Th-I response, and as such a dominance in Th-2 lymphocytes. The unheard of emergence of allergies and autoimmune diseases in undeveloped countries may follow differences not only in life style but also environmental factors, including diet, disease management, water, hygiene, breast feeding, refrigeration, chemical use, farming, vaccine use and excess electronic exposure. The apparent difference in the percent of individuals suffering from allergies in industrialized countries all point to the potential role of these factors in the functioning of the immune system. [0031] The environmental factors of industrialized countries may result in one or any number of immune response defects, resulting in mutations of proteinacious materials, amino acid sequences mismatching and pattern recognition errors. Any one of these errant processes can mimic infective elements and alter receptor sites, which then misinterpret the normal T lymphocyte response causing faulty immune activity. As it pertains to the immune system's need for exacting discrimination between self and non-self molecules, including foods, chemicals, beverages, environmental substances, fragrances, bacteria, viruses, spirochetes, cancers and infective microbes interaction at any receptor, synapses, cytokine, protein replication and other physiological systems, potential error in innate order becomes threatened.

[0032] The mechanism for immediate hypersensitive allergic reaction is presently understood to begin when an allergen is presented to a naive T lymphocyte. The T cell differentiates to a T helper cell (Th2) which through cytokine influence causes the B lymphocyte to secrete IgE immunoglobulin calling for mast cells, eosinophils and basophils. Immediate hypersensitive allergy thus results in the increased production of IgE. The IgE is tested as a clinical indicator of the presence of immediate hypersensitivity (allergy) to either inhalants, consumables or contact.

[0033] Although current allergy theories point to environmental or other allergens providing the basis of an allergic reaction, one alternative theory traces atopy to a defect in the processing of allergens by the immune system. For example, the medical literature contains instances where allergy has its basis in cross-reactivity between otherwise unrelated proteins. The basis for such cross-reactivity of proteins of different organisms is thought to be due to the similarity of the epitope of the individual proteins which otherwise are unrelated. In one such case dog dander was cross reacting with human prostate specific antigen. Further examples of cross reactivity have also been shown between Candida, human tissue and food. In still other studies there have been examples of allergic reactions specific to both bacteria and to virus resulting in immunoglobulin evidence of such reactivity.

[0034] Numerous researchers have looked at mechanisms of action ranging from partial amino acid sequence matches to molecular mimicry to receptor site abnormalities. No study has yet given a definitive answer as to cause, although some investigators have offered further evidence that the allergenic immune reaction can improperly read vital substances, chemicals, environmental elements and even self as a faulty immune opportunity.

[0035] Bacteria receive much of their attention from the devastation caused by the illnesses they create. Bacteria's role in odor, oral hygiene, allergy, acne, veterinarian dermatology, hair growth and autoimmune disease take a back seat by comparison. Products and methods which presently exist only offer limited symptomatic results for the emergence of illness and bring with them significant side effects for users.

[0036] Science has shown that bacteria are selectively susceptible to invasion and destruction by specific viruses. These viruses invade such bacteria and take over certain functions of the bacteria. The invading virus thus replicate and bacterial phage offspring selectively invade additional specific bacteria of the same or similar family and genus. As all the susceptible bacteria are destroyed by such invasion the viral aggressor is unable to sustain life having lost its host and environment of replication. In nature the control of bacterial populations are most likely held in check by invading virus resulting in bacterial phage which in turn limits the viral population as well. To date multiple bacteriophage have been identified and studied. Russian scientists have developed phage applications for the treatment of many health conditions. All phage to date have required the use of a virus which was once an infective agent, lending the possibility of adverse side effects or secondary infections from improper or ineffective neutralization techniques. For at least these reasons, as well as the lack of phage identification for other infective diseases, the application of this technology has not received widespread application or acceptance in traditional medicine.

[0037] Disclosed herein are novel methods for the treatment of microbial or pathogenic infection or growth, including but not limited to platforms to match a susceptible microbial or pathogen to a selective virus or bacteria for treatment or eradication of the microbial or pathogenic growth or infection. These relationships can be identified using multiple methodologies; including medical testing, bioelectric methods such as bioresonance, galvanic skin response testing, energetic testing using muscle testing, dermal screening as well as acupuncture point testing/pulse diagnosis.

[0038] The advantage of the bioelectrical methods is that subtle relationships between bacteria and virus can be identified non-invasively and effectively. Traditional scientific methods for identification of microbial or pathogenic infections or growth are not as sensitive to the subtle footprint of the infective agents, making relationships more difficult and costly to identify. Moreover, bioelectric methods, including bioresonant replication of identified bacterial and/or viral relationships can be carried out without risk of infection or adverse side effects common with classically produced bacteriophage. [0039] The splicing and bonding of bioelectric replicas of infective agents permit the manipulation of the relationships between elements. The inversions and/or reversals of either the bacterial data or the viral data are dependent upon the intended application, including the treatment or eradication of a microbial or pathogenic infection or growth. These data packets can be held electromagnetically, biophotometrically or as digital data packets in a software format. The resultant data packets no matter how imprinted can be combined or bonded by any of the above methods in several different proprietary and non proprietary analogue carriers; polymers, fabric, oils, plasmas, plastics, soaps, waxes, creams, pastes, foods, liquids, amulets or makeup. Stock products of various manufacturers can thus be treated during manufacturing or post manufacturing without harm to the product or packaging or in any way adversely affecting its intended use. This technique allows piggybacking of data packets into common use items for treatment regimens, product enhancement or subtle treatment applications.

[0040] Such carriers many also be contained in sprays, pellets, pearls, oils, capsules, liquids, yogurt, tablets, gel caps, injections, suppositories, patches, creams, lotions, jells, plasters, mouth wash, salve, lollipop, roll-ons or the like. Because of the intrinsic ability to splice, combine and bond the various agents to identified targets, the targets and carriers are limitless. Clothing, foods, drinks, toiletries, detergents, air fresheners, upholstery, surgical masks and scrubs may all become vehicles for specific delivery systems.

[0041] Immediate and proven applications include allergy elimination, acne elimination, dental caries elimination and hair loss prevention, skin cancer preventative, halitosis elimination, feminine hygiene, and foot odor elimination, hot spot elimination for veterinarian application, excessive pet grooming elimination and cystic back acne. Any target so affected by bacterial, microbial and/or pathogens can be selected for such bioelectrically modeled product therapy. [0042] The methods and compositions of the embodiments disclosed herein can also be used in the diagnosis and treatment of adverse reactions related to disorders of the immune system. The practices employed herein, unless otherwise indicated, include conventional techniques for determining adverse reactions to antigens, including environmental allergens. For example, allergy testing to detect and/or quantify reactive immunoglobulins from an individual patient may be employed with the embodiments disclosed herein. Such testing may include RAST (radioallergosorbent test), PRIST, skin prick testing or any other means of measuring immunoglobulins, including IgE, IgA, IgG or IgM. One exemplary method of detecting immunogenicity to a defined environmental allergen is the RAST test. The RAST test measures the immunogenic reaction to a specific allergen. For example, the allergen of interest, e.g. ragweed pollen or animal dander, is bound to a solid surface. A biological sample, such as blood, is added to the bound allergen, wherein only IgE antibody specific to the bound allergen reacts in the test sample. After the initial incubation, non-specific IgE antibody and other proteins are removed by washing. A labeled antibody specific to IgE antibodies is then added to detect the bound IgE antibodies to the solid platform. Phadia's ImmunoCAP^® (Phadia, Uppsala Sweden) specific IgE blood test is one commercial example of a RAST test specific to IgE antibody detection. Other assays for use in conjunction with the methods disclosed herein include biometric tests, including heart rate variability tests, bioimpedance analysis, hormonal assays, urine amino acid testing, urinary neurotransmitted testing, including Cortisol quantification and qualitative assays, as well as decreased secretory IgA markers, food allergies and specific biomarkers for various diseases, including but not limited to Crohn's disease, type I diabetes, multiple sclerosis, parasites and other diseases. Other tests may include energetic evaluations of patients. Decreased energy production is often accompanied by abonormalities of the immune system, which may result in an inability to maintain an immune response under static or stressed conditions.

[0043] Additionally, techniques for the identification of reactivity between identified antigens, for example allergens, and multiple infective agents may also be employed, including the sequential use of one or all of the following: electrophoresis, immunoblotting, PCR (polymerase chain reaction), ELISA (enzyme-linked immunosorbent assay), radioimmunoassay, immunofluorescence, bio-resonant matching, electromagnetic testing for similarity or like techniques with or without reagents, which serve to open the diagnostic window for specific DNA or RNA identification.

[0044] Identification of the underlying infective agent(s) that are reactive with environmental antigens will allow the design and construction of specific therapies, including administration of a vaccine, to the identified microbial pathogens. Vaccines may then be prepared using either standard vaccine protocols known to those of skill in the art, or bioelectric replications using computer generated electromagnetic signals. The bioelectric replication vaccine is a digital representation of the infective agent; yet as a homeopathic like substance carries none of the infective agent, but purely the digital imprint capable of stimulating an immunoglobulin response and immunity to the targeted allergen. See U.S. Patent No. 6,142,927, incorporated by reference in its entirety herein.

[004SJ Also included herein is a library for the detection of infective agents or pathogens and the determination of bacterial and/or viral relationships for treatment of the infective agents or pathogens in samples, including biological samples, environmental samples or organic or non-organic surfaces or samples. A library may be defined as a set of bioelectric replication signals of antigens or molecule, such as environmental allergens that may react immunologically with at least some of the affected individuals. In some embodiments, it is preferable to select bioelectric replication signals of antigens or molecules in the library that are representative of microbes or pathogens responsible for a large percentage of infection or growth in a biological sample, environmental sample or organic or non-organic surface or sample. In other embodiments it is preferable that some bioelectric replication signals of antigens or molecules in the library may not be completely specific. The library may be immobilized onto a solid platform.

[0046] The underlying microbial or pathogenic infectious agents may also be identified using a bioelectric signature detection assay. Such bioelectric signature detection assays include the use of galvanic skin response assays or acupuncture point testing. Galvanic skin response assays, also known as electrodermal response, psychogalvanic reflex or skin conductance response, measure changes in the electrical resistance of skin. Acupuncture point testing includes the use of acupuncture points, or meridians, to measure an individual's response to an agent. Acupuncture point testing may include the use of bioelectric current generators (see, e.g. BioMeridian's MSA (Meridian Stress Assessment) device) at meridian test points to measure changes in resistance at each point.

[0047] The underlying microbial or pathogenic infectious agents may also be identified through conventional means. Such tests, for example, may utilize polymerase chain reaction (PCR) to identify the molecular fingerprint of each microbial or pathogenic infective agent. To do this, each separate compartment or area of a solid platform, for example a 96- well microtiter plate, contains a probe set to a specific microbial agent, for example E. coli or Helicobacter pylori. PCR probes to specific microbial agents, which alternatively may be labeled, are well known to those of ordinary skill in the art, and may be designed using nucleotide sequences unique or specific to each microbial agent. For example, U.S. Patent No. 7,294,490, which is incorporated by reference herein, employs amplification means, including PCR, for detecting and identifying specific microbial agents in a biological sample. Each solid platform may contain probe sets specific to a microbial agent group, for example, a panel of bacterial agents. The PCR test may be repeated on other platforms directed specifically to other groups of microbial agents, for example, viral agents, spirochetes, bacteriophages, parasites and other microbial agents or pathogens. Each subsequent assay provides a precise DNA fingerprint of the underlying microbial infective agents, allowing identification of specific bacterial and/or viral species responsible for the allergic reaction. The results from each PCR test will be compared to the results obtained from the environmental allergen testing stage, and correlated thereto. [0048] Quantitative real-time PCR enhanced immunoassay is a preferred means of detecting and identifying the underlying infectious agent in an individual. The methods for performing quantitative real-time PCR (QRT-PCR) are well known to practitioners. QRT-PCR uses RNA as a template prepared from a biological sample, and allows accurate and precise quantification of specific RNA sequences in the sample. QRT-PCR enhanced immunoassay takes advantage of the high sensitivity through amplification of a specific RNA sequence, for example bacterial or viral antigen, captured by a specific immunoglobulin in a patient's sample. For example, previous studies have measured viral immunoglobulin M (IgM) antibody by first capturing IgM in the patient's sample onto anti-IgM attached to a solid support substrate. See Elfaitouri et al., 2005, Clin. Diag. Lab. Immun. 12:235-241. Enteroviral antigen is then allowed to bind to the captured IgM. Any RNA bound to the IgM is released through denaturation of the complex, and amplified via QRT-PCR. Quantification of a patient's IgM specific to enteroviral antigen allows analysis of any recent exposure to an enteroviral infectious agent. [0049J A "subject," "individual" or "patient" is used interchangeably herein, and refers to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets. Tissues, cells and their progeny of a biological entity obtained in vivo are also encompassed. [0050] As used herein, "sample" encompasses a variety of sample types and origins, such as blood and other liquid samples of biological origin, solid tissue samples such as a biopsy specimen or tissue cultures or cells derived therefrom, and the progeny thereof. The term "sample" encompasses a clinical sample, and also includes cells in culture, cell supernatants, cell lysates, serum, plasma, biological fluid, and a pure or enriched bacterial or viral sample derived from any of these, for example, as when a sample is cultured in order to increase, enrich and substantially purify a bacterial or viral sample therefrom. The term "sample" further encompasses environmental samples, such as water or soil samples. A sample can be from a microorganism, e.g., bacteria, yeasts, viruses, viroids, molds, fungi, plants, animals, including mammals such as humans. A sample may comprise a single cell or more than a single cell. These samples can be prepared by methods known in the art such as lysing, fractionation, purification, including affinity purification, FACS, laser capture microdissection (LCM) or isopycnic centrifugation. The term "sample" can also include products of subcellular fractionation methods used to create enriched cellular or subcellular fractions, such as subcellular organelles including nuclei, mitochondria, golgi apparatus, endoplasmic reticulum, chloroplasts, heavy and light membranes and cytoplasm. The term "sample" may also include samples of inorganic or organic origin, including samples taken from solid surfaces, such as kitchen or bathroom countertops, floor surfaces, carpet, fabric, or other surface or material. Furthermore, the term "sample" may also include electromagnetically imprinted information capsules, which contain binary codes that represent digital representations of analogues. Such digital analogues may be seen by the body and the immune system as replicas of the original infective agent, but do not contain the infective agent. [0051] Samples may be obtained from any subject by any technique known in the art. Samples derived from an animal or human can include, e.g., whole blood, sweat, tears, ear flow, sputum, lymph, bone marrow suspension, lymph, urine, saliva, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions of the respiratory, intestinal or genitourinary tracts fluid. Samples comprising whole blood or plasma are preferred. Methods of separating cells and cellular components from whole blood are well known in the art. Samples comprising biopsy tissue are not preferred, although such samples can be used to practice the present invention and may be collected by any technique known in the art. [0052] To obtain a blood sample, any technique known in the art may be used, e.g. a syringe or other vacuum suction device. A blood sample can be optionally pre-treated or processed prior to enrichment. Examples of pre-treatment steps include the addition of a reagent such as a stabilizer, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagent, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross-linking reagent. In some embodiments, a blood sample can be combined with an agent that selectively lyses one or more cells or components in a blood sample. Whole cells, cell fragments, but preferably proteins will be isolated from the samples by any technique known in the art. |0053] Preparation of samples are described herein and well known in the art. It is understood that a sample comprising bacteria or virus can be removed from its source (e.g., an individual, food, air, water, and other environmental samples); grown in culture, whereby the bacteria and/or virus is multiplied, enriched and/or purified (in some embodiments, substantially purified) prior to preparation of protein sample. Proteins can prepared from a whole cell extract or can be pre- fractionated based on subcellular location (e.g., membrane and cytoplasmic) or based on different physical and functional properties. In some embodiments, serum suspected of comprising bacteria and/or virus is depleted of the major serum proteins prior to analysis using digital antibodies. Methods for depleting, reducing and/or removing the major serum proteins are well known in the art. Proteins can also be extracted from the supernatant of a culture. In some embodiments, the sample is comprised of (derived from) mammalian cells (in some embodiments, vertebrate cells), such as human, murine, primate, or rodent. In some embodiments, the cell is of a non-human mammal (in some embodiments, of a non-human vertebrate). [0054] Detection assays employing radioactive or fluorescent labels are contemplated within the present invention. The particular label or detectable moiety used and the particular assay are not critical aspects of the invention. The detectable moiety can be any material having a detectable physical or chemical property. Such detectable labels have been well developed in the field of gels, columns, and solid substrates, and in general, labels useful in such methods can be applied to the present invention. Thus, a label is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Furthermore, it will be recognized that fluorescent labels are not to be limited to single species organic molecules, but include inorganic molecules, multi-molecular mixtures of organic and/or inorganic molecules, crystals, heteropolymers, and the like.

[0055] Useful labels in the present invention include fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like), enzymes (e.g., LacZ, CAT, horse radish peroxidase, alkaline phosphatase, F-galactosidase, β- galactosidase, and glucose oxidase, acetylcholinesterase and others, commonly used as detectable enzymes), quantum dot- labels, chromophore-labels, enzyme-labels, affinity ligand-labels, electromagnetic spin labels, heavy atom labels, probes labeled with nanoparticle light scattering labels or other nanoparticles, fluorescein isothiocyanate (FITC), TRITC, rhodamine, tetramethylrhodamine, R-phycoerythrin, Cy-3, Cy-5, Cy-7, Texas Red, Phar-Red, allophycocyanin (APC), epitope tags such as the FLAG or HA epitope, and enzyme tags such as and hapten conjugates such as digoxigenin or dinitrophenyl, or members of a binding pair that are capable of forming complexes such as streptavidin/biotin, avidin/biotin or an antigen/antibody complex including, for example, rabbit IgG and anti-rabbit IgG; fluorophores such as umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, tetramethyl rhodamine, eosin, green fluorescent protein, erythrosin, coumarin, methyl coumarin, pyrene, malachite green, stilbene, lucifer yellow, Cascade Blue, dichlorotriazinylamine fluorescein, dansyl chloride, phycoerythrin, fluorescent lanthanide complexes such as those including Europium and Terbium, molecular beacons and fluorescent derivatives thereof, a luminescent material such as luminol; light scattering or plasmon resonant materials such as gold or silver particles or quantum dots; or radiolabels including ¹⁴C, ¹²³1, ¹²⁴1, ¹³¹1, ¹²⁵I, Tc99m, ³²P, ³⁵S or ³H; or spherical shells, and probes labeled with any other signal generating label known to those of skill in the art, as described, for example, in Principles of Fluorescence Spectroscopy, Joseph R. Lakowicz (Editor), Plenum Pub Corp, 2nd edition (July 1999) and the 6* Edition of the Molecular Probes Handbook by Richard P. Hoagland. [0056] Semi-conductor nanocrystals such as quantum dots (i.e., Qdots) described in U.S. Pat. No. 6,207,392, are commercially available from Quantum Dot Corporation and include nanocrystals of Group H-VI semiconductors such as MgS, MgSe, MgTe, CaS, CaSe, CaTe, SrS, SrSe, SrTe, BaS, BaSe, BaTe, ZnS, ZnSe, ZnTe, CdS, CdSe, CdTe, HgS, HgSe, and HgTe as well as mixed compositions thereof; as well as nanocrystals of Group III-V semiconductors such as GaAs, InGaAs, InP, and InAs and mixed compositions thereof. The use of Group IV such as germanium or silicon, or the use of organic semiconductors, may also be feasible under certain conditions. The semiconductor nanocrystals may also include alloys comprising two or more semiconductors selected from the group consisting of the above Group III-V compounds, Group H-VI compounds, Group IV elements, and combinations of same. Examples of labels can also be found in U.S. Patent Nos. 4,695,554; 4,863,875; 4,373,932; and 4,366,241. Colloidal metals and dye particles are disclosed in U.S. Pat. Nos. 4,313,734 and 4,373,932. The preparation and use of non-metallic colloidals are disclosed in U.S. Pat. No. 4,954,452. Organic polymer latex particles for use as labels are disclosed in U.S. Pat. No. 4,252,459.

[0057] In addition to the previously mentioned labels, other labels which rely on proximity or quenching can be utilized. One such example of a proximity-dependent label is the AlphaScreen system available from PerkinElmer which allows for identification without the need for solid support. Quenching and other methods for detecting the binding of two antibodies to a single ligand have been described and are well known in the art. See, e.g., U.S. Pat. Nos. 4,199,559; 5,672,475; 5,783,453; and 6,013,457.

[0058] The label may be coupled directly or indirectly to the protein according to methods well known in the art. Methods for attaching and/or linking (either covalently or noncovalently, directly or indirectly, e.g., via a linker) label to protein are well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on the sensitivity required, ease of conjugation of the compound, stability requirements, available instrumentation, and disposal provisions. Non-radioactive labels are often attached by indirect means. In some embodiments, a ligand molecule (e.g., biotin) is covalently bound to a polymer. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound. A number of ligands and anti-ligands can be used. Where a ligand has a natural anti-ligand, for example, biotin, thyroxine, and Cortisol, it can be used in conjunction with labeled anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody. [0059] Labels can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore. Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, fluorescent green protein, and the like. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.

[0060] Means of detecting labels are well known to those of skill in the art. Thus, for example, where the label is a radioactive label, means for detection include a scintillation counter, proximity counter (microtiter plates with scintillation fluid built in), or photographic film as in autoradiography. Where the label is a fluorescent label, it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence, e.g., by microscopy, visual inspection, via photographic film, by the use of electronic detectors such as charge coupled devices (CCDS) or photomultipliers and the like. Similarly, enzymatic labels may be detected by providing appropriate substrates for the enzyme and detecting the resulting reaction product. Finally simple colorimetric labels are often detected simply by observing the color associated with the label.

[0061] Solid or semi-solid supports suitable for immobilizing environmental allergens or microbial or pathogenic substrates, and binding or reacting biological samples are well known in the art. Examples of a solid support include: a bead (including magnetized beads), microwell plate, a protein microarray (e.g., technology owned by Zyomyx, Inc. See, e.g. U.S. Pat. No. 6,365,418). Thus, for example, CdSe-CdS core-shell nanocrystals enclosed in a silica shell can be easily derivatized for coupling to a biological molecule. Bruchez et al. (1998) Science 281: 2013-2016. Similarly, highly fluorescent quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. Warren and Nie (1998) Science 281 : 2016-2018. Fluorescently labeled beads are commercially available from Luminex and Quantum Dot. In addition, pads, film, nanowells, or microfluid channels can also serve as a solid support. In some embodiments, reactive antibodies may be immobilized, bound or linked on a solid or semi-solid surface such as polyvinylidene difluoride, nitrocellulose, agarose, and/or polyacrylamide gel pads. Glass slides activated with aldehyde, polylysine, or a homofunctional cross-linker can also been used.

[0062] PCR - The most commonly used methods known in the art for detection of nucleic acids in a sample, for example, expression of mRNA in a biological sample include southern blotting, northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283 (1999)); RNAse protection assays (Hod, Biotechniques 13:852-854 (1992)); and PCR-based methods, such as RACE (rapid amplification of cDNA ends) or reverse transcription polymerase chain reaction (RT-PCR) (Weis et al., Trends in Genetics 8:263-264 (1992)). Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS), Comparative Genome Hybridisation (CGH), Chromatin Immunoprecipitation (ChIP), Single nucleotide polymorphism (SNP) and SNP arrays, Fluorescent in situ Hybridization (FISH), Protein binding arrays and DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array), or RNA microarrays. [0063] Reverse Transcriptase PCR (RT-PCR): One of the most sensitive and most flexible quantitative PCR-based gene expression profiling methods is RT-PCR, which can be used to compare mRNA levels in different samples to characterize patterns of gene expression, to discriminate between closely related mRNAs, or to analyze RNA structure. [0064] The first step is the isolation of mRNA from a biological sample. For example, the starting material can be typically total RNA isolated from blood or tissue. mRNA can also be extracted, for example, from frozen or archived fixed tissues, for example paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples. General methods for mRNA extraction are well known in the art and are disclosed in standard textbooks of molecular biology, including Ausubel et al., Current Protocols of Molecular Biology, John Wiley and Sons (1997).

[0065] In particular, RNA isolation can be performed using purification kit, buffer set and protease from commercial manufacturers, according to the manufacturer's instructions. RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation. As RNA cannot serve as a template for PCR, the first step in gene expression profiling and identification by RT-PCR is the reverse transcription of the RNA template into cDNA, followed by its exponential amplification in a PCR reaction. The two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling. The derived cDNA can then be used as a template in the subsequent PCR reaction.

[0066] To minimize errors and the effect of sample-to-sample variation, RT-PCR is usually performed using an internal standard. The ideal internal standard is expressed at a constant level among different tissues, and is unaffected by the experimental treatment. RNAs most frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and β-actin.

[0067] A more recent variation of the RT-PCR technique is real time quantitative PCR, which measures PCR product accumulation through a dual-labeled fluorigenic probe. Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR.

[0068] In addition to RT-PCR, identification of microbial agents may also be obtained through amplification of genomic DNA. Amplification of unique non-coding regions, for example, operons, upstream control elements or other regions of a specific microbial infective agent may allow for specificity when designing probes sets for carrying out these assays. To accomplish, genomic DNA may be obtained using any conventional means possible. Extraction of genomic DNA is well known to those of skill in the art, and can be performed, for example, using CsCl gradient purification, or through the use of commercial kits available for the purpose of isolating genomic DNA for PCR amplification.

[0069] Some embodiments of the invention include immunoassay for the identification of nucleic acid or proteins specific to the microbial infective agent and/or environmental allergen. In immunoblotting, e.g. western blots, proteins are electrophoretically separated and then identified through binding of its antibody. An immunoassay can be a competitive binding immunoassay where an analyte competes with a labeled antigen for a limited pool of antibody molecules (e.g. radioimmunoassay, EMIT). An immunoassay can also be non-competitive, where antibody is present in excess and is labeled. As analyte antigen complex is increased, the amount of labeled antibody-antigen complex may also increase (e.g. ELISA). Antibodies can be polyclonal if produced by antigen injection into an experimental animal, or monoclonal if produced by cell fusion and cell culture techniques. In immunoassay, the antibody may serve as a specific reagent for the analyte antigen.

[0070] Without limiting the scope and content of the present invention, some of the types of immunoassays are, by way of example only, RIAs (radioimmunoassay), enzyme immunoassays like ELISA (enzyme-linked immunosorbent assay), EMIT (enzyme multiplied immunoassay technique), microparticle enzyme immunoassay (MEIA), LIA (luminescent immunoassay), and FIA (fluorescent immunoassay). These techniques can be used to detect biological substances in the biological samples used herein. The antibodies - either used as primary or secondary ones - can be labeled with radioisotopes (e.g. 1251), fluorescent dyes (e.g. FITC) or enzymes (e.g. HRP or AP) which may catalyse fluorogenic or luminogenic reactions, as described above.

[0071] Biotin, or vitamin H is a co-enzyme which inherits a specific affinity towards avidin and streptavidin. This interaction makes biotinylated peptides a useful tool in various biotechnology assays for quality and quantity testing. To improve biotin/streptavidin recognition by minimizing steric hindrances, it can be necessary to enlarge the distance between biotin and the peptide itself. This can be achieved by coupling a spacer molecule (e.g., 6-aminohexanoic acid) between biotin and the peptide.

[0072] The biotin quantitation assay for biotinylated proteins provides a sensitive fluorometric assay for accurately determining the number of biotin labels on a protein. Biotinylated peptides are widely used in a variety of biomedical screening systems requiring immobilization of at least one of the interaction partners onto streptavidin coated beads, membranes, glass slides or microtiter plates. The assay is based on the displacement of a ligand tagged with a quencher dye from the biotin binding sites of a reagent. To expose any biotin groups in a multiply labeled protein that are sterically restricted and inaccessible to the reagent, the protein can be treated with protease for digesting the protein. [0073] EMIT is a competitive binding immunoassay that avoids the usual separation step. A type of immunoassay in which the protein is labeled with an enzyme, and the enzyme-protein-antibody complex is enzymatically inactive, allowing quantitation of unlabelled protein. Some embodiments of the invention include an ELISA assay to analyze the environmental allergens and/or microbial infective agents. ELISA is based on selective antibodies attached to solid supports combined with enzyme reactions to produce systems capable of detecting low levels of proteins. It is also known as enzyme immunoassay or EIA. The protein is detected by antibodies that have been made against it, that is, for which it is the antigen. Monoclonal antibodies are often used.

[0074] The test may require the antibodies to be fixed to a solid surface, such as the inner surface of a test tube, and a preparation of the same antibodies coupled to an enzyme. The enzyme may be one (e.g., β-galactosidase) that produces a colored product from a colorless substrate. The test, for example, may be performed by filling the tube with the antigen solution (e.g., protein) to be assayed. Any antigen molecule present may bind to the immobilized antibody molecules. The antibody-enzyme conjugate may be added to the reaction mixture. The antibody part of the conjugate binds to any antigen molecules that were bound previously, creating an antibody-antigen-antibody "sandwich". After washing away any unbound conjugate, the substrate solution may be added. After a set interval, the reaction is stopped (e.g., by adding 1 N NaOH) and the concentration of colored product formed is measured in a spectrophotometer. The intensity of color is proportional to the concentration of bound antigen. [0075J ELISA can also be adapted to measure the concentration of antibodies, in which case, the wells are coated with the appropriate antigen. The solution (e.g., serum) containing antibody may be added. After it has had time to bind to the immobilized antigen, an enzyme-conjugated anti- immunoglobulin may be added, consisting of an antibody against the antibodies being tested for. After washing away unreacted reagent, the substrate may be added. The intensity of the color produced is proportional to the amount of enzyme-labeled antibodies bound (and thus to the concentration of the antibodies being assayed).

[0076] The filter membrane method may be needed when receptors cannot be fixed to 96 well plates or when ligand binding needs to be done in solution phase. In other words, after ligand-receptor binding reaction in solution, if the reaction solution is filtered through nitrocellulose filter paper, small molecules including ligands may go through it and only protein receptors may be left on the paper. Only ligands that strongly bound to receptors may stay on the filter paper and the relative affinity of added compounds can be identified by quantitative analysis of the standard radioactive ligands. [0077] Some embodiments of the invention may include fluorescence immunoassays for the identification and analysis of microbial infective agents and/or environmental allergens. Fluorescence based immunological methods are based upon the competitive binding of labeled ligands versus unlabeled ones on highly specific receptor sites. The fluorescence technique can be used for immunoassays based on changes in fluorescence lifetime with changing analyte concentration. This technique may work with short lifetime dyes like fluorescein isothiocyanate (FITC) (the donor) whose fluorescence may be quenched by energy transfer to eosin (the acceptor). A number of photoluminescent compounds may be used, such as cyanines, oxazines, thiazines, porphyrins, phthalocyanines, fluorescent infrared-emitting polynuclear aromatic hydrocarbons, phycobiliproteins, squaraines and organo-metallic complexes, hydrocarbons and azo dyes.

[0078] Fluorescence based immunological methods can be, for example, heterogenous or homogenous. Heterogenous immunoassays comprise physical separation of bound from free labeled analyte. The analyte or antibody may be attached to a solid surface. The technique can be competitive (for a higher selectivity) or noncompetitive (for a higher sensitivity). Detection can be direct (only one type of antibody used) or indirect (a second type of antibody is used). Homogenous immunoassays comprise no physical separation. Double-antibody fluorophore— labeled antigen participates in an equilibrium reaction with antibodies directed against both the antigen and the fluorophore. Labeled and unlabeled antigen may compete for a limited number of anti-antigen antibodies.

[0079] Some of the fluorescence immunoassay methods include simple fluorescence labeling method, fluorescence resonance energy transfer (FRET), time resolved fluorescence (TRF), and scanning probe microscopy (SPM). The simple fluorescence labeling method can be used for receptor-ligand binding, enzymatic activity by using pertinent fluorescence, and as a fluorescent indicator of various in vivo physiological changes such as pH, ion concentration, and electric pressure. TRF is a method that selectively measures fluorescence of the lanthanide series after the emission of other fluorescent molecules is finished. TRF can be used with FRET and the lanthanide series can become donors or acceptors. In scanning probe microscopy, in the capture phase, for example, at least one monoclonal antibody is adhered to a solid phase and a scanning probe microscope is utilized to detect antigen/antibody complexes which may be present on the surface of the solid phase. The use of scanning tunneling microscopy eliminates the need for labels which normally is utilized in many immunoassay systems to detect antigen/antibody complexes. [0080] Protein identification methods: By way of example only, protein identification methods include low-throughput sequencing through Edman degradation, mass spectrometry techniques, peptide mass fingerprinting, de novo sequencing, and antibody-based assays. The protein quantification assays include fluorescent dye gel staining, tagging or chemical modification methods (i.e. isotope-coded affinity tags (ICATS), combined fractional diagonal chromatography (COFRADIC)). The purified protein may also be used for determination of three-dimensional crystal structure, which can be used for modeling intermolecular interactions. Common methods for determining three-dimensional crystal structure include x-ray crystallography and NMR spectroscopy. Characteristics indicative of the three-dimensional structure of proteins can be probed with mass spectrometry. By using chemical crosslinking to couple parts of the protein that are close in space, but far apart in sequence, information about the overall structure can be inferred. By following the exchange of amide protons with deuterium from the solvent, it is possible to probe the solvent accessibility of various parts of the protein. [0081] In one embodiment, fluorescence-activated cell-sorting (FACS) is used to identify cells that express the microbial infectious agent. FACS is a specialised type of flow cytometry. It provides a method for sorting a heterogenous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell. It provides quantitative recording of fluorescent signals from individual cells as well as physical separation of cells of particular interest. In yet another embodiment, microfluidic based devices are used to evaluate expression of the identified differentially regulated genes.

[0082] Mass spectrometry can also be used to characterize expression of microbial infective agents from patient samples. The two methods for ionization of whole proteins are electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). In the first, intact proteins are ionized by either of the two techniques described above, and then introduced to a mass analyser. In the second, proteins are enzymatically digested into smaller peptides using an agent such as trypsin or pepsin. Other proteolytic digest agents are also used. The collection of peptide products are then introduced to the mass analyser. This is often referred to as the "bottom-up" approach of protein analysis. [0083] Whole protein mass analysis is conducted using either time-of-flight (TOF) MS, or Fourier transform ion cyclotron resonance (FT-ICR). The instrument used for peptide mass analysis is the quadrupole ion trap. Multiple stage quadrupole- time-of-fiight and MALDI time-of-flight instruments also find use in this application.

[0084] Two methods used to fractionate proteins, or their peptide products from an enzymatic digestion. The first method fractionates whole proteins and is called two-dimensional gel electrophoresis. The second method, high performance liquid chromatography is used to fractionate peptides after enzymatic digestion. In some situations, it may be necessary to combine both of these techniques.

[0085] There are two ways mass spectroscopy can be used to identify proteins. Peptide mass uses the masses of proteolytic peptides as input to a search of a database of predicted masses that would arise from digestion of a list of known proteins. If a protein sequence in the reference list gives rise to a significant number of predicted masses that match the experimental values, there is some evidence that this protein was present in the original sample.

[0086] Tandem MS is also a method for identifying proteins. Collision-induced dissociation is used in mainstream applications to generate a set of fragments from a specific peptide ion. The fragmentation process primarily gives rise to cleavage products that break along peptide bonds. [0087] A number of different algorithmic approaches have been described to identify peptides and proteins from tandem mass spectrometry (MS/MS), peptide de novo sequencing and sequence tag based searching. One option that combines a comprehensive range of data analysis features is PEAKS. Other existing mass spec analysis software include: Peptide fragment fingerprinting SEQUEST, Mascot, OMSSA and XITandem).

[0088] Proteins can also be quantified by mass spectrometry. Typically, stable (e.g. non-radioactive) heavier isotopes of carbon (C 13) or nitrogen (Nl 5) are incorporated into one sample while the other one is labelled with corresponding light isotopes (e.g. C12 and N14). The two samples are mixed before the analysis. Peptides derived from the different samples can be distinguished due to their mass difference. The ratio of their peak intensities corresponds to the relative abundance ratio of the peptides (and proteins). The methods for isotope labelling are SILAC (stable isotope labelling with amino acids in cell culture), trypsin-catalyzed Ol 8 labeling, ICAT (isotope coded affinity tagging), ITRAQ (isotope tags for relative and absolute quantitation). "Semi-quantitative" mass spectrometry can be performed without labeling of samples. Typically, this is done with MALDI analysis (in linear mode). The peak intensity, or the peak area, from individual molecules (typically proteins) is here correlated to the amount of protein in the sample. However, the individual signal depends on the primary structure of the protein, on the complexity of the sample, and on the settings of the instrument.

[0089] N-terminal sequencing aids in the identification of unknown proteins, confirm recombinant protein identity and fidelity (reading frame, translation start point, etc.), aid the interpretation of NMR and crystallographic data, demonstrate degrees of identity between proteins, or provide data for the design of synthetic peptides for antibody generation, etc. N- terminal sequencing utilises the Edman degradative chemistry, sequentially removing amino acid residues from the N- terminus of the protein and identifying them by reverse-phase HPLC. Sensitivity can be at the level of 100s femtomoles and long sequence reads (20-40 residues) can often be obtained from a few 10s picomoles of starting material. Pure proteins (>90%) can generate easily interpreted data, but insufficiently purified protein mixtures may also provide useful data, subject to rigorous data interpretation. N-terminally modified (especially acetylated) proteins cannot be sequenced directly, as the absence of a free primary amino-group prevents the Edman chemistry. However, limited proteolysis of the blocked protein (e.g. using cyanogen bromide) may allow a mixture of amino acids to be generated in each cycle of the instrument, which can be subjected to database analysis in order to interpret meaningful sequence information. C-terminal sequencing is a post- translational modification, affecting the structure and activity of a protein. Various disease situations can be associated with impaired protein processing and C-terminal sequencing provides an additional tool for the investigation of protein structure and processing mechanisms.

[0090] Vaccines - In another embodiment of the invention, the immunoreactive polypeptides (including allergens) or structural analogs of epitopes, may be prepared by conventional means into vaccines. Vaccines may be prepared from one or more immunogenic polypeptides isolated from the microbial infective agents. If made by recombinant technology, these polypeptides are suitably expressed in a variety of host cells (e.g., bacteria, yeast, insect, or mammalian cells). Alternatively, the antigens may be isolated from microbial preparations or prepared synthetically if the amino acid sequence is known. [0091] The preparation of vaccines which contain, as active ingredients, an immunogenic polypeptide or structural analog having epitopes is known to one skilled in the art. Typically, such vaccines are prepared as injectable liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in a liquid prior to injection are also prepared. The preparation may also be emulsified, or the protein encapsulated in liposomes. [0092] The active immunogenic ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine. [0093] The vaccines are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably l%-2%. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate,-sodium saccharine, cellulose, magnesiumcarbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations, oral sprays, transdermal patch or powders and contain 10%-95% of active ingredient, preferably 25%-70%. [0094] Vaccines within the present invention are administered in a manner compatible with the dosage formulation, and in such amount as will be prophylactically and/or therapeutically effective. The quantity to be administered, which is generally in the range of about 5 micrograms to about 250 micrograms of antigen per dose, depends on the subject to be treated, capacity of the subject's immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered may depend on the judgment of the practitioner and may be peculiar to each subject.

[0095] The vaccine may be given in a single dose schedule, or preferably in a multiple dose schedule. A multiple dose schedule is one in which a primary course of vaccination may be with 1-10 separate doses, followed by other doses given at subsequent time intervals required to maintain and or reenforce the immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose(s) after several months. The dosage regimen is also, at least in part, determined by the need of the individual and be dependent upon the judgment of the practitioner.

[0096] Alternatively, the vaccine may be prepared using bioelectric replications from computer-generated electromagnetic signals. One example of the use of electromagnetic signals for treatment of disease states in seen in U.S. Patent No. 6,142,927, which is fully incorporated by reference therein. A product capsule, which represents an identified bacteria, virus, microbe and/or an infective agent mathematical replica, may be held in either a programmable solution by a series of binary numbers or a computer memory. Such information may be transmitted via several methods; e.g. radio frequency, antenna, and other transmission means. This method may also enhance the strength of such solution by the number of binary sequences. The information of said infective agents may be represented by such binary memory capsules, thus carrying only the coded infective information and none of the infectivity of the infective sample. Such method then permits a non-infective replica to be safely used by the body as a mirage of the original, which can be rotated either cis or trans to stimulate an immune response as desired.

[0097] The administration of a variety of agents or processes may act to alter the resistance value in an individual. One means of altering resistance values include the application of electromagnetic signals to the individual. Such electromagnetic signals can be generated through the measurement of resistance values upon application of a defined electrical and magnetic energy to an individual. U.S. Patent No. 6,142,297 describes one means of defining and administering an electrical and magnetic signal, including the use of a computer generated binary value to define a resonant signal. A vaccine can be produced based on the electromagnetic binary value necessary to produce an alteration in resistance value, and administered to a patient to treat an underlying microbial infective agent.

[0098] Treatment - Also contemplated within the present invention is the treatment of an individual diagnosed with an allergic reaction. This method includes the steps of: 1) diagnosing the traditional allergen responsible; 2) determining the correlative underlying infectious agent; and 3) treating said patient with a medicament or system that may reduce or eliminate the infectious agent from the patient. Identification of the causative microbial infectious agent may be through the methods disclosed herein. Alternatively, treatment may occur based on questionnaires presented by said individual afflicted with the allergic reaction. The questionnaire may present a series of questions regarding the environmental factors or stimuli that may affect said patient. The questionnaire may also reveal previous tests performed, and results of the tests. For example, a skin prick test may have already revealed said patient's sensitivity to cat dander or pollen. Results from the questionnaire may be correlated with knowledge obtained previously on correlative tests performed to determine which underlying microbial infectious agent is involved in said patient's allergic reaction.

[0099] Another embodiments includes the treatment of an individual diagnosed with a limited or non- immune related disorder. This method includes the steps of: 1) identifying a biological or environmental agent in a biological sample; 2) determining a microbial or pathogenic infective agent that correlates with the identified biological or environmental agent from a correlative library comprising information correlating a known biological or environmental agent with a microbial or pathogenic infective agent; or alternatively, determining the underlying microbial or pathogenic infective agent through assays that identify such agents; and 3) treating the individual with an agent that eradicates or ameliorates the pathogenic or microbial infective agent.

[00100] Yet another embodiment includes the elimination or treatment of a microbial or pathogenic infective agent in an environmental source, which includes the steps of: 1) providing a sample from the environmental source; 2) identifying the infective pathogen or microbial agent in the environmental source; and 3) treating or eliminating the infective pathogen or microbe from the environmental source.

[00101] After identification of the causative microbial agent, conventional treatment with medicaments towards the reduction or eradication of the identified microbial agents are also contemplated. Such medicaments may include, but are not limited to, antibiotics, including pencillins, cephalosporins, tetracyclines, erythromycin, beta-lactams, sulfa drugs, including sulfonamides, and antifungal antibiotics, aminoglycosides, ansamycins, carbacepham, carbapenems, macrolides, quinolones, small molecule inhibitors polypeptides, anti-viral agents, including nucleoside analogues and interferon therapies, such as acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine and protease inhibitors.

[00102] Alternatively, phage therapy, either bacterial or viral, interleukin-interferon manipulation, or any other means of reducing or eliminating the underlying infectious agent, may be used to reduce or eliminate the underlying microbial infective agent. Phage therapy, either bacterial or viral, administers a viral-bacterial match or a bacterial/viral match whereby a practitioner identifies a virus that is capable of eliminating the identified bacteria in vivo or a bacteria which is capable of eliminating the identified virus in vivo. By selectively administering the specific virus or bacterial, targeting of the identified bacterial or viral species can be accomplished by invasion of the bacteria by the virus and/or providing the preferred bacteria for viral invasion and elimination in vivo. [00103] Formulations - Provided herein are formulations for oral or topical administration of the compositions disclosed herein. In certain aspects, the oral formulations are formulated with pharmaceutically acceptable carriers or excipients. Such carriers enable the compositions to be formulated as tablets, powders, pills, dragees, capsules, liquids, gels, syrups, elixirs, slurries, suspensions and the like, for oral, ingestion by a patient to be treated.

[00104] Methods for the preparation of compositions containing the active agents described herein include formulating the compounds with one or more inert, pharmaceutically acceptable excipients or carriers to form a solid, semi-solid or liquid. Solid compositions include, but are not limited to, powders, tablets, dispersible granules, capsules, cachets, and suppositories. Liquid compositions include solutions in which a compound is dissolved, emulsions comprising a compound, or a solution containing liposomes, micelles, or nanoparticles comprising a compound as disclosed herein. Semi-solid compositions include, but are not limited to, gels, suspensions and creams. In various embodiments, the compositions are in liquid solutions or suspensions, solid forms suitable for solution or suspension in a liquid prior to use, or as emulsions. These compositions optionally contain minor amounts of nontoxic, auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, and so forth.

[00105] In some embodiments, a composition comprising an agent described herein takes the form of a liquid where the agents are present in solution, in suspension or both. In some embodiments, when the composition is administered as a solution or suspension a first portion of the agent is present in solution and a second portion of the agent is present in particulate form, in suspension in a liquid matrix. In some embodiments, a liquid composition includes a gel formulation. In other embodiments, the liquid composition is aqueous.

[00106] In some embodiments, pharmaceutical preparations for oral use are obtained by mixing one or more solid excipient with one or more of the agents described herein, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as: for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others such as: polyvinylpyrrolidone (PVP or povidone) or calcium phosphate. If desired, disintegrating agents are optionally added, such as the cross-linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

[00107] In certain embodiments, compositions include orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. In some embodiments, the push- fit capsules contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In certain embodiments, in soft capsules, the active compounds are dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers are optionally added. In certain embodiments, the formulations for oral administration are in dosages suitable for such administration.

[00108] In certain embodiments, the oral compositions are formulated for buccal or sublingual administration. In certain embodiments, buccal or sublingual compositions take the form of tablets, lozenges, or gels formulated in a conventional manner. In certain embodiments, parenteral injections involve bolus injection or continuous infusion. In some embodiments, formulations for injection are presented in unit dosage form, e.g. , in ampoules or in multi-dose containers, with an added preservative. In some embodiments, the compositions disclosed herein are in a form suitable for parenteral injection as a sterile suspension, solution or emulsion in oily or aqueous vehicles, and optionally contains formulatory agents such as suspending, stabilizing and/or dispersing agents. In some embodiments, suspensions of the active compounds are prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. In certain embodiments, aqueous injection suspensions contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspensions also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. In alternative embodiments, the active ingredient is in powder form for constitution with a suitable vehicle, e.g. , sterile pyrogen-free water, before use.

[00109] In some embodiments, the active agents disclosed herein are administered topically, such as solutions, suspensions, lotions, gels, pastes, medicated sticks, balms, creams or ointments. Such compositions optionally contain solubilizers, stabilizers, tonicity enhancing agents, buffers and/or preservatives. Compositions suitable for topical application to a subject or to a non-physiological surface or system preferably take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers which may be used include Vaseline, lanolin, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof.

[00110] In certain embodiments, the compositions provided herein are formulated for transdermal administration. In some embodiments, administration of such compositions employs transdermal delivery devices and transdermal delivery patches. Such patches include those constructed for continuous, pulsatile, or on demand delivery of pharmaceutical agents. In some embodiments, transdermal delivery of the compounds described herein is accomplished by use of iontophoretic patches and the like. In certain embodiments, the rate of absorption is slowed by using rate-controlling membranes or by trapping the compound within a polymer matrix or gel. Conversely, absorption enhancers are optionally used to increase absorption. Absorption enhancer and carrier include absorbable pharmaceutically acceptable solvents that assist in passage of the compound through the skin. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.

[00111] In certain embodiments, the compositions are formulated for administration by inhalation. In certain embodiments, in such pharmaceutical compositions formulated for inhalation, the compounds described herein are in a form as an aerosol, a mist or a powder. In some embodiments, pharmaceutical compositions described herein are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifiuoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In certain aspects of a pressurized aerosol, the dosage unit is determined by providing a valve to deliver a metered amount. In certain embodiments, capsules and cartridges of, such as, by way of example only, gelatin for use in an inhaler or insufflator is formulated containing a powder mix of the compound described herein and a suitable powder base such as lactose or starch. [00112] In some embodiments, the compositions are formulated in rectal compositions such as enemas, rectal gels, rectal foams, rectal aerosols, suppositories, jelly suppositories, or retention enemas. In certain embodiments, rectal compositions optionally contain conventional suppository bases such as cocoa butter or other glycerides, as well as synthetic polymers such as polyvinylpyrrolidone, PEG, and the like. In certain suppository forms of the compositions, a low-melting wax such as, but not limited to, a mixture of fatty acid glycerides, optionally in combination with cocoa butter is first melted. [00113] In certain embodiments, the compositions include at least one pharmaceutically acceptable carrier, diluent or excipient and a therapeutic agent described herein. In some embodiments, the compositions described herein include other medicinal or pharmaceutical agents, carriers, adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure, and/or buffers. In additional embodiments, the compositions described also contain other therapeutically valuable substances.

EXAMPLES

Treatment of Allergy Subjects

[00114] Patients suitable for allergy treatment range in age from toddlers and children to older adults in their 60's and 70's. Most patients appear after they have seen a number of both traditional physicians and sometimes alternative physicians without clinical result. Types of cases include autism, Lyme disease, Parkinson's disease, chronic fatigue, skin issues, chronic allergies, chronic infections and emotional/psychiatric disorders.

[00115] An examination is performed to determine if an altered autonomic nervous system response is present. Such examinations include a Heart Rate Variability Test, as well as a Bio Impedance Analysis, which may show decreased intracellular hydration and increased extracellular hydration, as well as changes in cellular phase angle. Other specific laboratory tests include circadian Cortisol release, as well as decreased secretory IgA markers, food allergies and specific biomarkers for various diseases; Crohn's disease, type I diabetes, multiple sclerosis, parasites and other specific and known laboratory markers. In addition to the laboratory tests, energetic evaluations are also performed. Decreased energy production in a patient is often accompanied by abnormalities of immune function resulting in an inability to maintain an immune response under static or stressed conditions.

[00116] A blood sample from the patient is drawn and a RAST test is performed on the sample. The RAST assay identifies immunoreactivity of a sample to known allergens, including animal dander, food allergens and other environmental allergens. Identified allergens or antigens are noted for the patient and the results compared to test results identifying microbes or pathogens found in the patient.

[00117] Cross-matching or manually biopanning a patient's response to multiple bacterial samples is also performed. A candidate for further testing is then selected. The positive response to the bacterial sample is then cross tested to identify the type of reactivity, either allergic or infective. Further testing of the selected bacteria along with a neutralizer may show reactivity to viral samples. This cross reactivity of the neutralized bacterial sample to the target virus is also done in a manual biopanning method until the target virus or pathogen and/or serotype is identified. Other techniques include short cycling peptidic immune response to induce amino acid sequence modifications and resultant stimulation of the THl or TH2 response. Other assays for determining relationships may include amino acid sequence determination, structural pattern recognition, automated biopanning, B.L.A.S.T. searches and real time PCR. The ultimate result of this technique identification process would be the automation of a testing platform. A less immediate goal is the identification of a bacterial/viral relationship for specific phage like treatment protocol resultant from the tests above. Phage display and any method of biopanning suitable for automation may also be used in the identification of bacterial/viral relationship for a specific phage-like treatment.

[00118] Once the virus, bacteria or pathogen is identified, a bioelectrical inversion and/or modification of the virus, bacteria or pathogen is tested to determine efficacy in the elimination of patient test responses. Final treatment is with a bioelectrical or bio resonant inversion and/or modified footprint of the causative agent (virus or bacteria), as what may be thought of as a homeopathically phage either bacterial or viral - i.e. Homeophage™. In an allergy protocol the allergen is cross tested to bacterial samples or bioelectric libraries in a manual or automated biopanning manner. The resultant matching bacteria is then further cross matched to the virus for Homeophage preparation.

REFERENCES

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9. Guameri et al, Identification of Potentially Cross-Reactive Peanut-Lupine Proteins by Computer-Assisted Search for Amino Acid Sequence Homology, Allergy and Immunology 138(4) (2005)

10. Czerkinsky et al, IgA Antibody-Producing Cells in Peripheral Blood after Antigen Ingetion:Evidence for a Common Mucosal Immune System in Humans, PNAS 84(8):2449-2453 (Apr. 1987)

11. Basagana et al, Allergy to human seminal fluid:Cross-reactivity with dog dander, J Allergy Clin Immunol, (Nov. 2007)

12. Holgate, Stephen T, Science, medicine, and the future; Allergic disorders, BMJ 320:231-234 (Jan. 2000)

13. Meitin et al, Influenza immunization: intranasal live vaccinia recombinant contrasted with parenteral inactivated vaccine, Vaccine 9(10):751-6 (Oct. 1991)

14. Moldoveanu et al, Human immune responses to influenza virus vaccines administered by systemic or mucosal routes, Vaccine 13(l l):1006-12 (Aug. 1995)

15. Weisz-Carrington et al, Organ and Isotype Distribution of Plasma Cells Producing Specific Antibody after Oral Immunization: Evidence for A Generalized Secretory Immune System, Journal of Immunology 123:1705-1708 (1979)

16. Wines et al, IgA receptors in health and disease, Tissue Antigens 68(2):103-l 14 (Aug. 2006)

17. Elfaitouri et al., Quantitative PCR-enhanced immunoassay for measurement of enteroviral immunoglobulin M antibody and diagnosis of aseptic meningitis, Clin. Diagnostic Lab. Immun. 12:235-241 (Feb. 2005). [00119] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

WHAT IS CLAIMED IS:

1. A method for creating a correlative library for detecting and identifying an underlying microbial or pathogenic infective agent in individuals afflicted with an immune disorder, the method comprising:

(a) providing a biological sample from a plurality of individuals afflicted with an immune disorder;

(b) reacting each biological sample from the plurality of individuals with an antigen library;

(c) detecting the presence of antigen-immunoglobulin complexes in each sample in (b) and identifying the antigen in said antigen-immunoglobuling complex(es);

(d) identifying the underlying infective pathogen in said plurality of individuals;

(e) correlating the identified antigen(s) with the identified underlying infective pathogen in said individuals; and

(fj collecting said correlative information to create a correlative library for detecting and identifying said underlying microbial or pathogenic infective agent.

2. The method of claim 1, wherein the assay to identify the antigen is RAST.

3. The method of claim 1, wherein the immunoglobulin is IgG, IgM, IgA or IgE.

4. The method of claim 1, wherein the immunoglobulin is IgE.

5. The method of claim 1, wherein the assay to identify the underlying infective microbe or pathogen is PCR.

6. The method of claim 5, wherein the PCR assay is QRT-PCR enhanced immunoassay.

7. The method of claim 1, wherein the assay to identify the underlying infective microbe or pathogen is a bioelectric signature detection assay.

8. The method of claim 7, wherein the bioelectric signature detection assay is galvanic skin response or acupuncture point testing.

9. A method for creating a correlative library for detecting and identifying an underlying microbial or pathogenic infective agent in individuals afflicted with a limited or non-immune system related disorder, the method comprising:

(a) providing a biological sample from a plurality of individuals afflicted with a limited or nonimmune system related disorder;

(b) identifying a biological or environmental agent in said biological sample;

(c) identifying the underlying infective pathogen or microbe in said plurality of individuals;

(d) correlating the identified antigen(s) with the identified underlying infective pathogen or microbe in said individuals; and

(e) collecting said correlative information to create a correlative library for detecting and identifying said underlying microbial or pathogenic infective agent in individuals afflicted with a limited or nonimmune system related disorder.

10. The method of claim 9, wherein the assay to identify the biological or environmental agent is PCR.

11. The method of claim 10, wherein the PCR assay is QRT-PCR enhanced immunoassay.

12. The method of claim 9, wherein the assay to identify the biological or environmental agent is an immunoassay.

13. The method of claim 12, wherein the immunoassay is ELISA, RIA, EMIT, MEIA, LIA or FIA.

14. The method of claim 9, wherein the assay to identify the underlying infective microbe or pathogen is a bioelectric signature detection assay.

15. The method of claim 14, wherein the bioelectric signature detection assay is galvanic skin response or acupuncture point testing.

16. The method of claim 9, wherein the assay to identify the underlying infective microbe or pathogen is PCR.

17. The method of claim 16, wherein the PCR assay is QRT-PCR enhanced immunoassay.

18. A method for treatment of an individual afflicted with an immune disorder, the method comprising the steps of:

(a) identifying an allergenic antigen in the individual afflicted with an immune disorder;

(b) determining a microbial or pathogenic infective agent that correlates with said identified antigen from a correlative library of claim 1 ; and

(c) treating said individual with an agent that inhibits the microbial infective agent.

19. The method of claim 18, wherein the assay for identifying the allergenic antigen is RAST.

20. The method of claim 19, wherein the immunoglobulin antibody detected in the RAST assay is IgG, IgM, IgA or IgE.

21. The method of claim 19, wherein the immunoglobulin antibody detected in the RAST assay is IgE.

22. The method of claim 18, wherein the assay for identifying the allergenic antigen is PCR.

23. The method of claim 22, wherein the PCR assay is QRT-PCR enhanced immunoassay.

24. The method of claim 18, wherein the individual is treated with at least one anti-microbial agent, phage therapy, interleukin manipulation, interferon therapy, or a combination thereof.

25. The method of claim 18, wherein the individual is treated with an anti-microbial agent.

25. The method of claim 25, wherein the anti-microbial agent is an antibiotic, a penicillin, a cephalosporin, a tetracycline, an erythromycin, a beta-lactam, a sulfa drug, a sulfonamide, an antifungal antibiotic, an aminoglycoside, an ansamycin, a carbacepham, a carbapenem, a macrolide, aquinolone, a small molecule inhibitor, a polypeptide, an anti-viral agent, a nucleoside analog, an interferon, acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine, a protease inhibitor, or a mixture thereof.

26. The method of claim 18, wherein the individual is treated with phage therapy.

27. The method of claim 26, wherein the phage therapy is bacterial phage therapy or viral-phage therapy.

28. The method of claim 26, wherein the phage therapy is bioelectric bacterial phage therapy or bioelectric viral-phage therapy.

29. The method of claim 18, wherein the immune disorder is an allergy, a chronic illness, chronic fatigue, fibromyalgia, Lyme disease, Parkinson's disease, an autoimmune disorder, a skin condition, hair loss, asthma, polycystic liver disease, polycystic kidney disease, autism, cancer, mental illness or combinations thereof.

30. A method for treatment of an individual afflicted with an allergic reaction, the method comprising the steps of:

(a) identifying an allergen through a patient questionnaire form;

(b) determining a microbial or pathogenic infective agent that correlates with said identified antigen from a correlative library of claim 1; and (c) treating said individual with an agent that eradicates or ameliorates the pathogenic or microbial infective agent.

31. The method of claim 30, wherein the individual is treated with at least one anti-microbial agent, phage therapy, interleukin manipulation, interferon therapy, or a combination thereof.

32. The method of claim 30, wherein the individual is treated with an anti-microbial agent.

33. The method of claim 32, wherein the anti-microbial agent is an antibiotic, a penicillin, a cephalosporin, a tetracycline, an erythromycin, a beta-lactam, a sulfa drug, a sulfonamide, an antifungal antibiotic, an aminoglycoside, an ansamycin, a carbacepham, a carbapenem, a macrolide, aquinolone, a small molecule inhibitor, a polypeptide, an anti-viral agent, a nucleoside analog, an interferon, acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine, a protease inhibitor, or a mixture thereof.

34. The method of claim 30, wherein the individual is treated with phage therapy.

35. The method of claim 34, wherein the phage therapy is bacterial phage therapy or viral-phage therapy.

36. The method of claim 34, wherein the phage therapy is bioelectric bacterial phage therapy or bioelectric viral-phage therapy.

37. The method of claim 30 wherein the immune disorder is an allergy, a chronic illness, chronic fatigue, fibromyalgia, Lyme disease, Parkinson's disease, an autoimmune disorder, a skin condition, hair loss, asthma, polycystic liver disease, polycystic kidney disease, autism, cancer, mental illness or combinations thereof.

38. A vaccine for treatment of an individual afflicted with an allergic reaction, wherein the vaccine comprises an epitope to an identified microbial infective agent.

39. The vaccine of claim 38, wherein the epitope is a product capsule of the identified microbial infective agent.

40. A method for treatment of an individual afflicted with a limited or non-immune system related disorder, the method comprising:

(a) identifying a biological or environmental agent in a biological sample;

(b) determining a microbial or pathogenic infective agent that correlates with said identified biological or environmental agent from a correlative library of claim 9; and

(c) treating said individual with an agent that eradicates or ameliorates the pathogenic or microbial infective agent.

41. The method of claim 40, wherein the assay to identify the biological or environmental agent is PCR.

42. The method of claim 41, wherein the PCR assay is QRT-PCR enhanced immunoassay.

43. The method of claim 40, wherein the assay to identify the biological or environmental agent is an immunoassay.

44. The method of claim 43, wherein the immunoassay is ELISA, RIA, EMIT, MEIA, LIA or FIA.

45. The method of claim 40, wherein the individual is treated with at least one anti-microbial agent, phage therapy, interleukin manipulation, interferon therapy, or a combination thereof.

46. The method of claim 40, wherein the individual is treated with an anti-microbial agent.

47. The method of claim 46, wherein the anti-microbial agent is an antibiotic, a penicillin, a cephalosporin, a tetracycline, an erythromycin, a beta-lactam, a sulfa drug, a sulfonamide, an antifungal antibiotic, an aminoglycoside, an ansamycin, a carbacepham, a carbapenem, a macrolide, aquinolone, a small molecule inhibitor, a polypeptide, an anti-viral agent, a nucleoside analog, an interferon, acyclovir, gancyclovir, zidovudine, lamivudine, ribavirin, amantidine, a protease inhibitor, or a mixture thereof.

48. The method of claim 53, wherein the individual is treated with phage therapy interleukin manipulation, interferon therapy, or a combination thereof.

49. The method of claim 40, wherein the individual is treated with phage therapy.

50. The method of claim 49, wherein the phage therapy is bacterial phage therapy or viral-phage therapy.

51. The method of claim 49, wherein the phage therapy is bioelectric bacterial phage therapy or bioelectric viral-phage therapy.

52. A method for eliminating or treating a microbial or pathogenic infective agent in an environmental source, the method comprising:

(a) providing a sample from the environmental source;

(b) identifying the infective pathogen or microbe in the environmental source;

(c) treating or eliminating the infective pathogen or microbe from the environmental source with a phage therapy.

53 The method of claim 52, wherein the assay to identify infective pathogen or microbe in the environmental source is

PCR.

54. The method of claim 53, wherein the PCR assay is QRT-PCR enhanced immunoassay.

55. The method of claim 52, wherein the assay to identify the infective pathogen or microbe in the environmental source is an immunoassay.

56. The method of claim 55, wherein the immunoassay is ELISA, RIA, EMIT, MEIA, LIA or FIA.

57. The method of claim52 , wherein the assay to identify the infective pathogen or microbe is a bioelectric signature detection assay.

58. The method of claim 57, wherein the bioelectric signature detection assay is galvanic skin response or acupuncture point testing.

59. The method of claim 52, wherein the sample is an air or water sample.

60. The method of claim 52, wherein the sample is from an environmental surface.

61. The method of claim 52, wherein the phage therapy is bacterial phage therapy or viral-phage therapy.

62. The method of claim 52, wherein the phage therapy is bioelectric bacterial phage therapy or bioelectric viral-phage therapy.