Abstract:
The present disclosure provides immunogenic materials and methods useful for reducing the risk of fungal infections, particularly valley fever. The disclosure also provides assays for identifying compounds useful to treat valley fever, as well as methods for ameliorating the symptoms of valley fever.

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application claims the benefit of U.S. Provisional Application No. 61/776,770 filed Mar. 11, 2013, and U.S. Provisional Application No. 61/777,845 filed Mar. 12, 2013, the disclosures of which are incorporated herein by reference. 
     
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
       [0002]    This invention was made with government support under Grant No. PO1 AI061310 awarded by the National Institutes of Health (NIH). The government has certain rights in the invention. 
     
    
     REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB 
       [0003]    This application is being filed electronically via the USPTO EFS-WEB server, as authorized and set forth in MPEP§1730 II.B.2(a)(A), and this electronic filing includes an electronically submitted sequence (SEQ ID) listing. The entire content of this sequence listing is herein incorporated by reference for all purposes. The Sequence Listing, filed electronically and identified as 3726 — 54785_SEQ_LIST_UA12-127, was created on Mar. 7, 2014, is 34,266 kb in size. 
       SEQUENCE LISTING BRIEF DESCRIPTIONS 
       [0004]      
         [0000]    
       
         
               
               
             
           
               
                   
               
               
                 SEQ ID NO 
                 Brief Description 
               
               
                   
               
             
             
               
                 1 
                 Reference CPS1 gene product; protein; amino acid 
               
               
                   
                 sequence 
               
               
                 2 
                 Reference CPS1 genomic DNA; nucleic acid sequence 
               
               
                 3-10 
                 Primers 
               
               
                   
               
             
          
         
       
     
       BACKGROUND OF INVENTION 
       [0005]      Coccidioides  species ( C. immitis  and  C. posadasii ) are the causative agents of coccidioidomycosis (Valley Fever), an important emerging disease endemic to the southwestern US as well as parts of Mexico and central and South America. Infection begins with inhalation of arthroconidia that initiate the parasitic phase in lungs and can result in a respiratory infection or if not controlled, a more serious disseminated disease. 
         [0006]      Coccidioides  spp. are dimorphic and produce a unique parasitic phase structure, the spherule, via a switch from polar to isotrophic growth with the spherule expanding from a barrel-shaped arthrocondium that is 3-6 μm by 2-4 μm in size to a sphere 80-100 microns in diameter. Internal septation and spore formation results in production of hundreds of endospores that if released can disseminate and reinitiate spherule formation at other places in the body. Most infections are mild and resolve without medical intervention although about 30% of infections cause flu-like symptoms that may take 1-4 months to resolve. 
         [0007]    A variety of approaches have been used to understand genes important for the parasitic phase of these and other fungi. These include random mutagenesis, targeted disruption of parasitic phase-specific genes and targeted mutagenesis of genes identified in other pathogens as virulence factors. In addition, expression analyses have been performed to identify phase-specific or phase-induced genes. For  Coccidioides , both expression analyses and the latter two mutagenesis approaches have been used, resulting in a number of mutants, some of which are altered in virulence. For example, SOWgp and MEP1 have been knocked out and the resulting mutant strains are reduced in virulence. 
         [0008]    Over the last 50 years, many approaches to vaccination against coccidioidomycosis have been tried, including whole killed cells, live mutant vaccines that have been modified in virulence, partially purified cellular extracts, and recombinant proteins that were identified by a myriad of both low and high technology methods. To date, killed whole cell vaccines provide the best protection in mice but are not transferable to humans because of intolerable adverse effects and poor efficacy. Recombinant proteins offer the safest approach but have modest efficacy in mice and have not been tried in a higher species. 
       SUMMARY OF THE INVENTION 
       [0009]    Without being held to any particular theory, the inventors have discovered a gene in fungi, which, if disrupted, results in leaky or otherwise more vigorous immune response-provoking variations on the wild type fungus. Further, these cyclic peptide synthase Cps1 analog (CPS1), “CPS1 analog” deletion mutant fungal spores are not virulent; introduction of the immunogens will not result in immunogen-induced pathology in an animal exposed to the immunogen. 
         [0010]    The inventors demonstrate herein that CPS1 is essential for virulence in the mouse model of coccidioidomycosis and that pre-infection of mice with a CPS1 mutant strain protects mice against subsequent infection with wild type  Coccidioides.    
         [0011]    The present disclosure therefore provides compositions comprising a fungus having a dysfunctional CPS1 gene product, wherein the composition is avirulent and capable of inducing an immune response in a mammal. 
         [0012]    Also provided are such compositions, wherein the dysfunctional CPS1 gene product is a result of a deletion of at least a portion of the CPS1 gene. 
         [0013]    Also provided are such compositions, wherein the dysfunctional CPS1 gene product is a result of a deletion in a region of the CPS1 gene selected from the group consisting of: at least about the entire CPS1 gene; at least about the entire DMAP region of the CPS1 gene; at least about an entire AMP binding domain region of the CPS1 gene; a regulatory element of the CPS1 gene; at least the coding sequence of the CPS1 gene; at least about 90% of the CPS1 gene; at least about 80% of the CPS1 gene; at least about 70% of the CPS1 gene; at least about 60% of the CPS1 gene; at least about 50% of the CPS1 gene; at least about 40% of the CPS1 gene; at least about 30% of the CPS1 gene; at least about 20% of the CPS1 gene; at least about 10% of the CPS1 gene. 
         [0014]    Also provided are such compositions, wherein the dysfunctional CPS1 gene product is a result of deletion of the entire CPS1 gene. 
         [0015]    Also provided are such compositions, wherein the composition is capable of inducing an immune response as a result of secretion of a metabolite or small molecule. 
         [0016]    Also provided are such compositions, wherein the composition is capable of inducing an immune response selected from the group consisting of: neutrophil invasion; granuloma formation; resistance to mycosis; and immunity to mycosis. 
         [0017]    Also provided are such compositions, wherein the fungus is a  Coccidioides  spp. 
         [0018]    Also provided are such compositions, wherein the composition is capable of inducing resistance to coccidioidomycosis (valley fever). 
         [0019]    Also provided are such compositions, wherein the composition is capable of inducing immunity to coccidioidomycosis (valley fever). 
         [0020]    Also provided are such compositions, wherein the fungal cell is selected from the group consisting of:  Coccidioides immitis; Coccidioides posadasii; Aspergillus fumigatus; Aspergillus flavus; Histoplasma capsulatum; Blastomyces dermatitidis; Cryptococcus neoformans; Cryptococcus laurentii  and  Cryptococcus albidus; Cryptococcus gattii; Candida albicans; Candida glabrata; Saccharomyces boulardii; Candida tropicalis; Candida krusei ; and  Candida parapsilosis.    
         [0021]    Also provided are such compositions, wherein the fungal cell is  Magnaporthe oryzae.    
         [0022]    Also provided are such compositions, which are formulated as a vaccine. 
         [0023]    Also provided are such compositions, wherein the composition comprises further avirulence protection means. 
         [0024]    Also provided are such compositions, wherein the further avirulence protection means is selected from the group consisting of; amino acid biosynthesis knockout; truncation; aging; modification; killing; formulation; resistance to reversion to wild type; and fusion. 
         [0025]    Also provided are such compositions, which is a mammalian immunogen. 
         [0026]    Also provided are such compositions, which is a human immunogen. 
         [0027]    The present disclosure also provides methods of preparing a pharmaceutical composition for passive immunization of an individual in need of immunization comprising: mixing a composition herein with a suitable excipient or carrier, thereby forming a pharmaceutical composition. 
         [0028]    The present invention also provides methods of eliciting an immune response in a mammal comprising administering to a mammal a pharmaceutically-effective dose of a composition herein. 
         [0029]    Also provided are such methods wherein the composition is administered by injection. 
         [0030]    Also provided are such methods wherein the composition is administered intranasally. 
         [0031]    Also provided are such methods wherein the pharmaceutical composition is formulated for subcutaneous, intramuscular, and/or intraperitoneal administration. 
         [0032]    Also provided are such methods wherein the pharmaceutical composition is formulated for intranasal administration. 
         [0033]    Also provided are such methods wherein the fungal virulence is attenuated or eliminated in any mammal susceptible to the fungus. 
         [0034]    Also provided are such methods wherein the mammalian subject is selected from the group consisting of: laboratory animal; companion animal; draft animal; meat animal; zoo animal; and human. 
         [0035]    Also provided are such methods wherein the subject is a mammal selected from the group consisting of: cat; dog; horse; bovine; camelids; and human. 
         [0036]    Also provided are such methods wherein the dose of composition administered is selected from the group consisting of: at least about 500 spores of the composition; at least about 1,000 spores of the composition; at least about 10,000 spores of the composition; at least about 20,000 spores of the composition; at least about 30,000 spores of the composition; at least about 40,000 spores of the composition; at least about 50,000 spores of the composition; at least about 60,000 spores of the composition; at least about 70,000 spores of the composition; at least about 80,000 spores of the composition; at least about 90,000 spores of the composition; at least about 100,000 spores of the composition; at least about 150,000 spores of the composition; at least about 200,000 spores of the composition; at least about 300,000 spores; at least about 500,000 spores. 
         [0037]    Also provided are such methods which further comprise administering at least a second subsequent dose of the composition to the mammal. 
         [0038]    Also provided are such methods wherein the at least second subsequent dose is administered at a time interval selected from the group consisting of: approximately one week after the first dose; approximately two weeks after the first dose; approximately three weeks after the first dose; approximately four weeks after the first dose; approximately five weeks after the first dose; approximately six weeks after the first dose; approximately seven weeks after the first dose; and approximately eight weeks after the first dose. 
         [0039]    The present disclosure also provides methods to reduce the pathogenic effects of  Coccidioides , comprising administering a siRNA complementary to CPS1 mRNA transcripts. 
         [0040]    The present disclosure also provides methods for screening compounds useful to treat coccidioidomycosis, comprising expressing CPS1 in a test model, introducing a test compound to the test model, and identifying those compounds which disrupt the function of CPS1 gene product as useful to treat coccidiodiodomycosis. 
     
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         [0041]    The patent or application file may contain one or more drawings executed in color and/or one or more photographs. Copies of this patent or patent application publication with color drawing(s) and/or photograph(s) will be provided by the Patent Office upon request and payment of the necessary fee. 
           [0042]      FIG. 1 . C57BL/6 mice challenged with intranasal doses of Δcps1 strain ranging from 50-4400 spores. All survived infection for 28 days, while 100% of mice challenged with WT  C. posadasii  succumbed by day 18 (p&lt;0.01). Closed circles, open circles, closed diamonds, and open diamonds are CPS1 deletion mutants (Δcps1) with spore doses of 50, 211, 810, and 4400, respectively; open triangles: WT, 59 spores. 
           [0043]      FIG. 2 . Protection of C57BL/6 mice by live vaccination with Δcps1 strain. Quantitative total lung colony forming units (CFU) 14 days following challenge with 90 spores of WT  C. posadasii  were significantly reduced in mice vaccinated with ΔCPS1 strain intraperitoneally (Δcps1 IP) or subcutaneously (Δcps1 SC) compared to the positive control chimeric Ag (Chim Ag) or adjuvant alone (Adj only) (P=0.001). 
           [0044]      FIG. 3 . Spherule morphology comparison: NSG and C57 mice. A. NSG mice (NOD-SCID—No lymphocytic origin cells, no NK cells) were challenged with 10,000 spores intranasally (IN) of Δcps1 and sacrificed for histopathology. Spherules are occasional, thin-walled, and irregularly shaped. B. WT spherules in C57BL/6 mice after infection with 50 spores showing thick walls and very round shape of normal spherules. 
           [0045]      FIG. 4 . Spherule morphology comparison between WT and Δcps1 strains: A. WT Silveira  C. posadasii  strain, day 3, C57BL/6. B-D. Δcps1  C. posadasii -strain day 3. 
           [0046]      FIG. 5 . Spherule morphology comparison: BALB/c mice with Δcps1 strain. A. 10× imagine of very few spherules observed in NSG mice. B. 40× image of the area represented by the circle in A. 
           [0047]      FIG. 6 . Effects of vaccination of BALB/c mice with attenuated Δcps1 strain on wild type infection. Proportion of mice surviving following injection with wild type Silveira strain following vaccination with Δcps1 strains intranasally (circles), Δcps1 strain injected subcutaneously (triangle), positive control chimeric Ag (squares) or adjuvant alone (diamonds). 
           [0048]      FIG. 7 . Lung fungal burden of vaccinated BALB/c mice surviving 28 days after infection. Total lung colony forming units (CFU) was measured in surviving mice 28 days after infection with 46 spores of the wild type strain Silveira. Group 1 represents those that received intranasal vaccination with Δcps1 strain. Group 2 represents those that received subcutaneous vaccination with Δcps1 strain. 
           [0049]      FIG. 8 .  Coccidioides -specific staining showing wild type strain spherule formation. Characterized by thick walls with well-developed endospores at day 4; very little host inflammatory reaction surrounding it. Swiss-Webster mouse, high magnification. 
           [0050]      FIG. 9 .  Coccidioides -specific staining showing variable sized spherules following Δcps1 inoculation. Two NOD-SCID and two BALB/c mice were infected intranasally with 10,000 spores of Δcps1. The sections were stained specifically for  Coccidioides  at day 3 following infection. A. Low magnification view. B. Larger magnification view 
           [0051]      FIG. 10 . H&amp;E staining of Δcps1 spherule on day 3. High magnification shows collapsing and degenerating spherule wall of the mutant strain with abundant host inflammation surrounding it and inside it. 
           [0052]      FIG. 11 . H&amp;E staining of Δcps1 spherules following rupture between day 4 and 5. Lung sections between day 4 and 5 were harvested and stained with H&amp;E to show neutrophils around and within the degenerating spherules at low magnification. The majority of these are dead. 
           [0053]      FIG. 12 . Δcps1 spherule day 5 post-infection. The endospores are heavily surrounded by host neutrophils and are not dispersing or enlarging to make new spherules.  Coccidioides -specific stain, 40× magnification. 
           [0054]      FIG. 13 . Spherules at 10 days following infection with Δcps1. 10 days following infection lung sections were taken and stained to show scattered granulomas with fewer than a dozen empty spherules within. A. H/E staining, low magnification B.  Coccidioides -specific staining, higher magnification. 
           [0055]      FIG. 14 . Lung fungal burden following IP and SC vaccinations of Δcps1 spores, Δryp1 spores, and controls. Box plot of lung fungal burden from mice vaccinated with Δcps1 or Δryp1 spores, either IP or SC, compared to controls. 
       
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
       [0056]    The inventors designed and characterized a  Coccidioides  cyclic peptide synthase Cps1 (herein referred to as CPS1) mutant and determined its usefulness as a potential immune response-provoking agent for protection against coccidioidomycosis (Valley fever). 
         [0057]    The inventors constructed a targeted gene-replacement strain of  C. posadasii  strain Silveira deleting the gene CIMG — 03303.3 (misannotated as CPSG — 02657.2 and CPSG — 02658.2 in Silveira) using  Agrobacterium -mediated transformation. This gene encodes an 1879 amino acid protein that exhibits 78% similarity to  C. heterostrophus  CPS1 and contains two conserved AMP-binding domains and an N-terminal DMAP1 binding domain, herein referred to as cyclic peptide synthase Cps1 (CPS1). 
         [0058]    The hyphal growth rate of the deletion mutant CPS1 (Δcps1) strain was somewhat reduced compared to Silveira at 24° C., but there was no significant difference at 37° C. In vitro analysis of the parasitic phase indicated that the Δcps1 mutant is able to form spherules although they are reduced in size relative to Silveira. 
         [0059]    Surprisingly, the inventors discovered that when Δcps1 arthroconidia were introduced into susceptible C57BL/6 mice via intranasal inoculation, no disease occurred, demonstrating it is avirulent and that Cps1 protein is a virulence factor in  Coccidioides . For C57BL/6 mice, 50 arthroconidia are a lethal dose, while for Δcps1 strains, even when mice were inoculated with 5000 spores, no signs of disease were observed; and all mice remained healthy. In only one of the 20 mice inoculated with &gt;800 Δcps1 spores, was any  Coccidioides  recovered, a single colony from the lung of that mouse. The inventors herein describe that Δcps1 fungi can induce protection against further infection and act as a live vaccine. 
         [0060]    As exemplified herein, the inventors injected C57BL/6 mice either intraperitoneal or subcutaneously with 50,000 Δcps1 spores and boosted with the same amount after two weeks. Four weeks later, the mice were challenged intranasally with 90 spores of  Coccidioides  strain Silveira. 
         [0061]    The control mice all developed disease, but the inventors show that the Δcps1 mutant provides complete protection against infection, with no sign of disease in infected mouse lungs or other organs. 
         [0062]    Interestingly, at the site of injection of Δcps1 arthroconidia, all mice had evidence of granulomatous lesions, indicating local reproduction of the mutant. The present disclosure therefore provides, inter alia, mutant strains of fungus as live vaccines against fungal pathologies, including coccidioidomycosis. 
         [0063]    Further, via metabolite analysis of WT and the Δcps1 mutant, the inventors have observed small molecule differences between the strains. 
         [0064]    The small metabolite product and the gene are targets for drug therapeutics. Because this gene is conserved among fungi, it is a general target for therapeutics in treatment of fungal diseases. 
         [0065]    Previous efforts at development of fungal vaccines were based on either whole cell extracts, partially purified extracts or recombinant proteins. None of the previous attempts produced the protection seen with the present mutant strains. 
         [0066]    Unlike other live attenuated vaccines, Cps1 may be part of an enzyme complex that produces one or more small molecules that may have a role in virulence. The invention of the CPS1 mutant could lead to a vaccine or to targets for treatment either through binding of the small molecules involved in virulence or by binding or disrupting the protein involved in making the small molecules required for virulence. 
       DEFINITIONS 
       [0067]      Coccidioides  cyclic peptide synthase Cps1, herein referred to as Cps1, is a protein encoded by a CPS1 gene product and CPS1 mRNA, and may encode either wild type or a mutant. A wild type or mutant CPS1 gene product will encode for a Cps1 protein. 
         [0068]    The term “dysfunctional,” “non-functional,” “inactivated,” or “inactivation” when referring to a gene or a protein means that the known normal function or activity of the gene or protein has been eliminated or highly diminished. For example, inactivation of CPS1 can be effected by inactivating the CPS1 gene. Inactivation which renders the gene or protein dysfunctional includes such methods as deletions, mutations, substitutions, interruptions or insertions in the nucleic acid gene sequence. 
         [0069]    General techniques of genetic recombination, including vector construction, transformation, selection of transformants, host cell expression, etc., are further described in Maniatis et al, 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Ausubel et al., 1989, Current Protocols in Molecular Biology, Greene Publishing Associates &amp; Wiley Interscience, N.Y.; Innis et al. (eds), 1995, PCR Strategies, Academic Press, Inc., San Diego, Calif.; and Erlich (ed), 1992, PCR Technology, Oxford University Press, New York.  Agrobacterium  transformation and replacement of  Coccidioides  genes was as described in Abuodeh et al. 2000, Genetic Transformation of  Coccidioides immitis  facilitated by  Agrobacterium tumefaciens . Journal of Infectious Diseases, 181:2106-2110 and Kellner et al., 2005,  Coccidioides posadasii  contains a single 1,3-beta-glucan synthase gene that appears to be essential for growth, Eukaryotic Cell, 4:111-120. 
         [0070]    As used herein, a “therapeutically effective amount” means a quantity of a specified pharmaceutical or therapeutic compound or composition sufficient to achieve a desired effect in a subject, or in a cell, being treated with the compound or composition. The effective amount of the agent will be dependent on several factors, including, but not limited to, the subject or cells being treated, and the manner of administration of the therapeutic composition. 
         [0071]    As is conventional in the art, the term “attenuated” refers to a cell, culture, or strain of fungus (e.g.  Coccidioides  spp.) exhibiting a detectable reduction in infectivity or virulence in vitro and/or in vivo as compared to that of the parent strain of the fungus from which the attenuated cell, culture, or strain is derived. Reduction in virulence encompasses any detectable decrease in any attribute of virulence, including infectivity in vitro and/or in vivo, or any decrease in the severity or rate of progression of any clinical symptom or condition associated with infection. 
         [0072]    The term “avirulent”, as used herein, does not mean that a microbe of that genus or species cannot ever function as a pathogen, but that the particular microbe being used is avirulent with respect to the particular animal being treated. The microbe may belong to a genus or even a species that is normally pathogenic but must belong to a strain that is avirulent. The microbe may also be modified genetically or through avirulence protection means to make the microbe avirulent. Examples of avirulent means include, but are not limited to, genetic engineering to knock out genes required for virulence, amino acid biosynthesis knockout, truncation of the viral genome, aging, killing, formulation, resistance to reversion to wild type, and fusion. “Pathogenic,” as used herein, means capable of causing disease or impairing normal physiological functioning. An “avirulent strain” is incapable of inducing the full set of symptoms of the disease that is normally associated with its virulent pathogenic counterpart. The term “microbes,” as used herein, includes bacteria, protozoa, and fungi. Derivatives of avirulent  Coccidioides  spp. are also contemplated to be within the scope of this disclosure. By “derivative” it is meant sexually or asexually derived progeny and mutants of the avirulent strains including single or multiple base substitutions, deletions, insertions or inversions which retain the inability to produce functional Cps1 protein. For example, the  Coccidioides posadasii  Silveira strain that has a deletion of the CPS1 gene described herein. 
         [0073]    The term “immunogen,” “immunogens,” “antigen,” or “antigens” means a material that can induce an immune response and is therefore antigenic. By “immune response” means any reaction by the immune system. These reactions include the alteration in the activity of an organism&#39;s immune system in response to an antigen and may involve, for example, antibody production, induction of cell-mediated immunity, complement activation or development of immunological tolerance. Immune response to antigens is well studied and widely reported. A survey of immunology is given in Barrett, James, T., Textbook of Immunology: Fourth Edition, C. V. Mosby Co., St. Louis, Mo. (1983). More specifically, the present disclosure provides a live, attenuated fungus (e.g.  Coccidioides  spp.) that can be used as an immunogenic composition or a vaccine. It will be appreciated that the attenuated fungus contains a dysfunctional CPS1 gene. 
         [0074]    “Vaccine,” as used herein, means an agent used to stimulate the immune system of a living organism so that protection against future harm is provided “Immunization” refers to the process of inducing a continuing high level of antibody and/or cellular immune response in which T-lymphocytes can either kill a pathogen and/or activate other cells (e.g., phagocytes) to do so in an organism, which is directed against a pathogen or antigen to which the organism has been previously exposed. 
         [0075]    The term “adjuvant” is intended to mean a composition with the ability to enhance an immune response to an antigen generally by being delivered with the antigen at or near the site of the antigen. Ability to increase an immune response is manifested by an increase in immune mediated protection. Enhancement of humoral immunity can be determined by, for example, an increase in the titer of antibody raised to the antigen. Enhancement of cellular immunity can be measured by, for example, a positive skin test, cytotoxic T-cell assay, ELISPOT assay for IFN-gamma or IL-2. Adjuvants are well known in the art. Exemplary adjuvants include, for example, Freud&#39;s complete adjuvant, Freud&#39;s incomplete adjuvant, aluminum adjuvants, MF59 and QS21. 
         [0076]    As used herein, “inhibit,” “inhibiting,” or “inhibition” includes any measurable or reproducible reduction in the infectivity of a fungus in the subject. “Reduction in infectivity” means the ability of the subject to prevent or limit the spread of the fungus in tissues or organs exposed to or infected by the fungus. Furthermore, “amelioration,” “protection,” “prevention,” and “treatment” mean any measurable or reproducible reduction, prevention, or removal of any of the symptoms associated with fungal infectivity, and particularly, the prevention, or amelioration of infection and resultant pathology itself. 
         [0077]    As used herein, “subject” means a patient or individual having symptoms of, or at risk for, fungal infection, coccidioidomycosis, or other malignancy. A subject may be human or non-human and may include, for example, laboratory animal, companion animal; draft animal, meat animal, zoo animal, and human. The subjects may include either adults or juveniles (e.g., children). Moreover, subject may mean any living organism, preferably a mammal (e.g., human or non-human) that may benefit from the administration of compositions contemplated herein. 
         [0078]    Compositions 
         [0079]    The current disclosure provides compositions comprising a fungus having a dysfunctional CPS1 gene product. The compositions may be formulated as an ingredient in a pharmaceutical composition, and this formulation can aid in administration of the composition. The compositions may routinely contain pharmaceutically acceptable concentrations of salts, buffering agents, preservatives and various compatible carriers or diluents. For all forms of delivery, the vectors may be formulated in a physiological salt solution. In one embodiment, the composition is a vaccine. 
         [0080]    The preferred formulations of the composition may depend on the method of administration of the composition. It is contemplated that the composition will include one or more conventional pharmaceutically acceptable carriers, adjuvants, other immune-response enhancers, and/or vehicles (collectively referred to as “excipients”). Such excipients are generally selected to be compatible with the active ingredient(s) in the composition. Use of excipients is generally known to those skilled in the art. Suitable pharmaceutical carriers, excipients, adjuvants and the preparation of dosage forms are described in, for example, Remington&#39;s Pharmaceutical Sciences, 17th Edition, (Gennaro, Ed., Mack Publishing Co., Easton, Pa., 1985. 
         [0081]    Mucosal compositions may be, for example, liquid dosage forms, such as pharmaceutically acceptable emulsions, solutions, suspensions, syrups, and elixirs. Excipients suitable for such vaccine preparations include, for example, inert diluents commonly used in the art, such as, water, saline, dextrose, glycerol, lactose, sucrose, starch powder, cellulose esters of alkanoic acids, cellulose alkyl esters, talc, stearic acid, magnesium stearate, magnesium oxide, sodium and calcium salts of phosphoric and sulfuric acids, gelatin, acacia gum, sodium alginate, polyvinylpyrrolidone, and/or polyvinyl alcohol. Excipients also can comprise various wetting, emulsifying, suspending, flavoring (e.g., sweetening), and/or perfuming agents. 
         [0082]    The compositions may be formulated for intranasal administration with a pharmaceutically acceptable carrier such as water, buffered saline, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol and the like) suitable mixtures thereof, or vegetable oils. If necessary, the action of contaminating microorganisms may be prevented by various antibacterial agents, such as parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. It will often be preferable to include in the formulation isotonic agents, for example, glucose or sodium chloride. Such formulation may be administered intranasally as an aerosol or atomized spray, or as liquid drops. 
         [0083]    Oral mucosal compositions also may, for example, be tableted or encapsulated for convenient administration. Such capsules or tablets can contain a controlled-release formulation. In the case of capsules, tablets, and pills, the dosage forms also can comprise buffering agents, such as sodium citrate, or magnesium or calcium carbonate or bicarbonate. Tablets and pills additionally can be prepared with enteric coatings. 
         [0084]    “Parenteral administration” includes subcutaneous injections, submucosal injections, intravenous injections, intramuscular injections, intrasternal injections, and infusion. Injectable preparations (e.g., sterile injectable aqueous or oleaginous suspensions) can be formulated according to the known art using suitable excipients, such as vehicles, solvents, dispersing, wetting agents, emulsifying agents, and/or suspending agents. These typically include, for example, water, saline, dextrose, glycerol, ethanol, corn oil, cottonseed oil, peanut oil, sesame oil, benzyl alcohol, benzyl alcohol, 1,3-butanediol, Ringer&#39;s solution, isotonic sodium chloride solution, bland fixed oils (e.g., synthetic mono- or diglycerides), fatty acids (e.g., oleic acid), dimethyl acetamide, surfactants (e.g., ionic and non-ionic detergents), propylene glycol, dextran, lactose, trehalose, and/or polyethylene glycols. Excipients also may include small amounts of other auxiliary substances, such as pH buffering agents. 
         [0085]    The compositions may include one or more adjuvants that enhance a subject&#39;s immune response (which may include an antibody response, cellular response, or both), thereby increasing the effectiveness as a vaccine. The adjuvant (s) may be a substance that has a direct (e.g., cytokine or Bacille Calmette-Guerin (BCG)) or indirect effect (liposomes) on cells of the subject&#39;s immune system. Examples of often suitable adjuvants include oils (e.g., mineral oils), metallic salts (e.g., aluminum hydroxide or aluminum phosphate), bacterial components (e.g., bacterial liposaccharides, Freund&#39;s adjuvants, and/or MDP), plant components (e.g., Quil A), cytokines and/or one or more substances that have a carrier effect (e.g., bentonite, latex particles, liposomes, and/or Quil A). Adjuvants also include, for example, CARBIGEN adjuvant and carbopol. It should be recognized that this disclosure encompasses both compositions that include an adjuvant (s), as well as compositions that do not include any adjuvant. 
         [0086]    “Cytokines” used in the compositions and methods described herein, refer to small proteins secreted primarily, but not exclusively, by cells of the immune system that promote the proliferation and/or differentiative functions of other cells. Examples of cytokines include interleukins, interferons, hematopoietic colony stimulating factors (CSF), and proinflammatory factors such as tumor necrosis factor (TNF). It is contemplated that the compositions may be freeze-dried (or otherwise reduced in liquid volume) for storage, and then reconstituted in a liquid before or at the time of administration. Such reconstitution may be achieved using, for example, vaccine-grade water. 
         [0087]    Administration of the Compositions 
         [0088]    In accordance with particular embodiments, the composition comprising fungi having a dysfunctional CPS1 gene product is used in a vaccine preparation. In general, the vaccine is administered in an immunologically effective amount, which is an amount sufficient to induce a protective immune response in the subject against fungal infection (e.g.  Coccidioides  spp.). The live attenuated fungi described herein are capable of triggering an immune response that protects a mammal against fungal infection or colonization after one or more administrations as a live vaccine. A “protective immune response” refers to any immunological response, either antibody or cell-mediated immunity, or both, occurring in the subject that either prevents or detectably reduces subsequent infection, or eliminates or detectably reduces the severity, or detectably slows the rate of progression, of one or more clinical symptoms or conditions associated with fungal infection. 
         [0089]    The immunogenicity level may be determined experimentally by challenge dose titration study techniques generally known in the art. Such techniques typically include vaccinating a number of subjects with the vaccine at different dosages, and then challenging the subjects with the virulent fungi to determine the minimum protective dose. 
         [0090]    Factors affecting the preferred dosage regimen may include, for example, the age, weight, sex, diet, activity, and condition of the subject; the route of administration; the efficacy, safety, and duration-of-immunity profiles of the particular vaccine used; whether a delivery system is used; and whether the vaccine is administered as part of a drug and/or vaccine combination. Thus, the dosage actually employed can vary. Determining such dosage adjustments is generally within the skill of those in the art using conventional means. 
         [0091]    In one embodiment, the composition is administered at a dose of at least about 500 spores of the composition, at least about 1,000 spores of the composition, at least about 10,000 spores of the composition, at least about 20,000 spores of the composition, at least about 30,000 spores of the composition, at least about 40,000 spores of the composition, at least about 50,000 spores of the composition, at least about 60,000 spores of the composition, at least about 70,000 spores of the composition, at least about 80,000 spores of the composition, at least about 90,000 spores of the composition, at least about 100,000 spores of the composition, at least about 150,000 spores of the composition, and at least about 200,000 spores of the composition. 
         [0092]    It is contemplated that the compositions may be administered to a subject at a single time; or, alternatively, two or more times over days, weeks, months, or years. In some embodiments, the composition is administered at least two times. In some such embodiments, for example, the compositions are administered twice, with the second dose (e.g., the booster) being administered approximately one week after the first dose, approximately two weeks after the first dose, approximately three weeks after the first dose, approximately four weeks after the first dose, approximately five weeks after the first dose, approximately six weeks after the first dose, approximately seven weeks after the first dose, and approximately eight weeks after the first dose. In the above embodiments, the first and subsequent dosages may vary, such as, for example, in amount and/or form. Often, however, the dosages are the same as to amount and form. 
         [0093]    In certain embodiments, the compositions are administered to a subject that is immunogenically naive to the fungi, e.g., the subject has not been vaccinated for the fungus or exposed to the fungus. In accordance with this embodiment, the composition is administered before the subject recipient is infected with the fungus. In such embodiments, the vaccine preparation may, for example, be administered to prevent, reduce the risk of, or delay the onset of  Coccidioides  spp. infection or one or more (typically two or more)  Coccidioides  spp. symptoms. 
         [0094]    In some embodiments, the compositions are administered to subjects in a population after a subject in the population has been infected with the fungus. In such embodiments, the compositions may, for example, ameliorate, suppress, or eradicate the fungus or one or more (typically two or more) fungal symptoms in the subjects of the population. 
         [0095]    The compositions can be administered by conventional means, including, for example, mucosal administration, (such as intranasal, oral, intratracheal, and ocular), and parenteral administration (such as, without limitation, intraperitoneal, subcutaneous or intramuscular administration). The compositions may also be administered intradermally or transdermally (including, without limitation, via a skin patch or topical administration). Mucosal administration is often particularly advantageous for live attenuated vaccines. 
         [0096]    Cyclic Peptide Synthase Cps1 (CPS1) 
         [0097]    CPS1 gene was originally identified as a potential non-ribosomal peptide synthase component, because it encodes an 1879 amino acid polypeptide with two AMP binding domains related to the adenylation domains in bacterial non-ribosomal peptide synthases. However it also contains a putative N-terminal DMAP1b domain. In mammals, this domain binds the DMAP1 transcriptional co-repressor that has been shown to bind regulatory proteins and is proposed to act as a co-repressor of transcription. 
         [0098]    The present CPS1 deletion strains are non-pathogenic but do initiate the formation of spherules (the infectious form of  Coccidioides ). The mutants also form spherules in vitro. The CPS1 mutant appears to have great potential as an attenuated vaccine since it protects from infection. When susceptible mice are challenged with wild type  C. posadasii  after inoculation with the Δcps1 mutant strain, nearly all experience extended survival of at least four weeks and have low fungal burdens. Innoculation with the CPS1 deletion mutant results in animals that are completely resistant to infection. Other fungi can be genetically engineered to make a fungal strain having a dysfunctional CPS1 gene to make vaccines useful to treat a number of different fungal infections. 
         [0099]    In some embodiments, the dysfunctional CPS1 gene is a result of a deletion of at least a portion of the CPS1 gene. In certain embodiments, the dysfunctional CPS1 gene product is a result of a deletion of at least about the entire CPS1 gene, at least about the entire DMAP region of the CPS1 gene, at least about an entire AMP binding domain region of the CPS1 gene, a regulatory element of the CPS1 gene, at least the coding sequence of the CPS1 gene, at least about 90% of the CPS1 gene, at least about 80% of the CPS1 gene, at least about 70% of the CPS1 gene, at least about 60% of the CPS1 gene, at least about 50% of the CPS1 gene, at least about 40% of the CPS1 gene, at least about 30% of the CPS1 gene, at least about 20% of the CPS1 gene, and at least about 10% of the CPS1 gene. In another embodiment, the dysfunctional CPS1 gene product is a result of deletion of the entire CPS1 gene. 
         [0100]    Coccidioidomycosis (Valley Fever) 
         [0101]    Coccidioidomycosis is a fungal infection (Valley Fever) caused by the endemic fungal species,  Coccidioides immitis  and  Coccidioides posadasii . The disease can range from an asymptomatic infection that renders humans immune for life to a fatal respiratory or disseminated infection. Approximately 40% of 150,000 people infected annually become sick, and approximately 5% develop severe and life-threatening illness that may leave them disabled, under continuous treatment, or deceased. Among patients that develop disseminated disease, most are treated for months to years, and many who discontinue treatment suffer relapse at some point because the current drugs available suppress but do not eradicate the fungus from the body. Treatment with antifungal medication may cost between $5000-$20,000 per year, not including the costs of ancillary care such as hospitalization, rehabilitation, frequent medical care, and disability. Better vaccines and medications to treat illness, e.g., short morbidity and reduce the severity and life time sequelae of coccidioidomycosis, are desperately needed because currently available medications are primarily fungistatic and fail in a significant number of disseminated cases. 
         [0102]    Coccidioidomycosis is commonly known as cocci or “Valley Fever”, as well as “California Fever”, “desert rheumatism”, and “San Joaquin Valley Fever”, is endemic in certain parts of Arizona, California, Nevada, New Mexico, Texas, Utah and northern Mexico. 
         [0103]      Coccidioides immitis  or  Coccidioides posadasii  resides in the soil in certain parts of the southwestern United States, most notably in California and Arizona. It is also prevalent in northern Mexico, and parts of Central and South America. It is dormant during long dry spells, then develops as a mold with long filaments when the rains come and that matures to break off into spores. The spores, known as arthroconidia, are swept into the air by disruption of the soil, such as during construction, farming, windstorms or an earthquake. 
         [0104]    Infection is caused by inhalation of the particles. The disease is not transmitted from person to person. The infection ordinarily resolves leaving the patient with a specific immunity to re-infection. However, in some cases the infection may manifest itself repeatedly or permanently over the life of the host.  Coccidioides immitis  or  Coccidioides posadasii  is a dimorphic saprophytic organism that grows as a mycelium in the soil and produces a spherule form in the host organism. 
         [0105]    Coccidioidomycosis is confined to the western hemisphere between 40° N and 40° S. Dry soil, especially in the Lower Sonoran Life Zone, is supportive of the pathogenic fungi growth. In harmony with mycelium life cycle, incidence increases with periods of dryness after a rainy season; this phenomenon, termed “grow and blow,” refers to growth of the fungus in wet weather, producing spores which are spread by the wind during succeeding dry weather. 
         [0106]    Besides humans, dogs, and cats, the fungus can be shown to infect most mammals, even if they do not get sick from it very often. Species in which Valley Fever has been found include livestock such as cattle and horses; llamas; marine mammals, including sea otter; zoo animals such as monkeys and apes, kangaroos, tigers, etc; and wildlife endemic to the geographic area such as cougar, skunk, and javelina. 
         [0107]    In soil,  Coccidioides  spp. exists in filament form. It forms hyphae in horizontal and vertical direction. With time, cells within hyphae degenerate to form alternating barrel shaped cells, approximately 3-5 microns in size, called arthroconidia. Arthroconidia are lightweight and carried by air currents. They can easily be inhaled without the person knowing. On arriving in alveoli, they enlarge in size and internal septations are developed, forming a structure termed a spherule. Internal spores, termed endospores develop within the spherule as it matures. Rupture of the spherules release these endospores, which in turn repeat the cycle and spread the infection locally and can disseminate to any organ via the blood and lymph systems. Nodules can form in lungs surrounding these spherules. When these rupture, they release their contents into bronchus, forming thin-walled cavities. These cavities can result in symptoms like characteristic chest pain, meoptysis and persistent cough. 
         [0108]    Aspergillosis 
         [0109]      Aspergillus  spp. are fungi whose spores are present in the air we breathe, but does not normally cause illness. However an individual with a weakened immune status may be susceptible to infection by some  Aspergillus  species, primarily  Aspergillus fumigatus.    
         [0110]    Aspergillosis is a group of diseases which can result from  Aspergillus  infection and includes invasive aspergillosis, ABPA, CPA and aspergilloma. Some asthma patients with very severe asthma may also be sensitised to fungi like  Aspergillus  (SAFS). 
         [0111]    Aspergillosis may affect patients whose immune system may be compromised—including those with leukaemia, chemotherapy patients or those on steroids, transplant patients, cystic fibrosis, HIV or AIDS, chronic obstructive pulmonary disease (COPD), chronic granulomatous disease (CGD), severe asthma with fungal sensitivity (SAFS) and many others. 
         [0112]      Aspergillus  does not solely affect humans; birds and animals can also develop aspergillosis, and some plant diseases and food spoilage may be due to  Aspergillus  infection. Especially serious are those  Aspergillus  species that produce the highly carcinogenic mycotoxin, aflatoxin, which can cause serious acute and chronic health problems in people who accidentally ingest it. Primarily aflatoxin producing species are  A. flavus  and  A. parasiticus , which can contaminate foods such as maize, peanuts and cottonseeds. 
         [0113]    Histoplasmosis 
         [0114]    Histoplasmosis is a disease caused by the fungus  Histoplasma capsulatum . The fungus lives in the environment, usually in association with large amounts of bird or bat droppings. Lung infection can occur after a person inhales airborne, microscopic fungal spores from the environment; however, many people who inhale the spores do not get sick. The symptoms of histoplasmosis are similar to pneumonia, and the infection can sometimes become serious if it is not treated. 
         [0115]    Blastomycosis 
         [0116]    Blastomycosis is a disease caused by the fungus  Blastomyces dermatitidis . The fungus lives in moist soil and in association with decomposing organic matter such as wood and leaves. Lung infection can occur after a person inhales airborne, microscopic fungal spores from the environment; however, many people who inhale the spores do not get sick. The symptoms of blastomycosis are similar to flu symptoms, and the infection can sometimes become serious if it is not treated.  Blastomyces dermatitidis  can also infect dogs. 
         [0117]    Candidiasis 
         [0118]      Candida  is a yeast and the most common cause of opportunistic mycoses worldwide. It is also a frequent colonizer of human skin and mucous membranes.  Candida  is a member of normal flora of skin, mouth, vagina, and stool. As well as being a pathogen and a colonizer, it is found in the environment, particularly on leaves, flowers, water, and soil. While most of the  Candida  spp. are mitosporic, some have known teleomorphic state and produce sexual spores. 
         [0119]    Infections caused by  Candida  spp. are in general referred to as candidiasis. The clinical spectrum of candidiasis is extremely diverse. Almost any organ or system in the body can be affected. Candidiasis may be superficial and local or deep-seated and disseminated. Disseminated infections arise from hematogenous spread from the primarily infected locus.  Candida albicans  is the most pathogenic and most commonly encountered species among all. Its ability to adhere to host tissues, produce secretory aspartyl proteases and phospholipase enzymes, and transform from yeast to hyphal phase are the major determinants of its pathogenicity. 
         [0120]    Cryptococcosis 
         [0121]      Cryptococcus neoformans  is an encapsulated yeast and the causative agent of cryptococcosis. Given the neurotropic nature of the fungus, the most common clinical form of cryptococcosis is meningoencephalitis. The course of the infection is usually subacute or chronic. Cryptococcosis may also involve the skin, lungs, prostate gland, urinary tract, eyes, myocardium, bones, and joints. The most commonly encountered predisposing factor for development of cryptococcosis is AIDS. Less commonly, organ transplant recipients or cancer patients receiving chemotherapeutics or long-term corticosteroid treatment may develop cryptococcosis. 
         [0122]    Kits 
         [0123]    The present disclosure further includes kits that are suitable for use in performing the methods described above. The kits can includes a dosage form of the compositions in an appropriate container and can also optionally include at least one additional component, and, typically, instructions for using the compositions with the additional component(s). The additional component(s) may, for example, be one or more additional ingredients (such as, for example, one or more of the excipients discussed above) that can be mixed with the compositions before or during administration. The additional component (s) may alternatively (or additionally) include one or more apparatuses for administering the compositions to the subject. Such an apparatus may be, for example, a syringe, inhaler, nebulizer, pipette, forceps, or any medically acceptable delivery vehicle. In some embodiments, the apparatus is suitable for subcutaneous administration of the compositions. In some embodiments, the apparatus is suitable for intranasal administration of the vaccine preparation. 
         [0124]    The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims. Whenever a range is given in the specification, all intermediate ranges and sub-ranges, as well as all individual values included in the ranges given are intended to be included in the disclosure. When a Markush group or other grouping is used herein, all individual members of the group and all combinations and sub-combinations possible of the group are intended to be individually included in the disclosure. 
       EXAMPLES 
     Example 1 
     Material and Methods 
       [0125]    Strains, Media and Growth Conditions 
         [0126]      Coccidioides posadasii  strain Silveira (ATCC 28868) was cultured on 2×GYE medium (2% glucose, 1% yeast extract and 1.5% agar) at room temperature. All manipulations of viable cultures were performed in the Keating Building Select agent biosafety level 3 (BSL3) laboratory, using standard operating procedures developed for working with this select agent and approved by the Centers for Disease Control (CDC). Δcps1 strains were selected and maintained on 2×GYE media supplemented with hygromycin at 50 μg/ml. Arthroconidia of Silveira were harvested from four-week old cultures grown on 2×GYE at room temperature using sterile water by the mini-stir bar method described previously (Huppert et al. Antimicrobial Agents and Chemotherapy, 1:367-372, 1972). Arthroconidia were washed with sterile dH 2 O and stored in sterile dH 2 O at 4° C. Spore counts were made with a hemacytometer counts and viable counts determined by plating. Spherules were generated by growth of strains in modified Converse medium at 37° C., 20% CO 2  and shaken at 180 rpm as described in J Bacteriol., 78:231-239 (1959). Spherules were harvested at 24-hour intervals up to 120 hours, fixed in 10% formaldehyde and stained with cotton blue. At least 50 spherules were measured to estimate their size at each time point. Statistical analysis was performed using SAS (version 9.1, SAS Institute Inc., Cary, N.C.) and the size of spherule is presented as mean±SD. 
         [0127]    Construction of CPS1 Gene Deletion Cassette 
         [0128]    The CPS1 gene of  Coccidioides , CIMG — 03303.3, was identified via homology to the  Cochlibolus heterostrophus  CPS1 gene. A CPS1 gene deletion cassette was constructed in multiple steps using primers listed in Table 1 . C. posadasii  strain Silveira DNA was used as a template to generate PCR fragments representing the 5′ and 3′ flanking regions of the CPS1 gene using primers OAM 1190 and OAM 1192, and OAM 1193 and OAM 1194 respectively. Primers OAM 1192 and OAM 1193 contain sequences complementary to the ends of the hygromycin resistance gene cassette (hphB) of plasmid pCB 1004. The hygromycin (hphB) gene was amplified from plasmid pCB 1004 using primers OAM597 and OAM 598. The PCR products of the CPS1 5′ and 3′ flanking regions were mixed with that of the hphB gene and amplified with nested primers OAM 1191 and 1195, that contain EcoRI sites. The resulting PCR product was then ligated into pGEM®-T Easy (Promega, Madison, Wis.). The construct, designated pAM1567, was verified by restriction analysis and PCR and the hphB insert gene of the plasmid was sequenced to determine that no mutations had been introduced. The gene replacement construct from pAM1567, containing the CPS1 5′flank-hphB-CPS1 3′flank was cloned into the binary vector pAM1145 as an EcoRI fragment, producing plasmid pAM1594. Plasmid pAM1594 was transformed into  Agrobacterium tumefaciens  strain EHA105 by electroporation and the resulting strain was named as A1594. 
         [0000]    
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Primers Used 
               
             
          
           
               
                   
                 Sense or 
                 Primer sequence  
                 SEQ 
               
               
                 Primer 
                 Anti-sense 
                 (5′-3′) 
                 ID 
               
               
                   
               
               
                 5′ UTR 
                   
                   
                   
               
               
                 OAM1190 
                 Sense 
                 GTGGGTATCAGTTGT 
                  4 
               
               
                   
                   
                 TTGTAGGAAG 
                   
               
               
                   
               
               
                 OAM1192 
                 Anti-sense 
                 GCTCCTTCAATATCA 
                  5 
               
               
                   
                   
                 GTTAACGTCGAGTTA 
                   
               
               
                   
                   
                 AACGCCAATCAGTAT 
                   
               
               
                   
                   
                 CGTCGTTTCG 
                   
               
               
                   
               
               
                 3′ UTR 
                   
                   
                   
               
               
                 OAM1193 
                 Sense 
                 AGATGCCGACCGGGA 
                  6 
               
               
                   
                   
                 ACCAGTTAACATAGA 
                   
               
               
                   
                   
                 CATGAGGATTGCTCG 
                   
               
               
                   
                   
                 GCTTTGTC 
                   
               
               
                   
               
               
                 OAM1194 
                 Anti-sense 
                 TCACGATGTCGTACG 
                  7 
               
               
                   
                   
                 GGCCAGTTTG 
                   
               
               
                   
               
               
                 Nested 
                   
                   
                   
               
               
                 OAM1191 
                 Sense 
                 GGGAATTC GAATTC G 
                  8 
               
               
                   
                   
                 CGTGGTCTGGTAGTC 
                   
               
               
                   
                   
                 GCGTTGAGAGCC 
                   
               
               
                   
               
               
                 OAM1195 
                 Anti-sense 
                 GAGCCG GAATTC CCT 
                  9 
               
               
                   
                   
                 AAATGCATAGCCATT 
                   
               
               
                   
                   
                 CCACAAATAC 
                   
               
               
                   
               
               
                 CPS1 Intern 
                   
                   
                   
               
               
                 OAM1288 
                 Sense 
                 CAACCGCAGGTCAGT 
                 10 
               
               
                   
                   
                 GTATG 
               
               
                   
               
             
          
         
       
     
         [0129]    Targeted Disruption of the  C. posadasii  CPS1 Gene in Strain Silveira 
         [0130]      C. posadasii  strain Silveira was transformed using  A. tumefaciens  strain A1594 as described previously in Eukaryotic Cell 4:111-120 (2005). Briefly, 1×10 7  arthroconidial germilings and 1×10 9    A. tumefaciens  cells were mixed and dispersed onto six sterile 0.45 nM, 82 mm diameter nitrocellulose filters (Millipore Corporation, Bedford, Mass., USA) on plates containing AB induction media. Following co-cultivation at room temperature for 48 hours, the nitrocellulose filters were transferred onto selection plates containing 2×GYE media supplemented with 50 ng/ml hygromycin (selection for transformed strains) and 100 μg/ml kanamycin (counter selection to prevent further growth of  A. tumefaciens ). Transformants were isolated after incubation at room temperature for 1-2 weeks and grown on selection plates for sporulation. Monoconidial isolates were selected via two conidial passages as described in Eukaryotic Cell 4:111-120 (2005). 
         [0131]    DNA Isolation and Confirmation of Transformants 
         [0132]    Genomic DNA was isolated from putative transformants as described previously in Eukaryotic Cell 4:111-120 (2005). Briefly, mycelium from a young colony was scraped from plates and mechanically disrupted with acid-treated glass beads in lysis buffer (50 mM Tris-HCl, [pH7.5], 100 mM EDTA [pH8.0], 100 mM NaCl, 0.5% SDS and 100 mM DTT) by vortexing at 3000 rpm for 10 minutes. DNA was then purified by extraction with phenol:chloroform:isoamyl alcohol. Following precipitation, the DNA was treated with RNase A and then extracted using CTAB. The DNA was precipitated, resuspended in 50 μl sterile dH 2 O and stored at −20° C. 
         [0133]    Transformed  C. posadasii  strains were analyzed by Southern blot analysis to verify replacement of the CPS1 gene by the hphB gene using standard procedures as described previously in Eukaryotic Cell 4:111-120 (2005). Probes for hybridization included the hphB gene, generated by PCR amplification from plasmid pCB 1004 using primers OAM597 and OAM 598, an internal fragment of CPS1 generated by amplification from Silveria genomic DNA using primers OAM1288 and OAM1289 and a 5′ flanking fragment (Table 1). 
         [0134]    Measurement of In Vitro Growth and Spherulation 
         [0135]    To determine whether the Δcps1 strains were altered in hyphal growth and conidiation, colonial radial growth was compared to strain Silveira. Three day-old monoconidial cultures were placed on 2×GYE petri plates containing or lacking 50 μg/frit hygromycin. Strains were plated in triplicate and the growth rate was assessed at room temperature (24° C.) and at 37° C. Colony diameters were recorded at three-day intervals for 21 days. Statistical analysis was performed using SAS (version 9.1, SAS Institute Inc., Cary, N.C.) and the data is presented as mean±SD. 
         [0136]    Mice 
         [0137]    8-week-old female C57/BL6 mice, were purchased from Harlan-Sprague-Dawley (Indianapolis, Ind.) and maintained according to National Institutes of Health guidelines. All studies were conducted with the approval of the Institutional Animal Care and Use Committee at the University of Arizona. 
       Example 2 
     In Vivo Studies 
       [0138]    Pathogenicity of the Δcps1 strain was assessed in two independent mouse studies in the Animal BSL3 facility at the Department of Veterinary Sciences and Microbiology at the University of Arizona. Mice were infected intranasally following i.p. anesthetization with ketamine-xylazine as described previously in Infection and Immunity 70:3287-3289 (2002). Twelve mice were inoculated per treatment with two mice sacrificed at 14 days for histopathology and the other 10 maintained for 28 days or until they appeared moribund. Mice were treated with the following spore doses (design/actual): Silveira, 50/59 arthroconidia/mouse, Δcps1, 50/50, 250/211, 1000/810 spores/mouse. In the second study, a higher dose was used to further assess avirulence. Strain Silveira was inoculated at 50/53 arthroconidia/mouse (design/actual), while Δcps1 was infected with 4400 arthroconidia. Mice were inoculated intranasally and monitored as in the first study. 
         [0139]    An additional mouse study was performed to test whether the Δcps1 strain could provide protection against subsequent inoculation with wild type  C. posadasii . In this study, groups of eight mice were inoculated twice, two weeks apart, with 50,000 spores of the Δcps1 strain introduced either subcutaneously or intraperitoneally. They were then challenged intranasally four weeks after the second (booster) dose with 90 spores of wild type parental  C. posadasii , strain Silveira. As controls, eight mice were vaccinated with a positive control chimeric antigen, Ag2/ PRA1-106  fused to CSA, and eight were vaccinated with adjuvant alone, a combination of MPL-SE (25 μg/mouse) and CpG (10 μg/mouse). The lungs of mice were weighed and quantitatively cultured two weeks after challenge. 
         [0140]    Mice in the control group had mean lung fungal burdens of 5.3×10 7  (800-11.9×10 7 ), while the mean fungal burden of all the mice vaccinated with CPS1 knockout was 212 cfu (range 1-1650). This avirulent strain afforded a high level of protection in a susceptible mouse, while causing no evidence of disease in 48 mice challenged with doses up 4400 spores intranasally. 
       Example 3 
     Identification of the  Coccidioides posadasii  CPR Gene 
       [0141]    The CPS1 gene of  Coccidioides  spp. was identified using the  C. heterostrophus  sequence as a query (AF332878). The  C. immitis  strain RS gene CIMG — 03303.3 encodes a protein of 1879 amino acids with a predicted molecular mass of 208 kDa. Alignment with the  C. heterostrophus  protein encoded by AF332878, indicated  C. immitis  CPS1 exhibited 55% identity and 13% similarity. The inventors note that the annotation for AF332878 was determined to represent a truncated form of the  C. heterostrophus  CPS1 ORF, lacking the N-terminal end of the protein which was determined based on RT-PCR (B. G. Turgeon, personal communication). Thus there is greater overall similarity between these proteins. Using BLASTX with CIMG — 03303.3 against the  C. posadasii  Silveira genome identified two adjacent genes CPSG — 02657.2 and CPSG — 02658.2 that align consecutively with the RS CPS1 gene. Further alignment and analysis of these protein sequences with CIMG — 03303.3 suggest an annotation error in Silveira; combining these proteins formed a complete open reading frame encoding the CPS1 protein. CIMG — 03303.3 from  Coccidioides immitis  strain RS showed 99% identity to a  C. posadasii  strain C735 protein ( C. posadasii  strain C735 delta SOWgp, XP — 003068865) and 83% identity with UREG — 07134 ( Uncinocarpus reesii  1704). The degree of similarity to  Paracoccidioides brasiliensis  ranged from 88 to 92% between the strains. The Cps1 protein is conserved in most ascomycete fungi with varying degrees of similarity to the query sequence and is related to proteins found in animals including the Dip2 proteins identified in  Drosophila  and found in mammals. 
         [0142]      C. immitis  Cps1 contains a DMAP1 binding domain at the N-terminus and two acyl-CoA synthetase (AMP-forming)/AMP-acid ligases II (CaiC) domains. The DMAP1 is known to act as a transcriptional co-repressor and the CaiC domains were found to function in lipid metabolism and secondary metabolite biosynthesis, transport and catabolism. 
       Example 4 
     Construction of a CPS1 Deletion Mutant 
       [0143]    To understand the effect of CPS1 on virulence of  C. posadasii , the inventors constructed Δcps1 strains using  Agrobacterium  mediated gene replacement. The deletion construct contained the hygromycin B gene from  Escherichia coli  between a 1.1 kb CPS1 5′ flanking segment and a 1.2 kb CPS1 3′U flanking segment. The entire construct (5′flank-hph-3′flank) was cloned into pAM1145 between T-DNA border sequences at EcoRI site and transformed into  Agrobacterium tumefaciens  strain AD965 and the resulting strain designated as A1594. The  C. posadasii  Δcps1 strains were generated by co-cultivation of A1594 and  C. posadasii  germlings on induction medium, followed by the selection of transformants on plated containing hygromycin. Forty-eight hygromycin resistant transformants were picked and purified by successive re-streaking on plates containing hygromycin for three times. The CPS1 gene deletion was assessed by both PCR and Southern hybridization. DNA was extracted from 24 hygromycin resistant strains and tested for deletion cassette using primers for hph gene and the CPS1 gene in an attempt to determine if the hygromycin resistant strains were homokaryons or heretokaryons. Based on the results obtained from PCR, Southern hybridization was performed on the DNA of 17 transformants and wild type Silveira DNA restricted with EcoRI, using the hph gene, CPS1 gene, 5′flanking sequence and 3′flanking sequence amplicons as probes. When hybridized with the hph gene probe, strains 11, 19, 28 and 30, contained a 10.2 kb fragment indicative of homologous gene replacement event. All other transformants had varying sized fragments indicating ectopic integration of the deletion cassette. The transformants were further tested with wild type CPS1 gene probe and the putative gene replacement strains (11, 19, 28 and 30) lacked the wild type gene. Those which had a wild-type copy of the CPS1 gene had a fragment of 5.1 kb, including the wild-type, Silveira. 
         [0144]    To confirm the above result the inventors tested six transformants (namely 6, 11, 13, 19, 30 and 48) and wild type with 5′flanking sequences and 3′ flanking sequences as probes. All the homokaryotic transformants had a fragment of 10.2 kb with both the probes. These results support the conclusion that at least four of the transformants (11, 13, 19 and 30) tested arose from a single homologous integration event of the CPS1 deletion cassette and other strains had a non-homologous integration resulting in ectopic transformants. 
       Example 5 
     Growth Rate and Spherule Size of CPS1 Mutants 
       [0145]    The growth rate of the Δcps1 mutant was assessed at 24° C. and 37° C. on media containing with and without hygromycin as selectable marker. Except for minor differences, no major defects in growth rates were observed between the Δcps1 and wild type during the initial growth phase. At day 5, a slightly significant difference was observed between the Δcps1 cultures grown on media containing with or without hygromycin (p=0.0474). However, by day 14, significant differences in growth rates between the Δcps1 and wild-type were observed in cultures grown at 24° C., where the Δcps1 had a reduced growth when compared to the wild-type. This reduced growth in the mutant might be due to the accumulation of secreted metabolites in the media. In contrast, the growth rate was almost similar between the Δcps1 and wild-type at 37° C. and correlated with the lower accumulation of the putative metabolite. 
         [0146]    To understand the effect of the CPS1 deletion on spherule size, the inventors inoculated induction media with arthroconidia and measured the size of spherules at 24 hour intervals for a span of five days. Significant differences in spherule size were observed between the Δcps1 and wild-type at all stages of spherulation (p&lt;0.0001). On day five, the maximum size of Δcps1 spherules were 7.8 μM in diameter while the wild-type spherules measured 9.9 μM. 
       Example 6 
     Comparison of Virulence of Wild-Type and ΔCps1 Strains 
       [0147]    BALB/c mice were intranasally infected with 50, 211, 810 and 4400 viable arthroconidia of Δcps1 and with 59 arthroconidia of the strain Silveira, the wild-type parental strain, to assess the virulence of Δcps1 mutants ( FIG. 1 ). Each concentration was tested in 12 different mice and the mice were followed for 30 days post-infection. Mice challenged with arthroconidia derived from wild-type strain showed high rates of mortality and nearly 30% of the animals died by day 15; all animals were dead by 19 days post-challenge. Interestingly, all animals infected with arthroconidia from Δcps1 mutant survived the length of the study (30 days). The number of Δcps1 arthroconidia used for intranasal infections has no effect on the survival and the differences in the survival rate of mice between the wild-type and Δcps1 were significant. 
         [0148]    The fungal burden in the mice infected with Δcps1 arthroconidia was assessed by harvesting lungs and spleens at 30 days post-challenge. From the 44 mice infected with the Δcps1 strain, only a single colony was recovered from the homogenate of the lung of one mouse infected with the 810 dose. No CFU were recovered from the spleens of the mice. Testing of the single colony recovered from the 810-dose mouse determined that it was a Δcps1 strain by PCR analysis. 
       Example 7 
     ΔCps1 Strains Provide Protection Against Infection by Wild-Type  C. posadasii    
       [0149]    To assess whether the avirulent Δcps1 strains are able to protect mice against subsequent infection by wild type  Coccidioides , C57BL/6 mice were vaccinated, either intraperitoneally or subcutaneously, with 50,000 Δcps1 arthroconidia, at two weeks boosted with the same number of spores and after four weeks, infected with 90 arthroconidia of Silveira, a stringent challenge as 50 spores is a lethal dose. The protective effects of the Δcps1 strain was assessed two weeks after challenge. Both lung weights and quantitative culturing of lungs revealed that the Δcps1 strain provided significant protection against infection, with a 3 log reduction in fungal burden compared to the Ag2/PRA-CSA chimeric antigen and almost a 5 log reduction compared to the adjuvant alone controls ( FIG. 2 ). 
       Example 8 
     Sensitivity to Hydrogen Peroxide 
       [0150]    To test whether the CPS1 deletion has any effect on resistance to oxidative stress, the inventors examined the growth of Δcps1 at different concentrations of hydrogen peroxide as a measure of oxidative stress. 2×GYE media was supplemented with different concentrations of H 2 O 2  (0 mM to 20 mM), inoculated with either Δcps1 or wild-type strain Silveira and growth assessed at either 24° C. or 37° C. Silveira was not able to resist more than 2 mM H 2 O 2  where as the Δcps1 was able to grow even at 8 mM H 2 O 2 . There were significant differences between the growth of Δcps1 and wild-type at both the temperatures (24° C. and 37° C.). Hygromycin in media had an effect on oxidative stress; the Δcps1 strain was sensitive above 5 mM H 2 O 2  when hygromycin was present in the media while in the absence of hygromycin the mutant was able to grow on media up to 8 mM H 2 O 2  at 37° C., or 6 mM H 2 O 2  at 24° C. These results collectively indicate that the Δcps1 mutant was able to withstand oxidative stress at a higher level compared to the wild-type strain. 
       Example 9 
     Degenerate Spherule and Endospore Formation in an Avirulent Mutant Strain of  Coccidioides posadasii  that Induces Protection in Mice 
       [0151]    Animals: Female BALB/c mice were purchased from Harlan-Sprague-Dawley. NOD-SCID (NSG) mice were a generous gift from Jeffrey Frelinger (Dept Immunobiology, The University of Arizona). Animals were housed and utilized according to NIH guidelines and all procedures were approved by the University of Arizona Institutional Animal Care and Use Committee. NSG mice, which lack NK and all T- and B-cells and are severely immunodeficient, were housed under SPF (specific pathogen free) conditions until transfer into the ABSL3 laboratory for infection with  Coccidioides.    
         [0152]      Coccidioides  strains:  C. posadasii  (Cp), strain Silveira, was grown to maturity on glucose yeast extract agar plates at room temperature and arthroconidia were harvested by the spin bar method. This was used as the virulent wildtype (WT) strain for challenge of vaccinated mice and as historical controls for histopathology slides to compare with Δcps1. The Δcps1 strain was transferred by plugs placed on fresh GYE plates with hygromycin in the medium and grown to maturity (8 weeks). Arthroconidia were harvested as for WT. 
         [0153]    Mouse Studies: For lung histopathology, NSG and BALB/c mice were anesthetized with 80 mg/kg ketamine and 8 mg/kg xylazine IP and the target inoculum was instilled intranasally in 30 μl sterile saline for injection. Mice were observed and weighed to monitor clinical condition. They were sacrificed using an overdose of inhalant anesthetic and lungs fixed in 10% buffered formalin or zinc acetate fixative. Serial or step sections were cut and stained with H&amp;E. Some studies were also stained with a  Coccidioides -specific immunohistochemical stain. 
         [0154]    For the protection study, 6-week old female BALB/c mice were vaccinated intranasally or subcutaneously with 10,000 viable arthroconidia of Δcps1 twice two weeks apart and challenged four weeks later with a target dose of 50 spores of strain Silveira. Control groups were vaccinated subcutaneously with MPL-SE adjuvant alone or 2 μg/mouse of chimeric antigen with adjuvant, which is known to prevent death following lethal infection in &gt;90% of C57BL/6 mice. Mice were observed for 28 days and moribund animals were euthanized as necessary throughout the study. On day 28, surviving mice were sacrificed, and the lungs weighed, scored, and processed for quantitative determination of fungal burden. Colonies were enumerated after 3 days&#39; incubation at 37° C. Spleens were plated whole on GYE plates and incubated up to one week at 37° C. to determine if disease disseminated. 
         [0155]    Histopathology: For early studies, entire lungs of two mice per time point were cut in 5 μm sections and every fifth section was affixed to slides and stained with hematoxylin and eosin (H&amp;E). For later studies involving higher numbers of infectious arthroconidia, two serial sections were cut for every fifth step section and 10 steps total were prepared on slides. One slide from each series was stained by H&amp;E and one slide was immunohistochemically stained with a polyclonal goat anti-Ag2/PRA antibody that is specific for  Coccidioides  as previously described (Shubitz et al. Infection and Immunity 76:5553-5564, 2008). 
         [0156]    Statistical Analysis: Lung fungal burdens were log transformed and compared by ANOVA (Systat 10.0). 
         [0157]    Results 
         [0158]    NSG Mice Infected with 1030 Spores. 
         [0159]    Six NSG mice were infected intranasally with 1030 spores of the Δcps1 mutant strain. Mice were observed daily for lethargy, ruffled fur, inactivity, and dehydration. On day 6, two mice were sacrificed and lungs fixed in formalin. One mouse had occasional, pinpoint reddish-grey lesions scattered throughout and the other was grossly normal. Examination of step sections (every 5 th  section) through the entire lungs revealed no spherules. There were clusters in the alveolar spaces of large, foamy macrophages that appeared to correlate with the grossly observable lesions, but there were no fungal forms associated with these areas. The remaining mice were observed until day 14 and all were clinically normal at sacrifice with maintenance of body weight. At necropsy, two animals had occasional reddish-grey lesions (&lt;12) as observed in one of the mice at day 6 and the other two appeared normal. Two mice had lungs fixed in formalin and sectioned and the entire lungs of the other two were quantitatively cultured. One animal had no fungal growth and 8200 colony-forming units were recovered from the other. Again, no fungal organisms were observed in step sections through the entire lung of the two fixed mice, but the clusters of foamy macrophages in the alveolar spaces were observed. However, the recovery of 8200 colonies from one mouse suggests expansion of the infection in at least one animal because that is an 8-fold increase over the target challenge. 
         [0160]    NSG and BALB/c Mice Infected with 10,000 Spores. 
         [0161]    Two NOD-SCID and two BALB/c mice were infected intranasally with 10,000 spores of Δcps1 strain and one mouse of each strain was sacrificed on day 1 and day 3 post infection. Two serial sections were cut every five steps for a total of 10 steps (20 slides); one slide from each serial pair was stained with H&amp;E and the other was stained specifically for  Coccidioides . No organisms were seen with either stain on day 1 post infection, but the  Coccidioides -specific stain revealed low numbers of variably sized spherules on day 3 ( FIGS. 9A and 9B ). There were more spherules in the NOD-SCID mice than the BALB/c mice, but the pathology in both strains was minimal. Spherules generally appeared thin walled and degenerating and were surrounded by clusters of neutrophils. This is in contrast to wildtype spherules of strain Silveira in mice at day 3, which appear to have thicker walls and are very round, often with dark-staining contents. Though abnormal spherule forms can be seen in tissue due to cutting artifact, the degenerating condition of the Δcps1 spherules appears to be constitutional. While day 3 spherules of strain Silveira appear to have one to a few layers of macrophages surrounding them, the Δcps1 spherules are surrounded, and sometimes invaded, by neutrophils. ( FIGS. 9A and 9B ). Neutrophils do not become a significant cell type around normal spherules until rupture between day 4 and 5 ( FIG. 10 ). It has been previously reported that spherule rupture and endospore release attracts neutrophils to the site. Whether the degenerating condition of the walls of Δcps1 spherules is a chemoattractant for neutrophils or whether the neutrophils have a role in the condition of the spherules is currently unknown; however,  FIGS. 3A and 3B  show that some spherules of Δcps1 appear abnormal without a neutrophilic infiltrate and it is possible that a defect in fungal wall structure may be allowing substances that normally only attract neutrophils upon rupture to escape from the Δcps1 spherules during earlier development. BALB/c mice (very susceptible, doses as low as 10 spores IN lethal) were vaccinated IN and subcutaneously (SC) with Δcps1 strain, challenged with 50 spores WT  Coccidioides . First the mice were infected with 1030 spores, sacrificed on days 6 and 14 post-infection for histopathology. Histopathology from about 150 serial sections that were stained with H&amp;E (routine stain) were negative for organisms. None of the mice became ill or died. For mice infected with 10,000 spores; no mice became ill and were sacrificed on days 1 and 3. Serial sections were stained with a  Coccidioides -specific stain. Spherules were visualized at Day 3 using the  Coccidioides -specific stain in both strains of mice; more spherules were present in the in NSG mice; the spherules look degenerate ( FIGS. 3A and 3B ). 
         [0162]    Upon initial scanning, spherules were not observed on the H&amp;E stained slides due to the paucity of organisms and the degenerating walls that either take up stain poorly or do not stain at all. Because the inventors had serial sections to examine, the H&amp;E stained slides were reviewed again after locating spherules with the  Coccidioides -specific stain. Low power scanning of the slides revealed the sites of neutrophil accumulation and examination of several of these sites at higher power (400-1000×) revealed remnants of spherule walls, or outlines of walls with neutrophils both surrounding the original spherule and filling it in, leaving an outline where the wall existed or where fragments may still be seen at high power ( FIG. 10 ). One small, empty, thin-walled spherule was observed intact, but clearly is not undergoing endosporulation. ( FIG. 10 ). 
         [0163]    BALB/c Mice Infected with 25 Million Spores. 
         [0164]    Mice were given an overwhelming dose of Δcps1 spores in order to make more observations of the spherules in vivo and to determine the fate of the spherules over time since in all previous studies (n=3) where lower doses were used, the organism was entirely cleared and there was no residual lung inflammation by day 14 post-infection. Eight BALB/c mice were given 25×10 6  spores intranasally; two mice were sacrificed on day 1 post-infection, one mouse each on day 3 and day 4, two mice on day 5, one mouse on day 7 and one mouse on day 10. Clinically, the mice began to look lethargic and have ruffled fur on day 3 and two mice, instead of one, were sacrificed on day 5 because they appeared ill enough that maintaining them longer would constitute unnecessary suffering. The remaining two mice improved clinically after day 5 and appeared outwardly normal at the time of sacrifice. 
         [0165]    All mice had grossly visible lesions in the lung except for the mice sacrificed at 24 hours. The lesions of mice on days 3-5 were diffuse, large, and pale and appeared edematous or “wet” rather than having discrete 0.5-1.0 mm granulomas typical of early coccidioidal infection in mice. The mice sacrificed on days 7 and 10 had grossly normal lungs. Five pairs of serial sections were made for each mouse and one of each pair was stained with H&amp;E and the other with the  Coccidioides -specific stain. H&amp;E stains revealed that the mice developed a severe suppurative pneumonia with edema by day 3. The beginnings of this are apparent on day 1, but it is diffuse by day 3. The neutrophil is the primary inflammatory cell present. In addition, there are vast numbers of developing Δcps1 spherules in clusters in the middle of the suppurative response. As with the sporadically visualized spherules from the mice infected with 10,000 spores, they are highly variable in size and many are degenerating, but some appear to be attempting to endosporulate. 
         [0166]    On day 4, the largest proportion of the Δcps1 spherules have been invaded by neutrophils, but structures that appear to be endospores are readily visible within spherules. They are highly variable in size and have thin walls like the Δcps1 spherules themselves. WT spherules rupture between day 4 and 5. 
         [0167]    On day 5 the Δcps1 spherules appear similar to day 4, however, they are distinct from WT in that the endospores have not been released or spread out from the spherule as happens with normally rupturing spherules. ( FIG. 10 ). All of the endospores, even those where the walls of the parent spherule are degenerated, are completely surrounded by neutrophils which appear to be containing them in their original position. In terms of the general inflammatory response, by day 5 a granulomatous component is seen. Macrophages have moved into peripheral positions surrounding the neutrophils and early granuloma formation is present. With wildtype spherules, the macrophages are present prior to the arrival of the neutrophils in the early lesion. 
         [0168]    By day 7 post-infection, the Δcps1 spherules appear to be decreased by &gt;90% compared to day 5 (visual estimate) and the inflammation is characterized by granulomas with a core of neutrophils and spherules. 
         [0169]    By day 10, the infection is reduced to small, scattered granulomas with fewer than a dozen primarily empty spherules within ( FIG. 12 ). 
         [0170]    Protection of BALB/c Mice by Intranasal or Subcutaneous Vaccination with Viable ΔCps1. 
         [0171]    The inventors have previously demonstrated that C57BL/6 mice can be significantly protected against lethal  Coccidioides  infection by immunizing with live spores of Δcps1. Because the inventors have been able to show good protection of C57BL/6 mice but poorer protection of BALB/c mice with recombinant vaccines in the past, and because in these experiments BALB/c mice are more susceptible to infection than C57BL/6 mice, the inventors compared BALB/c mice vaccinated with Δcps1 versus the Ag2/PRA-CSA chimeric recombinant vaccine that protects approximately 90% of C57BL/6 mice against challenges of 50 spores. 
         [0172]    BALB/c mice vaccinated with the recombinant antigen or adjuvant only all died between days 13-15 post-infection, whereas all but one of the mice vaccinated with Δcps1 survived until day 28 (P&lt;0.001) ( FIG. 6 ). There was no statistical difference between the route of vaccination with the Δcps1. Lung fungal burdens were quantified for surviving mice on day 28 and even though the intranasally vaccinated mice had lower fungal burdens ( FIG. 7 ), there was no statistical difference between the groups (P=0.241). 
       Example 10 
     Virulence of Mutant Strains Compared to Wild Type Silveira in Susceptible Mice 
       [0173]    8 week old C57BL/6 female mice were infected with target doses as listed in Table 2 with spores counted in the lungs. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Type and Amount of Spores Inoculated and Present in Lungs. 
               
             
          
           
               
                   
                   
                 Spores 
                 Number 
                 Spores counted 
               
               
                 Group 
                 Fungus 
                 inoculated 
                 of mice 
                 in lungs 
               
               
                   
               
             
          
           
               
                 1 
                 WT 
                 50 
                 12 
                 59 
               
               
                 2 
                 Δcps1 
                 50 
                 12 
                 51 
               
               
                 3 
                 Δcps1 
                 250 
                 12 
                 211 
               
               
                 4 
                 Δcps1 
                 1000 
                 12 
                 810 
               
               
                 5 
                 ΔLOM 
                 50 
                 12 
                 51 
               
               
                 6 
                 ΔLOM 
                 250 
                 12 
                 310 
               
               
                 7 
                 ΔLOM 
                 1000 
                 12 
                 900 
               
               
                   
               
             
          
         
       
     
         [0174]    Mice in the L-ornithine monooxygenase mutant (ΔLOM) 1000 spore and 250 spore groups started to become moribund on day 9 and day 10, respectively. All of the 1000 spore mice were euthanized on day 9 and the 250 spore mice were euthanized on days 10 and 11. Disease scores were high in all animals, except a single mouse (#10) in ΔLOM 1000 group. The animal lungs were positive for growth, but likely this mouse received only a fraction of the target dose. Wild type mice (59 spores) became moribund on days 13-19, and the ΔLOM 50 mice on days 13-16. These two groups appeared clinically similar and had similar disease scores at necropsy. 
         [0175]    The Δcps1 infected mice remained healthy throughout the observation period of 4 weeks. Though the original plan was to quantitate the fungal burden at the end of the study with any remaining mice, a modified plan was made to plate entire lungs and spleens if animals had no gross evidence of disease at necropsy. None of the mice had observable lesions at day 28 post-infection, and none of the slides from day 11 post-infection. showed any pockets of spherules or any inflammation, not even perivascular/peribronchial infiltrates. Tissues were incubated on GYE agar plates for 9 days. 
         [0176]    One mouse (#9, 1000 Δcps1 spore group) had growth in the lung but not the spleen. The strain that grew from this lung was saved for analysis. Statistical analysis of the survival curves was performed using a Kruskal-Wallis. 1) ΔLOM at each dose was statistically different from the other doses (p&lt;0.001). 2) ΔLOM 50 sp was significantly different from WT 59 spores (p&lt;0.001), with the mutant mice having earlier deaths than the WT mice. This occurred with a Δste12  C. posadasii  mutant as well. Histologically, no differences were seen between the WT mice and ΔLOM mice on HE stained slides. 3) ΔLOM at the higher doses was also significantly different from WT 59 sp. 4) None of the Δcps1 groups was different from each other (p=1.0), and all were different from the other strains. 
         [0177]    Histopathology: The ΔLOM mice did not appear different from the WT mice when inoculated with a similar dose (˜50 spores). The ΔLOM mice inoculated with higher doses had enormous numbers of spherules/endospores in all fields of the lungs. Δcps1 infected mice had no evidence of infection or inflammation in the lung sections examined. Though entire lungs were submitted in 10% formalin, only a single slide with a single slice of tissue was reviewed. 
         [0178]    Fungal burden: Nothing was quantitated in this study because of the moribund condition of 4 groups prior to the scheduled date of sacrifice and the lack of gross lesions in the remaining 3 groups of mice. For moribund mice, disease scores were 3-4 L with 6 mice also having visible lesions on the spleen. Growth was present in both lungs and spleen of most mice (with the exception of 2 ΔLOM 1000 mice which had no growth in spleen). For the healthy-appearing Δcps1 infected mice, plating of entire lungs and spleens yielded growth from the lung of a single mouse inoculated with 810 spores. This confirms that the mutant strain can reproduce in the host, but that the virulence of the strain is greatly diminished. 
       Example 11 
     Evaluation of a RYP1 Knockout in  Coccidioides    
       [0179]    The RYP1 gene (Nguyen and Sil, 2008, Proceedings of the National Academy of Sciences, USA 105:4880-4885) was knocked out in  Coccidioides  strain Silveira. Deletion of the RYP1 gene leads to avirulence in  Histoplasma capsulatum  because the mold cannot switch to the pathogenic yeast phase. In  Coccidioides , deletion of the RYP1 gene (CIMG — 02671.3) appears to inhibit the change to the spherule/endospore phase in vitro and is therefore anticipated to be entirely avirulent. This strain was compared with high doses of Δcps1. 
         [0180]    8 week old C57BL/6 mice were challenged with Δryp1 spores, Δcps1 spores and WT spores in doses shown in Table 3, with the post infection plate count. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Infection of Mice with Δryp1, Δcps1 and WT Spores. 
               
             
          
           
               
                   
                 Type of 
                 Amount of 
                 Number of 
                 Post infection plate 
               
               
                   
                 spores 
                 spores 
                 mice 
                 count 
               
               
                   
                   
               
             
          
           
               
                   
                 WT 
                 50 
                 12 
                 53 
               
               
                   
                 Δcps1 
                 1000 
                 12 
                 4400 
               
               
                   
                 Δryp1 
                 50 
                 12 
                 47 
               
               
                   
                 Δryp1 
                 1000 
                 12 
                 994 
               
               
                   
                   
               
             
          
         
       
     
         [0181]    Mice infected with the WT strain began to become moribund on day 12 post-infection. The largest proportion were moribund on day 14. By day 19, all WT mice were dead except one animal that demonstrated weight gain and was suspected to be uninfected. The Δcps1 and Δryp1 inoculated mice remained clinically normal. The #11 and #12 mice from each group were sacrificed for histopathology on day 14. Mice challenged with Δcps1 and both doses of Δryp1 had no weight loss and no observable lung lesions. The #11 WT mouse was also negative for lung lesions and had no weight loss, but #12 was as expected. At sacrifice at 28 days, the living WT mouse had one medium sized granuloma in the lung and two splenic granulomas. All the mutant Δcps1 and Δryp1 inoculated mice were grossly negative. Organs were plated in toto on GYE plates. 
         [0182]    All the organs plated except from the WT mouse were negative, both spleens and lungs, after 8 days of incubation. Histopathology of organs of the Δcps1 and Δryp1 infected mice 14 days post-infection showed no organisms in any of the mice. A couple of animals had mild, focal, inflammatory lesions, only 1 per mouse. No organisms were seen. WT #11 had no histologic evidence of disease, while #12 had a score of 4/5 for lungs, plus abscesses that consist almost exclusively of neutrophils and spherules/endospores in the spleen. Average days survived and average infection and sacrifice weights are provided in Table 5. 
         [0183]    The Δcps1 strain appears in this corroborative study to be nonpathogenic, and the Δryp1 strain was also nonpathogenic, as expected based on work done with the ortholog of this gene in  Histoplasma capsulatum  (Nguyen and Sil, 2008, Proceedings of the National Academy of Sciences, USA 105:4880-4885). The survival of two WT mice was unusual and likely due to technical issues, such as the mouse swallowing the dose instead of inhaling it. It is seldom observed that C57BL16 survive to 4 weeks if infected, but this animal did have systemic disease as evidenced by growth of  Coccidioides  from the spleen as well as lungs. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 Survival and Weights of Mice Used in Study. 
               
             
          
           
               
                   
                   
                 Avg. Day 
                 Avg. Infection 
                 Avg. Sacrifice 
               
               
                   
                 Mouse# 
                 survived 
                 weights 
                 Weights 
               
               
                   
                   
               
               
                   
                 Δryp1 50 
                 24.9 
                 19.2 
                 21.3 
               
               
                   
                 Δryp1 100 
                 24.9 
                 19.8 
                 22.0 
               
               
                   
                 Δcps1 5000 
                 24.9 
                 19.9 
                 22.1 
               
               
                   
                 WT 50 
                 15.5 
                 19.3 
                 15.2 
               
               
                   
                   
               
             
          
         
       
     
       Example 13 
     Evaluation of Immunity Provided by Avirulent  Coccidioides  Mutants Following Inoculation 
       [0184]    A study was performed to determine if two of the avirulent  Coccidioides  mutants will provide immunity to mice as a vaccine. Δryp1 and Δcps1 knockouts are the most interesting of the avirulent strains studied. Ryp1 is required to form spherules/endospores as the lack of the gene prevents the fungus from undergoing the transformation. Cps1 is involved in small molecule synthesis, and the gene product is required for pathogenicity. 
         [0185]    6 week old, female, C57BL/6 mice were inoculated with Δryp1 spores, Δcps1 spores, Chimeric Ag2/PRA-CSA antigen only (Chim Ag), HSPvar only (HSF), and Adjuvant plus Sac Supe (Sac Supe) with the amount and injection method shown in Table 6. SC=subcutaneously. IP=intraperitoneal. Average lung weights are also shown in Table 6. 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 Effects of Δryp1 and Δcps1 Inoculation on Lung Weights. 
               
             
          
           
               
                   
                   
                 Spores 
                   
                 Number 
                 Avg Lung 
               
               
                   
                 Group 
                 inoculated 
                 IP/SC 
                 of Mice 
                 weight (g) 
               
               
                   
                   
               
             
          
           
               
                   
                 Δcps1 
                 50000 
                 IP 
                 8 
                 0.3 
               
               
                   
                 Δcps1 
                 50000 
                 SC 
                 8 
                 0.3 
               
               
                   
                 Δryp1 
                 50000 
                 IP 
                 8 
                 0.79 
               
               
                   
                 Δryp1 
                 50000 
                 SC 
                 8 
                 0.8 
               
               
                   
                 HSF 2 μg 
                   
                 SC 
                 8 
                 0.6 
               
               
                   
                 Chim Ag 2 μg 
                   
                 SC 
                 8 
                 0.4 
               
               
                   
                 Sac Supe 2 μg 
                   
                 SC 
                 8 
                 0.7 
               
               
                   
                   
               
             
          
         
       
     
         [0186]    Mice receiving the mutant strains were given 5000 viable arthroconidia of the respective strain intraperitoneally or subcutaneously. All animals were boosted at 2 weeks, then rested for 4 weeks before being challenged intranasally with 50 arthroconidia of  C. posadasii  WT strain Silveira. Mice were sacrificed two weeks after challenge. Peritoneal lesions and subcutaneous injection sites had culture and histopathology performed at necropsy. 
         [0187]    Mice were challenged intranasally with wild type strain Silveira 4 weeks after boosting. Post-infection plate counts revealed that the mice received 90 spores. The 90 spores is a pretty stringent challenge. 
         [0188]    Mice had weight loss in groups 3, 4, 5, and 7 by day 10 post-infection. With fluid support, most mice survived. Two mice died. Disease scores were recorded, but this time lung weights were captured as a better form of data to subject to statistical analysis. Disease scores and lung weights correlated pretty well, but the lung weights are not subjective and don&#39;t depend on separating a continuum of disease, especially in mice that are borderline between 2 and 3 and 3 and 4 disease scores. Almost all mice injected with Δcps1 mutant strain had visible granulomas in the subcutaneous tissues or 1-2 mm white lesions in the omentum. These were collected for culture. 
         [0189]    The injection of the Δcps1 mutant strain either IP or SC resulted in the lowest lung weights in this experiment. All animals had evidence of a granulomatous lesion at the injection site, indicating that the mutant strain may have reproduced locally, providing sufficient antigen to result in a memory response that led to protection. A few IP injected animals also had 1-2 mm granulomas in the omentum. The Δryp1 strain appeared to provide no protection to the mice. This could be because it undergoes no growth at all in the host and the 25,000 arthroconidia are not sufficient to induce a memory response in the mice. 
         [0190]    Quantitative Lung Cultures: Box plot of the CFU from the seven groups in the study. It is clear that the Δcps1 mutant offered the greatest protection with a 2 log lower average lung weight compared to the positive control chimeric antigen group ( FIG. 14 ). None of the other vaccine groups showed protection compared to control and the statistical analysis of both lung weights and total lung CFU bear this out. 
         [0191]    Chimeric antigen, the “gold standard” resulted in 2 logs higher lung fungal burden than the Δcps1 strain but had significant reduction (˜3 logs) in fungal burden compared to controls. Mice looked pretty comparable to those in other studies with a similar challenge (˜100 spores). While this is the positive control antigen in the studies, it was known that there is room for a better antigen and this study again reinforces that.