BACKGROUND OF THE INVENTION U. S. Patent No. 4, 740, 585 discloses peptide vaccines for urinary tract infections prepared from synthetic peptides based on short sequences contained in HUR849 pilin A.

U. S. Patent No. 4, 736, 017 discloses peptide vaccines for urinary tract infections prepared from purified whole Gal-Gal pilus proteins or fragments thereof.

Baga et al., Cell, 49 (1987) : 241-251, disclosepapH deletion mutants in one strain of Escherichia coli. The reference indicates that, in these papH deletion mutants, 50%-70% of total pilus antigen was found free of cells in the form of polymerized structures. Further, the dissociated and purified pili from these mutants are stated to agglutinate erythrocytes, though data is not disclosed, The reference does not indicate whether such dissociated pili from the papH niutant in polymerized form are effective as vaccines or whether these pili from the papH mutant would have altered antigenicity. In addition, the reference does not give the exact sequences of the two papH deletion mutants from the one strain of E. coli.

Van Die proposed (J. Bacteriology, 170 : 5870-5876, 1988) using a gapped- duplex method with the Fll pap operon for insertion of a foreign peptide. However, his site of insertion did not correspond to the immunodominant site of papA.

SUMMARY OF THE INVENTION An embodiment of the present invention is immunogenic pili presenting at least one foreign peptide in an immunodominant region of papA.

Another embodiment of the present invention is an immunogenic composition, including a vaccine against E. coli urinary tract infections or for other microbial infections/disease, where at least one epitope is expressed at the immunodominant region of PapA, comprising dissociated pili that are obtained after standard shearing methods from a Gal-Gal pilus-producing bacteria having at least one peptide inserted into the immunodominant epitope region of PapA that normally does not contain such a peptide sequence. The foreign epitope may be from another region of papA that is not immunodominant, or it may be entirely foreign to papA such as an HIV epitope.

Another embodiment of the present invention is a process for producing pili and vaccines comprising pili (including vaccines for urinary tract infections and other microbial infections/diseases) of the invention comprising culturing a recombinant Gal-Gal pilus-producing bacteria which expresses at least one foreign peptide at the immunodominant region of a PapA region that normally does not contain such a peptide, recovering dissociated pili, and formulating a vaccine comprising these pili. Preferably, these pilus-producing bacteria harbor at least one papH mutation that facilitates detachment of the pili from the bacteria relative to a wild type strain.

Another embodiment of the present invention is a method of treating or preventing a urinary tract infection or other microbial infection/disease disease where protective epitopes are expressed at the immunodominant region of PapA comprising administration to a subject in need thereof a vaccine produced according to the invention.

Another embodiment of the present invention are E. coli bacteria having novel mutations that result in hybrid pili that can express one or more foreign antigens in the immunodominant region of papA, which optionally further include a mutation that facilitates detachment of pili from the surface of bacteria relative to a wild type strain.

Preferably, the mutation that facilitates detachment is a mutation in papH.

Another embodiment of the present invention is a plasmid that allows for the constant expression of immunologically novel pili at the surface of bacteria. This plasmid,

which preferably is a shuttle vector, could be used to transform live, attenuated microbes (e. g., aromatic mutant Escherichia coli, Salmonella typhi, Salmonella typhimurium, Actinobacillus pleuropneumoniae) as vaccine vehicles for small peptides (preferably spanning less than 20 amino acids). Also, simultaneous incorporation of the unique papA cassette and papH mutants provide for the constant release of hybrid Gal-Gal binding pili by transformed live attenuated microbes in vivo in animals and humans. Thus, the invention provides a method for either transient or chronic antigenic stimulation of a host with epitopes constituting protective immunity.

BRIEF DESCRIPTION OF THE DRAWINGS Fig. 1 shows a genetic and physical map of recombinant plasmids used in the present papH invention.

Fig. 2 (a) provides the papH DNA sequence of pHUR849, Fig. 2 (b) pDAL201B papH, Fig. 2 (c) pDAL210B papH, and Fig. 2 (d) pDAL200A.

Fig. 3 provides a comparison of the pa pDAL200A, pDAL201B, and pDAL210B.

Fig. 4 gives a comparison of deduced amino. acide sequences of papH genes for pHUR849, pDAL200A, pDAL201B, and pDAL210B.

Fig. 5 (a) shows the amino acids (which are underlined) that are deleted from papH in pHUR849 and Fig. 5 (b) shows the amino acids (which are underlined) that are deleted from papH in pDAL201B, pDAL210B, and pDAL200A.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT An embodiment of the present invention is an immunogenic composition, including a vaccine for urinary tract infections, comprising dissociated pili from a recombinant pilus-producing bacteria, said pili comprising at least one immunogenic peptide inserted into a PapA region that does not normally contain such a peptide in the corresponding wild type. The inserted immunogenic peptide (s) may be a non-pilus- associated peptide or a pilus-associated peptide, including the substitution of PapA immunogenic epitopes located normally in other regions of the PapA. For example, cryptic

immunogenic PapA epitopes located at the amino terminal (corresponding to Residues 4 through 15) can be inserted into the immunodominant region and be rendered antigenic and immunogenic in the expressed hybrid Gal-Gal binding pili. Preferred immunogenic peptides to be inserted in the PapA region for the prevention of E. coli urinary tract infections are set out in the examples below. Preferably, the peptide is inserted into a position between amino acid residues 64 through 80 of the papA region. In another preferred embodiment, the foreign peptide is inserted by replacing 18 to 60 bases at the DNA level, which is a location within papA that corresponds to the immunodominant region of papA moiety and that corresponds to amino acid residues 65 through 75 in wild type papA.

Preferably, the pili of this embodiment are produced by culturing a bacteria having at least one mutation that facilitates detachment of the pili from the bacteria relative to a wild type strain. Preferably, the mutation is one that impairs or eliminates the anchoring function of papH.

Another embodiment of the present invention is a process for producing pili or a vaccine comprising pili for urinary tract infections comprising culturing a recombinant pilus-producing bacteria expressing pili comprising at least one immunogenic peptide inserted into a papA region that normally does not contain such a peptide and recovering detached pili from the culture. Optionally, the method further comprises formulating a vaccine comprising the pili for the prevention of E. coli or the treatment or prevention of other microbial infections/diseases if foreign protective epitopes are inserted into the immunodominant region of PapA. Preferably, detached pili are recovered from the culture by centrifugation and further purified by cycles of magnesium sulfate precipitation and tris solubilization. Still more preferably, the recombinant hybid PapA Gal-Gal pilus-producing bacteria further includes at least one mutation that facilitates detachment of the pili from the bacteria.

In one particular embodiment of the pili production method, a one-liter TSB culture yields about 10 mg of purified pili after 18 hours growth at 37 °C from each of the 4 recombinant strains that harbor PapH mutations.

Another embodiment of the present invention is a method of treating or preventing a urinary tract infection or other microbial infections/diseases (e. g., patients infected with HIV-1 or HIV-2 with or without AID-defining illness) if the protective epitope is inserted into the PapA immunodominant region comprising administering to a subject in need thereof a vaccine produced according to the invention.

Another embodiment of the present invention are E. coli bacteria having novel mutations that facilitate detachment of pili from the surface of bacteria by impairing or eliminating. the anchoring function of PapH.' Another embodiment of the present invention relates to creation of novel protein-base immunogenic sequences set out in the examples below.

Preferably, the pilus-producing bacteria of the invention is E. coli, more preferably those disclosed in the examples below.

In the present invention, any mutation may be used that facilitates detachment of pili from the bacteria relative to a wild type strain. Preferably, the mutation impairs the anchoring function of PapH relative to a wild type pilus-producing bacteria, thereby increasing the amount of dissociated pili from the bacteria found in the culture supernatant relative to a wild type pilus-producing bacteria. Preferably, the mutation is a deletion mutation in the DNA encoding PapH, but other types of mutations achieving the same function may be used, such as insertion mutations.

Vaccines comprising the dissociated pili of the invention are formulated according to known methods, including those described in U. S. Patent No. 4, 736, 017.

Suitable adjuvants may be used in the vaccines. The method of preventing E. coli urinary tract infections includes those described in U. S. Patent No. 4, 736, 017.

Adherence of Escherichia coli to uroepithelial cells is an important pathogenic step in the development of urinary tract infections. There are a number of adhesins expressed by uropathogenic E. coli, which may mediate uroepithelial attachment ; however, pyelonephritogenic strains are characterized by the high frequency of pili associated with the a-D-Galp- (1-4)-p-D-Galp (Gal-Gal) binding. The Gal-Gal binding phenotype is considered critical to the pathogenesis of unobstructive, ascending urinary tract infection in anatomically normal, otherwise healthy young women. This is probably

due to the absence of a natural host defense factor in urine to prevent the Gal-Gal binding to uroepithelial cells. Digalactoside-binding adherence is mediated by pili, which are also known as Pap pili, or P pili because they bind to the P, blood group antigen (a globoside containing Gal-Gal) that is present on human erythrocytes and all epithelial cells.

The. pap operon consists of at least 9 genes (1) that are required for the expression of the Pap pilus-adhesion complex (see Figure 1). PapA is the major (structural) fimbrial-subunit. PapH is involved in both the termination of pilus growth and is required to anchor the fully grown pilus to the cell surface. PapC is located in the outer membrane and forms the assembly platform for pilus growth. PapD is a periplasmic which protein that forms complexes intracellularly with the pilus subunits before assembly. PapE, PapF, and PapG are tip pilus components. PapG is the adhesion molecule conferring Gal-Gal binding specificity. PapF complexes with PapG, and PapE attaches to PapA moieties, as well as, attaches and orients the PapF-PapG complex so that the adhesin is at the tip of the pilus.

The present invention is further illustrated by, though in no way limited-to, the construction of hybrid PapA pili and likely protective epitopes against E. coli urinary tract infection to be inserted into the immunodominant region of PapA.

The immunodominant regions of F71, F72, F9, and F13 have been localized to the PapA moiety, specifically residing between residues 65-77, residues 65-77, residues 65-75, and residues'65-75, within the operon of pDal201B, pDal210B, pDal 200, and pHU849, respectively.

Furthermore, immunodominant fine deletion mutants in plasmids harboring the F operon for F71, F72, F9, and F13 (viz., pDal201B, pDal210B, pDal 200, and pHU849) have been performed. Linearized pDal201B, pDal210B, pDal 200, and pHU849 have been treated with endonuclease enzymes as recommended by the manufacturer. They were used to cleave the operon specifically at sites encompassing or within the immunodominant PapA region and without generation of too many or ambiguous-fragments during digestion. The strategy included the following :

F type Endonuclease restriction deletion Deletion location at Pap F71 CviJI 58-74 F72 AciI 71-91 F9 CviJI 57-76 F13 MseI 67-77 Oligonucleotide primers corresponding to the cleavage sites in proper orientation separated by desired sequences to be incorporated into the chimeric papA template are synthesized by conventional techniques. They are used to fill the cleaved recessed termini. A salmonella flagellin epitope corresponding to 6 amino acids and an epitope of human interleukin-4 peptide corresponding to 20 amino acids have been inserted into papA genetic cassettes. These genetic templates in Escherichia coli HB101 strain result in pili being expressed at the surface of the bacterium as demonstrated by electron microscopy and expression of hybrid pili as demonstrated by simultaneous binding of a single protein band in SDS-PAGE gels by Western blotting using polyclonal murine antibody to the pili and foreign epitopes. Cohorts of 5 mice each immunized with the hybrid product can elicit antibodies to. the foreign epitope as demonstrated in ELISA tests.

The following peptide conjugate vaccines were demonstrated to be protective after serial parenteral administration in the BALB/c murine model of experimental pyelonephritis after intravesicular administration : F serotvpe Structural Pilin Sequence Residue Position (R) F13 PQGQGKVT R 5-12 F13 AKFGGMGAKKG R 65-65 Identification of additional protective epitopes of Pap pili and F1C structural pilin epitopes for the protection of pyelonephritis and cystitis, respectively, was accomplished. It should be noted the identified protective Fll epitope corresponding to residues 4 through 15 within the pilin A is essentially identical with F13 protective epitope in this region. However, a longer sequence was used for demonstrative purposes.

Peptides were synthesized by conventional solid phase techniques using tertiary butyloxycarbonyl-protected amino acids and amino acid polystyrene resins. As side chain protecting groups, O-benzyl esters were used for Asp, Glu, Thr and Ser, and tosyl groups were used for Arg and His. Cys was protected by p-methoxybenzyl, Lys by o- chorobenzyloxy-carbonyl, and Try by 2, 6-dichlorobenzy. Couplings were performed with molar excess of-c-Boc amino acid and dicyclohexylcarbodiiniide (DCC). If Asn or Gln was to be coupled, a molar excess of N-hydroxytriazole was included. Anydrous hydrogen fluoride in the presence of dimethylsulfide and anisol was used to cleave the protecting groups and the resin simultaneously. After either washing and/or acetic acid extraction, the purity of the final product was determined by reverse phase high performance liquid chromatography. The peptides were considered to be > 98 % pure following this conventional technique.

Conjugation of peptides to thyroglobulin or bovine serum albumin was performed using m-maleinimidobenzoyl N-hydroxysuccinimide ester (MBS) and succinimidyl 4-(N-maleinimido-methyl) cyclohexane-l-carboxylate (SMCC), respectively.

The resulting peptide carrier conjugate was subsequently isolated by gel filtration. The molar ratio of conjugated peptides to carrier protein was determined by comparing the amino acid composition of the carrier before and after conjugation. In general,"10 to 15 moieties of peptide per carrier moiety were conjugated by this conventional conjugation technique.

The following peptide thyroglobulin and bovine serum albumin conjugate vaccines were made : F serotvpe Structural Pilin Sequence Residue Position (R) F71 PQGQGEVSF R 5-12 F71 NFKQLQGGAAKKG R 65-77 F72 PQGQGKVTF R 5-12 F72 NFKKAAGGGGAKT R 65-75 F9 QGSGQVNFKG R 4-12 F9 NFKKAATPGGAAKT R 65-75 Fll IPQGQGKVTFNG R 4-15 F12 IPEGQGKVT R 2-12 FIC NGGTVHFKGEVVN R5-12 F1 TTVTVNGGTVHF R4-15

The intravesicular BALB/c experimental model of pyelonephritis and cystitis, as originally described by O'Hanley, was employed to evaluate the protective capacity of structural pilin synthetic peptide conjugate vaccines to prevent subsequent renal and/or bladder colonization by homologous piliated strains at 48 hours after bacterial bladder inoculation. Cohorts of 20 mice per group were vaccinated via intramuscular administration on two occasions with the experimental thyroglobulin and bovine serum albumin conjugate pilin A vaccines (i. e., day 0 and day 14). Each intramuscular dose of experimental vaccine consisted of-200 ug in 100 ul saline emulsified in 100 ul incomplete Freund's adjuvant. Control vaccines consisted of thyroglobulin and bovine serum albumin emulsified in saline and incomplete Freund's adjuvant. These control vaccines were administered in similar fashion and schedule as the experimental vaccines. Challenge for pilin A vaccinated mice entailed bladder inoculation of 108 CFU of an Escherichiå coli strain that expressed homologous pili. In contrast, the cohort size for control animals was 5 per challenge strain. The table below summarizes the challenge strategy.

F pilin A vaccine status Wild-type challenge strain (F serotype expression) F71 KD201B strain (HB101 transformed with pDA201B) expressing recombinant F71 pili F72 KD210 B strain (HB101 transformed with pDAL210B) expressing recombinant F72 pili F9 3669 pyelonephritis strain (F9 pili) Fll J96 strain expressing F13, plus mannose binding pili F12 C1979 pyelonephritis strain (F12) F1C P2 (F1C) Fl J198 expresses only mannose binding pili and no Gal-Gal or X binding pili Protection against subsequent renal colonization and bladder colonization by the challenge strain was defmed by >90% of the experimental animals in a cohort (i. e., 18 of 20 vaccinated experimental mice) having no bacterial growth from aliquots of homogenized whole right kidney and aliquots of homogenized whole bladders and none of the experimental animals having heavy bacterial growth from the challenge strain in renal or bladder specimens (viz., the absence of + + + + colonization density or > 500 CFU of the challenge strain per 0. 1 gram of renal or bladder tissue) compared to heavy growth of

the challenge strain in both renal and bladder specimens (+ + + + colonization density or >500 CFU per 0. 1 gm of renal or bladder tissue) by the challenge strain in > 80 % of control animals (i. e. > 4 of 5 control mice).

Results indicated the following : F serotyp Pilin A Sequence Residue Positions Homologous Protection F71 PQGQGEVT R 5-12 Yes F71 PQGQGEVA R 5-12 Yes F71 NFKQLQGGAAKKG R 65-77 Yes F72 PQGQGKVT R 5-12 Yes F72 NFKKAAGGGGAKT R 65-77 Yes F9 TTVNGGTVH R 4-12 Yes F9 NFKKAATPGGAAKT R 65-75. Yes F11 IPQGQGKVTFNGTV R 4-17 Yes F12 IPEGQGKVT R 4-12 Yes F1C NGGTVHFKGEVVN R 5-15 Yes Fl TTVTVNGGTVHF R4-15 Yes One or a combination of pilin A vaccines comprising one or more of the following amino acid sequences that correspond to published and unpublished F pilin primary sequences would be protective against ascending, non-obstructive Escherichia coli urinary tract infections in anatomically normal women and males : Pilin A Residue Urinary Tract New or F serotype Pilin A Sequence Positions Protection Potential Old Claim F71 PQGQGEVT R 5-12 Pyelonephritis New F71 PQGQGEVA R 5-12 Pyelonephritis New F71 NFKQLQGGAAKKG R 65-77 Pyelonephritis New F72 PQGQGKVT R 5-12 Pyelonephritis New F72 NFKKAAGGGGAKT R 65-77 Pyelonephritis New F9 TTVNGGTVH R 4-12 Pyelonephritis New F9 NFKKAATPGGAAKT R 65-75 Pyelonephritis New Fl l IPQGQGKVTFNGTV R 4-17 Pyelonephritis New F12 IPEGQGKVT R 4-12 Pyelonephritis New F13 PQGQGKVT R 5-12 Pyelonephritis Old F13 AKFGGMGAKKG R 65-65 Pyelonephritis Old F1C NGGTVHFKGEWN R 5-15 Cystitis New Fl TTVTVNGGTVHF R4-15 Cystitis New A particularly useful method to produce such a vaccine employs whole pap pili corresponding to F71, F72, F9, and F13 (since they comprise >90% of the wild-type strains responsible for non-obstructive Escherichia coli in anatomically normal woman) and

pili expressing R5-12, R4-12, R4-17,-and/or R5-15 by insertion into the immunodominant PapA pilin region (R 65-76) using a genetic cassette with mutated papA and papH cistrons.

In the following examples, mutagenesis of the papH structural gene, which is responsible for anchoring the globoside-binding pili to the cell surface, is utilized. The papH gene was mutagenized of 4 Gal-Gal pilus recombinants, [pHUR849 (pap-5), pDAL201B (Pap-21), pDAL210B (pap-17), and pDAL200A (pap-200A)], which encode for the serotypes F13, F71, F72, and F9 (2), respectively. This was accomplished by creating deletions of 237 or 300-bp within the papH gene of each strain. These deletions encode for 79 or 100 amino acids respectively, and leads to a truncated form of the PapH protein which allows for the mutant recombinant piliated strains to secrete newly synthesized pili into the culture medium. Since PapH or its truncated form is not required in the secretion or the assembly of the pilin-subunit (3), the growing Pap pilus can be detached because of unstable interaction between PapA and the cell envelope. In addition, the complete nucleotide and deduced amino acid sequences of papH genes in all 4 recombinant strains and their deletion derivatives are disclosed herein.

Experimental Procedures Bacterial strains, plasmids, and growth conditions Bacterial strains and plasmids used for these papH examples are listed in Table 1 (below) and Figure 1. The source of the chromosal DNA for pDAL210B was E. coli strain 3669, originally isolated from a woman with acute pyeionephritis (2). The source of the chromosomal DNA for pDAL210B and pDAL210B was E. coli strain C1212, originally isolated from a woman with acute cystitis (2). The source of the chromosomal DNA for pHUR849 was isolated from E. coli strain J96, originally isolated from a woman with acute pyelonephritis (4). All bacteria were cultured in Luria broth or on Luria-agar plates, containing 40 pg/ml X-gal and 20 mM IPTG. Antibiotics were used at the indicated final concentrations : ampicillin, 100, ug/ml, and tetracycline 34 j-ig/ml, for the selection of plasmid-containing strains. Bacterial transformation were performed as previously described (5).

Table 1. Plasmids used in this stlJdy Plasmid Description Reference or source E call HBIO1 F- (gpt-pro)62, leu B6, sup E44, ara-4: gal K2, lac Y1 Stratagene #(mcr C-mmr), rsp L20(Strr), xyl-5, mtl-1, recA13 XL-1 Blue recA (recAl, lac', end A1, gyrA96, th 1, hsdr R7, Stratagem supE44, relA1, (F proAB, lac 1q, lac Z#M15, Tn10) SURE e14* (mcr A), #(mcr CB-hsd SMR-mmr)171, end A1, sup Stratagene E44, thi 1, gyr A96, rel A1, lac, recB, rec), sbcC, umuC ::Tn5(kanr), uvr C, (F' proAB, lac i, lac Z#M15, Tn10] DL844 DL1784 irp::mTn10 D.Low Plasmids pDAL200A puca containing a 9 kb sau 3a DNA fragment encoding (2) for the pap-200A operon DNA sequence (see Fig. 1) pDAL210B pUCB containing a 11 kb Eco RI-Sal I DNA fragmerd (2) encoding for the pap-21 operon DNA sequence (see Fig. 1) pDAL pBR322 containing a 13. 5 kb Bam Wt DNA fragment (2) encoding for the pap-17 operon DNA sequence (see Fig. 1) pHUR849 pBR322 containing a 11. 1 kb Eco RI-Bam Hl DNA (4) fragment encoding for the pap 5 operon DNA sequence (see Fi. 1) pKTD-1 pBluescript II containing a 16-bp deletion which removes This study the Xba !-Sma I multiple cloning site (MCS), of the vector SK-a pKTD-2 pKTDt containing a 8-bp deletion which removes the Cia This study i-Hinc it MCS of the vector SK- PKTD-3 pBtuescript 11 containing a 8-bp deletion Which removes This study the Eco Rt-Hind iII MCS of the vector SK- pKD201 B-1 pBluescript II containing a 7. 1 kb Eco Rt-Kpn 1 pap-17 DNA Thie study fragment derived from pDAL210B pKD201 B-2 pKTD-2 containing a 4. 1 kb Hind ici DNA fragment derived This study from pKD2018-1 pKD201B-3 pKD201B-2 containing 3.86 kb Hind III DNA fragment, This study which contains a 237-bp Cla I-Sma I deletion of papH, derived from pKD201B-2 pKD201B-4 pBluescript II containing a 237-bp Cla I-Sma I DNA This study fragment derived from pKD201B-2 pKD201B-5 pBluescript II containing a 700 bp Eco RI-Cla I DNA This study fragment derived from pKD201B-2 pKD201B-6 pKD201B-2 containing a 3. 2 kb DNA fragment, which This study contains a 937-bp Eco Sma l deletion' pKD201B-7 pBluescript II containing a 6. 86 kb Eco Rt-Kpn t DNA This study fragment, which resulted from the libation of a 3. 86 kb Hind III DNA fragment derived from pKD201B-3, which contains a 237-bp deletion of papH, to a 3 kd DNA fragment, derived from pKD201B-1 pKD201B-8 pUC8 containing a 10. 86 kb pap-21 operon DNA This study sequence, which resulted from the ligation of a 6. 86 kb Eco RI-Kpn I fragment derived from pKD201B-7, which contains a 237-bp detetion of pap H, to a 4 kb Eco Rt-Sa ! t fragment, derived from and pDAL2108 pKD200A-1 pKTD-3 containing a 6. 4 kb Sal I-Kpn I fragment derived This study from pDAL200A pKD200A-2 pKTD-2 containing a 4. 1 kb Hind ! M fragment derived from This study pKD200A-1. pKD200A-3 pK0200A-2 containing 3. 86 kb Hind III DNA fragment. This study which contains a 237-bp Cla I-Sma I deletion of papH pKD200A-4 pBluescript II containing a 237-bp Cla I-Sma I DNA This study fragment derived from pKD200A-2 pKD200A-5 pBluescript ! ! containing a 700-bp Eco RI-Cla I DNA This study fragment derived from pKD200A-2 pKD200A-6 pKD200A-2 containing a 3.16 kb DNA fragment. which This study contains a 937-bp Eco Rl-Sma # deletion pKD200A-7 pBluescript II containing a 6.16 kb Sal I-Kpn I DNA This study fragment which resulted from the ligation of a 3. 86 kb Hind III DNA fragment derived from pKD200A-3 to a 2. 3 kd Sal I-Kpn I DNA fragment, derived from pKD200A-1 pKD200A-8 pUC8 containing a 8. 76 kb pap 200A operan DNA This study sequence, which resulted from the ligation of a 2. 6 Sal I-Kpn t DNA fragment derived pDAL200A, to a 616 kb Sal I-Kpn I DNA fragment, which contains a 237-bp deletion of P pKD210B-1 pKTD-3 containing 13. 5 kb hm H ! DNA fragment This study encoding for the pap-17 operon DNA sequence derived from pDAL210B pKD210B-2 pKTD-2 containing a 6 kb Hind III DNA fragment derived This study from pKD210B-1 pKD210B-3 pBluescript II cortaining a 237-bp Cla I-Sma I DNA This study fragment derived from pKD210B-2 pKD210B-4 pBluescript II containing a 2. 5 kb Eco Rl-tla I DNA This study fragment derived from pKD210B-2 pKD210B-5 pBluescript II containing a 3. 26 kb Cla I-Kpn I DNA This study fragment derived from pKD2t08-2 pKD210B-6 pBluescript II containing a 2. 5 kb Eco Rt-Stna # fusion-Hind This study III DNA fragment derived from pKD210B-5 pKD210B-7 pBluescript II containing a 2. 5 kb Bam HI-Hind III DNA This study fragment derived trom pKD2tOB-t pKD210B-8 pBluescript II containing a 3. 3 kb Sma I-Kpn I DNA This study fragment derived. from pKD21OB-5 pKD21 OB-9 pBluescdpt 11 contain a 5. 77 kb Eco BI-Kpn I DNA This study fragment resulting from the tigaHon of a 3. 26 kb Sma I-KPN I DNA fragment derived from pKD210B-5, to pKD2108-4 linearized with Cla I-Kpn I, the fusion of Cla I-Sma I creates a 237-bp deletion of papH pKD2108-10 pBluescript 11 containirg a 13. 3 kb Barn Ht DNA fragment This study derived from the ligation of a 5. 76 kb Hind Ht DNA fragment derived from pKD210B-9, to a 7. 5 kb Hind III DNA fragment derived from pKD2tOB-f

pKD210B-11 pBR322 containing a 13. 3 kb Bam Hl DNA fragment pap This study -17 operon DNA sequence derived from pKD210B-10 which contains a 237-bp deletion of papH pKD849-1 pKTD-2 containing a 4. 1 kb Hind iii DNA fragment derived This study from pHUR 849 pKD849-2 pBluescript II containing a 4. 1 kb Hind III D. NA fragment This study derhed from pHUR 849 PKD849-3 pBluescript 11 containing a 3. 2 kb Sma I DNA fraoment This study derived from pKD849-2 pKD849-4 pBluescript II containing a 3. 85 ! cb DNAfr. agment derived This study from the ligation of a 645-bp PCR product derived from pHUR 849, to pKD849-3 linearized with $tia I, which contains a 300-bp deletion of papH pKD849-5 pBR322 containing a 10. 8 kb Eco RI-Bam HI DNA This study fragment encoding for the pap-5 operon DNA sequence, which resulted from the ligation pHUR849 linearized with Hind iil, to a 3. 85. Hind ! it DNA fragment derived from pKD849-4 which contains a 300-bp deletion ouf papy a MCS of SK-Is 657-759 bp, and is flanked by T3 and T7 promoters.

Nucleic acid isolation and manipulations Large scale plasmid DNA isolation was carried out using a QIAGEN Plasmid Kit (QIAGEN, Inc., Chatsworth, CA). Small scale plasmid mini-preps used for routine DNA analysis were performed using the alkaline lysis method 6). Each protocol provided DNA of sufficient purity to obtain reproducible co-amplification PCR results.

The lysozyme boiling miniprep method (7) was used for the isolation of double-stranded DNA templates for sequencing.

Restriction endonucleases, T4 DNA ligase, Kienow fragment of polymerase I, T4 DNA polymerasa, and deoxynucleoside-triphosphates were used according to the conditions recommended by the commercial suppliers (New England BioLabs, Beverly.

MA, and Boehringer Mannheim, Indianapolis, IN). After digestion with restriction endonucleases, DNA fragments larger than 1 kb were separated by electrophoresis on 0. 7% agarose gels ; whereas, separation of smaller DNA fragments was done on 1. 5 or 2% agarose gels. Electrophoresis was carried out in TAE buffer (40-mM Tris acetate with 1 mM EDTA [pH 8. 0]). DNA fragments were isolated from agarose gels using GENE CLEAN (BIO 101 Inc., La Jolla, CA), or QAlquick Gel Extraction (QIAGEN, Inc., Chatsworth, CA), according to recommendations of the manufacturer.

Oligonucleotide synthesis Oligonucleotide primers were synthesized by standard phosphoramidite chemistry on a 345 DNA/RNA synthesizer (Applied Biosystems, Foster City, CA). After de-blocking at room temperature for 24 h, the primers were recovered by precipitation at room temperature in 1/10 vol of 3 M NaOAc pH 5. 2, 2 Vol 100% ETOH. After centrifugation, the pellets were dried under vacuum and resuspended in 200 PLI of distilled water. The amount of nucleic acid was estimated by their absorbance at 260nm. All samples were adjusted to the same concentration. Table 2 lists the thirteen different DNA primers used for both sequencing and PCR analysis. PCR amplification was used to determine the orientation of sub-clones containing deletions within the papi gene of each construct.

DNA sequencing and sequence analysis Double-stranded DNA sequencing was performed using the dideoxynucteotide chain-termination method (8), using [aSS]-thio-dATP (1000 Ci mol'\ Amersham, Arlington Heights, 1L), and T7. DNA polymerase (Sequenase, U. S.

Biochemicals, Cleveland, OH). Sequencing reactions were performed in both directions to confirm the analysis. The oligonucleotide primer 200aRE was used for sequence analysis of the final deletion constructs pKD200A-8 and pKD210B-ll. The oligonucleotide PapHRE was used for sequence confirmation of the final deletion constructs pKD201B-8 and pKD849-5. Analysis of DNA and protein sequences used programs distributed'through the University of Wisconsin Genetics Computer Group. Nucleotide and Amino Acid sequences were aligned with LINEUP and PRETTY programs (9).

TABLE 2. Primers used in khis study Primera Oligonucleotlde sequence T3 S'ATTAACCCTCACTAAAG 3'anneals to multiple cloning site of SK- T7 5' AATACGACTCACTATAG 3' anneals to multiple cloning site of SK- Reverse 5' AACAGCTATGACCATG 3' anneals to multiple cloning site of SK- PapHFD 5' ATGAGACTGCGATTCTCTGT 3' anneals to the TAC translational start region of i 4 pap H genes PapHRE 5' TCCGTTTCTCACAATTCTGA 3' anneals to bp 509-528 of the pap H gene of pDAL201B, pap-21 and pHUR 849, pap-5 21 ObFD 5'CCTGAAATACGAGAATATTA 3'anneals 93-bp upstream of the TAC transtatfonal start region of the pap A gene of pHUR849, pap-5 (2) 210bRE 5' TAATATTCTCGTATTTCAGG 3' the complement of 210bFD and anneals to the same 83 zon as described for 210bFD FOR210b 5' TGGACTGGTATAACAATCGA 3' anneals 2.9 kb upstream of the TAC transiational start region of the pap H gene of pDAL210B, pap-21 200aRE 5' tccgtttcgcacaattctga 3' anneals to bp 511-528 of the pap H gene of pDAL210B, pat17, and pap 200a, respectively PapFORa 5' AGTGGATTCATGCAGCATTTCT anneals to bp 258-270 of the pap A Ne of pHUR849, pap-5 (2) FORSEQ 5'TGGACCTCCTGAGCTA 3'anneata to bp 456-474 of the pap A gene of pHUR849. pap-S (2) PapREVb 5' GGGGCAGCCCTGCCGTCCCAA anneals to bp 122-142 of the pap H AT 3' gene of pHUR849, pap-5 REVSEQ 5' AAACACCATGAAACACACA 3' anneals to bp 41-61 of the pap H gene of pHUR849 $ contains a single Bam Mi reswdion site single undediried. b contains a single Sma I blunt end restriction site double underlined.

DNA amplification DNA amplification was carried out with 50 ng of plasmid DNA : 0 : 75 uM of each oligonucleotide in distilled H20, supplemented with 1 % Triton X-100, 2mM MgCI2, 200 pM each dNTP, and 1. 25 U Taq DNA Polymerase (Promega, Madison, WI), in a final volume of 100 jul. PCRs were performed in a Epicomp DNA Thermal Cycler (Epicomp, San Diego, CA). All manipulation were carried out with dedicated DNA-free pipettes using Elkay filter pipet tips (Applied Scientific, San Francisco, CA), in a sterile field to minimize the risk of contamination. All reagents were added together except-for the Taq DNA Polymerase. The reaction mixture was overlaid with 100 all of sterile mineral oil and was denatured in the thermal cycler at 95°C for 2 min. Then, Taq polymerase was added and amplification was earned out over 35 cycles, as follows : a 2 mm denaturation step at 94°C,'a 1 min annealing step at 50°C, a 1 min primer extension step at 72°C, and finally, products were extended for 7 mm at 72°C. The reaction mixture was held at room temperature until required. Blank control tubes containing all reagents except the template DNA or primers were also run. The amplified DNA fragments were electrophoresed on 1. 5% agarose in TAE butter and visualized by staining with ethidium bromide, and the products were photographed under UV light. PCR was used to establish the correct orientation of the DNA fragments bearing the 237 or 300-bp deletions of the papH gene of each of the four deletion derivatives. The amplification of each construct employed at least one or more different pairs of DNA primers. For each deletion derivative, the DNA primers were as follows : REVERSE and 200aRE for pKD200A-7, REVERSE and PapHRE for pKD201B-7, PapFOR and 200aRE or 210bRE for pKD210B-9, and PapFOR and PapHRE for pKD849-4.

Electron Microscopy A single colony of each papH mutants, their parent recombinants, and the original wild type strains was isolated from a 18 h 37°C growth on agar, suspended in 500 ul of saline, and processed for standard negative staining for transmission electron microscopy. Also, the broth culture of each bacterial strain was processed for negative staining for observation in the electron microscope.

Hemagglutination Assay Binding properties of strains were determined by slide agglutination using human P1 erythrocyctes as described previously (10). Also, the agglutination of purified pili was performed as described by Normark et al (11), using 2-fold serial dilution's starting at 500 llg/ml of protein. A positive reaction was determined macroscopically.

Pili Purification After 24 h incubation at 37°C in selective broth medium, bacteria were harvested by centrifugation and pili were purified essentially according to the method of Korhonen et al (12). The purity of pili preparations was analyzed on SDS-PAGE by silver staining.

Immunoreactivity The purified pili from each papH mutant were assessed for immunoreactivity against polyclonal murine and rabbit antibody reactivity in standard ELISA tests and polyclonal murine and rabbit antibody in Western blotting tests.

Vaccine Efficacy The efficacy of purified pili from each papH mutant was assessed in the standard experimental BALB/c model of pyelonephritis. Cohorts of 20 female mice that were 14 weeks old were immunized intramuscularly on day 0 and day 14 with 50 ug of purified pili from each papH mutant, as determined by Lowry technique. Each vaccinal administration consisted of 100ul of'pili-incomplete Freund's adjuvant emulsion. Mice were challenged intravesicularly on day 30 by 106 bacteria expressing the homologous pili antigen. Challenge strains included : J96 for KD849-5 vaccine recipients ; 3669 for KD2001- 8 vaccine recipients ; KD201 for KD201-8 vaccine recipients ; and KD210B for KD210B-11 vaccine recipients. Protection against renal colonization by the challenge strain was assessed at day 2 after challenge. Positive controls included cohorts of 5 non-vaccinated mice challenged with each strain of bacteria. The pili vaccine conferred protection if the right renal homogenates did not reveal any bacterial growth in >90% of the cohort and

none of the renal homogenates in the cohort had more than 5 CFU per gram of tissue. For comparative purposes, all right kidney homogenates from control animals needed to have > 100 CFU of the challenge strain per gram of tissue.

Results Nucleotide, sequences and deduced PapH primary structures The plasmids pHUR849 (pap-5), pDAL201B (pap-21), pDAL210B (pap-17) and, pDAL200A (pap-200A), in E coli strain HB101 express digalactose-binding of the serotypes F13, F71, F72 and F9, respectively. The pap gene cluster responsible for regulation and biogenesis of these pili from E. coli strains J96, C1212 and, 3669 is diagrammed in Figure 1. Sequence analysis of papH genes from pDAL201B (pap-21), pDAL210B (pap-17) and, pDAL200A (pap-200A), was compared to the known nucleotide sequence of papH gene of pHUR849 (pap-5) (3). Figures 2 shows a single 588-bp open reading frame with the same polarity as papA (2, 4). Analyses of these papH sequences revealed many typical features of prokaryotic gene organization. All four papH gene sequences contained a potential ribosome-binding sites, ATG initiation codon signal sequence, and a TGA termination codon. A potential initiation codon ATG at position-22, preceded by a sequence corresponding to-AGGGT, which showed homology to ribosome- binding sites, was found 13-bp upstream in all four papH sequences. A protein initiated here and ending at the TGA triplet'at position 586 would encode a 195 amino acid polypeptide with a calculated molecular weight of 21. 9 kd. The mature PapH protein contains 173 amino acid residues. The NH2-terminal amino acid sequence of the open reading frame has all the features of a signal peptide sequence. The deduced putative signal sequence for the papH was located 22 codons upstream of their terminal Ala (Figure 2).

These sequences contained a highly hydrophobic region comprising an amino acids stretch of Ser-Val-Pro-Leu-Phe-Phe-Phe. There was a positively charge amino acid residue (Arg) at the position-21. The suggested cleavage sites between Ala-1 and gly +1 conforms to rules of prokaryotic signal cleavage sites and was similar to most other bacterial genes (12).

In addition, the final papH deletion derivatives, pKD849-5 (pap-5), pKD201B (pap-21), pKD210B-ll (pap-17) and pKD200A-8 bap-200A), were also sequenced. In addition,

sequencing into the papA and papC genes which flank the papH gene (Figure 1) of all four papH deletion derivatives was carried out in order to insure that all three genes were in frame. Finally, the codon usage of the papH genes of pDAL201B, pDAL210B and, pDAL200A, and papH gene of pHUR849 were analyzed using a codon frequency computer program (13). The pattern of codon utilization was not significantly different among the genes.

Comparison of papH nucleotide and PapH amino acid sequences LINEUP and PRETTY computer programs (9) were used to calculate the overall percent homology of the predicted PapH polypeptide at the nucleotide and amino acid level. Figures 3 and 4 compare the deduced nucleotide and amino acid sequences of the papH genes of pDAL201B, pDAL210B and, pDAL200A, to the known nucleotide and amino acid sequences of the papH gene of pHUR849. The overall homology among pDAL201B, pDAL210B and, pDAL200A, papH genes was greater than 99% at the nucleotide level and 100% at the amino acid level. Compared to the nucleotide sequence corresponding of papH gene of pHUR849, there was 98 % and-99 % homology at the nucleotide level and amino acid level, respectively. The amino acid differences among these three papH genes were evaluated and compared to the amino acid sequence of the papH gene for pHUR849 and are shown in Figures 4. Comparisons of the substituted amino acid between pDAL201B, pDAL210B, pDAL200A and, pHUR849 papH genes shows that there were only two amino acid changes among these genes, and both these changes were non conserved amino acid substitutions. The first non-conserved substitution is Gly-Cys, at amino acid residue-13 of the putative signal sequence, and the second non- conserved substitution Is ValeAla at amino acid residue 121 of the mature PapH protein.

The deduced mature PapH protein. of 173 amino acid residues shares many structural features'with known E. coil pilins. PapH contains two cysteine residues 38 amino acids apart in the NH2-terminal half of the protein, a tyrosine residue as the penultimate amino acid, and shows an overall sequence similarity to other E. coli piIins, especially from Gly 23 to Gly 50 and in the COOH-terminal region (3). These data show that there is genetic

conservation of the papH genes among these strains at both the nucleotide and amino acid level.

PapH deletion mutants Figure 5 compares the deduced amino acid sequence of the papH deletion mutants, pKD201B-B, pKD210B11, and pKD200A-8, to the amino acid sequence of the deletion mutant of pKD849-5 The final construct pKD849-5 (pap-5), contains a 300-bp deletion (nucleotides 145-445, Figure 2), which encodes for 100 amino acids residues (R 27-126). This deletion mutant now contains an open reading frame (ORF) of 219-bp which encodes for a mature fusion protein of 73 amino acids. As shown in Figure 5, the final constructs pKD201B-8 (pap-21), pKD210B-ll (pap-17) and, pKD200A-8 (pap- 200A), all contain a 237-bp deletion (nucleotides 207-445, Figure 2), which encodes for 79 amino acids residues (R 48-126), respectively. All three mutants, carry ORF's of 282-bp, which encodes for a mature fusion protein of 94 amino acids. The 94 amino acids are identical among these constructs. In addition, pKD201B-8, pKD210B-ll and pKD200A-8 each contain, one non conserved amino acid substitution at amino acid residue 121 (ValoAla). Among these strains, this single amino acid substitution within each gene due to a change in the coding sequence of papH gene. This alteration in the coding sequence of the final constructs (Table 1, Figures 2 and 5) arose following the self-ligations of the end- filled Cla 1 to Sma 1 restrictions sites in the intermediate constructs pKD201B-3, pKD210B-9 and pKD200A-3, respectively.

Electron Microscopy Each of the negative stained papH mutants viewed under the transmission electron microscope revealed essentially few if any protruding pili-like structures from the cell surface. In contrast, negative stained bacteria from the parent recombinants and their original wild type strains reveal great numbers of pili-like structure protruding from the cell surface under similar condition of preparation. Also, broth cultures from each papH mutant processed for electron microscopy revealed pili free of cellular debris.

Pap H Mutations Affect Cell Association of Pap Pili

E. coli strain HB101 harboring pHUR849, pDAL201B, pDAL210B, and pDAL200a and their papH mutants, pKD849-5, pKD201B-8, pKD210B-ll, and PkD200A-8, respectively, were assessed for hemagglutination. A single CFU of each strain grown on agar agglutinated human P1 erythrocytes. Also, purified pili from the recombinant strains with an intact pap operon'or a papH mutant agglutinated human PI erythrocytes. The culture supernatants of papH mutants were sufficient to hemagglutinate PI erythrocytes ; whereas, the parenteral recombinants would only hemaggluttinate erythrocytes when pelleted cells were used. These results suggest that papH mutants secrete functional Gal-Gal pili into culture supernatant. prepared from these strains.

Pili Isolation and Pili Characterization from papH Mutants The pili from each papH mutant purified by a standard method (10) revealed a single band in SDS-PAGE corresponding to the putative PapA moiety of the respective PapA of the parent recombinant and their original wild type strain.

The amount of purified pili from each papH mutant strain obtained from 1 liter 18 h broth culture was estimated to be > 10 mg. This was calculated by taking the average of 3 protein determinations of aliquots of known diluted purified pili preparation.

A Lowry technique was used to estimate protein concentration.

Each purified pili preparation from papH mutants was bound by homologous murine and rabbit antisera raised against whole pili of the respective parent recombinant and their original wild type strain in ELISA tests. Identical binding patterns and kinetics were observed among the pili preparations from papH mutants, recombinant pili, and wild type pili with these antisera. Also, identical immunoreactivity of the purified pili from papH mutants was demonstrated by Western blots with murine and rabbit antisera elicited against whole pili of the respective parent recombinant and their original wild type.

In addition, cohorts of mice immunized with purified pili from each papy mutant were protected from subsequent renal colonization./infectivity by the challenge strain. None of the control mice were protected from renal colonization/infectivity by the challenge strain.

Summary The inventors have mutagenized the papH gene of 4 Gal-Gal pilus recombinants, pHUR849 (pap-5), pDAL201B (pap-21), pDAL210B (papl7), and pDAL200A (pap-200A). These recombinants encode for the serotypes F13, F71, F72, and F9 (2) respectively. They are intended to be used in large-scale pili vaccine production.

This was accomplished by cloning the papH gene of these recombinant strains to determine the nucleotide and deduced amino acid sequence of these genes. When compared to the previously published nucleotide and amino acid sequence of the papH gene of pHUR849 (3), the recombinant stains pDAL201B, pDAL210B, and pDAL200A were 98% and 99% homologous at the nucleotide level and amino acid level respectively. Based on these sequences, employing PCR and standard recombinant DNA techniques, it was possible to create specific deletions within each papH gene. This resulted in'4 recombinant deletion derivatives of pHUR849, pDAL201B, pDAL210B, and pDAL200A, known as pHUR949- 5, pDAL201B-8, pDAL210B-11, and pDAL2-A-8. The recombinantpKD849-5, contains a 330-bp deletion that encodes for 100 amino acid residues. This deletion derivative contains an open reading frame of 219-bp that encodes for a mature fusion protein of 73 amino acids. The final constructs pKD201B-8, pKD210B-ll, and pKD200A-8 carry 237- bp deletion that encodes for an identical mature fusion protein of 94 amino acids. In addition, we also sequenced into the papA and papC genes that flank the papH gene of all four deletion derivatives to insure that all three genes were in frame for each recombinant.

This extended sequence analysis was vital for two reasons. First, the papA, papH, and papC genes are coregulated at the transcription level. The transcriptional activity of these genes is dependent on the transcriptional activity of papI and papB genes (3, 14-17).

Second, mutations in both papA and papC completely abolish pilus formation and the expression of the adhesion on the cell surface ; whereas mutations in papC alone do not affect the pilin antigen produced within the cells (18).

Broth culture results using the E. coli bacterial strain HB101 containing these deletion derivatives show that these constructs now release newly synthesized pili fibers into the culture medium. Moreover, these results are consistent with other studies on

the regulation and biogenesis of Pap pili (1, 3, 11, 14-20). In studies, carried out by Nomark and co-workers (3, 18), they have shown that in two different mutations in the papH gene in one strain that 50%-70% of the total pilus antigen was found free of the cells in the culture supernatant in the form of a polymerized structure. The results of the present invention indicate that high amounts of newly synthesized pili fibers are released into the supernatant by the present papH mutants. It is also important to note that these pili from the papH mutants have identical PapA pilin molecular weights as their parent recombinant and wild type strain. Furthermore, they are immunologically similar to the parent recombinant pili and wild type pili by allowing specific antibody binding to occur in ELISA tests and Western blots. From a vaccine production perspective, these pili can be readily isolated and purified and retain their protective vaccine capacity as demonstrated by their eliciting protection against experimental BALB/c pyelonephritis. Since our data confirm the highly conserved nature of the anchoring gene of Gal-Gal binding piliated bacteria, this strategy of mutagenizing the anchoring gene of the pilus by deletions or other means will be used for other Gal-Gal binding pili belonging to classical F8, F10, Fll, F12 serotypes and variant piliated strains (F1C) and uncharacterized pili types in order to collect dissociated pili in broth culture.

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13. Devereux, J. Nucl. Acid. Res., 12 (1985) : 378-395 ; 14. Norgren et al., EMBO J., 3 (1984) : 1159-1165 ; 15. Blyn et al., EMBO J., 9 (1990) : 4045-4054 ; 16. Braaten et al., J. Bact., 173 (1991) : 1789-1800 ; 17. Braaten et al., Proc. Natl. Acad. Sci. USA, 89 (1992) : 4250-4254 ; 18. Norgren et al., J. Mol. Biol., 1 (1987) : 169-178 ; 19. Linberg et al., Nature, 328 (1987) : 84-87 ; and 20. Baga et al., J. Bact., 157 (1984) : 330-333.

The invention has been described above with reference to specific examples.

Further modifications and variations known to those of ordinary skill based on the description herein are contemplated to be within the invention.

The disclosures of all cited references are expressly incorporated herein to the same extent as if each was individually incorporated by reference.