US20050142611A1 - Method of isolation and self-assembly of small protein particles from blood and other biological materials - Google Patents

Method of isolation and self-assembly of small protein particles from blood and other biological materials Download PDF

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US20050142611A1
US20050142611A1 US11/005,416 US541604A US2005142611A1 US 20050142611 A1 US20050142611 A1 US 20050142611A1 US 541604 A US541604 A US 541604A US 2005142611 A1 US2005142611 A1 US 2005142611A1
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proteons
subsample
blood
pnc
plasma
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Vitaly Vodyanoy
Alexandre Samoylov
Oleg Pustovyy
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Auburn University
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids

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  • the present invention relates generally to compositions and methods for the isolation and manipulation of misfolded proteins and their nucleation centers.
  • Heinz bodies aggregates of denatured hemoglobin called Heinz bodies were found in aged erythrocytes. See Schluter et al. (supra). Further, Kannan et al. (supra) described a protein aggregation from sickle erythrocytes that is mostly composed of globin. Particles resembling those described by Enderlein (1925) Bakterien - Cyclogenie (Verlag de Gruyter & Co, Berlin), were isolated from the blood of cancer patients and determined to be composed of mainly denatured hemoglobin (Gemer (1997) Blut. Curr. Onkol. 7:6P12).
  • Aggregated proteins associated with disorders are found in other biological materials, as well. For example, proteinaceous particles isolated from brain were identified as causing scrapie (Prusiner (1982) Science 216:136-144). Since then, these particles and their structure have represented important areas of study (Prusiner (1991) Science 252:1515-1522; Wille et al. (2002) Biophysical J. 82:825; Wille et al. (2002) PNAS 99:3563-3568; Geschwind et al. (2002) Neurology 58:A135-A135; Dyson et al. (2002) Biophysical J. 82:824), and methods for the sensitive detection of prion-related disorders using ultrasound have been developed.
  • compositions and methods for the isolation and manipulation of misfolded, or partially misfolded, proteins present in blood and other biological materials are provided.
  • the compositions hereinafter termed “proteons,” are comprised of misfolded proteins.
  • PNCs are comprised of metallic nanoclusters.
  • Proteons can be visualized by microscopy of biological materials, for example fluids such as blood samples of mammals and homogenates of vegetable matter. As proteons are comprised of misfolded proteins, detection of proteons and identification of the proteins can be used to diagnose and measure progression of disease states. For example, proteons isolated and purified from blood and blood plasma lack detectable nucleic acids, but contain two major polypeptide populations with high homology to the alpha chain of hemoglobin.
  • methods for the amplification and detection of misfolded protein in a biological sample are provided. Additionally, methods for the clearance of misfolded protein from a sample of biological material are provided. The method can be manipulated by subjecting the sample to heat or pressure, or by carrying out various numbers of seeding steps. Methods for amplification include heat and pressure treatment of a sample. Likewise, subjecting a biological sample to or treating it with metal clusters increases the concentration of proteons.
  • proteons are formed by a mechanism involving the reversible polymerization and aggregation of proteins, particularly misfolded proteins, on a nucleation center.
  • the nucleation centers are referred to as “proteon nucleation centers” or “PNCs.”
  • the PNCs of the invention are unexpectedly pro-apoptotic when added to cultured animal cells. Accordingly, pro-apoptotic compositions and methods for their production are also provided herein.
  • FIG. 1 shows various electron micrographs of proteons in thin sections.
  • Transmission electron microscopy (TEM) was used to prepare electron micrographs of type 1 proteons. See FIG. 1A and FIG. 1B . Also shown are TEM of type 2 proteons. See FIG. 1C and FIG. 1D .
  • TEM of negatively stained type 2 proteons are shown in FIG. 1E and FIG. 1F .
  • An electron micrograph of a type 2 proteon prepared using scanning electron microscopy (SEM) is shown in FIG. 1G . Scale bars (in microns): FIG. 1A : 5; FIG. 1B - 1 F: 0.5; FIG. 1G : 1.
  • FIG. 2 shows proliferation of proteons.
  • Proteons in purified water and blood plasma incubated at 37° C. in an atmosphere of ambient air, showing the number of proteons visible in the dark-field microscope as a function of time. See FIG. 2A .
  • Proteons and plasma were incubated in tissue culture media. ⁇ , ⁇ —proteons and plasma in culture growth medium, respectively; ⁇ , ⁇ —D5648 and D6429 growth medium, respectively.
  • FIG. 2C Assembly and disassembly of proteons in the presence of urea is shown in FIG. 2C .
  • the urea was then removed from the suspension of proteons by dialysis. Cyclic amplification of proteons in plasma is shown in FIG. 2D .
  • the first sample was incubated for 15 minutes at 65° C. and normal pressure. Treated samples of 5 ⁇ L were serially introduced into untreated sample and subjected to a heat cycle, up to 6 cycles.
  • FIG. 3 shows characterization of Cu nanoparticles using TEM, with a-Fe particles shown for comparison.
  • a BF image showing clusters of crystalline, metallic Cu nanoparticles is shown in FIG. 3A .
  • a BF image of the amorphous matrix is shown in FIG. 3B .
  • a SAD pattern identifying the nanoparticles in FIG. 3A as an FCC phase with a lattice parameter of approximately 360 pm and a random crystallographic orientation is shown in FIG. 3C .
  • Centered DF image prepared using a portion of the ⁇ 111 ⁇ FCC ring is shown in FIG. 3D .
  • the nanoparticles appear bright, on a dark background, indicating that the ⁇ 111 ⁇ FCC diffraction maxima originated from the nanoparticles and not the matrix (since the Cu particles are randomly oriented, many of the particles are out of contrast).
  • the inset shows clumped and individual a-Fe particles (DF from a portion of the ⁇ 110 ⁇ BCC ring).
  • Scale bars shown in Figs. A, B, and D represent 50 nm. Scale bars in the insert represent 20 mn.
  • FIG. 4 shows the effect of PNC on cell viability.
  • FIG. 4A shows the viability of cultured cells after 20 hours of exposure to PNC obtained from the shark blood at different concentrations of PNC/ml: (1)—1.7 ⁇ 10 11 ; (2)—9.1 ⁇ 10 10 ; (3)—9.9 ⁇ 10 9 ; (4)—0.
  • F98, RG2 rat and mouse brain glioma cells, respectively, CTX—rat transfected astrocytes).
  • FIG. 4B shows dark-field photomicrographs of the mouse rat glioma cells.
  • FIGS. 4 B 1 and 4 B 2 show cells before and after exposure to 7.7 ⁇ 10 11 PNC/ml, respectively.
  • FIG. 4B 3 shows cells after exposure to 1.0 ⁇ M staurosporine.
  • FIG. 4 Fluorescence photomicrograph of RG2 glioma cell exposed to 7.7 ⁇ 10 11 PNC/ml for 20 h and stained with Annexin V and propidium iodide (400X).
  • compositions and methods for identifying and characterizing disease states are provided.
  • the compositions comprise misfolded proteins and misfolded proteins aggregated on a nucleation center.
  • the aggregated proteins are referred to herein as proteons.
  • the nucleation centers are referred to as proteon nucleation centers (PNCs).
  • proteons are intended protein bodies, generally on the order of a few tens of nanometers up to several microns across, comprised of misfolded or partially misfolded proteins surrounding a PNC.
  • the diameter of the proteon can be (but is not limited to) sizes of at least 10 nm, 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 0.1 ⁇ m, 0.2 ⁇ m, 0.25 ⁇ m, 0.3 ⁇ m, 0.4 ⁇ m, 0.5 ⁇ m, 0.6 ⁇ m, 0.7 ⁇ m, 0.8 ⁇ m, 0.9 ⁇ m, 1 ⁇ m, 2 ⁇ m, 3 ⁇ m, 4 ⁇ m, 5 ⁇ m, 6 ⁇ m, 7 ⁇ m, 8 ⁇ m, 9 ⁇ m, 10 ⁇ m, 20 ⁇ m, 30 ⁇ m, 40 ⁇ m, 50 ⁇ m, 60 ⁇ m, 60
  • proteons can be isolated from blood, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood.
  • proteons can be isolated from plasma, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit and rat plasma.
  • PNC metallic nucleation centers isolated as described herein.
  • PNCs can be isolated from the blood, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood.
  • PNCs can be isolated from plasma, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat plasma.
  • PNCs may be comprised of, but not limited to, at least 1 nm, at least 2 nm, at least 3 nm, at least 4 nm, at least 5 nm, at least 10 nm or larger metallic clusters containing at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more metal or metalloid atoms.
  • metal (or metallic) cluster also termed nanocluster
  • metal (or metallic) cluster it is intended an aggregate of bonded metal atoms wherein valence electrons are delocalized and/or shared among constituent atoms, including but not limited to metals such as Cu, Zn, Fe, Mn, Cr, Mo, Sn, V, Ni and the like, as well as metalloids such as Se, Si, As, B, and the like, for example.
  • Atoms that comprise such particles may be found in combination with other metals, such as for example in alloys. Atoms comprising the cluster may be in any reduction state.
  • plasma is intended the supernatant produced by the centrifugation of blood or other suspension of biological material, including but not limited to dilutions of such supernatants with diluents.
  • seeding is intended adding an amount of either a PNC or proteon to a biological sample.
  • the proteons of the invention can be identified and quantified in biological samples.
  • biological samples include serum, blood, other bodily fluids, tissue including brain, other organ tissue, and the like.
  • tissue is homogenized in a fluid or liquid.
  • Proteons can be isolated from biological samples of any mammal including but not limited to human, primate, bovine, cattle, horse, sheep, pig, cat, dog, rabbit, rat, deer, ox, mouse, and the like. They can also be detected in samples from fish (including but not limited to teleosts such as sharks), chicken, turkey, duck, and the like.
  • proteons are comprised of misfolded proteins.
  • the proteon compositions of the invention show an apple-green birefringence when stained with congo-red. This staining pattern is analogous to that obtained with prions and other amyloid proteins, all of which are included in the class of congophilic proteins. See Kelly (1996) Curr. Opin. Struct. Biol. 6:11-17. These proteins are associated with various disorders or disease states. Thus, the identification of proteons comprised of such proteins is indicative of a disorder or disease state. Likewise, the number of proteons in a sample comprised of such proteins is predictive of the progression of the disease. That is, the number of proteons in a sample correlates with progression of a disease state.
  • proteons in a sample is useful for determining or diagnosing the stage of disease or disorder and can help in planning treatments or therapies for the disease.
  • Examples of disorders involving misfolded proteins and the relevant proteins that can be utilized in the methods of the present invention are set forth in Table 1, below.
  • the disorders associated with congophilic proteins are set forth in Table 2, below.
  • proteons must not only be identified, but also the misfolded protein in the proteon must be identified.
  • Methods for protein purification and identification include antibody binding, amino acid sequencing, and the like. TABLE 1 Conformational diseases. Protein Disease Hemoglobin Sickle cell anemia and aggregates Heinz bodies in aged erythrocytes Unstable hemoglobin inclusion body hemolysis Drug induced inclusion body hemolysis Aggregates regulate apoptosis in cancer patients Atherosclerosis Malaria Infections Auto-immune disorders Toxic reactions Internal bleedings Prion protein Creutzfeld-Jacob disease (CJD) New variant CJD Bovine spongiform encephalopathy (BSE) Gerstmann-Straussler-Schheinker disease Fatal familial insomnia Kuru ⁇ -amyloid Alzheimer's disease Down's syndrome Familial Alzheimer's ⁇ -Synuclein Parkinson's disease, Lewy bodies Tau protein Frontotemporal dementia, Pick bodies Serpins ⁇ 1 -
  • Immunohistochemical assays have been developed for the proteins listed in Tables 1 and 2. See, e.g., Hardt et al. (2000) J. Comp. Path. 122:43-53 (antibodies for the detection of the prion protein, PrP). However, many of these proteins are only abundant in the late stages of the disease and may be undetectable utilizing standard assay techniques. Thus, in one embodiment, the methods of the present invention may be combined with an immunochemical assay for the protein or proteins selected from Tables 1 and 2. These proteins, or their functional derivatives, may be detectably labeled with any appropriate marker such as a radioisotope, an enzyme, a fluorescent label, a paramagnetic label, or a free radical linked to an antibody capable of binding these proteins.
  • any appropriate marker such as a radioisotope, an enzyme, a fluorescent label, a paramagnetic label, or a free radical linked to an antibody capable of binding these proteins.
  • Assay techniques useful in the present invention include, but are not limited to, assays comprising incubating a biological sample from a subject suspected of having such a condition in the presence of a detectably labeled binding molecule (e.g., antibody) capable of identifying the relevant protein, and detecting the binding molecule which is bound in a sample.
  • a detectably labeled binding molecule e.g., antibody
  • the proteins contained in a particular sample of proteons can be identified by screening against a panel of phage antibodies in which the displayed peptide is a domain of the antibody molecule that includes the site that binds antigen.
  • Phage-antibody libraries can be constructed including billions of clones, displaying billions of antibodies with different antigen specificities. For a review of this technique, see Petrenko and Vodyanoy (2003) J. Micro. Meth. 53:253-262.
  • proteons themselves can be detected and quantitated by dark-field microscopy. Under high-resolution dark-field microscopy proteons are visualized as bright spherical shapes. Techniques for dark-field microscopy are known in the art. See, e.g., Bradbury and Bracegirdle (1998), Introduction to Light Microscopy ( Microscopy Handbooks, No 42), 2d ed.; (Springer Verlag). In particular, proteons are small, ball-like bodies of different sizes, estimated in the range of 50-250 nm. By contrast, healthy erythrocytes appear as bright void circles of about 7 microns diameter in the dark-field view, whereas neutrophils are roughly 7-15 microns.
  • proteons When a blood sample becomes aged, the morphology and number of the proteons change, with some estimated to be 500 nm in diameter. Some appear attached to the internal surface of the erythrocyte membrane. Proteons are found in fresh blood of species including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood.
  • Proteons can be isolated from blood or plasma, i.e., the supernatant produced by centrifuging a biological material. Centrifugal separation may be carried out by any means known in the art using any method, apparatus, time, temperature, or speed as appropriate for the biological sample.
  • the relative centrifugal force (R.C.F) applied can be at least 300 ⁇ g, 500 ⁇ g, 600 ⁇ g, 700 ⁇ g, 800 ⁇ g, 900 ⁇ g, 1,000 ⁇ g, 1,100 ⁇ g, 1,200 ⁇ g, 1,300 ⁇ g, 1,400 ⁇ g, 1,500 ⁇ g, 1,600 ⁇ g, 1,700 ⁇ g, 1,800 ⁇ g, 1,900 ⁇ g, 2000 ⁇ g, 2,500 ⁇ g, 3,000 ⁇ g, 4,000 ⁇ g, 4,500 ⁇ g, 5,000 ⁇ g, 5,500 ⁇ g, 6,000 ⁇ g, 6,500 ⁇ g, 7,000 ⁇ g, 7,500 ⁇ g, 8,000 ⁇ g, 8,500 ⁇ g, 9,000 ⁇ g, 9,500 ⁇ g, 10,000 ⁇ g, 11,000 ⁇ g, 12,000 ⁇ g, 12,800 ⁇ g, 13,000 ⁇ g, 14,000 ⁇ g, 15,000 ⁇ g, 16,000 ⁇ g, 17,000 ⁇ g, 18,000 ⁇ g, 19,000 20,000 ⁇ g, or more.
  • the time of centrifugation to obtain separation can be adjusted based on the R.C.F.
  • the temperature of the sample may be maintained within a suitable range before during, and/or after separation, such as for example at least 4° C., 14° C., 25° C., 37° C., 40° C., 42° C., 56° C., 65° C., 90° C., or more
  • proteons can be formed by incubating plasma at 37° C. under sterile conditions over a thirteen day period. At the end of this period, the numbers of proteons observed under dark-field light microscopy are greatly increased.
  • large numbers of proteons are produced by subjecting plasma to 120° C. at 20 psi for two hours.
  • the visible number of proteons is amplified by subjecting plasma to a single step of elevated temperature.
  • Efficiency of proteon production is enhanced by taking a small portion of an amplified sample, adding it to an untreated sample, and heating the untreated sample. These steps can be repeated a number of times, each iteration yielding an increased quantity of proteons. Accordingly, by dividing the sample into a number of subsamples, subjecting the first subsample to heat or pressure, then aliquoting a small amount of the proteons from the first subsample into the second subsample and carrying out the heating step, a greater concentration of proteons can be produced from the second subsample than was produced from the first subsample. These seeding steps can be repeated multiple times until, after several iterations, the concentration of proteons produced per volume of sample eventually plateaus.
  • the first two cycles result in a small but significant increase of proteon population, whereas the third cycle brings about a dramatic increase in the number of proteons. Generally, the next three cycles result in saturation of the proteon population.
  • a test sample containing a small amount of misfolded proteins is subjected to a single heating step.
  • the amplified proteons are quantitated by dark-field microscopy and verified by immunofluorescent techniques to detect the misfolded protein.
  • a small amount of seeds such as the PNCs described above can be added to a test sample to increase the sensitivity of the single step methods.
  • Roughly 5 ⁇ 10 13 PNC/ml are produced by initial filtration of plasma through at least a 5 kDa nominal molecular weight (NMW) cutoff filter, at least a 4 kDa NMW cutoff filter, at least a 3 kDa NMW cutoff filter, at least a 2 kDa NMW cutoff filter, at least a 1 kDa NMW cutoff filter, at least a 500 Da NMW cutoff filter, or smaller, or a combination thereof.
  • NMW nominal molecular weight
  • the sample may be optionally prefiltered using a 0.5 micron filter, a 0.22 micron filter, a 0.2 micron filter, at least a 100 kDa NMW cutoff filter, a 50 kDa NMW cutoff filter, a 30 kDa NMW cutoff filter, any filter within the range of 5 kDa to 10, 20, 30, or higher molecular weight cutoff, or any combination thereof.
  • This concentration then can be increased by a factor of roughly 100 by evaporation.
  • addition of 5 ml of 5 ⁇ 10 13 PNC/ml to a 1 ml sample increases the concentration of PNC in a sample by 2.5 ⁇ 10 11 PNC/ml. This concentration is increased by a factor of 100 if pre-concentrated PNC are added. If the initial concentration of PNC varies from 10 8 to 10 11 PNC/ml, the sensitivity can be increased by a factor of between 250 to 250,000.
  • the first step amplification described above is carried out, then a small portion of amplified sample is introduced into the untreated sample and subjected to heat again. Then, the small portion of the second amplified sample is added to the third untreated sample, heated, and so on.
  • the number of cycles depends on the initial concentration of misfolded proteins. Suitable numbers of cycles include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or more.
  • the detection and identification can be done as a single-step method.
  • Apparatus for subjecting a sample to heat and/or pressure are recognized in the art and include without limitation, PCR thermocyclers, autoclaves, etc.
  • both the single- and multiple-step methods can be manipulated by varying the temperature, pressure, or temporal parameters.
  • Suitable temperatures include at least 4, 15, 25, 37, 40, 45, 50, 55, 56, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120° C., or higher.
  • Suitable pressures include at least ambient pressure, as well as at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 psi, or higher.
  • Suitable times of treatment include at least 1, 5, 10, 15, 20, 25, 30, 25, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120 minutes, or more and may include times oftreatment of at least, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days.
  • these methods can be utilized to clear misfolded proteins from a biological sample such as blood. Because low temperatures can be utilized with long time periods, this can be accomplished without damaging the biological sample.
  • these methods can detect misfolded proteins involved in congophilic disorders. See Kelly (1996) Curr. Op. Struc. Biol. 6:11-17; Kelly (1996) 8:101-106. For instance, there is a demonstrated structural homology between prion and hemoglobin proteins. Korth et al. (1997) Nature 390:74-77. There is evidence that prions are present in lymphoid organs and blood. See, e.g., Brown et al. (2001) J. Lab. Clin. Med. 137:5-13; Aguzzi (2000) Lab. Clin. Med. 137:5-13; Aguzzi (2001) Nature Medicine 7:289-290; Wadsworth et al. (2001) Lancet 358:171-180. Accordingly, the methods of the present invention can be utilized for amplification of a congophilic protein, thus allowing early detection of disorders related to these proteins.
  • PNC of roughly 1-2 nm and containing about 40-300 atoms play an important role in capturing hemoglobin released into blood plasma. While released hemoglobin is normally captured by protein haptoglobin and endocytosed by macrophages, released hemoglobin can be collected by PNCs. Roughly 7 ⁇ 10 13 PNC are present in each milliliter of human blood, while only 0.003% of the whole pool of PNC is normally linked to proteins and made into proteons. However, a proteon of medium size of 160 nm can collect about 100,000 protein molecules of similar size to hemoglobin. Thus, the strong protein scavenging properties of metal nanoparticles allow them to collect proteins including misfolded hemoglobin (Kristiansen et al. (2001) Nature 409:198).
  • the present methods can be utilized for amplification of proteins involved in intravascular hemolysis and resulting in aggregation of hemoglobin, including, without limitation, sickle cell anemia, atherosclerosis, malaria, infections and their complications, auto-immune disorders, internal bleedings and intravascular hemolysis due to internal prosthetic devices, and toxic reactions.
  • proteins involved in intravascular hemolysis and resulting in aggregation of hemoglobin including, without limitation, sickle cell anemia, atherosclerosis, malaria, infections and their complications, auto-immune disorders, internal bleedings and intravascular hemolysis due to internal prosthetic devices, and toxic reactions.
  • samples for single-step or cyclic amplification can be prepared from homogenates of small tissue fragments, or from biological fluids such as blood, cerebrospinal, lymph, etc.
  • tissue homogenates and biological fluids from such sources are known. See Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual , Vols. 1-3 (2d ed; Cold Spring Harbour Laboratory Press, Plainview, N.Y.); and Ausubel et al., eds. (1994) Current Protocols in Molecular Biology , (Greene Publishing Associates, Inc. and John Wiley & Sons, Inc.).
  • PNCs can be produced from plasma by filtration through an ultrafiltration membrane.
  • plasma is filtered consecutively through a 30 kDa and a 5 kDa CentriconTM filter from Millipore before heat treatment.
  • the centrifuge filtration is carried out using an initial volume of 80 ml centrifuged at 3,500 g for 20 minutes, 20° C.
  • Adsorption spectra of the filtrate reveals the presence of metals, including copper, zinc, and iron, indicating that PNCs comprise metals.
  • the filtrate was precipitated with 1.2 mM MgSO 4 and TEM studies were carried out. Such procedures are known in the art. See, e.g., Shindo and Oikawa, Analytical Electron Microscopy for Materials Science , Springer-Verlag (2002). It was found that the precipitated extract contained crystalline metallic nanoparticles of roughly 1-2 nm diameter. Selected area diffraction patterns were consistent with the presence of face centered cubic (FCC) or body centered cubic (BCC) metals or solid-solution alloys such as FCC copper and BCC iron.
  • FCC face centered cubic
  • BCC body centered cubic
  • the PNCs of the invention are characterized by small size, a few nm or smaller. Additionally, the PNCs are present in large quantities, about 10 12 -10 13 PNC/cm 3 of blood or tissue, are abundant, present binding sites and strong affinity to proteins, exhibit variability to bind different proteins, and resist extreme physical and biochemical conditions.
  • the PNCs of the invention comprise a novel reagent for use in inducing apoptosis, as well as a process for its production.
  • aliquots from 1 to 40 ⁇ l containing about 1 ⁇ 10 12 to 4 ⁇ 10 13 PNCs were added to 100 ⁇ l wells of 96-well ELISA plate.
  • Such compounds and processes are of great usefulness to those of skill in the art. See, e.g., U.S. Pat. No. 5,344,926 to Murakata et al., titled “Process for producing staurosporine derivatives”; U.S. Pat. No. 4,973,552 to Schroeder et al., titled “Staurosporine fermentation process”; and U.S. Pat. No. 6,518,032 to Fritz et al., titled “Rapid methods for identifying modifiers of cellular apoptosis activity.”
  • concentrations of PNCs and or proteons can be used to mediate biological effects. For example, concentrations of at least 5 ⁇ 10 11 , 1 ⁇ 10 11 ; 5 ⁇ 10 10 ; 1 ⁇ 10 10 , 5 ⁇ 10 9 ; 1 ⁇ 10 9 , 5 ⁇ 10 8 ; 1 ⁇ 10 8 , 5 ⁇ 10 7 ; 1 ⁇ 10 7 , 5 ⁇ 10 6 ; 1 ⁇ 10 6 , 5 ⁇ 10 5 ; 1 ⁇ 10 5 , 5 ⁇ 10 4 ; 1 ⁇ 10 4 or less may be used.
  • a 30 ⁇ l sample of freshly drawn full blood from a healthy human male was obtained and diluted in 1000 ⁇ l of purified water (Direct QTM, Millipore, 17 MOhm) in a 1.5-ml plastic vial, and centrifuged at 2200 ⁇ g (6000 rpm) to obtain plasma.
  • An additional aliquot of the blood was taken and prepared for optical dark-field microscopy.
  • the plasma was transferred to a 4-ml glass vial with a plastic cap and a teflon liner.
  • An aliquot of plasma was again retained for dark-field microscopy.
  • the vial and contents were subjected to heating at a temperature of 120° C. and 20 psi of pressure for two hours.
  • An aliquot of the heat-treated plasma was prepared for dark-field microscopy.
  • the fresh full blood sample was found to contain approximately 3 ⁇ 10 8 proteons/ml, whereas the diluted sample contained roughly 9 ⁇ 10 6 proteons/ml.
  • N 0 is the initial number of particles
  • b is the growth coefficient. If N, N 0 , and t are substituted with the experimental values found in the above experiment, one can estimate that the growth coefficient (b) for this case is equal to 5.2 l/hour, and the proteon population is doubled every 8 minutes.
  • a summary of the data is presented in TABLE 3 Cyclic amplification methods a . b Number of Time, proteons in Number of Temperature, ° C.
  • Plasma 8 12 days 37 d 1 cycle, 7.0 ⁇ 10 10 Plasma 8 12 days 37 d 1 cycle, 3.5 ⁇ 10 11 Growth 8 12 days media 1 37 d 1 cycle, 3.0 ⁇ 10 11 Growth 8 12 days media 2 40 1 cycle, 3.6 ⁇ 10 8 Plasma 8 90 min 40 6 cycles/ 1.4 ⁇ 10 8 Plasma 8 15 min 56 1 cycle/ 1.8 ⁇ 10 9 Plasma 8 15 min 56 6 cycles/ 2.0 ⁇ 10 9 Plasma 8 15 min 65 3 cycles/ 2.5 ⁇ 10 11 Plasma 15 15 min 65 6 cycles/ 2.5 ⁇ 10 11 Plasma 15 min 90 1 cycle/ 5 ⁇ 10 11 Plasma 9 3 min 120° C., 1 cycle/ ⁇ 1 8 ⁇ 10 11 Plasma 12 140 kPa min 120° C., 1 cycle/2 8 ⁇ 10 11 Plasma 245 140 kPa hours a The first sample was incubated for 15 minutes at temperatures shown herein.
  • b Number of proteons was estimated by counting with high resolution dark-field microscope and electron microscopy.
  • Electron microscopy analysis was also carried out on samples obtained before and after heat treatment.
  • Transmission electron microscope (TEM) images obtained from pre- and post-heat-treatment samples reveal small proteons appearing as dark discs with a rough and fibrous appearance.
  • An analysis of the TEM images revealed the size distribution of this characteristic small proteon to reach a maximum about 150 nm.
  • proteon Another characteristic form of proteon was observed, a coconut-shaped particle of about 1-5 microns with a structure resembling one or more nuclei and a cell-like appearance.
  • the nuclei look very similar to the small proteons described above.
  • a cross-sectional view of a larger proteon reveals a very distinctive external membrane-like structure. This membrane-like structure, however, looks very different from the bacterial wall or the mammalian cell membrane, appearing as a curly fibrous shell of 10-12 nm thick. Some fiber-like structures and a few nuclei are visible inside the proteon. Images obtained by scanning electron microscopy (SEM) confirm the presence of both small and large characteristic proteons.
  • the chemical composition was determined by energy dispersive X-ray spectroscopy using a JEOL JSM-840 SEM system using standard procedures for identifying and quantifying elemental composition. Such procedures are known in the art. See, e.g., Shindo and Oikawa (2002) Analytical Electron Microscopy for Materials Science (Springer-Verlag).
  • proteons suspended in distilled water was deposited on the aluminum SEM mount and dried in a vacuum for 24 hours.
  • the X-ray spectra were obtained with an electron beam size of 200 nm at 80 kV for 90 s.
  • Spectra revealed that the proteons were composed of carbon, oxygen, nitrogen, and sulfur, and the presence of potassium, sodium, chloride, silicon, and copper was also detected.
  • the presence of carbon, nitrogen, and sulfur was confirmed by analytical chemical analysis (Leco Corporation, Michigan, USA). Notably phosphorus, a necessary element of DNA, was never detected in the proteon samples. On the other hand, all the elements needed for amino acids and proteins are available.
  • Plasma 56° C., 0.72 ⁇ 0.04 0.98 ⁇ 0.2 normal pressure, 10 min Plasma, 80° C., 0.68 ⁇ 0.04 1.0 ⁇ 0.2 normal pressure, 10 min Proteons, 120° C., 0.71 ⁇ 0.04 1.7 ⁇ 0.2 20 psi, 2 hours
  • proteons from rabbit blood were disassembled by sodium dodecyl sulfate (SDS), a negatively charged detergent. The fragments of proteins were electrophoresed down and made distinctive bands in the polyacrylamide gel. The proteins were identified by N-terminal amino acid sequencing, yielding the partial sequence VLSPA(D/E)(E/K)TN(A/I) that shows 100% homology with the rabbit alpha chain of hemoglobin. Amino acid analysis showed that proteons are enriched by hydrophilic negatively charged amino acids, glutamic and aspartic acids. Additionally, such proteons show a similar hydropathy index to hemoglobin.
  • SDS sodium dodecyl sulfate
  • Optical observation of proteons was performed with an OLYMPUSTM microscope fitted with a 100-W mercury lamp illumination source, a polarizer, a Naessens dark-field condenser (COSE Corp., Canada) and a 100 ⁇ objective (oil, NA 1.4).
  • the dark-field images were directed to a DEI-470T OPTRONICSTM CCD Video Camera System (Optronics Engineering, CA) utilizing the methods described in Vodyanoy et al. (1994) Langmuir 10:1354-1357.
  • a direct count of proteons was used to determine their concentrations in liquid samples, and IMAGE PROTM (Creative Software, Inc.) was used to quantify the number of proteons.
  • Proteons and plasma in tissue culture media (Group 3 and 4, respectively) exhibited the same growth curves and reached the same number of proteons after 13 days of incubation ( FIG. 2B ).
  • Plasma was prepared as described in Example 1. The samples of plasma were combined with the guanidine hydrochloride or urea to a final concentration of 0, 0.01, 0.1, 1, 4, and 8 M, respectively. These chaotropic compounds are known to unfold and denature proteins.
  • the experimental samples displayed a diffuse distribution of proteins or fragments of proteins with no sharp bands of proteins of the high molecular mass range.
  • concentration of urea increased, the intensity of the diffusion staining decreased, and almost fully disappeared at the 8 M concentration of urea.
  • the proteon sample displays a 14,400 Da band that coincides with a similar band found in plasma.
  • guanidine hydrochloride or urea was added to proteons produced without the chaotropic compounds, heat of 120° C. and pressure of 20 psi resulted also in a great reduction of number of proteons visible by dark-field microscopy. Dialysis of these samples restored the population of the proteons.
  • PNCs were removed from blood plasma by filtering the plasma through 5 kDa CENTRICONTM filters from Millipore according to the manufacturer's protocol.
  • the protein level in the retentate was quantitated and compared to that of unfiltered plasma.
  • Assay kits were obtained from Bio-Rad Laboratories, and quantitative studies were carried out according to the manufacturer's instructions.
  • the amount of protein in the filtered plasma was the same as that measured in the non-filtered sample. No protein was detected in the filtrate. After filtration, proteons could not be produced until the filtered fraction was returned to the plasma. The number of proteons was dependent on the amount of filtrate returned to the retentate.
  • EDTA ethylene diamine tetra acetate
  • Adsorption spectra of the filtrate determined by energy dispersive x-ray spectroscopy (EDS) and inductively coupled plasma-atomic emission spectrometry (GTW Analytical Services, TN), revealed the presence of metals, including Cu, Zn, and Fe.
  • TEM transmission electron microscopy
  • composition of microstructural features was determined (qualitatively) by means of energy dispersive x-ray spectroscopy (EDS).
  • EDS energy dispersive x-ray spectroscopy
  • This work employed an Oxford Instruments' ultra-thin window (UTW) detector, attached to the JEM 2010TM, together with an Oxford Instruments' ISISTM analyzer.
  • UW ultra-thin window
  • the bulk of the blood precipitate from rabbit plasma was amorphous. However, this extract was found to contain crystalline metallic nanoparticles, with diameters of around 1-2 nm and above. SAD patterns originating from different regions of the samples were consistent with the presence of both face centered cubic (FCC) and body centered cubic (BCC) metals (or possibly solid-solution alloys), with lattice parameters (a 0 ) of approximately 360 and 290 pm respectively.
  • FCC face centered cubic
  • BCC body centered cubic
  • the surface energy of the particles provides a driving force for larger particles to cannibalize smaller particles (the surface area to volume ratio for a 1-nm particle is 6 ⁇ 10 9 m ⁇ 1 and this drops by an order of magnitude for a 10-nm particle).
  • Metallic materials have relatively high solid-vapor interfacial energies ( ⁇ SV ) and those for copper and ⁇ -iron are around the middle of the range for metallic materials (at ⁇ 2.2 and 3.2 J m ⁇ 2 , respectively; Muir (1975) Interfacial Phenomena in Metals and Alloys (Addison-Wesley; reprinted by TechBooks, Herdon, Va.)).
  • the metal-organic matrix interface has an interfacial energy ( ⁇ SM ) that is such that ⁇ SM ⁇ SV , there would remain a significant thermodynamic driving force for coarsening.
  • ⁇ SM interfacial energy
  • room-temperature coarsening would occur at a negligible rate (solid-state sintering involves bulk diffusion, interfacial diffusion, free surface diffusion and evaporation and re-condensation, all of which would be very slow for Cu or ⁇ -Fe at room temperature).
  • Ashby (1974) Acta Metallurgica 22(3):275-289.
  • Swinkels and Ashby (1981) Acta Metallurgica 29(2):259-281 See also, Swinkels and Ashby (1981) Acta Metallurgica 29(2):259-281.
  • the presence of the organic liquid matrix raises possibilities for mass transport, it appears that the matrix did not provide a path for the rapid transfer of metal atoms since many of the nanoparticles of served in the present work remained
  • RG2 mouse brain glioma
  • F98 rat brain glioma
  • Hs683 human brain glioma
  • CTX TNA2 rat transfected astrocyte
  • H9c2[2-1] rat heart myocardium
  • 27FR rat skin fibroblast
  • SVGp12 human brain astroglia
  • DMEM Product No. D5648,Sigma
  • FCS HyClone
  • PNC aliquots, 100 ⁇ l, 5 ⁇ 10 9 ⁇ 3 ⁇ 10 11 PNC/ml
  • PNCs were isolated from blood obtained from shark, dog, and rabbit using the ultrafiltration protocol described in Example 5. PNCs were autoclaved at 120° C. and 20 psi for 15 minutes before adding to the cell cultures.
  • MTT tetrazolium salt
  • FIG. 4C shows the viability of RG2 glioma cells exposed to PNCs from different sources. It takes about 1 ⁇ 10 12 PNC/ml to fully suppress these glioma cells. This concentration accounts for not more than 10% of the full concentration of PNCs in a healthy animal.
  • a progressively increased number of proteons can be produced from plasma subjected to increasing temperatures.
  • seven 1 ml samples of plasma were prepared for cyclic amplification. After the initial number of proteons was quantitated by a dark-field microscope, the first sample was incubated for 15 minutes at 65° C. and normal pressure. Five ⁇ l of the treated first sample was introduced to seed the untreated second sample, and the second sample was incubated for 15 minutes at 65° C. and normal pressure. This step was repeated: 5 ⁇ l of the second amplified sample was added to the third untreated sample. This process was repeated up to 6 cycles.
  • a control series was run by adding of five ⁇ l of purified water (instead of seeds) to 1 ml of untreated plasma.
  • the first two cycles resulted in a small but significant (p ⁇ 0.001) increase of proteon population, whereas the third cycle brought about a dramatic increase in the number of proteons.
  • the next three cycles resulted in saturation of the proteon population. In contrast, the control samples showed no dramatic increase of the proteon population. See FIG. 2 .
  • Nanobacteria gave a positive signal, while all freshly prepared proteons showed no interaction. Proteons incubated in cell culture media for 13 days, at 37° C. (with and without CO 2 ) show a positive reaction. However, the culture media alone incubated for 13 days, at 37° C. also gave a positive reaction, while freshly prepared culture media was negative, indicating that nanobacteria antigen appeared from the culture media during the incubation.
  • Fresh blue shark ( Prionace ) tissue was homogenized in purified water (1: 1, w/w) and suspension was centrifuged at 12,800 ⁇ g for 40 minutes at 4° C. The final filtrate was obtained by filtering the supernatant consecutively through 30-kDa and 5-kDa CENTRICONTM filters (Millipore). Liquid obtained by filtration was autoclaved at 20 psi for 15 minutes. Micrometer and sub-micrometer particles were isolated from shark extracts. It was initially observed that shark's blood contains approximately 5-fold more PNCs/ml than rat or rabbit blood. Specifically, one microliter of shark extract contained approximately 5 ⁇ 10 13 proteon nucleating centers (PNC). PNCs such as these are generally comprised of 1-2-nm metallic nanoclusters containing 40-300 atoms.
  • the shark's body and liver were stored in ice for approximately 12 h.
  • the tissue was homogenized using various methods. Specifically, 50 g of liver was homogenized in 150 ml H 2 O (DIRECT-QTM water purification system, Millipore) in a blender. Additionally, 50 g of liver was homogenized in 150 ml of 0.2% NaCl/H 2 O solution in a blender, and 50 g of liver was also homogenized in 150 ml of 0.9% NaCl and 0.9% Ethanol solution. Blood was diluted approximately 1:10 in water.
  • the homogenates were centrifuged at 12,800 g-13,000 g for 40 min. on a Beckman (Model J2-21TM) centrifuge in a JA 10TM rotor. The pellet was discarded and the supernatant was filtered through 30,000 Da CENTRICON PLUS-80TM centrifugal filter devices (Millipore). Samples were combined and filtered through a 5,000 Da CENTRICON PLUS-80TM centrifugal filter device, yielding a PNC “seed solution.”
  • Plasma was obtained by adding 10 ml of rabbit blood to 290 ml H 2 O (DIRECT-QTM water purification system, Millipore) (1:30). The solution was mixed and centrifuged for 40 min at 13,000 g on a Beckman (Model J2-21TM) centrifuge in a JA 10TM rotor. The pellet was discarded and the supernatant was used for seed preparation.
  • PNC were obtained by filtering plasma through 30,000 Da and then 5,000 Da CENTRICON PLUS-80TM centrifugal filter devices (Millipore).
  • Example A The pH of the seed solution was changed to 7 approximately by adding 1N NaOH. A white deposit was formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter AllegraTM 21R centrifuge in a S4180TM bucket rotor for 15 min.
  • Example B The pH of the remaining PNC suspension was changed from 7 to 8 by adding 1N NaOH. A white deposit was again formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter AllegraTM 21R centrifuge in a S4180TM bucket rotor for 15 min.
  • Example C The pH of the remaining PNC suspension was changed from 8 to 12 by adding 1N NaOH. A white deposit was again formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter AllegraTM 21R centrifuge in a S4180TM bucket rotor for 15 min.
  • Rabbit blood, dog blood, and human blood were each diluted in H 2 0 (DIRECT-QTM water purification system, Millipore). Specifically, 25 ml of rabbit blood was diluted in 150 ml of water; 10 ml of dog blood was diluted in 150 ml water; and 60 ⁇ l of human blood was diluted in 0.97 ml of H 2 O.
  • Rabbit and dog plasma were centrifuged at 12,800-13,000 g for 40 min on a Beckman (Model J2-21TM) centrifuge in a JA 10TM rotor. The pellet was discarded and the supernatant was used for PNC preparation.
  • Human plasma was centrifuged at 6,500 rpm for 5 min on table centrifuge. The pellet was discarded and the supernatant was used for PNC preparation.
  • PNC were obtained by sequentially filtering the supernatants though 30,000 Da and 5,000 Da CENTRICON PLUS-80TM centrifugal filter devices (Millipore). The filtered PNC suspensions (2 ml) were autoclaved in 4 ml bottles for 15 min at 20 psi and used for cultured cells experiments.

Abstract

Compositions and methods for the isolation and manipulation of misfolded, or partially misfolded, proteins present in blood and other biological materials are provided. In one aspect of the invention, the compositions, hereinafter termed “proteons” are comprised of misfolded proteins. Also provided are compositions and methods for the isolation and manipulation of proteon nucleation centers (PNCs) upon which the proteons of the present in blood and other biological materials form. In another aspect of the invention, the PNCs are comprised of metallic nanoclusters.

Description

    CROSS-REFERENCE TO RELATED APPLICATION
  • This application is a continuation-in-part of copending U.S. patent application Ser. No. 10/674,750 filed on Sep. 30, 2003 which claims the benefit of U.S. Provisional Application Ser. No. 60/415,108 filed on Sep. 30, 2002, which is hereby incorporated in its entirety by reference herein.
    • FIELD OF THE INVENTION
  • The present invention relates generally to compositions and methods for the isolation and manipulation of misfolded proteins and their nucleation centers.
    • BACKGROUND OF THE INVENTION
  • There are many disorders that are thought to arise from the same general mechanism based upon misfolding and aggregation of underlying proteins, including prion-related disorders, neurodegenerative diseases, and several systemic disorders. See, for example, Schluter et al. (1986) PNAS 83:6137-6141; Kannan et al. (1988) J. Biol. Chem. 263:3766-13773; Carrell and Lomas (1997) Lancet 350:134-138; Carrell and Gooptu (1998) Curr. Op. Struc. Biol. 8:799-809; Soto (2001) FEBS Letters 498,:204-207; Jaikaran and Clark (2001) Biochimica et Biophysica Acta 1537:179-203; Ursini et al. (2002) Trends Mol. Med. 8:370-374; and Davis et al. (2002) Lancet 359:2242-2247.
  • One of the suggested mechanisms of protein aggregation is seeded polymerization, in which initial seeds nucleate the deposition of monomers. For example, aggregates of denatured hemoglobin called Heinz bodies were found in aged erythrocytes. See Schluter et al. (supra). Further, Kannan et al. (supra) described a protein aggregation from sickle erythrocytes that is mostly composed of globin. Particles resembling those described by Enderlein (1925) Bakterien-Cyclogenie (Verlag de Gruyter & Co, Berlin), were isolated from the blood of cancer patients and determined to be composed of mainly denatured hemoglobin (Gemer (1997) Blut. Curr. Onkol. 7:6P12).
  • Aggregated proteins associated with disorders are found in other biological materials, as well. For example, proteinaceous particles isolated from brain were identified as causing scrapie (Prusiner (1982) Science 216:136-144). Since then, these particles and their structure have represented important areas of study (Prusiner (1991) Science 252:1515-1522; Wille et al. (2002) Biophysical J. 82:825; Wille et al. (2002) PNAS 99:3563-3568; Geschwind et al. (2002) Neurology 58:A135-A135; Dyson et al. (2002) Biophysical J. 82:824), and methods for the sensitive detection of prion-related disorders using ultrasound have been developed. See Saborio (2001) Nature 411:810-813. Recently, micrometer-sized particles were identified in the cerebrospinal fluid of patients with schizophrenia (Wetterberg et al. (2002) Neurosci Lett. 329:91-5). Accordingly, new compositions and methods for the formation, isolation, and detection of misfolded, aggregated proteins are required.
    • BRIEF SUMMARY OF THE INVENTION
  • Compositions and methods for the isolation and manipulation of misfolded, or partially misfolded, proteins present in blood and other biological materials are provided. In one aspect of the invention, the compositions, hereinafter termed “proteons,” are comprised of misfolded proteins. Also provided are compositions and methods for the isolation and manipulation of proteon nucleation centers (PNCs), upon which the proteons of the present invention form. The PNCs are comprised of metallic nanoclusters.
  • Proteons can be visualized by microscopy of biological materials, for example fluids such as blood samples of mammals and homogenates of vegetable matter. As proteons are comprised of misfolded proteins, detection of proteons and identification of the proteins can be used to diagnose and measure progression of disease states. For example, proteons isolated and purified from blood and blood plasma lack detectable nucleic acids, but contain two major polypeptide populations with high homology to the alpha chain of hemoglobin.
  • Accordingly, methods for the amplification and detection of misfolded protein in a biological sample are provided. Additionally, methods for the clearance of misfolded protein from a sample of biological material are provided. The method can be manipulated by subjecting the sample to heat or pressure, or by carrying out various numbers of seeding steps. Methods for amplification include heat and pressure treatment of a sample. Likewise, subjecting a biological sample to or treating it with metal clusters increases the concentration of proteons.
  • While the present invention is not bound to any particular mode of action, it is believed that proteons are formed by a mechanism involving the reversible polymerization and aggregation of proteins, particularly misfolded proteins, on a nucleation center. For convenience, the nucleation centers are referred to as “proteon nucleation centers” or “PNCs.”
  • The PNCs of the invention are unexpectedly pro-apoptotic when added to cultured animal cells. Accordingly, pro-apoptotic compositions and methods for their production are also provided herein.
    • BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S)
  • FIG. 1 shows various electron micrographs of proteons in thin sections. Transmission electron microscopy (TEM) was used to prepare electron micrographs of type 1 proteons. See FIG. 1A and FIG. 1B. Also shown are TEM of type 2 proteons. See FIG. 1C and FIG. 1D. TEM of negatively stained type 2 proteons are shown in FIG. 1E and FIG. 1F. An electron micrograph of a type 2 proteon prepared using scanning electron microscopy (SEM) is shown in FIG. 1G. Scale bars (in microns): FIG. 1A: 5; FIG. 1B-1F: 0.5; FIG. 1G: 1.
  • FIG. 2 shows proliferation of proteons. Proteons in purified water and blood plasma incubated at 37° C. in an atmosphere of ambient air, showing the number of proteons visible in the dark-field microscope as a function of time. See FIG. 2A. Proteons and plasma were incubated in tissue culture media. ▪, ●—proteons and plasma in culture growth medium, respectively; ▴, ▾—D5648 and D6429 growth medium, respectively. The insert shows a linear fit of the experimental data to the logistic equation Ln(L/N−1)=k(T1/2−t), where L=maximal number of proteons, N=number of proteons at time t, and T1/2=time when N=L/2 (Jarman, 1970). See FIG. 2B. Assembly and disassembly of proteons in the presence of urea is shown in FIG. 2C. After the proteons were assembled in the presence of urea, the urea was then removed from the suspension of proteons by dialysis. Cyclic amplification of proteons in plasma is shown in FIG. 2D. The first sample was incubated for 15 minutes at 65° C. and normal pressure. Treated samples of 5 μL were serially introduced into untreated sample and subjected to a heat cycle, up to 6 cycles.
  • FIG. 3 shows characterization of Cu nanoparticles using TEM, with a-Fe particles shown for comparison. A BF image showing clusters of crystalline, metallic Cu nanoparticles is shown in FIG. 3A. A BF image of the amorphous matrix is shown in FIG. 3B. A SAD pattern identifying the nanoparticles in FIG. 3A as an FCC phase with a lattice parameter of approximately 360 pm and a random crystallographic orientation is shown in FIG. 3C. Centered DF image prepared using a portion of the {111}FCC ring is shown in FIG. 3D. The nanoparticles appear bright, on a dark background, indicating that the {111}FCC diffraction maxima originated from the nanoparticles and not the matrix (since the Cu particles are randomly oriented, many of the particles are out of contrast). The inset shows clumped and individual a-Fe particles (DF from a portion of the {110}BCC ring). Scale bars shown in Figs. A, B, and D represent 50 nm. Scale bars in the insert represent 20 mn.
  • FIG. 4 shows the effect of PNC on cell viability. FIG. 4A shows the viability of cultured cells after 20 hours of exposure to PNC obtained from the shark blood at different concentrations of PNC/ml: (1)—1.7×1011; (2)—9.1×1010; (3)—9.9×109; (4)—0. (F98, RG2—rat and mouse brain glioma cells, respectively, CTX—rat transfected astrocytes). FIG. 4B shows dark-field photomicrographs of the mouse rat glioma cells. FIGS. 4B1 and 4B2 show cells before and after exposure to 7.7×1011 PNC/ml, respectively. FIG. 4B 3 shows cells after exposure to 1.0 μM staurosporine. 4—Fluorescence photomicrograph of RG2 glioma cell exposed to 7.7×1011 PNC/ml for 20 h and stained with Annexin V and propidium iodide (400X). FIG. 4C shows viability of RG2 glioma cultured cells after 20 hours of exposure to PNC obtained from the blue shark (Prionace) (▪), hound dog, (●), human (▴), and New Zealand white rabbit (Harland Sprague Dawley) (▾) blood at different concentrations. R=0.95, p<0.0001.
    • DETAILED DESCRIPTION OF THE INVENTION
  • The present invention now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the invention are shown. Indeed, the invention may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.
  • Compositions and methods for identifying and characterizing disease states are provided. The compositions comprise misfolded proteins and misfolded proteins aggregated on a nucleation center. The aggregated proteins are referred to herein as proteons. The nucleation centers are referred to as proteon nucleation centers (PNCs).
  • Definitions
  • By “proteons” are intended protein bodies, generally on the order of a few tens of nanometers up to several microns across, comprised of misfolded or partially misfolded proteins surrounding a PNC. Thus, the diameter of the proteon can be (but is not limited to) sizes of at least 10 nm, 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 0.1 μm, 0.2 μm, 0.25 μm, 0.3 μm, 0.4 μm, 0.5 μm, 0.6 μm, 0.7 μm, 0.8 μm, 0.9 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm, 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, or larger. In one aspect of the invention, proteons can be isolated from blood, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood. In another aspect of the invention, proteons can be isolated from plasma, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit and rat plasma.
  • By “PNC” is intended the metallic nucleation centers isolated as described herein. In one aspect of the invention, PNCs can be isolated from the blood, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood. In another aspect of the invention, PNCs can be isolated from plasma, including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat plasma. PNCs may be comprised of, but not limited to, at least 1 nm, at least 2 nm, at least 3 nm, at least 4 nm, at least 5 nm, at least 10 nm or larger metallic clusters containing at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more metal or metalloid atoms.
  • By metal (or metallic) cluster (also termed nanocluster) it is intended an aggregate of bonded metal atoms wherein valence electrons are delocalized and/or shared among constituent atoms, including but not limited to metals such as Cu, Zn, Fe, Mn, Cr, Mo, Sn, V, Ni and the like, as well as metalloids such as Se, Si, As, B, and the like, for example. Atoms that comprise such particles may be found in combination with other metals, such as for example in alloys. Atoms comprising the cluster may be in any reduction state.
  • By “plasma” is intended the supernatant produced by the centrifugation of blood or other suspension of biological material, including but not limited to dilutions of such supernatants with diluents.
  • By “seeding” is intended adding an amount of either a PNC or proteon to a biological sample.
  • The proteons of the invention can be identified and quantified in biological samples. Such samples include serum, blood, other bodily fluids, tissue including brain, other organ tissue, and the like. To identify the proteons in tissue, the tissue is homogenized in a fluid or liquid.
  • Proteons can be isolated from biological samples of any mammal including but not limited to human, primate, bovine, cattle, horse, sheep, pig, cat, dog, rabbit, rat, deer, ox, mouse, and the like. They can also be detected in samples from fish (including but not limited to teleosts such as sharks), chicken, turkey, duck, and the like.
  • As indicated, proteons are comprised of misfolded proteins. In one aspect, the proteon compositions of the invention show an apple-green birefringence when stained with congo-red. This staining pattern is analogous to that obtained with prions and other amyloid proteins, all of which are included in the class of congophilic proteins. See Kelly (1996) Curr. Opin. Struct. Biol. 6:11-17. These proteins are associated with various disorders or disease states. Thus, the identification of proteons comprised of such proteins is indicative of a disorder or disease state. Likewise, the number of proteons in a sample comprised of such proteins is predictive of the progression of the disease. That is, the number of proteons in a sample correlates with progression of a disease state. Therefore, quantification of proteons in a sample is useful for determining or diagnosing the stage of disease or disorder and can help in planning treatments or therapies for the disease. Examples of disorders involving misfolded proteins and the relevant proteins that can be utilized in the methods of the present invention are set forth in Table 1, below. The disorders associated with congophilic proteins are set forth in Table 2, below.
  • It is recognized that for proper diagnosis, proteons must not only be identified, but also the misfolded protein in the proteon must be identified. Methods for protein purification and identification include antibody binding, amino acid sequencing, and the like.
    TABLE 1
    Conformational diseases.
    Protein Disease
    Hemoglobin Sickle cell anemia and aggregates
    Heinz bodies in aged erythrocytes
    Unstable hemoglobin
    inclusion body hemolysis
    Drug induced inclusion
    body hemolysis
    Aggregates regulate apoptosis in
    cancer patients
    Atherosclerosis
    Malaria
    Infections
    Auto-immune disorders
    Toxic reactions
    Internal bleedings
    Prion protein Creutzfeld-Jacob disease (CJD)
    New variant CJD
    Bovine spongiform encephalopathy (BSE)
    Gerstmann-Straussler-Schheinker disease
    Fatal familial insomnia
    Kuru
    β-amyloid Alzheimer's disease
    Down's syndrome
    Familial Alzheimer's
    α-Synuclein Parkinson's disease, Lewy bodies
    Tau protein Frontotemporal dementia,
    Pick bodies
    Serpins α1-antitrypsin deficiency
    cirrhosis
    emphysema
    Antithrombin deficiency
    thrombosis
    C1-inhibitor deficiency
    angioedema
    Neuroserpin Neurodegenerative disease,
    Collins bodies
    Glutamate repeats Inherited neurodenegerative
    disorders
    Hungtington's disease
    Amylin Diabetes type II
    SOD Amyotrophic lateral sclerosis
    ApoB Atherosclerosis
    CFTR protein Cystic fibrosis
    Immunoglobulin Systemic amyloid light
    chain amyloidosis
    Amyloid light chain Nodular amyloidosis
    Serum amyloid A Reactive systemic amyloid
    A amyloidoses
    Chronic inflammatory disease
    Transthyretin Senile systemic amyloidosis
    Familial amyloid neuropathy
    Familial cardiac amyloid
    β2-microglobulin Hemodialysis amyloidosis
    Prostatic amyloid
    Apolipoprotein Al Familial amyloid polyneuropathy
    Familial visceral amyloid
    Cystatin C Hereditary (Icelandic)
    cerebral angiopathy
    Lysozyme Familial visceral amyloidosis

    See Carrel and Lomas (1997) Lancet 350: 134-138; Carrell and Gooptu (1998) Curr. Op. Struc. Biol. 8: 799-809.; Soto (2001) FEBS Letters 498: 204-207; Jaikaran and Clark (2001); Ursini et al. (2002) Trends Mol Med. 8: 370-374; Kannan et al. (1988) J. Biol. Chem. 263: 13766-13773; Schluter and Drenckhahn (1986) PNAS 83: 6137-6141; Gerner et al. (2002);
    # Davis et al. (2002) Lancet 359: 2242-2247; Fernandez et al. (2001) Atherosclerosis 158, 103-111 (atherosclerosis); Papalexis et al. (2001) Mol. Biochem. Parasitology 115: 77-86; Esievo et al. (1984) Veterinary Parasitology 15: 181-185; Igoe et al. (2002) Clin. Microb. Newsletter 24: 69-70; Kreidl et al. (2002) J. Am. Coll. Surgeons 194: 387; Beckers
    # (2001) Netherlands J. . Med 58: 204-207 (autoimmune diseases); Ismeno et al. (1999) Int'l J. Cardiology 69: 179-183; Klibansky et al. (1966) Toxicon 3: 213-216; Seibert et al. (2003) Toxicon 41: 831-839; Szabo et al. (2002) Thrombosis Research 107: 357-363; Kaioumova et al. (2001) Chemosphere 43: 801-805.
  • TABLE 2
    Congophilic disorders.
    Disorder Acronym Disorder Protein Involved
    CJD Spongiform Prion protein
    encepalopathies fragments
    APP Alzheimer Beta protein
    fragment 1{fraction (40/43)}
    HRA Hemodialysis-Related Beta-2 microglobin*
    Amyloidosis
    PSA Primary Systematic Immunoglobulin light
    Amyloidosis chain and fragments
    SAA 1 Secondary Systematic Serum amyloid A 78
    Amyloidosis residue rragment
    FAP I** Familial Amyloid Transthyretin fragments,
    Polyneuropathy I 50+ alleles
    FAP III Familial Amyloid Apolipoprotein A-1
    Polyneuropathy III fragments
    CAA Cerebral Amyloid Cystatin A minus 10
    Angiopathy residues
    FHSA Finnish Hereditary Gelsolin 71 residue
    Systemic Amyloidosis
    IAPP Type II Diabetes Islet amyloid
    polypeptide fragment
    ILA Injection-Localized Insulin
    Amyloidosis
    CAL Medullary Thyroid Calcitonin fragments
    Carcinoma
    ANF Atrial Amyloidosis Atrial natriuretic
    factor
    NNSA Non-Neuropathic Lysozyme and fragments
    Systemic Amylodosis
    HRA Hereditary Renal Fibrinogen fragments
    Amyloidosis

    See Kelly (1996) Curr. Opin. Struct. Biol. 6: 11-17.

    *Homologous to immunoglobin, thus a predicted paralogous disease.

    **Also called senile systemic amyloidosis, prealbumin is synonymous with transthyretin. See mad-cow.org/congo.html (the prefix “www” is required).
  • Immunohistochemical assays have been developed for the proteins listed in Tables 1 and 2. See, e.g., Hardt et al. (2000) J. Comp. Path. 122:43-53 (antibodies for the detection of the prion protein, PrP). However, many of these proteins are only abundant in the late stages of the disease and may be undetectable utilizing standard assay techniques. Thus, in one embodiment, the methods of the present invention may be combined with an immunochemical assay for the protein or proteins selected from Tables 1 and 2. These proteins, or their functional derivatives, may be detectably labeled with any appropriate marker such as a radioisotope, an enzyme, a fluorescent label, a paramagnetic label, or a free radical linked to an antibody capable of binding these proteins.
  • Methods of making and detecting such detectably labeled antibodies or their functional derivatives are well known to those of ordinary skill in the art, and are described in more detail below. See, for example, Klein (1982) Immunology: The Science of Self-Nonself Discrimination (John Wiley & Sons, New York 1982); Kennett et al. (1980) Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses, (Plenum Press, New York; Campbell (1984) Monoclonal Antibody Technology, Laboratory Techniques in Biochemistry and Molecular Biology, Volume 13, ed. Burdon et al. (Elsevier, Amsterdam; and Eisen (1980) in Microbiology, ed. Davis et al. 3d ed.; Harper & Row, Philadelphia. Methods for the generation of polyclonal antibodies are known, as are techniques for the generation of monoclonal antibodies See, e.g., Kohler and Milstein (1975) Nature 256:495-497.
  • Assay techniques useful in the present invention include, but are not limited to, assays comprising incubating a biological sample from a subject suspected of having such a condition in the presence of a detectably labeled binding molecule (e.g., antibody) capable of identifying the relevant protein, and detecting the binding molecule which is bound in a sample. See, e.g., Work et al. (1978) Laboratory Techniques and Biochemistry in Molecular Biology (North Holland Publishing Company, NY).
  • Alternatively, the proteins contained in a particular sample of proteons can be identified by screening against a panel of phage antibodies in which the displayed peptide is a domain of the antibody molecule that includes the site that binds antigen. Phage-antibody libraries can be constructed including billions of clones, displaying billions of antibodies with different antigen specificities. For a review of this technique, see Petrenko and Vodyanoy (2003) J. Micro. Meth. 53:253-262.
  • The presence of proteons themselves can be detected and quantitated by dark-field microscopy. Under high-resolution dark-field microscopy proteons are visualized as bright spherical shapes. Techniques for dark-field microscopy are known in the art. See, e.g., Bradbury and Bracegirdle (1998), Introduction to Light Microscopy (Microscopy Handbooks, No 42), 2d ed.; (Springer Verlag). In particular, proteons are small, ball-like bodies of different sizes, estimated in the range of 50-250 nm. By contrast, healthy erythrocytes appear as bright void circles of about 7 microns diameter in the dark-field view, whereas neutrophils are roughly 7-15 microns. When a blood sample becomes aged, the morphology and number of the proteons change, with some estimated to be 500 nm in diameter. Some appear attached to the internal surface of the erythrocyte membrane. Proteons are found in fresh blood of species including human, bovine, horse, pig, cat, dog, fish (including but not limited to teleosts such as sharks), rabbit, and rat blood.
  • Dark-field microscopy of proteons can be confirmed by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) methodology. Techniques for electron microscopy are known in the art. See, e.g., Slayter and Slayter (1992) Light and Electron Microscopy, (Cambridge University Press).
  • Proteons can be isolated from blood or plasma, i.e., the supernatant produced by centrifuging a biological material. Centrifugal separation may be carried out by any means known in the art using any method, apparatus, time, temperature, or speed as appropriate for the biological sample. The relative centrifugal force (R.C.F) applied can be at least 300×g, 500×g, 600×g, 700×g, 800×g, 900×g, 1,000×g, 1,100×g, 1,200×g, 1,300×g, 1,400×g, 1,500×g, 1,600×g, 1,700×g, 1,800×g, 1,900×g, 2000×g, 2,500×g, 3,000×g, 4,000×g, 4,500×g, 5,000×g, 5,500×g, 6,000×g, 6,500×g, 7,000×g, 7,500×g, 8,000×g, 8,500×g, 9,000×g, 9,500×g, 10,000×g, 11,000×g, 12,000×g, 12,800×g, 13,000×g, 14,000×g, 15,000×g, 16,000×g, 17,000×g, 18,000×g, 19,000 20,000×g, or more. The relative centrifugal force is a function of the rotor diameter and the revolutions per minute and is readily calculated from formula R.C.F.=1.118×10−5×r×N2 (where r=the rotating radius and N=revolutions per minute). The time of centrifugation to obtain separation can be adjusted based on the R.C.F. applied and, thus, may be at least 10 sec, 20 sec, 30 sec, 40 sec, 50 sec, 1 min, 5 min, 10 min, 15 min, 20 min, 30 min, 40 min, 50 min, 1 h, 1.5 h, 2 h, 2.5 h, 3 h, 4 h, 5 h, 6 h, 8 h, 10 h, 12 h, 14 h, 16 h, 18 h, 24 h, or more. The temperature of the sample may be maintained within a suitable range before during, and/or after separation, such as for example at least 4° C., 14° C., 25° C., 37° C., 40° C., 42° C., 56° C., 65° C., 90° C., or more
  • In one embodiment, proteons can be formed by incubating plasma at 37° C. under sterile conditions over a thirteen day period. At the end of this period, the numbers of proteons observed under dark-field light microscopy are greatly increased.
  • In another embodiment, large numbers of proteons are produced by subjecting plasma to 120° C. at 20 psi for two hours. The visible number of proteons is amplified by subjecting plasma to a single step of elevated temperature.
  • Efficiency of proteon production is enhanced by taking a small portion of an amplified sample, adding it to an untreated sample, and heating the untreated sample. These steps can be repeated a number of times, each iteration yielding an increased quantity of proteons. Accordingly, by dividing the sample into a number of subsamples, subjecting the first subsample to heat or pressure, then aliquoting a small amount of the proteons from the first subsample into the second subsample and carrying out the heating step, a greater concentration of proteons can be produced from the second subsample than was produced from the first subsample. These seeding steps can be repeated multiple times until, after several iterations, the concentration of proteons produced per volume of sample eventually plateaus.
  • Typically, the first two cycles result in a small but significant increase of proteon population, whereas the third cycle brings about a dramatic increase in the number of proteons. Generally, the next three cycles result in saturation of the proteon population.
  • In one embodiment, a test sample containing a small amount of misfolded proteins is subjected to a single heating step. The amplified proteons are quantitated by dark-field microscopy and verified by immunofluorescent techniques to detect the misfolded protein.
  • In another embodiment, a small amount of seeds such as the PNCs described above can be added to a test sample to increase the sensitivity of the single step methods. Roughly 5×1013 PNC/ml are produced by initial filtration of plasma through at least a 5 kDa nominal molecular weight (NMW) cutoff filter, at least a 4 kDa NMW cutoff filter, at least a 3 kDa NMW cutoff filter, at least a 2 kDa NMW cutoff filter, at least a 1 kDa NMW cutoff filter, at least a 500 Da NMW cutoff filter, or smaller, or a combination thereof. The sample may be optionally prefiltered using a 0.5 micron filter, a 0.22 micron filter, a 0.2 micron filter, at least a 100 kDa NMW cutoff filter, a 50 kDa NMW cutoff filter, a 30 kDa NMW cutoff filter, any filter within the range of 5 kDa to 10, 20, 30, or higher molecular weight cutoff, or any combination thereof. This concentration then can be increased by a factor of roughly 100 by evaporation. Thus, in one aspect, addition of 5 ml of 5×1013 PNC/ml to a 1 ml sample increases the concentration of PNC in a sample by 2.5×1011 PNC/ml. This concentration is increased by a factor of 100 if pre-concentrated PNC are added. If the initial concentration of PNC varies from 108 to 1011 PNC/ml, the sensitivity can be increased by a factor of between 250 to 250,000.
  • In another embodiment, the first step amplification described above is carried out, then a small portion of amplified sample is introduced into the untreated sample and subjected to heat again. Then, the small portion of the second amplified sample is added to the third untreated sample, heated, and so on. The number of cycles depends on the initial concentration of misfolded proteins. Suitable numbers of cycles include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or more.
  • In one embodiment, the detection and identification can be done as a single-step method. Apparatus for subjecting a sample to heat and/or pressure are recognized in the art and include without limitation, PCR thermocyclers, autoclaves, etc.
  • As will be recognized by one of skill in the art, both the single- and multiple-step methods can be manipulated by varying the temperature, pressure, or temporal parameters. Suitable temperatures include at least 4, 15, 25, 37, 40, 45, 50, 55, 56, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120° C., or higher. Suitable pressures include at least ambient pressure, as well as at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 psi, or higher. Suitable times of treatment include at least 1, 5, 10, 15, 20, 25, 30, 25, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120 minutes, or more and may include times oftreatment of at least, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more days.
  • In another embodiment, these methods can be utilized to clear misfolded proteins from a biological sample such as blood. Because low temperatures can be utilized with long time periods, this can be accomplished without damaging the biological sample.
  • In another embodiment, these methods can detect misfolded proteins involved in congophilic disorders. See Kelly (1996) Curr. Op. Struc. Biol. 6:11-17; Kelly (1996) 8:101-106. For instance, there is a demonstrated structural homology between prion and hemoglobin proteins. Korth et al. (1997) Nature 390:74-77. There is evidence that prions are present in lymphoid organs and blood. See, e.g., Brown et al. (2001) J. Lab. Clin. Med. 137:5-13; Aguzzi (2000) Lab. Clin. Med. 137:5-13; Aguzzi (2001) Nature Medicine 7:289-290; Wadsworth et al. (2001) Lancet 358:171-180. Accordingly, the methods of the present invention can be utilized for amplification of a congophilic protein, thus allowing early detection of disorders related to these proteins.
  • PNC of roughly 1-2 nm and containing about 40-300 atoms play an important role in capturing hemoglobin released into blood plasma. While released hemoglobin is normally captured by protein haptoglobin and endocytosed by macrophages, released hemoglobin can be collected by PNCs. Roughly 7×1013 PNC are present in each milliliter of human blood, while only 0.003% of the whole pool of PNC is normally linked to proteins and made into proteons. However, a proteon of medium size of 160 nm can collect about 100,000 protein molecules of similar size to hemoglobin. Thus, the strong protein scavenging properties of metal nanoparticles allow them to collect proteins including misfolded hemoglobin (Kristiansen et al. (2001) Nature 409:198).
  • Thus, in another embodiment, the present methods can be utilized for amplification of proteins involved in intravascular hemolysis and resulting in aggregation of hemoglobin, including, without limitation, sickle cell anemia, atherosclerosis, malaria, infections and their complications, auto-immune disorders, internal bleedings and intravascular hemolysis due to internal prosthetic devices, and toxic reactions. See Kannan et al. (1988) J. Biol. Chem. 263:13766-13773; Schluter and Drenckhahn (1986) PNAS 83:6137-6141 (sickle cell); Fernandez et al. (2001) Atherosclerosis 158, 103-111 (atherosclerosis); Papalexis et al. (2001) Mol. Biochem. Parasitology 115:77-86; Esievo et al. (1984) Veterinary Parasitology 15:181-185; Igoe et al. (2002) Clin. Microb. Newsletter 24:69-70; Kreidl et al. (2002) J. Am. Coll. Surgeons 194:387; Beckers (2001) Netherlands J. Med:58:204-207 (autoimmune diseases); Ismeno et al. (1999) Int'l J. Cardiology 69:179-183; Klibansky et al. (1966) Toxicon 3:213-216; Seibert et al. (2003) Toxicon 41:831-839; Szabo et al. (2002) Thrombosis Research 107:357-363; Kaioumova et al. (2001) Chemosphere 43:801-805.
  • Using standard techniques, samples for single-step or cyclic amplification can be prepared from homogenates of small tissue fragments, or from biological fluids such as blood, cerebrospinal, lymph, etc. Techniques for the preparation of tissue homogenates and biological fluids from such sources are known. See Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual, Vols. 1-3 (2d ed; Cold Spring Harbour Laboratory Press, Plainview, N.Y.); and Ausubel et al., eds. (1994) Current Protocols in Molecular Biology, (Greene Publishing Associates, Inc. and John Wiley & Sons, Inc.).
  • PNCs can be produced from plasma by filtration through an ultrafiltration membrane. In one embodiment, plasma is filtered consecutively through a 30 kDa and a 5 kDa Centricon™ filter from Millipore before heat treatment. The centrifuge filtration is carried out using an initial volume of 80 ml centrifuged at 3,500 g for 20 minutes, 20° C.
  • Filtration of plasma before heat treatment abolishes proteon formation in the retentate. However, recombination of the fractions results in the resumption of proteon formation, and the number of proteons formed is dependent upon the amount of filtrate added back to the retentate. Thus, the PNCs are present in the filtrate.
  • Adsorption spectra of the filtrate reveals the presence of metals, including copper, zinc, and iron, indicating that PNCs comprise metals. The filtrate was precipitated with 1.2 mM MgSO4 and TEM studies were carried out. Such procedures are known in the art. See, e.g., Shindo and Oikawa, Analytical Electron Microscopy for Materials Science, Springer-Verlag (2002). It was found that the precipitated extract contained crystalline metallic nanoparticles of roughly 1-2 nm diameter. Selected area diffraction patterns were consistent with the presence of face centered cubic (FCC) or body centered cubic (BCC) metals or solid-solution alloys such as FCC copper and BCC iron.
  • For a review of metal clusters, see Aiken and Finke (1998) J. Mol. Cat. A: Chem. 145:1-44; Gonzalez-Moraga (1993) Cluster Chemistry (Springer-Verlag, New York, N.Y.). High symmetry is one of the main characteristics of metal clusters (Gonzalez-Moraga (1993) (Supra). In addition, metal clusters bind proteins. See Broun et al. (2002) J. Mol. Biol. 321:341-353; Liu and Xu (2002) J. Inorganic Biochem. 88:77-86. Thus, in one embodiment, the PNCs of the invention are characterized by small size, a few nm or smaller. Additionally, the PNCs are present in large quantities, about 1012-1013 PNC/cm3 of blood or tissue, are abundant, present binding sites and strong affinity to proteins, exhibit variability to bind different proteins, and resist extreme physical and biochemical conditions.
  • To test the effects of PNCs isolated from the filtrate upon living cells, various amounts of PNCs obtained by ultrafiltration and sterilized by autoclaving were incubated for four hours with various animal cells in tissue culture. Significant effects upon cell viability were observed, such as apoptosis of cells and cell death. For instance, rat and mouse glioma cells demonstrated marked signs of cell death, as assessed both microscopically and by MTT assay. Accordingly, the PNCs of the invention comprise a novel reagent for use in inducing apoptosis, as well as a process for its production. In one embodiment, aliquots from 1 to 40 μl containing about 1×1012 to 4×1013 PNCs were added to 100 μl wells of 96-well ELISA plate. Such compounds and processes are of great usefulness to those of skill in the art. See, e.g., U.S. Pat. No. 5,344,926 to Murakata et al., titled “Process for producing staurosporine derivatives”; U.S. Pat. No. 4,973,552 to Schroeder et al., titled “Staurosporine fermentation process”; and U.S. Pat. No. 6,518,032 to Fritz et al., titled “Rapid methods for identifying modifiers of cellular apoptosis activity.”
  • Various concentrations of PNCs and or proteons can be used to mediate biological effects. For example, concentrations of at least 5×1011, 1×1011; 5×1010; 1×1010, 5×109; 1×109, 5×108; 1×108, 5×107; 1×107, 5×106; 1×106, 5×105; 1×105, 5×104; 1×104 or less may be used.
  • This invention is further illustrated by the following examples that should not be construed as limiting.
    • EXPERIMENTAL EXAMPLE 1 Production of Proteons from Blood and Analysis by Microscopy
  • A 30 μl sample of freshly drawn full blood from a healthy human male was obtained and diluted in 1000 μl of purified water (Direct Q™, Millipore, 17 MOhm) in a 1.5-ml plastic vial, and centrifuged at 2200×g (6000 rpm) to obtain plasma. An additional aliquot of the blood was taken and prepared for optical dark-field microscopy. The plasma was transferred to a 4-ml glass vial with a plastic cap and a teflon liner. An aliquot of plasma was again retained for dark-field microscopy. The vial and contents were subjected to heating at a temperature of 120° C. and 20 psi of pressure for two hours. An aliquot of the heat-treated plasma was prepared for dark-field microscopy.
  • Each aliquot retained for microscopy was analyzed by dark-field microscopy using an Olympus™ microscope fitted with a 100 W mercury lamp, a polarizer, and a Naessens dark-field condenser (COSE Corp., Canada).
  • After analysis, the fresh full blood sample was found to contain approximately 3×108 proteons/ml, whereas the diluted sample contained roughly 9×106 proteons/ml. The treated sample contained an estimated 3×1011 proteons/ml, a five-order of magnitude increase. Adjusted for the initial dilution of the blood sample, each milliliter of blood yielded roughly 1×1013 proteons. Thus, within two hours, the number of proteons increased by approximately 5 orders of magnitude. Assuming exponential growth, then the number of proteons (N) at any given moment of time (t) can be described by the equation:
    N=N0ebt   (1)
  • where N0 is the initial number of particles, and b is the growth coefficient. If N, N0, and t are substituted with the experimental values found in the above experiment, one can estimate that the growth coefficient (b) for this case is equal to 5.2 l/hour, and the proteon population is doubled every 8 minutes. A summary of the data is presented in
    TABLE 3
    Cyclic amplification methodsa.
    bNumber of
    Time, proteons in Number of
    Temperature, ° C. regime 1 ml cMedia experiments
    37 d1 cycle, 7.0 × 1010 Plasma 8
    12 days
    37 d1 cycle, 3.5 × 1011 Growth 8
    12 days media 1
    37 d1 cycle, 3.0 × 1011 Growth 8
    12 days media 2
    40 1 cycle, 3.6 × 108   Plasma 8
    90 min
    40 6 cycles/ 1.4 × 108   Plasma 8
    15 min
    56 1 cycle/ 1.8 × 109   Plasma 8
    15 min
    56 6 cycles/ 2.0 × 109   Plasma 8
    15 min
    65 3 cycles/ 2.5 × 1011 Plasma 15
    15 min
    65 6 cycles/ 2.5 × 1011 Plasma 15
    15 min
    90 1 cycle/   5 × 1011 Plasma 9
    3 min
    120° C., 1 cycle/<1   8 × 1011 Plasma 12
    140 kPa min
    120° C., 1 cycle/2   8 × 1011 Plasma 245
    140 kPa hours

    aThe first sample was incubated for 15 minutes at temperatures shown herein. Five microliters of the treated first sample are introduced as seeds in the untreated second one and subjected to the same heat again. Then, 5 microliters of the second amplified sample are added to the third untreated sample, heated and so on up to 6 cycles.

    bNumber of proteons was estimated by counting with high resolution dark-field microscope and electron microscopy.

    cMedia. Plasma was obtained from a blood as described herein. D5648, growth media 1, D5648 tissue culture media (Sigma) with 10% FBS (HyClone); D6429, growth media 2, D6429 tissue culture media (Sigma) with 10% FBS.

    dProliferation of proteons is characterized by a 5 day latent period, a 2 day exponential growth phase, and 5 days of saturation.
  • As a control, a suspension of phospholipids and cholesterol was subjected to the same protocol used for the blood sample. However, no structures resembling proteons were observed under dark-field microscopy.
  • Electron microscopy analysis was also carried out on samples obtained before and after heat treatment. Transmission electron microscope (TEM) images obtained from pre- and post-heat-treatment samples reveal small proteons appearing as dark discs with a rough and fibrous appearance. An analysis of the TEM images revealed the size distribution of this characteristic small proteon to reach a maximum about 150 nm.
  • Another characteristic form of proteon was observed, a coconut-shaped particle of about 1-5 microns with a structure resembling one or more nuclei and a cell-like appearance. The nuclei look very similar to the small proteons described above. A cross-sectional view of a larger proteon reveals a very distinctive external membrane-like structure. This membrane-like structure, however, looks very different from the bacterial wall or the mammalian cell membrane, appearing as a curly fibrous shell of 10-12 nm thick. Some fiber-like structures and a few nuclei are visible inside the proteon. Images obtained by scanning electron microscopy (SEM) confirm the presence of both small and large characteristic proteons.
    • EXAMPLE 2 Chemical Composition of Proteons
  • Energy Dispersive Spectroscopy Analysis
  • The chemical composition was determined by energy dispersive X-ray spectroscopy using a JEOL JSM-840 SEM system using standard procedures for identifying and quantifying elemental composition. Such procedures are known in the art. See, e.g., Shindo and Oikawa (2002) Analytical Electron Microscopy for Materials Science (Springer-Verlag).
  • A sample of proteons suspended in distilled water was deposited on the aluminum SEM mount and dried in a vacuum for 24 hours. The X-ray spectra were obtained with an electron beam size of 200 nm at 80 kV for 90 s. Spectra revealed that the proteons were composed of carbon, oxygen, nitrogen, and sulfur, and the presence of potassium, sodium, chloride, silicon, and copper was also detected. The presence of carbon, nitrogen, and sulfur was confirmed by analytical chemical analysis (Leco Corporation, Michigan, USA). Notably phosphorus, a necessary element of DNA, was never detected in the proteon samples. On the other hand, all the elements needed for amino acids and proteins are available.
  • Amino Acid Composition
  • Free amino acid composition of samples before and after heat and highpressure treatment were determined (LPSA, University of Arizona, Tucson, Ariz.). See Table 4.
    TABLE 4
    Amino acid composition (pmol/50 ul)
    No Amino acid Control* Proteons
    1 O-Phosphoserine 98.731 39.878
    2 Taurine 191.790 227.739
    3 O-Phosphoethanolamine 17.980 15.318
    4 Urea 220.811 62.573
    5 Aspartic Acid 137.212 123.086
    6 Threonine 365.225 214.981
    7 Serine 385.160 314.039
    8 Asparagine — 95.908
    9 Glutamic Acid 483.645 229.149
    10 Glutamine 287.073 3.920
    11 Glycine 985.419 922.430
    12 Alanine 443.165 448.792
    13 Citralline 81.803 —
    14 Valine 188.720 236.126
    15 Cystine 4.799 6.367
    16 Methionine — 77.583
    17 L-Cystathio-nine 12.301 16.417
    18 Isoleucine 82.836 76.302
    19 Leucine 121.941 139.060
    20 Tyrosine 68.636 75.682
    21 Phenylalanine 104.921 79.904
    22 y-Amino-butiric — 108.022
    Acid
    23 Etanolamine 36.578 35.605
    24 L-Ornithine 53.341 23.004
    25 Lysine 226.033 208.597
    26 Histidine 75.954 103.043
    27 Arginine 273.221 166.512

    *Pre-heat and high-pressure treatment plasma.

    Protein Concentrate
  • The quantitive analysis of proteins in the proteon samples was carried out by two different protein assays obtained from Bio-Rad Laboratories and Sigma according to the manufacturers' protocols. Samples of blood as described in the Example 1 were exposed to different temperatures and pressures. Results of the experiments are shown in
    TABLE 5
    Protein concentrations in proteon samples.
    BIO-RAD, SIGMA,
    Protein Protein
    concentration, concentration,
    Sample, Condition μg/ml μg/ml
    Plasma, control, 0.67 ± 0.05 0.85 ± 0.2
    25° C.
    Plasma, 56° C., 0.72 ± 0.04 0.98 ± 0.2
    normal pressure,
    10 min
    Plasma, 80° C., 0.68 ± 0.04  1.0 ± 0.2
    normal pressure,
    10 min
    Proteons, 120° C., 0.71 ± 0.04  1.7 ± 0.2
    20 psi, 2 hours
  • Gel electrophoresis of plasma and two major protein components of plasma, albumin and hemoglobin, treated with 120° C. heat and 20 psi pressure produce obvious bands of 66,200 Da and 14,400 Da. These are shared with albumin and hemoglobin, respectively. After the treatment, the albumin has two weak bands of 14,400 Da and ˜8,000 Da, which coincide with the same bands of proteons. The treated hemoglobin conserved only the 8,000 Da band. Proteons filtered through a 100 kDa filter conserved the 14,400 and ˜8,000 bands, while proteons washed from the filter contain practically all bands of plain proteons, indicating that misfolded albumin and hemoglobin may be present in proteons. The confirmation of this fact may be obtained from the immunoblotting analysis.
  • Proteons from rabbit blood were disassembled by sodium dodecyl sulfate (SDS), a negatively charged detergent. The fragments of proteins were electrophoresed down and made distinctive bands in the polyacrylamide gel. The proteins were identified by N-terminal amino acid sequencing, yielding the partial sequence VLSPA(D/E)(E/K)TN(A/I) that shows 100% homology with the rabbit alpha chain of hemoglobin. Amino acid analysis showed that proteons are enriched by hydrophilic negatively charged amino acids, glutamic and aspartic acids. Additionally, such proteons show a similar hydropathy index to hemoglobin. Proteons stained with congo-red show an apple-green birefringence with polarizing light indicating the anisotropic alignment of the dye molecules. Congo-red staining is indicative of a common structural feature shared by many amyloids. Specifically, they are stabilized in part by anti-parallel beta sheet extensions from one monomer to another. It is believed that the dye binds to inter-monomer clefts between anti-parallel beta edge strands. See Kelly (1996) Curr. Op. Struc. Biol. 6:11-17; Kelly (1996) Curr. Op. Struc. Biol. 8:101-106. One protein belonging to the congophilic family is the prion protein associated with the prion diseases. A structural homology between prion and hemoglobin proteins has been demonstrated (Korth et al. (1997) Nature 390:74-77). In particular, two prion PrP(121-231) molecules could be superimposed with two β subunits of the crystal lattice of sickle cell hemoglobin1HBS. The superposition included the backbone atoms of residues 145-154, 179-189, and 201-217 of the helices 1, 2, and 3 of PrP(121-231) and of residues 5-14,106-116, and 125-141 of the helices 1, 6, and 7 of hemoglobin S.
  • Absence of DNA in Proteons
  • An aliquot of blood pre- and post-treatment (see Example 1) was purified using the DN easy Tissue Kit™ (Qiagen) according to the manufacturer's standard protocols for animal blood and bacteria. After final elution, samples were loaded on 1% agarose gel. DNA bands were visualized with ethidium bromide. DNA was detected in pre-treatment sample and undetected in the post-treatment sample.
  • Similar results were obtained using a HIGH PURE™ PCR Template Preparation Kit from Roche for isolation of Nucleic Acids followed by fluorometric quantitation of double-stranded DNA using the PICOGREEN™ dsDNA Quantitation Reagent from Molecular Probes and a TECAN SPECTRAFLUOR PLUS™ equipped with DELTASOFT™ software for detecting fluorescence (excitation at 485 nm and emission at 535 nm). See Table 6.
    TABLE 6
    Fluorometric quantitation of DNA in blood and proteons.
    DNA concentration,
    Sample μg/ml
    Blood 45.1
    Blood after dilution 3.0
    and centrifugation
    Proteons, freshly 0.033
    prepared
    Proteons, 3 months <0.001
    old
    • EXAMPLE 3 Controlled Growth of Proteons
  • Two identical sets of samples were prepared for this experiment, in which the growth of proteons incubated at 37° C. in an atmosphere of ambient air was compared with the growth of proteons incubated in an atmosphere of 5% CO2. Each set included the following numbered groups:
      • Group 1. Three ml of freshly prepared proteons (as described in Example 1).
      • Group 2. Three ml of plasma after dilution and centrifugation (as described in Example 1).
      • Group 3. Ten μl of freshly prepared proteons added to 3 ml of D6429 tissue culture media (Sigma) with 10% FBS (HyClone).
      • Group 4. Ten μl of freshly prepared proteons added to 3 ml of D5648 tissue culture media (Sigma) with 10% FBS (HyClone).
      • Group 5. Ten μl of freshly prepared plasma added to 3 ml of D6429 tissue culture media (Sigma) with 10% FBS (HyClone).
      • Group 6. Ten μl of freshly prepared plasma added to 3 ml of D5648 tissue culture media (Sigma) with 10% FBS (HyClone).
  • The experiment was run in duplicate. Uninoculated media were used as a control. Samples were analyzed by dark-field and scanning electron microscopy at the time points of 0, 2,4, 8, and 13 days.
  • Optical observation of proteons was performed with an OLYMPUS™ microscope fitted with a 100-W mercury lamp illumination source, a polarizer, a Naessens dark-field condenser (COSE Corp., Canada) and a 100× objective (oil, NA 1.4). The dark-field images were directed to a DEI-470T OPTRONICS™ CCD Video Camera System (Optronics Engineering, CA) utilizing the methods described in Vodyanoy et al. (1994) Langmuir 10:1354-1357. A direct count of proteons was used to determine their concentrations in liquid samples, and IMAGE PRO™ (Creative Software, Inc.) was used to quantify the number of proteons.
  • The number of proteons incubated at 37° C. in an atmosphere of ambient air (Group 1) measured by dark-field microscope did not change significantly (p<0.01) during 13 days (FIG. 2A, line 1). The plasma at the same conditions (Group 2) showed a very small increase in population of proteons within 8 days of incubation, but the number increased dramatically and reached the number of proteons in group 1 after 13 days of incubation (FIG. 2A, line 2). Proteons and plasma in tissue culture media ( Group 3 and 4, respectively) exhibited the same growth curves and reached the same number of proteons after 13 days of incubation (FIG. 2B). The culture media alone incubated at the same conditions showed no proteons (FIG. 2B, bottom line). No significant (p<0.01) effect of CO2 was observed.
    • EXAMPLE 4 Reversibility of Construction and Deconstruction of Proteons In Vitro
  • Plasma was prepared as described in Example 1. The samples of plasma were combined with the guanidine hydrochloride or urea to a final concentration of 0, 0.01, 0.1, 1, 4, and 8 M, respectively. These chaotropic compounds are known to unfold and denature proteins.
  • Samples were subjected to heat of 120° C. and pressure of 20 psi. In the samples to which no chaotropic compounds were added, the numbers of proteons observed by dark-field microscopy was normally high. The number of proteons decreased as the concentration of chaotropic compounds was increased (FIG. 2C).
  • Samples of proteons grown at the suppressive presence of 8 M Urea were subjected to dialysis using a PIERCE SLIDE-A-LYSER™ 10K (20 h, 5 L, 20° C.) according to the manufacturer's instructions. The number of proteons found by dark-field microscope increased significantly. Samples of plasma treated with 120° C. heat and 20 psi pressure and urea at concentrations of 0.01-8 M were taken. Polyacrylamide gel electrophoresis was carried out on each sample with a 4-20% Tris-HCl READY GEL™, Bio-Rad according to the manufacturer's protocol. The control (proteons without chaotropic compounds) showed two characteristic bands of 14,400 and about 8,000 Da. The experimental samples (proteons in the presence of a chaotropic compound) displayed a diffuse distribution of proteins or fragments of proteins with no sharp bands of proteins of the high molecular mass range. As the concentration of urea increased, the intensity of the diffusion staining decreased, and almost fully disappeared at the 8 M concentration of urea. The proteon sample displays a 14,400 Da band that coincides with a similar band found in plasma. When guanidine hydrochloride or urea was added to proteons produced without the chaotropic compounds, heat of 120° C. and pressure of 20 psi resulted also in a great reduction of number of proteons visible by dark-field microscopy. Dialysis of these samples restored the population of the proteons. Gel electrophoresis of proteons and plasma treated with 120° C. heat and 20 psi pressure at the presence of urea, and then dialyzed, reveals two bands of 14,400 and about 8,000 Da in all samples, including those before and after dialysis.
    • EXAMPLE 5 Effect of Ultrafiltration on Proteon Formation
  • PNCs were removed from blood plasma by filtering the plasma through 5 kDa CENTRICON™ filters from Millipore according to the manufacturer's protocol. The protein level in the retentate was quantitated and compared to that of unfiltered plasma. Assay kits were obtained from Bio-Rad Laboratories, and quantitative studies were carried out according to the manufacturer's instructions. The amount of protein in the filtered plasma was the same as that measured in the non-filtered sample. No protein was detected in the filtrate. After filtration, proteons could not be produced until the filtered fraction was returned to the plasma. The number of proteons was dependent on the amount of filtrate returned to the retentate. Addition of 10 mM of the chelating agent, ethylene diamine tetra acetate (EDTA), known to form strong complexes with metals, also prevented the formation of proteons. Adsorption spectra of the filtrate, determined by energy dispersive x-ray spectroscopy (EDS) and inductively coupled plasma-atomic emission spectrometry (GTW Analytical Services, TN), revealed the presence of metals, including Cu, Zn, and Fe.
    • EXAMPLE 6 Analysis of PNCs
  • To characterize the nature of the PNC nanoparticles, transmission electron microscopy (TEM) was utilized. Transmission electron microscopy (TEM) was performed using a JEOL JEM™ 2010 instrument, operated at 200 kV. Brightfield (BF) imaging was used to provide an overview of the microstructure of the sample. Features of interest were characterized by selected area diffraction (SAD) and nanobeam diffraction (NBD), with the latter set up to produce a narrow (<50 nm diameter), yet near-parallel beam, so that SAD-like patterns were produced. Dark-field (DF) imaging was employed to determine which microstructural features gave rise to the diffraction maxima. The composition of microstructural features was determined (qualitatively) by means of energy dispersive x-ray spectroscopy (EDS). This work employed an Oxford Instruments' ultra-thin window (UTW) detector, attached to the JEM 2010™, together with an Oxford Instruments' ISIS™ analyzer.
  • Scanning electron micrographs were obtained using a JEPL JSM-840 SEM system. Plasma from rabbit blood was filtered consecutively through a 30 kDa and a 5 kDa CENTRICON™ filter from Millipore before heat treatment. PNCs were precipitated from the filtrate by 1.2 mM MgSO4 at pH 11.3 and transferred onto 400 mesh Ni/carbon grids (Electron Microscopy Sciences). Proteon samples for TEM were fixed with 3% gluteraldehyde, dehydrated with ethanol, and embedded in Durcupan ASM™ resin (Fluka).
  • The bulk of the blood precipitate from rabbit plasma was amorphous. However, this extract was found to contain crystalline metallic nanoparticles, with diameters of around 1-2 nm and above. SAD patterns originating from different regions of the samples were consistent with the presence of both face centered cubic (FCC) and body centered cubic (BCC) metals (or possibly solid-solution alloys), with lattice parameters (a0) of approximately 360 and 290 pm respectively. These combinations of Bravais lattice and a0 are close to those of FCC copper (a0=361.50 pm (International Centre Diffraction Data (2001), Powder Diffraction File, ICCD, Newtown Square, Pa.) and BCC α-iron (“ferrite”, a0=286.64 pm (International Centre Diffraction Data (2001), Powder Diffraction File, ICCD, Newtown Square, Pa.), respectively. Furthermore, both copper and iron were encountered in EDS spectra acquired from the regions containing the nanoparticles. Centered DF imaging demonstrated that the diffraction maxima in these patterns originated from the nanoparticles. When viewed in BF, the metallic nanoparticles were very difficult to distinguish from the amorphous background in most regions of the samples. Hence, such particles could easily have been overlooked in the BF imaging techniques used conventionally for biological electron microscopy.
  • The observed crystallography of non-clumped nanoparticles was that of metallic iron and copper, rather than of salts of these metals. Furthermore, the diffraction patterns encountered in this work were not produced by an organometallic structure. The production of even nanometer-sized metallic particles implies the assembly of a significant number of metal atoms. For example, a 1 nm diameter Cu particle has the same volume as around 10 Cu, or 20 α-Fe, unit cells. FCC metals have 4 atoms per unit cell and BCC metals 2 atoms per cell, indicating a particle containing around 40 atoms in both cases (similarly, a 3 nm diameter particle would contain over 1,000 atoms).
  • Individual metallic nanoparticles had a random crystallographic orientation. Thus, in cases where the particles had become clumped (in some cases, this appeared to involve flocculation, in others some of the particles had sintered together), a polycrystalline aggregate was produced. In contrast, within a number of relatively large (around 10 nm diameter or above) clumps of particles, significant (˜5-10 nm wide) regions were encountered with a constant crystallographic orientation. However, none of the clumps was a true single crystal. Some of these relatively large clumps contained a number of, as yet unidentified, second phases in addition to α-Fe and Cu.
  • Both Cu and Fe form stable oxides (for example the Gibbs free energy of formation of even the relatively low stability CuO phase is around −127 kJ mol−1 at 300 K). See Brandes and Brook (1992) Smithells Metals Reference Book (7th ed., Butterworth-Heinenmann, Oxford, UK). Furthermore, the initial stages of oxidation of these metals are rapid, even at room temperature. For example, logarithmic oxidation of initially bare iron, at an oxygen partial pressure of only 10 mPa, results in the growth of around 2 nm of oxide, after less than 20 minutes at 300 K. See Kruger, J. and Yolken (1964), cited by Lawless. (1974) Rep. Prog. Phys. 37(2):231-316. The presence of non-noble metallic nanoparticles implies that the surrounding organic matrix has either impeded oxygen access to the metallic particles and/or has a significant reducing effect.
  • Many of the nanoparticles survived coarsening. The surface energy of the particles provides a driving force for larger particles to cannibalize smaller particles (the surface area to volume ratio for a 1-nm particle is 6×109 m−1 and this drops by an order of magnitude for a 10-nm particle). Metallic materials have relatively high solid-vapor interfacial energies (γSV) and those for copper and α-iron are around the middle of the range for metallic materials (at ˜2.2 and 3.2 J m−2, respectively; Muir (1975) Interfacial Phenomena in Metals and Alloys (Addison-Wesley; reprinted by TechBooks, Herdon, Va.)). Thus unless the metal-organic matrix interface has an interfacial energy (γSM) that is such that γSM<<γSV, there would remain a significant thermodynamic driving force for coarsening. Given the kinetics of coarsening, if all that were present were the metallic nanoparticles, room-temperature coarsening would occur at a negligible rate (solid-state sintering involves bulk diffusion, interfacial diffusion, free surface diffusion and evaporation and re-condensation, all of which would be very slow for Cu or α-Fe at room temperature). See Ashby (1974), Acta Metallurgica 22(3):275-289. See also, Swinkels and Ashby (1981) Acta Metallurgica 29(2):259-281. Although the presence of the organic liquid matrix raises possibilities for mass transport, it appears that the matrix did not provide a path for the rapid transfer of metal atoms since many of the nanoparticles of served in the present work remained extremely fine.
    • EXAMPLE 7 In Vitro Effect of PNC on Cultured Cells
  • The impact of PNCs upon viability of various cultured cells was investigated using the tetrazolium salt (MTT) cell proliferation assay. RG2 (mouse brain glioma), F98 (rat brain glioma), Hs683 (human brain glioma), CTX TNA2 (rat transfected astrocyte), H9c2[2-1] (rat heart myocardium), 27FR (rat skin fibroblast), and SVGp12 (human brain astroglia) cells were obtained from American Type Culture Collection (ATCC™) and maintained as recommended by ATCC™. MTT cell proliferation assays are commercially available. See, e.g., MTT Cell Proliferation Assay from ATCC™.
  • Cells were plated in DMEM (Product No. D5648,Sigma)+10% FCS (HyClone) in polystyrene 96-well plates at a density 3×103 cells per well. Twenty-four hours after plating, the medium was replaced with DMEM with either staurosporine (100 μl, 1 μM) or PNC (aliquots, 100 μl, 5×109 −3×1011 PNC/ml). PNCs were isolated from blood obtained from shark, dog, and rabbit using the ultrafiltration protocol described in Example 5. PNCs were autoclaved at 120° C. and 20 psi for 15 minutes before adding to the cell cultures.
  • After 20 hours of treatment, a 20-μl aliquot of tetrazolium salt (MTT, 5 mg/ml in PBS) was added to the wells, and interaction was allowed to proceed for 4 hours at 37° C. MTT was reduced in metabolically active cells to form purple formazan crystals, which were dissolved by DMSO and quantified by a plate reader (BioRad). For each cell type, a linear relationship between cell number and absorbance is established, enabling accurate, straightforward quantification of changes in proliferation.
  • In two trials, the effect of PNCs on RG2 cells was studied utilizing the following protocol:
      • Day 1. Plate out RG2 cells at a density of 3×103 cells/well in D5648+10% FCS and incubate overnight.
      • Staurosporine (Sigrna S5921), 100 μg, FW 466.5. Dissolve 100 μg staurosporine into 214.3 μl
      • DMSO to equal a 1 mM stock solution. Store at −200° C. Dilute stock 1:10 in media to equal 0.1 mM or 100 μM stock.
      • Dilute as follows:
      • 466.5 gm/1 liter=1 M
      • 100 gm/0.214 L=1M
      • Dilute stock 1:10 10 μl stock+90 μl DMEM
      • 100 μg/2.143 ml=100 μM (frozen stock)−use 10 μl/well=1 μM
      • Day 2. Remove media and add DMEM+1% FCS (100 μl/well). TX put on late afternoon.
        • Add staurosporine, autoclaved shark PNC, and either 10%, 1%, or 0% FCS treatments to cells and incubate overnight.
  • The results of this study are shown in Tables 7 and 8, below. (Ab. Av.=Absorbance at 550 nm; St. Dv.=Standard Deviation)
    TABLE 7
    MTT assay on RG2 glioma cells, with 10%, 1% and 0% FCS
    Shark Seeds-autoclaved
    10% 10% 10% 10% 1% 1% 1% 1% 0%
    Shark FCS FCS FCS FCS FCS FCS FCS FCS FCS
    3 no tx 20 μl 10 μl 1 μl no tx 20 μl 10 μl 1 μl no tx
    0.533 0.298 0.404 0.482 0.731 0.408 0.496 0.707 0.866
    0.542 0.316 0.414 0.465 0.753 0.433 0.544 0.724 0.891
    0.577 0.374 0.425 0.526 0.74 0.394 0.533 0.605 0.695
    0.516 0.369 0.409 0.467 0.633 0.365 0.596 0.633 0.937
    0.5 0.321 0.431 0.466 0.684 0.411 0.571 0.612 0.799
    0.362 0.414 0.693 0.419 0.541 0.909
    0.285 0.373 0.636 0.384 0.573 0.928
    0.297 0.393 0.637 0.431 0.529 0.949
    Ab. 0.5336 0.32775 0.407875 0.4812 0.688375 0.405625 0.547875 0.6562 0.87175
    Av
    St. 0.029126 0.035568 0.018349 0.025994 0.049494 0.023482 0.031197 0.055432 0.085951
    Dv.
    stauro-
    Shark Seeds-autoclaved sporine 10% 1% 0%
    0% 0% 0% 10% FCS FCS FCS
    Shark FCS FCS FCS FCS water water water
    3 20 μl 10 μl 1 μl 1 μM 20 μl 20 μl 20 μl
    0.432 0.739 0.827 0.406 0.436 0.726 0.971
    0.464 0.653 0.895 0.411 0.462 0.701 0.74
    0.463 0.713 0.918 0.399 0.394 0.676 0.79
    0.429 0.618 0.833
    0.463 0.638 0.78
    0.479 0.677
    0.452 0.577
    0.551 0.574
    Ab. 0.466625 0.648625 0.8506 0.405333 0.430667 0.701 0.833667
    Av
    St. 0.038049 0.059625 0.055599 0.006028 0.034312 0.025 0.121533
    Dv.
  • TABLE 8
    MTT assay, RG2 cells in 1% FCS, with shark, rabbit and dogs 1 and 2 seeds, autoclaved.
    20 μl 10 μl 1 μl 20 μl 10 μl 1 μl
    no tx Shark Seeds Dog 1 seeds
    0.64 0.342 0.447 0.664 0.675 0.773 0.658
    0.694 0.344 0.616 0.596 0.633 0.705 0.598
    0.667 0.373 0.407 0.595 0.527 0.662 0.712
    0.678 0.322 0.499 0.676 0.57 0.613 0.625
    0.675 0.626 0.63 0.63 0.625
    0.634 0.728 0.675 0.639
    0.689 0.6 0.703 0.688
    0.596 0.719 0.629 0.61
    Ab 0.6708 0.34525 0.49225 0.6345 0.63525 0.67375 0.644375
    Av.
    St. 0.019817 0.020998016 0.090691326 0.038097619 0.07015035 0.05268437 0.03923168
    Dv.
    20 μl 10 μl 1 μl 20 μl 10 μl 1 μl stauro
    Dog
    2 seeds Rabbit seeds 1% FCS
    0.555 0.595 0.687 0.503 0.62 0.732 0.108
    0.568 0.642 0.541 0.582 0.577 0.676 0.095
    0.543 0.65 0.601 0.476 0.607 0.589 0.093
    0.529 0.648 0.534 0.512 0.6 0.647
    0.561 0.53 0.66 0.585 0.564 0.64
    0.526 0.638 0.623 0.584 0.604 0.61
    0.498 0.593 0.644 0.565 0.519 0.634
    0.566 0.658 0.559 0.536 0.554 0.649
    Ab 0.54325 0.61925 0.606125 0.542875 0.580625 0.647125 0.09866667
    Av.
    St. 0.024294326 0.04372887 0.05713752 0.0423402 0.03372976 0.0431292 0.00814453
    Dv.
  • Similar studies were carried out comparing the effect of shark PNCs with staurosporine. See Tables 9-12, below. A significant decrease in cell viability was observed for cultured cells incubated with PNCs for 20 hours (FIG. 4A). The viability of the rat and mouse glioma cells declined by 90% and 75%, respectively, while the viability of the rat astrocytes decreased by only 25% at the same conditions. Post-exposure morphological observations of cells under optical dark-field microscope showed signs of cell death. Cells were shrunken and rounded; nuclei were condensed and showed budding of cell bodies (FIG. 4B-2). Cell damage produced by the shark PNCs compares well with the injury made by 1 μM of staurosporine (a potent apoptosis-inducing reagent) (FIG. 4B-3). A significant effect on cell viability was also observed with Hs683 (human brain glioma), H9c2[2-1] (rat heart myocardium), 27FR (rat skin fibroblast), and SVGp12 (human brain astroglia) cells. Proteons and PNCs obtained from the blood plasma of healthy dog and rabbit also significantly affected the viability of the cultured mammalian cells.
  • FIG. 4C shows the viability of RG2 glioma cells exposed to PNCs from different sources. It takes about 1×1012 PNC/ml to fully suppress these glioma cells. This concentration accounts for not more than 10% of the full concentration of PNCs in a healthy animal.
    TABLE 9
    MTT assay on various cell lines with shark seeds and 0% FCS
    RG2 Fibroblast Myocard
    No
    20 No 20 No 20
    tx 1 μl 10 μl μl tx 1 μl 10 μl μl tx 1 μl 10 μl μl
    Plate
    1 1.075 0.964 0.856 0.597 0.658 0.503 0.595 0.342 0.509 0.452 0.496 0.376
    0% FCS 1.169 1.014 0.791 0.496 0.603 0.517 0.541 0.36 0.462 0.373 0.471 0.382
    1.103 1.016 0.688 0.523 0.558 0.556 0.492 0.375 0.494 0.438 0.462 0.33
    1.084 1.082 0.739 0.55 0.556 0.569 0.432 0.382 0.449 0.446 0.513 0.309
    Ab. 1.10775 1.019 0.7685 0.5415 0.59375 0.53625 0.515 0.36475 0.4785 0.42725 0.4855 0.34925
    Av.
    St. 0.042469 0.048401 0.07191 0.04307 0.048016 0.031298 0.609508 0.017727 0.027767 0.036619 0.023302 0.035491
    Dv.
    CTX astrocytes SVG astrocytes F98 glioma
    No
    20 No 20 No 20
    tx 1 μl 10 μl μl tx 1 μl 10 μl μl tx 1 μl 10 μl μl
    Plate
    1 0.622 0.596 0.555 0.429 0.678 0.688 0.441 0.275 1.045 0.914 0.367 0.213
    0% FCS 0.603 0.589 0.559 0.489 0.681 0.585 0.439 0.275 0.977 0.697 0.444 0.16
    0.59 0.645 0.561 0.396 0.676 0.587 0.462 0.251 0.966 0.643 0.415 0.196
    0.565 0.6 0.533 0.434 0.656 0.667 0.363 0.244 1.064 0.73 0.504 0.172
    Ab. 0.595 0.6075 0.552 0.42725 0.67275 0.63175 0.42625 0.26125 1.013 0.746 0.4325 0.18525
    Av.
    St. 0.02393 0.02541 0.01291 0.038549 0.011354 0.053525 0.043431 0.016132 0.048751 0.117601 0.057274 0.023796
    Dv.
  • TABLE 10
    MTT assay on various cell lines with shark seeds and 1% FCS
    RG2 Fibroblast Myocard
    Plate No
    20 No 20 No 20
    2 tx 1 μl 10 μl μl tx 1 μl 10 μl μl tx 1 μl 10 μl μl
    1% 0.839 0.606 0.536 0.36 0.503 0.44 0.5 0.307 0.404 0.43 0.317 0.317
    FCS
    0.734 0.551 0.723 0.419 0.475 0.452 0.44 0.316 0.43 0.444 0.349 0.326
    0.665 0.595 0.551 0.435 0.465 0.518 0.351 0.298 0.408 0.466 0.326 0.289
    0.723 0.656 0.564 0.445 0.457 0.547 0.308 0.371 0.425 0.458 0.321 0.377
    AbAV 0.74025 0.602 0.5935 0.41475 0.475 0.48925 0.39975 0.323 0.41675 0.4495 0.32825 0.32725
    CTX astrocytes SVG astrocytes F98 glioma
    Plate No
    20 No 20 No 20
    2 tx 1 μl 10 μl μl tx 1 μl 10 μl μl tx 1 μl 10 μl μl
    1% 0.521 0.501 0.501 0.355 0.602 0.509 0.352 0.248 0.746 0.687 0.376 0.137
    FCS
    0.507 0.564 0.426 0.415 0.597 0.496 0.37 0.238 0.971 0.524 0.334 0.154
    0.542 0.562 0.42 0.387 0.534 0.488 0.401 0.246 0.91 1.267 0.283 0.141
    0.538 0.641 0.439 0.471 0.48 0.547 0.394 0.26 0.864 0.521 0.309 0.139
    AbAv 0.527 0.567 0.4465 0.407 0.55325 0.51 0.37925 0.248 0.87275 0.74975 0.3255 0.14275
  • TABLE 11
    MTT assay on various cell lines with Staurosporine
    RG2
    Saurosp. 100 nm RG2 Fibro Fibro Myocard myocard
    Shark 7 0.305 0.12 0.257 0.168 0.402 0.154
    0.301 0.119 0.275 0.166 0.373 0.151
    Plate 3 0.279 0.119 0.275 0.171 0.172 0.159
    1% FCS 0.272 0.149 0.296 0.171 0.185 0.176
    Ab. Av. 0.28925 0.12675 0.27575 0.169 0.283 0.16
    St. Dv. 0.016215 0.014841 0.015945 0.002449 0.121362 0.011165
    CTX CTX SVG SVG F98 F98
    Saurosp. astro astro astro astro glioma glioma
    Shark 7 0.252 0.212 0.128 0.067 0.136 0.108
    0.518 0.122 0.12 0.066 0.138 0.108
    Plate 3 0.533 0.118 0.128 0.067 0.12 0.109
    1% FCS 0.21 0.126 0.136 0.068 0.139 0.109
    Ab. Av. 0.37825 0.1445 0.128 0.067 0.13325 0.1085
    St. Dv. 0.171002 0.045118 0.006532 0.000816 0.008921 0.000577
  • TABLE 12
    Effect of shark extracts on cultured cells as
    a percentage of metabolically active cells
    METABOLICALLY ACTIVE CELLS, %
    CELL LINES Shark extract Shark extract Shark extract Staurosporine
    (RAT) 1 μl 10 μl 20 μl 1 μM
    F98 glioma 73.6 ± 20.5 42.6 ± 18   18.2 ± 17.6 12.4 ± 11.4
    RG2 glioma 91.9 ± 8.5  69.3 ± 13.1 48.8 ± 11.7 17.1 ± 21.4
    Myocardium 89.2 ± 14.4 101.4 ± 10.6  72.9 ± 15.9 38.3 ± 10  
    CTX astrocytes 102.1 ± 8.2  92.7 ± 6.3  71.8 ± 13.0 27.4 ± 34.2
    Fibroblasts 90.3 ± 13.9 86.7 ± 21.5 61.4 ± 12.9 35.5 ± 5.6 
    SVG astrocytes 93.9 ± 10.1 63.3 ± 11.8 38.8 ± 7.8  12.1 ± 11.6
    • EXAMPLE 8 Cyclic Amplification of Proteons
  • A progressively increased number of proteons can be produced from plasma subjected to increasing temperatures. To examine a method of cyclic amplification, seven 1 ml samples of plasma were prepared for cyclic amplification. After the initial number of proteons was quantitated by a dark-field microscope, the first sample was incubated for 15 minutes at 65° C. and normal pressure. Five μl of the treated first sample was introduced to seed the untreated second sample, and the second sample was incubated for 15 minutes at 65° C. and normal pressure. This step was repeated: 5 μl of the second amplified sample was added to the third untreated sample. This process was repeated up to 6 cycles. A control series was run by adding of five μl of purified water (instead of seeds) to 1 ml of untreated plasma.
  • The first two cycles resulted in a small but significant (p<0.001) increase of proteon population, whereas the third cycle brought about a dramatic increase in the number of proteons. The next three cycles resulted in saturation of the proteon population. In contrast, the control samples showed no dramatic increase of the proteon population. See FIG. 2.
    • EXAMPLE 9 Comparison With Other Biological Particles
  • Experiments were carried out to compare the proteons obtained by the procedure described in the Example 1 with the nanobacteria isolated from blood by Kajander et al. (1996) Mol. Biol. Cell 7:3007-3007 using the NANOCAPTURE ELISA™, an Enzyme-Linked Immunosorbent Assay, for detection of nanobacterial antigens (Nanobac OY, Finland). The nanobacteria included in the Nanocapture ELISA were used as a positive control. The Microplate Manager 4.01 Bio-Rad was used to obtain the results of the ELISA. The assay procedure was carried out following the manufacturer's recommendations. The reaction was considered to be positive when the absorbance was significantly higher then the level of noise. Results of interaction of antibodies grown against nanobacteria with proteons and plasma are summarized in Table 13.
    TABLE 13
    Interaction of antibodies specific to
    nanobacteria with proteons and plasma.
    No Sample Condition Reaction
    1 Proteons, Freshly prepared -
    human 1 at 120° C.
    and 20 psi, 2 h
    2 Proteons, Freshly prepared -
    human 2 at 120° C.
    and 20 psi, 2 h
    3 Proteons, Freshly prepared -
    rabbit at 120° C.
    and 20 psi, 2 h
    4 Proteons, Incubated 13 days, -
    human 1 37° C. after
    preparation
    5 Plasma, Freshly prepared -
    human
    6 Plasma, Incubated 13 days, -
    human 1 37° C.
    7 Proteons, Incubated 13 days, +
    human 1, 37° C.
    in D5648a
    8 Proteons Incubated 13 days, +
    human 1, 37° C.
    in D6429b
    9 Plasma, Incubated 13 days, +
    human 1, 37° C.
    in D5648a
    10 Plasma, Incubated 13 days, +
    human 1, 37° C.
    in D6429b
    11 Proteons, Incubated 13 days, +
    human 1, 37° C.
    in D5648a
    12 Proteons Incubated 13 days, +
    human 1, 37° C.; 5%
    in D6429b CO2-95% air
    13 Plasma, Incubated 13 days, +
    human 1, 37° C.; 5%
    in D5648a CO2-95% air
    14 Plasma, Incubated 13 days, +
    human 1, 37° C.; 5%
    in D6429b CO2-95% air
    15 Proteons, Incubated 13 days, +
    human 1, 37° C.; 5%
    in D5648a CO2-95% air
    D5648a Incubated 13 days, +
    37° C.
    D6429b Incubated 13 days, +
    37° C.
    16 D6429b Freshly prepared -
    17 Waterc Freshly prepared -
    18 Brothd 120° C. and -
    20 psi, 2 h
    Nanobacteria +

    aD5648 tissue culture media (Sigma) with 10% FBS (HyClone).

    bD6429 tissue culture media (Sigma) with 10% FBS (HyClone).

    cPurified water (Direct QTM, Millipore, 17 MOhm)

    dLB-Medium (BIO 101, Inc.; 10 g Trypton-B, 5 g yeast extract-B, 10 h NaCl in 1 L of water).
  • Nanobacteria gave a positive signal, while all freshly prepared proteons showed no interaction. Proteons incubated in cell culture media for 13 days, at 37° C. (with and without CO2) show a positive reaction. However, the culture media alone incubated for 13 days, at 37° C. also gave a positive reaction, while freshly prepared culture media was negative, indicating that nanobacteria antigen appeared from the culture media during the incubation.
    • EXAMPLE 10 Methods of Shark PNC Preparation
  • A) Shark Blood
  • Fresh blue shark (Prionace) tissue was homogenized in purified water (1: 1, w/w) and suspension was centrifuged at 12,800×g for 40 minutes at 4° C. The final filtrate was obtained by filtering the supernatant consecutively through 30-kDa and 5-kDa CENTRICON™ filters (Millipore). Liquid obtained by filtration was autoclaved at 20 psi for 15 minutes. Micrometer and sub-micrometer particles were isolated from shark extracts. It was initially observed that shark's blood contains approximately 5-fold more PNCs/ml than rat or rabbit blood. Specifically, one microliter of shark extract contained approximately 5×1013 proteon nucleating centers (PNC). PNCs such as these are generally comprised of 1-2-nm metallic nanoclusters containing 40-300 atoms.
  • B) Shark Liver.
  • The shark's body and liver were stored in ice for approximately 12 h. The tissue was homogenized using various methods. Specifically, 50 g of liver was homogenized in 150 ml H2O (DIRECT-Q™ water purification system, Millipore) in a blender. Additionally, 50 g of liver was homogenized in 150 ml of 0.2% NaCl/H2O solution in a blender, and 50 g of liver was also homogenized in 150 ml of 0.9% NaCl and 0.9% Ethanol solution. Blood was diluted approximately 1:10 in water.
  • The homogenates were centrifuged at 12,800 g-13,000 g for 40 min. on a Beckman (Model J2-21™) centrifuge in a JA 10™ rotor. The pellet was discarded and the supernatant was filtered through 30,000 Da CENTRICON PLUS-80™ centrifugal filter devices (Millipore). Samples were combined and filtered through a 5,000 Da CENTRICON PLUS-80™ centrifugal filter device, yielding a PNC “seed solution.”
  • 1) PNC Formation for Metal Analysis (from “Seed Solution”)
  • 450 mg of MgSO4×7H2O was added to approximately 150 ml shark seed solution having a pH approximately 6-7. IN NaOH was added to the solution to raise pH to 11, approximately. White precipitate was formed, and the precipitate was centrifuged at 5000 rpm on a Beckman table centrifuge. Supernatant was discarded and the pellet was dissolved by lowering the pH to between 6-7 using a 1N solution of HCl. Analysis showed the presence of Zn, Cu and Mg in the solution.
  • 2) PNC Formation for Cell Culture (from “Seed Solution”)
  • 20 ml of the “seed solution was autoclaved for 15 minutes at 20 psi and used for cultured cell experiments.
  • C) Rabbit Blood
  • Plasma was obtained by adding 10 ml of rabbit blood to 290 ml H2O (DIRECT-Q™ water purification system, Millipore) (1:30). The solution was mixed and centrifuged for 40 min at 13,000 g on a Beckman (Model J2-21™) centrifuge in a JA 10™ rotor. The pellet was discarded and the supernatant was used for seed preparation. PNC were obtained by filtering plasma through 30,000 Da and then 5,000 Da CENTRICON PLUS-80™ centrifugal filter devices (Millipore).
  • Further preparation for electron microscopy of some samples included adding MgSO4×7H2O (Humco) to the PNC suspension (MgSO4×7H2O+360 ml of seeds solution, pH approximately 5-6). As series of precipitation were performed as follows
  • 1st precipitation. (Sample A). The pH of the seed solution was changed to 7 approximately by adding 1N NaOH. A white deposit was formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter Allegra™ 21R centrifuge in a S4180™ bucket rotor for 15 min.
  • 2nd precipitation. (Sample B). The pH of the remaining PNC suspension was changed from 7 to 8 by adding 1N NaOH. A white deposit was again formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter Allegra™ 21R centrifuge in a S4180™ bucket rotor for 15 min.
  • 3rd precipitation. (Sample C). The pH of the remaining PNC suspension was changed from 8 to 12 by adding 1N NaOH. A white deposit was again formed. The deposit was taken from the solution by pipetting and deposited on a 400 mesh nickel TEM grid. Then the rest of the sample was centrifuged at 5000 rpm on a Beckman-Coulter Allegra™ 21R centrifuge in a S4180™ bucket rotor for 15 min.
  • D) Mammalian Blood: Rabbit, Dog, and Human
  • 1. Rabbit blood, dog blood, and human blood were each diluted in H20 (DIRECT-Q™ water purification system, Millipore). Specifically, 25 ml of rabbit blood was diluted in 150 ml of water; 10 ml of dog blood was diluted in 150 ml water; and 60 μl of human blood was diluted in 0.97 ml of H2O. Rabbit and dog plasma were centrifuged at 12,800-13,000 g for 40 min on a Beckman (Model J2-21™) centrifuge in a JA 10™ rotor. The pellet was discarded and the supernatant was used for PNC preparation. Human plasma was centrifuged at 6,500 rpm for 5 min on table centrifuge. The pellet was discarded and the supernatant was used for PNC preparation.
  • PNC were obtained by sequentially filtering the supernatants though 30,000 Da and 5,000 Da CENTRICON PLUS-80™ centrifugal filter devices (Millipore). The filtered PNC suspensions (2 ml) were autoclaved in 4 ml bottles for 15 min at 20 psi and used for cultured cells experiments.
  • Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
  • All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
  • Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims (20)

1. A method for the cyclic amplification of proteons in a biological sample comprising:
a) centrifuging said biological sample until a supernatant is formed;
b) dividing said supernatant into a plurality of subsamples; and
c) heating a subsample for a period of time.
2. The method of claim 1, further comprising the steps of:
a) obtaining an aliquot of said heated subsample;
b) placing said aliquot into an unheated subsample;
c) heating the subsample of 2b) for a period of time; and
d) repeating steps 2a)-2c) with aliquots taken from the most recently heated subsample for a predetermined number of cycles.
3. The method of claim 2, wherein steps 2a)-2c) are repeated for a predetermined number of cycles until the number of proteons obtained in each heated subsample no longer increases, wherein the number of proteons in the subsample in which the number of proteons no longer increases is indicative of the amount of misfolded proteins present in the biological sample.
4. A method for the detection of a disorder selected from Table 1 or Table 2, comprising:
a) centrifuging a biological sample until a supernatant is formed;
b) dividing said supernatant into a plurality of subsamples;
c) heating a subsample for a period of time;
d) obtaining an aliquot of said heated subsample;
e) placing said aliquot into an unheated subsample;
f) heating the subsample of e) for a period of time; and
g) repeating steps d-f with aliquots taken from the most recently heated subsample for a predetermined number of cycles;
wherein the proteons produced from the most recently heated subsample are further contacted with an antibody that binds to a protein selected from Table 1 or Table 2, wherein the binding of said antibody is indicative of a disorder related to said protein.
5. The method of claim 2, wherein the subsamples are each 1 ml and the aliquot is 5 μl.
6. The method of claim 2, wherein the period of time for each cycle is two hours.
7. The method of claim 2, wherein the period of time for each cycle is one hour.
8. The method of claim 2, wherein the period of time for each cycle is 15 minutes.
9. The method of claim 6, wherein the temperature is 45° C.
10. The method of claim 7, wherein the temperature is 50° C.
11. The method of claim 8, wherein the temperature is 65° C.
12. The method of claim 9, wherein the number of cycles is 20.
13. The method of claim 10, wherein the number of cycles is 10.
14. The method of claim 11, wherein the number of cycles is 6.
15. An isolated proteon nucleation center (PNC) comprising a metal cluster.
16. A process for the purification of the PNC of claim 15 from a biological sample, comprising:
a) centrifuging said biological sample until a supernatant is formed;
b) filtering said supernatant through a 5,000 kDa nominal molecular weight limit ultrafiltration membrane; and
c) collecting the filtrate.
17. A PNC product produced by the process of claim 16.
18. The isolated PNC of claim 15, wherein said metal cluster is selected from the group consisting of copper, iron, magnesium, and zinc.
19. A method for inducing apoptosis in cells, comprising contacting a cell culture with at least one isolated PNC of claim 15.
20. A method for clearing misfolded proteins from blood comprising contacting a sample of blood with the PNC of claim 15.
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