Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in the genome. These procedures are less applicable to experiments with non-model organisms, which frequently comprise non-sequenced genomes with an unknown order of probe targets. We therefore present an additional analysis approach, which does not depend on the structural information of a reference genome, and quantifies the presence or absence of a probe target in an unknown genome. The principle is that intensity values of target probes are compared with the intensities of negative-control probes and positive-control probes from a control hybridization, to determine if a probe target is absent or present. In a test, analyzing the genome content of a known bacterial strain: Staphylococcus aureus MRSA252, this approach proved to be successful, demonstrated by receiver operating characteristic area under the curve values larger than 0.9995. We show its usability in various applications, such as comparing genome content and validating next-generation sequencing reads from eukaryotic non-model organisms.

Interorgan coordination of the murine adaptive response to fasting.

Starvation elicits a complex adaptive response in an organism. No information on transcriptional regulation of metabolic adaptations is available. We, therefore, studied the gene expression profiles of brain, small intestine, kidney, liver, and skeletal muscle in mice that were subjected to 0-72 h of fasting. Functional-category enrichment, text mining, and network analyses were employed to scrutinize the overall adaptation, aiming to identify responsive pathways, processes, and networks, and their regulation. The observed transcriptomics response did not follow the accepted "carbohydrate-lipid-protein" succession of expenditure of energy substrates. Instead, these processes were activated simultaneously in different organs during the entire period. The most prominent changes occurred in lipid and steroid metabolism, especially in the liver and kidney. They were accompanied by suppression of the immune response and cell turnover, particularly in the small intestine, and by increased proteolysis in the muscle. The brain was extremely well protected from the sequels of starvation. 60% of the identified overconnected transcription factors were organ-specific, 6% were common for 4 organs, with nuclear receptors as protagonists, accounting for almost 40% of all transcriptional regulators during fasting. The common transcription factors were PPARα, HNF4α, GCRα, AR (androgen receptor), SREBP1 and -2, FOXOs, EGR1, c-JUN, c-MYC, SP1, YY1, and ETS1. Our data strongly suggest that the control of metabolism in four metabolically active organs is exerted by transcription factors that are activated by nutrient signals and serves, at least partly, to prevent irreversible brain damage.

Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis.

The chemical legislation of the EU, Registration, Evaluation, and Authorization of Chemicals (REACH), stipulates that about 30 000 chemical substances are to be assessed on their possible risks. Toxicological evaluation of these compounds will at least partly be based on animal testing. In particular, the assessment of reproductive toxicity is a very complicated, time-consuming and animal-demanding process. Introducing microarray-based technologies can potentially refine in vivo toxicity testing. If compounds of a distinct chemical class induce reproducible gene-expression responses with a recognizable overlap, these gene-expression signatures may indicate intrinsic features of certain compounds, including specific toxicity. In the present study, we have set out the first steps towards this approach for the reproductive toxicity of phthalates. Male rats were treated with a single dose of either reprotoxic or non-reprotoxic phthalates, and were analyzed 24 h afterwards. Subsequently, histopathological and gene-expression profiling analyses were performed. Despite ambiguous histopathological observations, we were able to identify genes with differential expression profiles between the reprotoxic phthalates and the non-reprotoxic counterparts. This shows that differences in gene-expression profiles, indicative of the type of exposure, may be detected earlier, or at lower doses, than classical pathological endpoints. These findings are promising for 'early warning' biomarker analyses and for using toxicogenomics in a category approach. Ultimately, this could lead to a more cost-effective approach for prioritizing the toxicity testing of large numbers of chemicals in a short period of time in hazard assessment of chemicals, which is one of the objectives of the REACH chemical legislation.

Induction of arthritis in monkeys by immunization with type II collagen.

Immunization of two cynomolugus and three rhesus monkeys with purified type II collagen resulted in the development of polyarthritis. Arthritis first became clinically apparent 7 wk after primary immunization and persisted for 16 mo. Radiologic examination of the limbs demonstrated soft tissue swelling with severe joint destruction including loss of cartilage and bone. Involved joints eventually became ankylosed with permanent loss of some motion. All of the monkeys developed a response to the immunizing collagen as determined by ELISA of serum for antibodies. Arthritis was associated with weight loss and constitutional symptoms, including lethargy and refusal to eat. One monkey became so debilitated that it was necessary to euthanize it. Histologic examination of the joints showed synovial hypertrophy with pannus formation. A control monkey immunized with type I collagen suffered no apparent ill effects.

The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.

BACKGROUND: The Gram negative anaerobic bacterium Porphyromonas gingivalis has long been recognized as a causative agent of periodontitis. Periodontitis is a chronic infectious disease of the tooth supporting tissues eventually leading to tooth-loss. Capsular polysaccharide (CPS) of P. gingivalis has been shown to be an important virulence determinant. Seven capsular serotypes have been described. Here, we used micro-array based comparative genomic hybridization analysis (CGH) to analyze a representative of each of the capsular serotypes and a non-encapsulated strain against the highly virulent and sequenced W83 strain. We defined absent calls using Arabidopsis thaliana negative control probes, with the aim to distinguish between aberrations due to mutations and gene gain/loss. RESULTS: Our analyses allowed us to call aberrant genes, absent genes and divergent regions in each of the test strains. A conserved core P. gingivalis genome was described, which consists of 80% of the analyzed genes from the sequenced W83 strain. The percentage of aberrant genes between the test strains and control strain W83 was 8.2% to 13.7%. Among the aberrant genes many CPS biosynthesis genes were found. Most other virulence related genes could be found in the conserved core genome. Comparing highly virulent strains with less virulent strains indicates that hmuS, a putative CobN/Mg chelatase involved in heme uptake, may be a more relevant virulence determinant than previously expected. Furthermore, the description of the 39 W83-specific genes could give more insight in why this strain is more virulent than others. CONCLUSION: Analyses of the genetic content of the P. gingivalis capsular serotypes allowed the description of a P. gingivalis core genome. The high resolution data from three types of analysis of triplicate hybridization experiments may explain the higher divergence between P. gingivalis strains than previously recognized.

Elevated 8-hydroxydeoxyguanosine levels in DNA of diethylstilbestrol-treated Syrian hamsters: covalent DNA damage by free radicals generated by redox cycling of diethylstilbestrol.

The generation of free radicals by microsome-mediated redox cycling between catechol estrogens or diethylstilbestrol and their corresponding quinones has previously been demonstrated in vitro. However, the reaction of free radicals with DNA has not yet been detected in animals treated with estrogen and is the subject of this investigation. The reaction of guanine bases of DNA with hydroxyl radicals to form 8-hydroxydeoxyguanosine has been used as a monitor of free radical generation in kidney and liver of Syrian hamsters, a species prone to estrogen-induced carcinogenesis. Prior to in vivo measurements, the in vitro hydroxylation of guanine bases of DNA under conditions of redox cycling of estrogen was investigated. In incubations of DNA or deoxyguanosine with hamster kidney microsomes, NADPH, and diethylstilbestrol 4',4"-quinone, the hydroxylation of guanine bases of free deoxyguanosine or of DNA was 50 to 100% higher than in controls. When incubations were carried out in the presence of iron(III) chloride, the hydroxylation of guanine bases was 2.5- or 10-fold higher than control values. There was a 65% increase from control values in levels of 8-hydroxydeoxyguanosine in liver DNA of hamsters treated with 20 mg/kg/day diethylstilbestrol for 3 days and 100 mg/kg on the 4th day. In hamsters treated chronically with diethylstilbestrol implants for 15 days, 8-hydroxydeoxyguanosine levels more than doubled from control values in kidney but not liver DNA. Treatment of hamsters with estradiol for various time periods did not induce any changes in levels of hydroxylated guanine in either kidney or liver. It was concluded that in vitro and in vivo redox cycling of diethylstilbestrol hydroxylated guanine bases in DNA.

Horseradish peroxidase/hydrogen peroxide-catalyzed oxidation of the carcinogen N-hydroxy-N-acetyl-2-aminofluorene as effected by cyanide and ascorbate.

Horseradish peroxidase and H2O2 mediate N-hydroxy-N-acetyl-2-aminofluorene (N-OH-AAF) conversion into two more potent carcinogens, 2-nitrosofluorene and N-acetoxy-N-acetyl-2-aminofluorene. Optical studies of this system indicate that horseradish peroxidase is operating as a peroxidase with N-OH-AAF as the electron donor. Our studies confirm the earlier finding that 2-nitrosofluorene and N-acetoxy-N-acetyl-2-aminofluorene are the products of the type II enzyme-mediated oxidation of N-OH-AAF, but surprisingly, the results with the type VI enzyme indicate that more 2-nitrosofluorene was formed and, in addition, another product absorbing at 245 nm was formed. If ascorbate is present in the N-OH-AAF/horseradish peroxidase/H2O2 system, ascorbate is oxidized preferentially. Cyanide, a known inhibitor of the peroxidase, does not inhibit when N-OH-AAF is the electron donor. The reaction products are the same in the presence or absence of cyanide.

Lipid hydroperoxide activation of N-hydroxy-N-acetylaminofluorene via a free radical route.

The data presented here demonstrate that linoleic acid hydroperoxide in the presence of methemoglobin or hematin activated the carcinogen N-hydroxy-N-acetyl-2-amino-fluorene via the nitroxyl free radical intermediate into 2-nitrosofluorene and N-acetoxy-N-acetyl-2-aminofluorene. Ascorbate inhibited the activation, in which case the free radical intermediate was replaced by the ascorbate free radical. On the basis of optical kinetics, we have established that the rate of linoleic acid hydroperoxide decrease paraleled the rate of N-hydroxy-N-acetyl-2-aminofluorene decrease and also the rate of 2-nitrosofluorene increase. The stoichiometry of the reaction was such that, for every 2 linoleic acid hydroperoxide molecules consumed, 2 N-hydroxy-N-acetyl-2-aminofluorene molecules were oxidized and 1 2-nitrosofluorene and 1 N-acetoxy-N-acetyl-2 aminofluorene molecule was formed.

Inhibition by phenyl N-tert-butyl nitrone of early phase carcinogenesis in the livers of rats fed a choline-deficient, L-amino acid-defined diet.

Male Wistar rats were fed a choline-deficient, L-amino acid-defined (CDAA) diet alone or in combination with a nitrone-based free radical trapping agent, phenyl N-tert-butyl nitrone (PBN) in the drinking water at the concentrations of 0.013, 0.065, and 0.130% for 12 weeks. PBN inhibited the changes that are normally induced in the livers of rats by the CDAA diet feeding, i.e., development of putative preneoplastic lesions, proliferation of connective tissue, reduction of glutathione S-transferase activity, formation of 8-hydroxyguanine in DNA, and an increase in inducible cyclo-oxygenase (COX2) activity. PBN, however, did not prevent the increases in the COX2 mRNA or protein levels brought on by the CDAA diet These results indicate that the loss of glutathione S-transferase activity and COX2 induction may play significant roles in rat liver carcinogenesis by the CDAA diet and that PBN prevents neoplasia not only by its radical scavenging activity but also by inhibiting COX2 activity at the catalytic level.

Hydroxyl free-radical spin-adduct in rat brain synaptosomes. Observations on the reduction of the nitroxide.

Understanding the prevalence and action of hydroxyl free-radicals, damaging species in biological systems, is improved by spin-trapping techniques. The hydroxyl free-radical rapidly adds to the spin-trap 5,5-dimethyl-1-pyrroline-1-oxide (DMPO) to form a relatively stable nitroxyl free-radical spin-adduct (DMPO-OH), but it was found that DMPO-OH becomes diamagnetic, presumably by chemical reduction, when it is added to rat brain synaptosomes. DMPO-OH reduction by synaptosomes was a time-dependent process, starting immediately and continuing up to 20 min or more, when almost all the spin-adduct is reduced. During synaptosomal reduction, the electron paramagnetic resonance (EPR) high field line of DMPO-OH is broadened indicating restrictions on the motion of the nitroxide. This was not due to simple absorption of DMPO-OH to proteins. Experiments with the spin-adduct in glycerol at low temperatures showed that DMPO-OH experienced, during synaptosomal reduction, restricted motion having a correlation time of about 3.3 X 10(-9)s. This value would be expected if DMPO-OH was near the polar region of the hydrocarbon layer of a membrane bilayer. Synaptosomal membrane transport of DMPO-OH was tested by competition studies, since it was presumed that this nitroxide was transported and then reduced inside the synaptosomes. Several compounds tested, including amino acids, neurotransmitters, food dyes, and many others, that may have acted competitively in transport were not effective in slowing down reduction of DMPO-OH. However, it was found that azide, cyanide and heating of the synaptosomes markedly decreased the rate of synaptosomal reduction of DMPO-OH. Azide at 50 microM manifested one-half of its maximal inhibitory effect. Experiments with 1-octanol to obtain a measure of the membrane partition of DMPO-OH demonstrated that the octanol/water distribution was 1.83. Experiments with glass microfibre filtration to determine synaptosomal binding revealed that DMPO, as well as apparently DMPO-OH, were not specifically retained by synaptosomes. All of these results combined with past work on nitroxide reduction by biological systems, suggest that DMPO-OH reduction by synaptosomes is due to its interaction with and reduction by electron transport carriers of mitochondria within the synaptosomes.

Obligatory free radical intermediate in the oxidative activation of the carcinogen N-hydroxy-2-acetylaminofluorene.

We have demonstrated that the nitroxyl free radical form of the carcinogen N-hydroxy-2-acetylaminofluorene (OH-AAF) is an obligatory intermediate in the cumene hydroperoxide-hematin-induced oxidative activation of this carcinogen into 2-nitrosofluorene and N-acetoxy-2-acetylaminofluorene. Both the rate of N-OH-acetylaminofluorene oxidation and the amount of its nitroxyl free radical were experimentally observed as a function of reaction time. Rate equations were derived for a model in which the nitroxyl free radical form of OH-AAF was an obligatory intermediate in the reaction. Using this theory it was possible to compute one experimental variable, the rate of OH-AAF oxidation, utilizing the other experimental variable, the amount of nitroxyl free radical present at any time during the reaction. The theory also predicts a linear relationship between the rate of OH-AAF oxidation and the square of the free radical content; and this was found to be true experimentally. The dismutation rate constant of the nitroxyl free radical of OH-AAF was found to be 2.7-10(5) M-1-s-1.

Glutathione/Fe3+/O2-mediated DNA strand breaks and 8-hydroxydeoxyguanosine formation. Enhancement by copper, zinc superoxide dismutase.

Oxidative DNA damage reflected by the formation of 8-hydroxy-2'-deoxyguanosine (8-OH-dG) and strand breaks caused by a glutathione mixed-function oxidation system (GSH-MFO) comprised of Fe3+, O2, and glutathione as an electron donor was enhanced by copper, zinc superoxide dismutase (CuZnSOD) in a concentration-dependent manner. Unlike CuZnSOD, manganese SOD (MnSOD) as well as iron SOD (FeSOD) did not enhance either strand breaks or 8-OH-dH formation in DNA. The capacity of CuZnSOD to enhance damage to DNA was inhibited by 5,5-dimethyl-1-pyrroline N-oxide (DMPO), a spin trapping agent. The salicylate hydroxylation assay showed that hydroxyl radicals formed in the presence of the GSH-MFO system was increased by CuZnSOD. The GSH-MFO system caused the release of free copper from CuZnSOD. Based on these results, we interpret the effects of CuZnSOD on the GSH-MFO induced DNA damage as due to reactive oxygen species, probably .OH, formed by the reaction of free Cu2+, released from oxidatively damaged CuZnSOD, and H2O2 produced by the GSH-MFO system.

Hydroxyl free radical reactions with amino acids and proteins studied by electron spin resonance spectroscopy and spin-trapping.

It has recently been shown that Fe(I) complexes of ADP or ATP generate OH radicals with H2O2 in a Fenton-type reaction. The OH radicals can be detected by using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) as a spin trap in electron spin resonance spectroscopy. All the biologically occurring amino acids, some related compounds and several proteins (histone, bovine serum albumin, collagen) were tested as OH radical scavengers against DMPO. The tested compounds competed with DMPO in trapping OH radicals to various extents as shown by the decrease of signal intensity of DMPO-OH spin-adduct. The tested compounds did not oxidize Fe(II) itself, with the only exception being tyrosine, as revealed by properly designed ferrozine reaction. Some of the amino acids reacted also with the DMPO-OH spin-adduct to a certain extent, whereas others did not. The formation of carbon centered organic radicals of the amino acids could be detected under the influence of OH radicals by using the spin traps phenyl-tert-butylnitrone (PBN) and alpha-pyridyl-1-oxide-N-tert-butylnitrone (4-POBN). The proteins, however, did not react with these spin traps. One can conclude that the amino acids and proteins can be targets of OH radical damage even in vivo, and such phenomena may be of importance in the deterioration of the conformation of proteins, e.g., during aging or in some pathological processes.

Formation of long-lived hydroxyl free radical adducts of proline and hydroxyproline in a Fenton reaction.

Proline and hydroxyproline when exposed to the hydroxyl free radical generating system of ADP-Fe(II)-H2O2 yielded long-lived free radicals. An analysis of the electron paramagnetic resonance spectra of the long-lived hydroxyl free radical adducts of proline and hydroxyproline is consistent with a free electron on a nitroxyl group interacting with the nitrogen atom as well as with three separate protons. In the case of proline, nitroxide formation was observed under the influence of tert-butyl-hydroperoxide, giving a similar EPR spectrum (Lin, J.S., Tom, T.C. and Olcott, H.S. (1974) J. Agr. Food Chem. 22, 526-528); however, the hydroxyl free radical adduct of hydroxyproline has not been described yet. In the case of the proline nitroxide radical, two of the three protons involved interact with the free electron equivalently. The coupling constants for the hydroxyl free radical adduct of proline are AN = 1.58 mT, AH1 beta = AH2 beta = 2.13 mT, AH3 beta = 1.77 mT and for hydroxyproline are AN = 1.54 mT, AH1 beta = 2.56 mT, AH2 beta = 2.03 and AH3 beta = 1.51. The data are consistent with the amine nitrogen of proline and hydroxyproline being oxidized to a nitroxyl group and the free electron of the nitroxyl interacting with the beta-protons of these amino acid hydroxyl free radical adducts.

Thiol-dependent metal-catalyzed oxidation of copper, zinc superoxide dismutase.

Superoxide dismutase (SOD) is a key enzyme in the antioxidant system of the cells. When exposed to a metal-catalyzed oxidation (MCO) system composed of Fe3+, O2, and thiol as an electron donor copper, zinc SOD (CuZnSOD) was susceptible to oxidative modification and damage as indicated by the loss of activity, fragmentation and aggregation of peptide as well as by the formation of carbonyl groups. Oxidative damage to CuZnSOD was inhibited by diethylenetriaminepentaacetic acid as well as by free radical scavengers and spin-trapping agents. The results of the present study indicate that hydrogen peroxide may be generated from a thiol/Fe3+/O2 system and that hydroxyl free radicals, produced by metal-catalyzed Fenton reactions, may be the ultimate species mediating the SOD damage. Incubation with the MCO system resulted in the release of Cu ions from CuZnSOD. Incubation with the thiol-MCO did not significantly increase the formation of 2-oxohistidine in CuZnSOD. The lack of formation of 2-oxohistidine, as well as the pronounced preventive effect of spin-traps on the thiol-MCO-mediated damage to CuZnSOD, indicates that inactivation might actually be predominantly due to global oxidation rather than a site-specific oxidation. The thiol-MCO-mediated damage to SOD may result in the perturbation of cellular antioxidant defense mechanisms and subsequently lead to a pro-oxidant condition.

Studies on the effect of iron overload on rat cortex synaptosomal membranes.

Iron as ferrous ammonium sulfate was injected into the cerebral spinal fluid of rats. After three consecutive days of injection of 4 mumol of iron, the total iron content of brain cortex synaptosomes from the iron-treated animals was 2-fold higher than that from control animals receiving the saline vehicle only. Spin label studies of the synaptosomal membranes demonstrated that the lipid region of the membranes became more rigid and, in addition, the mobility of labeled SH groups of membrane proteins decreased after the iron treatment. The cholesterol content was significantly higher in iron-treated animals as compared to controls. Centrophenoxine pretreatment (100 mg/kg body weight daily for 6 weeks) diminished the iron effects. Synaptosomal membrane alterations observed after iron treatment were similar to changes observed previously during aging. This lends support to the notion that free-radical induced damage occurs in brain membranes with increasing age.

Spin-trapping of the trichloromethyl radical produced during enzymic NADPH oxidation in the presence of carbon tetrachloride or bromotrichloromethane.

Utilizing the spin-trapping agent phenyl-t-butyl nitrone, a free radical has been detected which is produced from carbon tetrachloride or bromotrichloromethane during the enzymic oxidation of NADPH by rat liver microsomes. The presence of NADPH is obligatory for generation of the radical. The formation of the trichloromethyl radical-phenyl-t-butyl nitrone adduct is an enzymic process, as evidenced by the inhibition of its formation in systems containing heated microsomes and in systems containing p-hydroxymercuribenzoate. A computer-simulated ESR spectrum for the trichloromethyl adduct of phenyl-t-butyl nitrone can reproduce the essential features of the spectrum of the spin-trapped radical produced enzymically from CCl4. A mechanism is proposed for the formation of the trichloromethyl radical from CCl4 or BrCCl3.

Biomarkers of oxidative stress study II: are oxidation products of lipids, proteins, and DNA markers of CCl4 poisoning?

Oxidation products of lipids, proteins, and DNA in the blood, plasma, and urine of rats were measured as part of a comprehensive, multilaboratory validation study searching for noninvasive biomarkers of oxidative stress. This article is the second report of the nationwide Biomarkers of Oxidative Stress Study using acute CCl4 poisoning as a rodent model for oxidative stress. The time-dependent (2, 7, and 16 h) and dose-dependent (120 and 1200 mg/kg i.p.) effects of CCl4 on concentrations of lipid hydroperoxides, TBARS, malondialdehyde (MDA), isoprostanes, protein carbonyls, methionine sulfoxidation, tyrosine products, 8-hydroxy-2'-deoxyguanosine (8-OHdG), leukocyte DNA-MDA adducts, and DNA-strand breaks were investigated to determine whether the oxidative effects of CCl4 would result in increased generation of these oxidation products. Plasma concentrations of MDA and isoprostanes (both measured by GC-MS) and urinary concentrations of isoprostanes (measured with an immunoassay or LC/MS/MS) were increased in both low-dose and high-dose CCl4-treated rats at more than one time point. The other urinary markers (MDA and 8-OHdG) showed significant elevations with treatment under three of the four conditions tested. It is concluded that measurements of MDA and isoprostanes in plasma and urine as well as 8-OHdG in urine are potential candidates for general biomarkers of oxidative stress. All other products were not changed by CCl4 or showed fewer significant effects.

Age effect on brain pH during ischemia/reperfusion and pH influence on peroxidation.

Older gerbils are more sensitive to ischemia/reperfusion injury (IRI) than younger ones. Utilizing 31P-NMR to monitor in vivo pH and high energy phosphates of brain cortex undergoing an IRI showed that cortical intracellular pH decreased to 6.35 after ischemia and then increased with reperfusion, but older gerbils required significantly more time to recover than younger animals. Brain high energy phosphates dropped during ischemia but rebounded within 20 min reperfusion in younger gerbil brain but remained significantly lower in older gerbil brain for 50 min. These data suggest that IRI-induced brain acidification may enhance oxidative damage. In an in vitro system it was shown in both young and old brain homogenate that peroxidation rate increased when the pH of the incubation medium was decreased from 7.4 to 6.4. This was true in the presence or absence of an ADP/Fe/Ascorbate system in both young and old brain homogenate. Enhancement of peroxidation rate by ADP/Fe/Ascorbate addition was much more pronounced at pH 7.4 (30- to 40-fold increase) as compared to pH 6.4 (7.8- to 9.5-fold increase). This data can be interpreted to indicate that the lower pH makes endogenous Fe more available to catalyze oxidative damage. The fact that brain pH and high energy phosphates remain lower in older gerbil brains during IRI suggests that brain mitochondria from older animals are less capable of responding to a large oxidative stress brought on by an IRI.(ABSTRACT TRUNCATED AT 250 WORDS)

Neuroinflammatory processes are important in neurodegenerative diseases: an hypothesis to explain the increased formation of reactive oxygen and nitrogen species as major factors involved in neurodegenerative disease development.

The hypothesis, as stated in the title, has arisen from the failure of simpler notions to explain a series of otherwise difficult to understand observations and the mounting evidence, in a broader sense, that inflammatory processes in the CNS are important etiologically in neurodegenerative diseases. Novel aspects include the primacy of inflammatory processes, within the CNS, which leads to increased formation of "proinflammatory" cytokines that lead to increased formation of reactive oxygen species (ROS) and mediation of the upregulation of genes that produce toxic products such as reactive nitrogen species (RNS). Here I utilize important background reports and synthesize ideas to help account for the noted increases in ROS and RNS and their biological reaction products in neurodegenerative diseases. The uniqueness of the CNS inflammatory processes include minimal damping of amplification processes, such as proinflammatory cytokine-mediated cascades, combined with unique genetic defects, that act in combination with other risk factors to repeatedly "spark" the inflammatory cascades to account for some of the major differences in neurodegenerative diseases. This hypothesis can be experimentally examined by development of definitive methods to quantitate unique products that are formed by processes predicted to occur under neurodegenerative conditions.