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The marginalization of hormesis.

Despite the substantial development and publication of highly reproducible toxicological data, the concept of hormetic dose-response relationships was never integrated into the mainstream of toxicological thought. Review of the historical foundations of the interpretation of the bioassay and assessment of competitive theories of dose-response relationships lead to the conclusion that multiple factors contributed to the marginalization of hormesis during the middle and subsequent decades of the 20th Century. These factors include the following: (a) the close association of hormesis with homeopathy, which led to the hostility of modern medicine toward homeopathy, thereby creating a guilt-by-association framework, and the carryover influence of that hostility toward hormesis in the judgements of medically based pharmacologists/toxicologists; (b) the emphasis of high-dose effects linked with a lack of appreciation of the significance of the implications of low-dose stimulatory effects; (c) the lack of an evolution-based mechanism(s) to account for hormetic effects; and (d) lack of appropriate scientific advocates to counter aggressive and intellectually powerful critics of the hormetic perspective.

Animals↗

Quantitative analysis of cell-type specific gene expression in the green alga Volvox carteri.

BACKGROUND: The multicellular alga Volvox carteri possesses only two cell types: mortal, motile somatic cells and potentially immortal, immotile reproductive cells. It is therefore an attractive model system for studying how cell-autonomous cytodifferentiation is programmed within a genome. Moreover, there are ongoing genome projects both in Volvox carteri and in the closely related unicellular alga Chlamydomonas reinhardtii. However, gene sequencing is only the beginning. To identify cell-type specific expression and to determine relative expression rates, we evaluate the potential of real-time RT-PCR for quantifying gene transcript levels. RESULTS: Here we analyze a diversified pool of 39 target genes by real-time RT-PCR for each cell type. This gene pool contains previously known genes with unknown localization of cellular expression, 28 novel genes which are described in this study for the first time, and a few known, cell-type specific genes as a control. The respective gene products are, for instance, part of photosynthesis, cellular regulation, stress response, or transport processes. We provide expression data for all these genes. CONCLUSION: The results show that quantitative real-time RT-PCR is a favorable approach to analyze cell-type specific gene expression in Volvox, which can be extended to a much larger number of genes or to developmental or metabolic mutants. Our expression data also provide a basis for a detailed analysis of individual, previously unknown, cell-type specifically expressed genes.

Algal Proteins↗

High mobility group A2 is a target for miRNA-98 in head and neck squamous cell carcinoma.

BACKGROUND: HMGA2 expression has been shown to be associated with enhanced selective chemosensitivity towards the topoisomerase (topo) II inhibitor, doxorubicin, in cancer cells. Although the roles of signaling cascades and proteins as regulatory factors in development, neoplasia and adaptation to the environment are becoming well established, evidence for the involvement of regulatory small RNA molecules, such as microRNAs (miRNAs) as important regulators of both transcriptional and posttranscriptional gene silencing is presently mounting. RESULTS: Here we report that HMGA2 expression in head and neck squamous cell carcinoma (HNSCC) cells is regulated in part by miRNA-98 (miR-98). Albeit HMGA2 is associated with enhanced selective chemosensitivity towards topoisomerase (topo) II inhibitor, doxorubicin in HNSCC, the expression of HMGA2 is thwarted by hypoxia. This is accompanied by enhanced expression of miRNA-98 and other miRNAs, which predictably target HMGA2. Moreover, we show that transfection of pre-miR-98trade mark during normoxia diminishes HMGA2 and potentiates resistance to doxorubicin and cisplatin. These findings implicate the role of a miRNA as a key element in modulating tumors in variable microenvironments. CONCLUSION: These studies validate the observation that HMGA2 plays a prominent role in governing genotoxic responses. However, this may only represent cells growing under normal oxygen tensions. The demonstration that miRNA profiles are altered during hypoxia and repress a genotoxic response indicates that changes in microenvironment in eukaryotes mimic those of lower species and plants, where, for example, abiotic stresses regulate the expression of thousands of genes in plants at both transcriptional and posttranscriptional levels through a number of miRNAs and other small regulatory RNAs.

Base Sequence↗

Gene expression profiling of human cancers.

DNA microarrays allow us to visualize simultaneously the expression of potentially all genes within a cell population or tissue sample-revealing the "transcriptome." The analysis of this type of data is commonly called "gene expression profiling" (GEP) because it provides a comprehensive picture of the pattern of gene expression in a particular biological sample. For this reason microarrays are revolutionizing life sciences research and are leading to the development of novel and powerful methods for investigating cancer biology, classifying cancers, and predicting clinical outcome of cancers. Several recent high-profile reports have revealed how clustering of GEP data can clearly identify clinically (and prognostically) important subtypes of cancer among patients considered by established clinicopathological criteria to have similar tumors. Accurate "prognostic signatures" can be obtained from GEP data, which represent relatively small numbers of genes. These signatures can be valuable in directing appropriate treatment and in predicting clinical outcome, and they generally outperform other systems based on clinical and histological criteria. In this paper the basic principles of DNA microarray technology and the different types of microarray platforms available will be introduced, and the power of the technique will be illustrated by reviewing some recent GEP studies on selected cancers, including a preliminary analysis of hepatocellular carcinoma from our Palermo laboratory. GEP is likely to be adopted in the future as a key decision-making tool in the clinical arena. However, several issues relating to data analysis, reproducibility, cross-comparability, validation, and cost need to be resolved before the technology can be adopted broadly in this context.

Carcinoma, Hepatocellular↗

Assessment of cognition in Parkinson's disease.

OBJECTIVE: To develop a short, practical instrument that is sensitive to the specific cognitive deficits in Parkinson's disease (PD) for comparing groups in research situations and for assessing change in cognitive functioning over time. METHODS: A literature search was conducted to identify the most frequently affected cognitive domains in PD and to select candidate items for the initial scale. This scale was tested in 85 patients and 75 age-, education-, and sex-matched control subjects. Items that met predefined criteria for data quality, reproducibility, and discriminative properties were included in the final scale. RESULTS: The final scale, the SCOPA-COG (SCales for Outcomes of PArkinson's disease-cognition), consists of 10 items with a maximum score of 43, with higher scores reflecting better performance. The test-retest reliability of the total score was 0.78 (intraclass correlation coefficient) and ranged from 0.40 to 0.75 for individual items (weighted kappa). Cronbach's alpha was 0.83. Construct validity of the scale was supported by the expected correlations with the CAMCOG (Cambridge Cognitive Examination) and the Mini-Mental State Examination (MMSE) and by differences found between groups of participants classified by dementia status and between patients grouped by disease severity. The scale showed a clear trend toward lower cognition scores for patients with more advanced PD. The coefficient of variation of the SCOPA-COG was higher than that of the CAMCOG or the MMSE, indicating a better ability to detect differences between individuals. CONCLUSION: The SCOPA-COG is a short, reliable, and valid instrument that is sensitive to the specific cognitive deficits in PD.

Aged↗

Photodynamic therapy for intracranial neoplasms: development of an image-based computer-assisted protocol for photodynamic therapy of intracranial neoplasms.

Photodynamic therapy is being studied as an adjuvant therapy for malignant gliomas. Therapeutic efficacy is based on photosensitizer uptake kinetics and the ability to deliver adequate light doses to an appropriate treatment volume at the optimal time. Our laboratory has developed an image-based, computer-assisted treatment-planning protocol to study the treatment variables leading to optimizing photodynamic therapy for intracranial neoplasms. Fifteen patients with recurrent malignant glial tumors underwent 16 treatments in the developmental phase of the project in which light treatment volume was progressively expanded. Group I (n = 4) received postresection intracavitary photoillumination only, Group II (n = 3) received limited interstitial/intracavitary photoillumination, and Group III (n = 9) received multiple interstitial/intracavitary photoillumination. Between 3 and 18 interstitial fiber probes were placed through optically lucent tumor access catheters. Computed three-dimensional image-based treatment planning provided reproducible data-based tumor volumes, treatment volumes, and stereotactic accuracy for tumor volume resection and interstitial light fiber insertion. Initial observations include: 1) treatment failures occur outside of the effective light treatment volumes; 2) effective light volumes can be expanded safely with multiple stereotactically implanted interstitial light fibers; and 3) optimal treatment involves individualized tailoring of light dose volume and geometry. This protocol allows standardized scientific study of the variables affecting the application of photodynamic therapy for intracranial neoplasms.

Adult↗

Predicting solubility of anthracene in non-aqueous solvent mixtures using a combination of Jouyban-Acree and Abraham models.

Quantitative structure property relationships were proposed to calculate the binary interaction terms of the Jouyban-Acree model using coefficients of Abraham solvational models. The applicability of the proposed methods for reproducing solubility data of anthracene in binary solvents has been evaluated using 56 solubility data sets collected from the literature. The mean percentage deviation (MPD) of experimental and calculated solubilities, using predicted mole fraction solubility of anthracene in solvents 1 and 2, has been computed as a measure of accuracy and the MPD of the proposed methods were 5.5 and 4.2%. The accuracy of the method was compared with that of a previously reported method where the MPD was 14.4% and the mean differences between proposed and previous methods was statistically significant. To provide a predictive model, solubility of anthracene was computed using Abraham solvational models and employed to predict the solubility in binary solvents using derived model constants of Jouyban-Acree model and the obtained MPDs were 37.9 and 22.2%, respectively.

Algorithms↗

Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms.

We present a new microRNA target prediction algorithm called TargetBoost, and show that the algorithm is stable and identifies more true targets than do existing algorithms. TargetBoost uses machine learning on a set of validated microRNA targets in lower organisms to create weighted sequence motifs that capture the binding characteristics between microRNAs and their targets. Existing algorithms require candidates to have (1) near-perfect complementarity between microRNAs' 5' end and their targets; (2) relatively high thermodynamic duplex stability; (3) multiple target sites in the target's 3' UTR; and (4) evolutionary conservation of the target between species. Most algorithms use one of the two first requirements in a seeding step, and use the three others as filters to improve the method's specificity. The initial seeding step determines an algorithm's sensitivity and also influences its specificity. As all algorithms may add filters to increase the specificity, we propose that methods should be compared before such filtering. We show that TargetBoost's weighted sequence motif approach is favorable to using both the duplex stability and the sequence complementarity steps. (TargetBoost is available as a Web tool from http://www.interagon.com/demo/.).

5' Untranslated Regions↗

Data quality in predictive toxicology: reproducibility of rodent carcinogenicity experiments.

We compared 121 replicate rodent carcinogenicity assays from the two parts (National Cancer Institute/National Toxicology Program and literature) of the Carcinogenic Potency Database (CPDB) to estimate the reliability of these experiments. We estimated a concordance of 57% between the overall rodent carcinogenicity classifications from both sources. This value did not improve substantially when additional biologic information (species, sex, strain, target organs) was considered. These results indicate that rodent carcinogenicity assays are much less reproducible than previously expected, an effect that should be considered in the development of structure-activity relationship models and the risk assessment process.

Animals↗

Use of the enzyme-linked immunosorbent assay (ELISA) in immunotoxicity testing.

Based on an earlier described macromethod for the routine measurement of IgM and IgG in rat sera, a mechanized micro enzyme-linked immunosorbent assay (ELISA) was developed. The assay was performed in the wells of microtiter plate thus minimizing the quantities of reagents and antisera needed. Data on reproducibility of the assay and calculation of IgM and IgG levels are provided. For the functional assessment of the humoral immunity of the rat, ELISA is a powerful tool. In an earlier report, assays for the titration of thymus-independent IgM antibodies to E. coli LPS and the IgM and IgG response to the thymus-dependent antigen tetanus toxoid were described. More recently it was shown that the antigen ovalbumin elicits a thymus-dependent IgM, IgG and IgE response which could be readily measured with the enzyme immunoassay, as well as a delayed-type hypersensitivity reaction. As the optimum ovalbumin concentration for both types of reactions was the same, it is concluded that the ovalbumin model offers the advantage that both humoral and cellular immunity can be studies simultaneously in the same animal.

Animals↗

The nutrition of active muscle flaps.

In the last 25 years, techniques utilising muscle flaps to perform mechanical work have become part of the reconstructive surgeon's repertoire. In this paper, these techniques and the particular physiological challenges faced by active flaps are discussed and a sub-classification of muscle flaps into passive and active is proposed. A series of experiments are described that were designed to compare local pO(2) and gaseous perfusion, at multiple sites in pedicled tibialis anterior muscle flaps and controls, using specially developed dual amperometric microelectrodes, in an in vivo rabbit model. No significant difference in perfusion was found comparing flaps and controls until the flap's vascular pedicles were divided and ligated, and then flap perfusion fell to zero. Flap and control oxygenation varied significantly only during mobilisation and again, after pedicle division and ligation (F[13,55] = 12.3; P < 0.001)]. This absence of functional ischaemia as a consequence of mobilisation in the model used suggests the practice of delaying electrical conditioning of muscle flaps in dynamic cardiomyoplasty and neoanal sphincteroplasty might be unnecessary if these data are reproduced in human latissimus dorsi muscle. The relevance of these findings to free flap oxygen consumption and to the delay phenomenon is discussed.

Animals↗

Computerized morphometric analysis of pathological prion protein deposition in scrapie-infected hamster brain.

Transmissible spongiform encephalopathies (TSEs or prion diseases) are characterized by a constellation of typical though variable pathological changes in the brain. Deposition of disease-associated abnormal prion protein (PrP(Sc)) is the pathological feature of TSEs most consistent and accessible for quantification. However, the evaluation of PrP(Sc) deposits detected by immunohistochemical techniques has been traditionally based on arbitrarily assigned semiquantitative scores. This approach is limited by its subjectivity and bias, yielding considerable variability. In this study, we used MetaMorph 6.1 image analysis software for quantitative analysis of immunostained PrP(Sc) deposits in the CNS of hamsters infected with the 263K strain of scrapie agent. Computerized morphometric analysis (CMA) allowed unambiguous detection of even minimal amounts of immunostained PrP(Sc). CMA values for intensity of staining and area stained correlated well with semiquantitative scores, providing reproducible quantitative data and objective criteria for analyzing PrP(Sc) deposition. CMA provides a simple and reliable method for improved and consistent diagnosis of TSEs that may also be used to quantify other immunostained biomarkers.

Animals↗

Bioconversion of cellulose into ethanol by nonisothermal simultaneous saccharification and fermentation.

The kinetic characteristics of cellulase and beta-glucosidase during hydrolysis were determined. The kinetic parameters were found to reproduce experimental data satisfactorily and could be used in a simultaneous saccharification and fermentation (SSF) system by coupling with a fermentation model. The effects of temperature on yeast growth and ethanol production were investigated in batch cultures. In the range of 35-45 degrees C, using a mathematical model and a computer simulation package, the kinetic parameters at each temperature were estimated. The appropriate forms of the model equation for the SSF considering the effects of temperature were developed, and the temperature profile for maximizing the ethanol production was also obtained. Briefly, the optimum temperature profile began at a low temperature of 35 degrees C, which allows the propagation of cells. Up to 10 h, the operating temperature increased rapidly to 39 degrees C, and then decreased slowly to 36 degrees C. In this nonisothermal SSF system with the above temperature profile, a maximum ethanol production of 14.87 g/L was obtained.

Bioreactors↗

Determination of gangliosides in human cerebrospinal fluid by high-performance thin-layer chromatography and direct densitometry.

A method for the separation and quantification of a complex ganglioside mixture from a clinically available amount (5 ml) of human cerebrospinal fluid (CSF) is described. After reduction of the CSF volume by ultrafiltration, gangliosides are extracted with methanol/chloroform, then separated and quantified by high performance thin layer chromatography (HPTLC) and direct densitometry. For purification of crude ganglioside extract, the method of choice was microdialysis against water. Recovery for the present method including all methodological steps was 78%. No delective loss of gangliosides was demonstrated. The CSF ganglioside pattern from 'normal' CSF samples resembles that of brain gangliosides, particularly cerebellum gangliosides. Based on chromatographic comparison with standards, the percentages of lipid-bound NeuAc-positive fractions were: GM1 = II3NeuAc-GgOse4Cer (3%), GD3 = II3NeuAc2-Lac-Cer (3%), GD1a = IV3NeuAc,II3NeuAc-GgOse4Cer (15%), X1 (3%), GD1b = II3(NeuAc)2-GgOse4Cer (16%), X2 (3%), GT1b = IV3NeuAc,II3NeuAc2-GgOse4-Cer (41%), and GQ1b = IV3NeuAc2-,II3NeuAc2-GgOse4-Cer (16%). The total ganglioside content varied between 616-944 micrograms/l. Within-run and between-run assay precision (relative standard deviation) for 'normal' pooled CSF ranged from 0.04 to 0.12 for the predominant CSF ganglioside fractions (GD1a, GD1b, GT1b, GQ1b), and from 0.13 to 0.23 for the less pronounced fractions (GM1, GD3).

Adult↗

The use of liquid chromatography-mass spectrometry for the identification and quantification of urinary iminodipeptides in prolidase deficiency.

It has been reported that the urine of patients with prolidase deficiency contains various iminodipeptides with a carboxyl-terminal proline (hydroxyproline). These iminodipeptides have hitherto been detected indirectly by acid hydrolysis or enzymatic digestion, followed by amino acid analysis. In the present study, it was shown that X-Pro could be distinguished from Pro-X when the iminodipeptides were analysed directly by liquid chromatography coupled with atmospheric pressure ionization mass spectrometry (LC/API-MS), with scanning of the protonated molecule ions ([M+H]+). The same procedure also successfully quantified urinary iminodipeptides from patients with prolidase deficiency. A quantitative investigation of two siblings with prolidase deficiency revealed that the patient with severe clinical symptoms excreted more iminodipeptides than the other who did not have serious symptoms. LC/API-MS also revealed iminodipeptides (Gly-Hyp and Pro-Hyp) in the urine of the mother of the patients and in normal volunteers. Patients excreted much more Pro-Hyp than normal volunteers, whereas no quantitative differences were found between the mother and controls. In patients, the excretion of large quantities of X-Pro is due to their very low prolidase activity towards this type of substrate. In the erythrocytes of patients, prolidase activity towards X-Hyp was extremely low; even in the mother and normal volunteers, it was remarkably low in comparison with the activity against X-Pro.

Amino Acid Sequence↗

[Characteristics of care to patients with stroke in a secondary hospital].

OBJECTIVE: To describe the assistance profile of stroke patients accomplished in Hospital Universitário of University of São Paulo (HU-USP), by the Internal Medicine team of the Emergency Room, as being a standard of non-tertiary hospital. METHOD: Retrospective analysis of 228 patients with cerebrovascular disease, assisted from 1989 to 1993. RESULTS: We found the following subgroup distribution: 53% of patients had ischemic strokes, 26%, had hemorrhagic strokes, 2% had association from both and 19% were not classified. Among risk factors, we found an incidence of 67,5% for arterial hypertension; 24.6% for cardiac disease (chronic atrial fibrillation being the most frequent); diabetes occurred in 20.2% of cases. Among complications, coma was present in 22.4% of cases; respiratory insufficiency occurred in 15%; infection, in 29%. Death rate was 14. 5%. Average permanence in hospital was 4.11 days. CONCLUSIONS: The epidemiological aspects and complications reproduced the data described in the literature. Some negative aspects were inadequacy of accommodations and the great incidence of pulmonary infections. However, the mortality rate was comparable to the lowest found in literature.

Adult↗

Modeling organic carbon dynamics and cadmium fate in long-term sludge-amended soil.

A model is described that may help to resolve uncertainty and controversy over the long-term consequences of sludge applications to arable land, especially with regard to the effects of sludge adsorption characteristics on trace metal solubility and bioavailability (e.g., the sludge "time bomb" or sludge "protection" hypotheses). Mass balances of organic and inorganic material derived from sludge and crop residues are simulated. Each pool has a potentially different adsorption affinity for trace metals, and this leads to changes in the adsorption capacity of sludge-amended soil that influence leaching and crop uptake. Model simulations were compared with measured changes in organic carbon and ethylenediaminetetraacetic acid (EDTA)-extractable cadmium contents in a clay loam soil following 41 years of sludge applications. The model adequately reproduced the data, although discrepancies in the vertical distribution of Cd were attributed to the effects of macropore transport and root-uptake driven recirculation. A Monte Carlo sensitivity analysis demonstrated that the most important parameters affecting leaching and crop uptake were the Cd loading and parameters controlling adsorption, especially the partition coefficient for sludge-derived inorganic material and the exponent regulating the effect of pH on sorption. Scenario simulations show that no general conclusions can be drawn with respect to the validity of the sludge "time bomb" and sludge "protection" hypotheses. Either may occur, or neither, depending on three key system parameters: the ratio of sludge adsorption capacity to the initial adsorption capacity of the soil, the proportion of the sludge adsorption capacity contributed by the inorganic fraction, and the sludge Cd loading.

Cadmium↗