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Biomedical subjects

A M Edwards

Publications and source records attributed to A M Edwards.

At least 19 recordsLinked to original sources
PubMed2006

Gene expression profiling of acute liver stress during living donor liver transplantation.

During liver transplantation, the donor graft is subjected to a number of acute stresses whose molecular basis is not well-understood. The effects of surgical stress, preservation and reperfusion injury were studied in 24 consecutive living donor liver transplant (LDLT) operations. Liver biopsies were taken early in the donor operation (OPENING), after transection of the donor liver (PRECLAMP) and following implantation of the graft (post hepatic artery, [PHA]); these were evaluated for histology, tissue glutathione content and gene expression using a 19K-human cDNA microarray. LDLT was associated with an ischemia/reperfusion injury, with accumulation of small numbers of neutrophils and decreased glutathione in the PHA biopsies. Following reperfusion, the expression of 129 genes increased and 106 genes decreased when compared to OPENING levels (> or <2-fold, p < 0.01). By real-time PCR a subset of 25 genes was verified (15 increased, 10 decreased). These genes were similarly altered in another condition of acute liver stress (the response to brain-death), but not in three chronic liver disease states (HCV, HBV and PBC). This study has identified a set of genes whose expression is altered in acute, but not chronic, liver stress, likely to play a central role in the pathogenesis of acute liver injury of liver transplantation.

Adult↗
PubMed2006

Thermoregulatory observations in soccer match play: professional and recreational level applications using an intestinal pill system to measure core temperature.

BACKGROUND: Technological limitations associated with oesophageal and rectal temperature probes have previously limited match play observations of body temperature. OBJECTIVE: To investigate the application of an intestinal pill system to measure core temperature during dynamic, field based, soccer matches. METHODS: Core temperature (T(c)) was assessed using the intestinal pill system (CorTemp 2000) and changes in plasma volume were calculated using the values for haemoglobin and packed cell volume obtained before and after recreational (n = 8) and the professional soccer (n = 7) matches. RESULTS: In the recreational match, there were significant post-match reductions in body mass (-1.6%, p<0.05) and plasma volume (-7.2%, p<0.01). Significant increases were observed in T(c) from rest to half time (p<0.01) and from half time to full time (p<0.05). In the professional match, body mass decreased by 1.9% (p<0.05) and plasma volume by 11.6% (p<0.01). T(c) increased from rest to half time (p<0.01) but was unchanged from half time to full time. Significant associations were observed between maximum oxygen consumption and match play heart rates in the second half of each match but these were not related to changes in plasma volume or T(c). CONCLUSIONS: Intestinal temperature proved a useful method of recording core temperature during soccer match play and assisted in the measurement of alterations in thermoregulatory variables in response to both professional and recreational level soccer matches; however, technological limitations still restrict the wider application of this method, especially at a competitive level.

Adolescent↗
PubMed2005

Efficacy and acceptability of a new topical skin lotion of sodium cromoglicate (Altoderm) in atopic dermatitis in children aged 2-12 years: a double-blind, randomized, placebo-controlled trial.

BACKGROUND: Atopic dermatitis (AD) is a common inflammatory allergic disease of children. The primary anti-inflammatory therapy is topical steroids. An effective treatment without the topical and systemic adverse effects of corticosteroids would be useful. Topical formulations of sodium cromoglicate have been researched in the past, but without consistent results. We report a trial of a new aqueous skin lotion of sodium cromoglicate (Altoderm) in children with AD. OBJECTIVES: To compare the efficacy, safety and acceptability of Altoderm lotion with a placebo control in the treatment of AD in children. METHODS: A double-blind, controlled study in which children aged 2-12 years with AD were randomized to 12 weeks of treatment with a lotion containing 4% sodium cromoglicate (Altoderm) or the lotion base. To be included subjects had to have a SCORAD score of > or = 25 and < or = 60 at both of two clinic visits 14 days apart. Subjects continued using existing treatment which included emollients and topical steroids. The primary outcome was the change in the SCORAD score. The two groups were compared for the change in the SCORAD score from the second baseline visit to the visit after 12 weeks of treatment using an analysis of variance. Secondary outcome measures included parents' assessment of symptoms, usage of topical steroids recorded on daily diary cards, and final opinions of treatment by parent and clinician. Parents were asked about adverse effects at each clinic visit and the responses recorded. RESULTS: Fifty-eight children were randomized to Altoderm and 56 to placebo and all were included in the intention-to-treat analysis. The mean +/- SD SCORAD scores at baseline were 41.0 +/- 9.0 (Altoderm) and 40.4 +/- 8.73 (placebo). These scores were reduced after 12 weeks by 13.2 (36%) with Altoderm and by 7.6 (20%) with placebo. The difference of 5.6 (95% confidence interval 1.0-10.3) is statistically significant (P = 0.018). Diary card symptoms improved with both treatments but the improvement was greater in the Altoderm-treated patients. Topical steroid usage was reduced in both groups and was larger in the Altoderm-treated patients. The differences were statistically significant for the mean of all symptoms, the overall skin condition and use of topical steroids. Those for itching and sleep loss were not. Treatment-related adverse events were reported in 11 subjects (Altoderm seven, placebo four). Most of these referred to irritation, redness and burning at the site of application. There were four reports of erythema and pruritus (Altoderm three, placebo one), and three reports of application site burning (Altoderm two, placebo one). None was reported as severe or very severe. CONCLUSIONS: These results show a clinically useful benefit of this sodium cromoglicate lotion in children with moderately severe AD.

Administration, Cutaneous↗
PubMed2004

Oxygen uptake kinetics and maximal aerobic power are unaffected by inspiratory muscle training in healthy subjects where time to exhaustion is extended.

The aim of this study was to determine whether 4 weeks of inspiratory muscle training (IMT) would be accompanied by alteration in cardiopulmonary fitness as assessed through moderate intensity oxygen uptake (V(.)O(2)) kinetics and maximal aerobic power (V(.)O(2max)). Eighteen healthy males agreed to participate in the study [training group (Tra) n=10, control group (Con) n=8]. Measurements of spirometry and maximal static inspiratory mouth pressure ( PI(max)) were taken pre- and post-training in addition to: (1) an incremental test to volitional exhaustion, (2) three square-wave transitions from walking to running at a moderate intensity (80% ventilatory threshold) and (3) a maximal aerobic constant-load running test to volitional fatigue for the determination of time to exhaustion ( T(lim)). Training was performed using an inspiratory muscle trainer (Powerbreathe). There were no significant differences in spirometry either between the two groups or when comparing the post- to pre-training results within each group. Mean PI(max) increased significantly in Tra ( P<0.01) and showed a trend for improvement ( P<0.08) in Con. Post-training T(lim) was significantly extended in both Tra [232.4 (22.8) s and 242.8 (20.1) s] ( P<0.01) and Con [224.5 (19.6) and 233.5 (12.7) s] ( P<0.05). Post-training T(lim) was significantly extended in Tra compared to Con ( P<0.05). In conclusion, the most plausible explanation for the stability in V(.)O(2) kinetics and V(.)O(2max) following IMT is that it is due to insufficient whole-body stress to elicit either central or peripheral cardiopulmonary adaptation. The extension of post-training T(lim) suggests that IMT might be useful as a stratagem for producing greater volumes of endurance work at high ventilatory loads, which in turn could improve cardiopulmonary fitness.

Adaptation, Physiological↗
PubMed2003

From tooth to hoof: treponemes in tissue-destructive diseases.

With the advent of new molecular and immunological tools, there is better understanding of the roles that difficult to cultivate bacteria, and not-yet-cultivated bacteria such as spirochaetes, play in polymicrobial diseases. Only relatively recently have studies implicated Treponema spirochaetes in human periodontal disease, a destructive condition of the tissues supporting the teeth. A number of different Treponema species have been isolated and their surface protein components that mediate adhesion, cytotoxicity, and tissue damage have been characterized. More recently Treponema strains closely related to human oral isolates have been cultivated from active lesions of digital dermatitis, an ulcerative condition affecting the feet of cows and sheep. This condition, like periodontal disease, appears to have a polymicrobial aetiology in which enrichment for Treponema may play a crucial part. This article reviews the known mechanisms by which Treponema interact with eukaryotic host cells and tissue proteins, and how these interactions may contribute to pathogenic diversity.

Animals↗
PubMed2003

Test performance indicators from a single soccer specific fitness test differentiate between highly trained and recreationally active soccer players.

AIM: The aim of this study was to investigate whether a single soccer specific fitness test (SSFT) could differentiate between highly trained and recreationally active soccer players in selected test performance indicators. METHODS SUBJECTS: 13 Academy Scholars (AS) from a professional soccer club and 10 Recreational Players (RP) agreed to participate in this study. Test 1--VO(2) max was estimated from a progressive shuttle run test to exhaustion. Test 2--The SSFT was controlled by an automated procedure and alternated between walking, sprinting, jogging and cruise running speeds. Three activity blocks (1A, 2A and 3A) were separated by 3 min rest periods in which blood lactate samples were drawn. The 3 blocks of activity (Part A) were followed by 10 min of exercise at speeds alternating between jogging and cruise running (Part B). RESULTS: Estimated VO(2) max did not significantly differ between groups, although a trend for a higher aerobic capacity was evident in AS (p<0.09). Exercising heart rates did not differ between AS and RP, however, recovery heart rates taken from the 3 min rest periods were significantly lower in AS compared with RP following blocks 1A (124.65 b x min(-1) +/-7.73 and 133.98 b x min(-1) +/-6.63), (p<0.05) and 3A (129.91 b x min(-1) +/-10.21 and 138.85 b x min(-1) +/-8.70), (p<0.01). Blood lactate concentrations were significantly elevated in AS in comparison to RP following blocks 2A (6.91 mmol x l(-1) +/-2.67 and 4.74 mmol x l(-1) +/-1.28) and 3A (7.18 mmol x l(-1) +/-2.97 and 4.88 mmol x l(-1) +/-1.50), (p<0.05). AS sustained significantly faster average sprint times in block 3A compared with RP (3.18 sec +/-0.12 and 3.31 sec +/-0.12), (p<0.05). CONCLUSION: The results of this study show that highly trained soccer players are able to sustain, and more quickly recover from, high intensity intermittent exercise.

Adolescent↗
PubMed2002

A comparison of two time-domain analysis procedures in the determination of .VO(2) kinetics by pseudorandom binary sequence exercise testing.

The purpose of this study was to apply and compare two time-domain analysis procedures in the determination of oxygen uptake (.VO(2)) kinetics in response to a pseudorandom binary sequence (PRBS) exercise test. PRBS exercise tests have typically been analysed in the frequency domain. However, the complex interpretation of frequency responses may have limited the application of this procedure in both sporting and clinical contexts, where a single time measurement would facilitate subject comparison. The relative potential of both a mean response time (MRT) and a peak cross-correlation time (PCCT) was investigated. This study was divided into two parts: a test-retest reliability study (part A), in which 10 healthy male subjects completed two identical PRBS exercise tests, and a comparison of the .VO(2) kinetics of 12 elite endurance runners (ER) and 12 elite sprinters (SR; part B). In part A, 95% limits of agreement were calculated for comparison between MRT and PCCT. The results of part A showed no significant difference between test and retest as assessed by MRT [mean (SD) 42.2 (4.2) s and 43.8 (6.9) s] or by PCCT [21.8 (3.7) s and 22.7 (4.5) s]. Measurement error (%) was lower for MRT in comparison with PCCT (16% and 25%, respectively). In part B of the study, the .VO(2) kinetics of ER were significantly faster than those of SR, as assessed by MRT [33.4 (3.4) s and 39.9 (7.1) s, respectively; P<0.01] and PCCT [20.9 (3.8) s and 24.8 (4.5) s; P<0.05]. It is possible that either analysis procedure could provide a single test measurement of .VO(2) kinetics; however, the greater reliability of the MRT data suggests that this method has more potential for development in the assessment of .VO(2) kinetics by PRBS exercise testing.

Adult↗
PubMed2002

Structural specificity of steroids in stimulating DNA synthesis and protooncogene expression in primary rat hepatocyte cultures.

Among the chemical compounds of varied structure which possess liver tumour-promoting are steroids, such as estrogens, pregnenolone derivatives and anabolic steroids. Although the mechanism(s) of tumour promotion in liver by these xenobiotics is not well understood, it is clear that growth stimulation is one important element in their action. As a basis for better defining whether steroids stimulate growth by a common mechanism or fall into sub-groups with differing actions, the effects of 46 steroids on DNA synthesis and the expression of protooncogenes c-fos and c-myc were examined in primary cultures of normal rat hepatocytes. Tentative groupings of steroids have been identified based on apparent structural requirements for stimulation of DNA synthesis, and effects of auxiliary factors in modulating this growth stimulus. For a "progestin" group, insulin appeared to be permissive for stimulation of DNA synthesis, and presence of an ester or hydroxyl group at 17alpha-position in combination with a non-polar group at C(6) appeared to be required for stimulation. For the pregnenes, dexamethasone was stimulatory. Structural requirements include a non-polar substitution at 16alpha-position and presence of a 6alpha-methyl group. Androgens were weak or ineffective stimulators of DNA synthesis. Anabolic steroids were weak to strong stimulators and alteration to A ring structure in combination with non-polar substitution at 17alpha-position appeared to be required for the activity. With the exception of the anabolic steroid, dianabol, there do not appear to be strong correlation between ability to stimulate DNA synthesis and ability to induce protooncogene expression among the steroids. This study provides a starting point for future more detailed examination of growth-stimulatory mechanism(s) of action of steroids in the liver.

Animals↗
PubMed2002

Protective effect of Boldo and tea infusions on the visible light-mediated pro-oxidant effects of vitamin B2, riboflavin.

The effect of Boldo and black tea infusions on the pro-oxidant effects of vitamin B2, riboflavin (RF), when exposed to the action of visible light was studied. The amounts of antioxidants present in Boldo and tea infusions were evaluated by a procedure based on the bleaching of preformed 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radical cations and were expressed as 6-hydroxy-2,5,7,8-tetramethyl-chroman-2-carboxylic acid equivalent concentrations. The quenching rate constants of singlet oxygen (1O2; [kq]Boldo = 6.0 x 10(7) M(-1) s(-1) and [kq]Tea = 3.2 x 10(7) M(-1) s(-1)) and triplet RF (3RF; [3RFkq]Boldo = 10 x 10(8) M(-1) s(-1) and [3RFkq]TEA = 3.2 x 10(8) M(-1) s(-1)) with Boldo and tea were determined by flash photolysis. These data allow a quantitative interpretation of the results obtained. Our data suggest that most of the oxygen consumption observed in the photolysis of RF in the presence of tea and Boldo infusions is caused by 1O2 reactions. The oxygen consumption quantum yield is considerably smaller than the fraction of RF triplets trapped by the additives (AH) present in the infusion, indicating that their interaction with 3RF does not lead to chemical reactions or that the AH*+ radical ions initially formed participate in secondary processes that do not consume oxygen. Boldo and tea infusions have a significant protective effect when a system containing RF and tryptophan (Trp) is exposed to visible light, not only by quenching the 1O2 and interfering with the Type-I mechanism but also by repairing the damage to Trp molecules associated with the latter mechanism.

Chromans↗
PubMed2001

Solution structure and dynamics of yeast elongin C in complex with a von Hippel-Lindau peptide.

Elongin is a transcription elongation factor that stimulates the rate of elongation by suppressing transient pausing by RNA polymerase II at many sites along the DNA. It is heterotrimeric in mammals, consisting of elongins A, B and C subunits, and bears overall similarity to a class of E3 ubiquitin ligases known as SCF (Skp1-Cdc53 (cullin)-F-box) complexes. A subcomplex of elongins B and C is a target for negative regulation by the von Hippel-Lindau (VHL) tumor-suppressor protein. Elongin C from Saccharomyces cerevisiae, Elc1, exhibits high sequence similarity to mammalian elongin C. Using NMR spectroscopy we have determined the three-dimensional structure of Elc1 in complex with a human VHL peptide, VHL(157-171), representing the major Elc1 binding site. The bound VHL peptide is entirely helical. Elc1 utilizes two C-terminal helices and an intervening loop to form a binding groove that fits VHL(157-171). Chemical shift perturbation and dynamics analyses reveal that a global conformational change accompanies Elc1/VHL(157-171) complex formation. Moreover, the disappearance of conformational exchange phenomena on the microsecond to millisecond time scale within Elc1 upon VHL peptide binding suggests a role for slow internal motions in ligand recognition.

Binding Sites↗
PubMed2001

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.

High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information about cloning, expression, purification, biophysical characterization and structure determination via NMR spectroscopy or X-ray crystallography. It will be essential to develop specifications and ontologies for standardizing this information to make it amenable to retrospective analysis. To this end we created the SPINE database and analysis system for the Northeast Structural Genomics Consortium. SPINE, which is available at bioinfo.mbb.yale.edu/nesg or nesg.org, is specifically designed to enable distributed scientific collaboration via the Internet. It was designed not just as an information repository but as an active vehicle to standardize proteomics data in a form that would enable systematic data mining. The system features an intuitive user interface for interactive retrieval and modification of expression construct data, query forms designed to track global project progress and external links to many other resources. Currently the database contains experimental data on 985 constructs, of which 740 are drawn from Methanobacterium thermoautotrophicum, 123 from Saccharomyces cerevisiae, 93 from Caenorhabditis elegans and the remainder from other organisms. We developed a comprehensive set of data mining features for each protein, including several related to experimental progress (e.g. expression level, solubility and crystallization) and 42 based on the underlying protein sequence (e.g. amino acid composition, secondary structure and occurrence of low complexity regions). We demonstrate in detail the application of a particular machine learning approach, decision trees, to the tasks of predicting a protein's solubility and propensity to crystallize based on sequence features. We are able to extract a number of key rules from our trees, in particular that soluble proteins tend to have significantly more acidic residues and fewer hydrophobic stretches than insoluble ones. One of the characteristics of proteomics data sets, currently and in the foreseeable future, is their intermediate size ( approximately 500-5000 data points). This creates a number of issues in relation to error estimation. Initially we estimate the overall error in our trees based on standard cross-validation. However, this leaves out a significant fraction of the data in model construction and does not give error estimates on individual rules. Therefore, we present alternative methods to estimate the error in particular rules.

Animals↗
PubMed2001

Stimulation of DNA synthesis by tumor promoters in primary rat hepatocytes is not mediated by arachidonic acid metabolites.

Studies in vivo using inhibitors of eicosanoid synthesis suggested that prostaglandins may play a role in mediating tumor promotion in liver by agents such as phenobarbital (PB). However, it is not clear whether any stimulation of arachidonic acid metabolism/prostaglandin formation results directly from the action of tumor promoters on hepatocytes or indirectly from effects of promoters on Kupffer cells or other non-hepatocytes. Our laboratory has been utilizing relatively pure populations of rat hepatocytes under the defined conditions of primary cultures, to investigate growth-stimulatory actions of tumor promoters, an important element in the promotion stage of carcinogenesis. It has been shown that most if not all liver tumor promoters tested stimulate hepatocyte DNA synthesis when added in combination with factors such as EGF, insulin, and glucocorticoid. In the present study, we sought evidence for a role of prostaglandins (PGs) in the direct growth-stimulatory actions of tumor promoters on hepatocytes. PGE(2), PGF(2 alpha), and PGD(2) cause concentration-dependent stimulation of hepatocyte DNA synthesis, while arachidonic acid was without any effect. PGE(2) and PGF(2 alpha) required the presence of dexamethasone to exert significant effects. These PGs did not further augment the stimulatory effect of EGF. In contrast, PGD(2) stimulated DNA synthesis in the presence or absence of insulin, dexamethasone, or EGF. The effect of tumor promoters on arachidonic acid metabolism, as measured by [(3)H]arachidonic acid release and PGE(2) production, was determined. The phorbol ester TPA significantly increased [(3)H]arachidonic acid release as well as PGE(2) formation in hepatocytes in line with known effects in other cell types. However, liver tumor promoters phenobarbital (PB), alpha-hexachlorocycohexane (HCH), 1,1-bis(p-chlorophenyl)-2,2,2-trichloroethane (DDT), and pregnenolone-16 alpha-carbonitrile (PCN) were without effects. Finally, inhibitors of arachidonic acid metabolism were tested for effects on the ability of TPA or liver tumor promoters to stimulate DNA synthesis by direct action on cultured hepatocytes. In all cases, lack of selective inhibition was observed. Taken together, the results show that while prostaglandins may directly stimulate DNA synthesis in hepatocytes, they are unlikely to mediate the direct growth-stimulatory actions of liver tumor promoters.

Animals↗
PubMed2001

The test-retest reliability of gas exchange kinetics in humans using a pseudo random binary sequence exercise test.

The purpose of this study was to compare the test-retest reliability of oxygen uptake (VO2) kinetics with carbon dioxide output (VCO2) kinetics using a pseudo random binary sequence (PRBS) exercise test. A reliable test of gas exchange kinetics would have the potential of being applied as a sports fitness test. Ten healthy male subjects agreed to participate in the study and all subjects completed two identical PRBS exercise tests (test 1 and test 2), separated by a 30 min period of inactivity. Three consecutive 300 s PRBS cycles were completed in each test with 20 s exercise intensity changes between 25 and 85 W using an electrically braked cycle ergometer. Fourier analysis was computed for frequencies 3.3, 6.7 and 10 mHz. Statistical analysis by two-way ANOVA with repeated measures did not reveal significant differences between test 1 and test 2 for either VO2 kinetics or VCO2 kinetics. Static gain of VO2 for test 1 [9.11 (SD 0.59) ml.min-1.W-1] and test 2 [9.23 (SD 0.64) ml.min-1.W-1] did not differ significantly between tests. The 95% limits of agreement for VCO2 kinetics displayed increased variability in comparison to VO2 kinetics at each frequency of amplitude ratio and phase shift. Systematic bias ranged between 0% and 4%, except at frequency 10 mHz of VCO2 kinetics phase shift which showed a 10% bias for slower VO2 kinetics in test 2. It is possible that the increased variability of VCO2 kinetics compared to VO2 kinetics might be attributable to a lower signal to noise ratio in VCO2 kinetics, variations in ventilation or the storage mechanisms of CO2. The lower variability of VO2 kinetics compared with VCO2 kinetics suggests that the PRBS test of VO2 kinetics has the greater potential for further development as an indicator of aerobic fitness.

Adult↗
PubMed2001

Hydration state of single cytochrome c monolayers on soft interfaces via neutron interferometry.

Yeast cytochrome c (YCC) can be covalently tethered to, and thereby vectorially oriented on, the soft surface of a mixed endgroup (e.g., -CH3/-SH = 6:1, or -OH/-SH = 6:1) organic self-assembled monolayer (SAM) chemisorbed on the surface of a silicon substrate utilizing a disulfide linkage between its unique surface cysteine residue and a thiol endgroup. Neutron reflectivities from such monolayers of YCC on Fe/Si or Fe/Au/Si multilayer substrates with H2O versus D2O hydrating the protein monolayer at 88% relative humidity for the nonpolar SAM (-CH3/-SH = 6:1 mixed endgroups) surface and 81% for the uncharged-polar SAM (-OH/-SH = 6:1mixed endgroups) surface were collected on the NG1 reflectometer at NIST. These data were analyzed using a new interferometric phasing method employing the neutron scattering contrast between the Si and Fe layers in a single reference multilayer structure and a constrained refinement approach utilizing the finite extent of the gradient of the profile structures for the systems. This provided the water distribution profiles for the two tethered protein monolayers consistent with their electron density profile determined previously via x-ray interferometry (Chupa et al., 1994).

Biophysical Phenomena↗
PubMed2001

Effect of visible light on selected enzymes, vitamins and amino acids.

In most cases, the presence of an endogenous photosensitizer is a requirement for visible light modification of biomolecules in animal tissues. Riboflavin (RF) is present in all aerobic cells and is a very efficient photosensitizer, presenting a complex photochemistry with a mixed type I-type II mechanisms. Visible light irradiation in the presence of RF diminished the enzymatic activity of horse radish peroxidase (HRP) only when this glyco-enzyme was deglycosilated. In contrast, the activity of catalase is inactivated via singlet oxygen, and that of lysozyme was efficiently inactivated by a mixed type I-type II mechanisms. The reactive species involved in the RF sensitized photoconversion of lysozyme and the aromatic amino acids tryptophan and tyrosine (both free in solution) is discussed. The role of ascorbate and the effect of RF photosensitized processes in biological complex systems, such as the ocular lens and tumoral cell in culture, is analyzed.

Amino Acids↗
PubMed2001

Unfolding of microarray data.

The use of DNA microarrays for the analysis of complex biological samples is becoming a mainstream part of biomedical research. One of the most commonly used methods compares the relative abundance of mRNA in two different samples by probing a single DNA microarray simultaneously. The simplicity of this concept sometimes masks the complexity of capturing and processing microarray data. On the basis of the analysis of many of our microarray experiments, we identified the major causes of distortion of the microarray data and the sources of noise. In this study, we provide a systematic statistical approach for extraction of true expression ratios from raw microarray data, which we describe as an unfolding process. The results of this analysis are presented in the form of a model describing the relationship between the measured fluorescent intensities and the concentrations of mRNA transcripts. We developed and tested several algorithms for inference of the model parameters for the microarray data. Special emphasis is given to the statistical robustness of these algorithms, in particular resistance to outliers. We also provide methods for measurement of noise and reproducibility of the microarray experiments.

Computational Biology↗