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PubMed1996

Assessing the stability of cystatin/cysteine proteinase complexes using mildly-denaturing gelatin-polyacrylamide gel electrophoresis.

A method for assessing the stability of cystatin/cysteine proteinase complexes using mildly-denaturing gelatin-polyacrylamide gel electrophoresis (gelatin-PAGE) is described. As suggested by the use of well-known cystatins (human stefins A and B, and oryzacystatins I and II) and the plant cysteine proteinase papain, the ability of cystatin/cysteine proteinase complexes to remain stable during electrophoresis is associated with the degree of affinity between the enzyme and the inhibitor (and inversely associated with the Ki values), at least with the disulfide bond-lacking cystatins. Complexes with Ki values > or = 10(-8) M (weak interactions) are partly or completely dissociated under the conditions used, while those with lower Ki values (strong interactions) remain stable. As shown by the differential effects of two plant cystatins, oryzacystatins I and II, against a cysteine proteinase present in crude (complex) extracts from a plant pest -- the two-spotted spider mite (Tetranychus urticae Koch), the gelatin-PAGE procedure is suitable for studying the ability of cystatins to form highly stable complexes with cysteine proteinases, without the need for prior purification steps. Considering the well-recognized potential of proteinase inhibitors for pest and pathogen control, this analytical approach will be useful for rapidly assessing the respective potential of various cystatins for protection of plants, animals, and humans.

Animals↗

PubMed1998

Separation of cis/trans conformers of human and salmon calcitonin by low temperature capillary electrophoresis.

Conformer-specific recognition of peptides and proteins has often been proved with the aid of indirect methods. Here we provide an analytical approach for a direct investigation of separated isomers. Cis/trans conformers of the peptide hormones human (hCT) and salmon (sCT) calcitonin exhibit different migration properties in capillary zone electrophoresis at subambient temperatures. Calcitonin consists of 32 amino acids with two proline residues incorporated. It is the longest unstructured peptide for which a conformer separation by capillary electrophoresis has yet been achieved. Lowering the temperature yielded a splitting into two and three peaks for sCT and hCT, respectively, in acidic buffer. The peak ratios of 66:34 for sCT and 71:23 for hCT are in good agreement with the conformer distribution previously reported from nuclear magnetic resonance (NMR) studies. The addition of different organic modifiers (5-20% v/v) to the running buffer does not improve the separation. The observed merging of conformer peaks in buffer containing 20% v/v 2,2,2-trifluoroethanol (TFE) is attributed to structure formation.

Amino Acid Sequence↗

PubMed2003

Capillary electrophoresis-mass spectrometry: 15 years of developments and applications.

Since its introduction in 1987, capillary electrophoresis-mass spectrometry (CE-MS) has developed to a well accepted multidimensional analytical approach complementary and/or competitive to classical MS-hyphenated separation techniques. The threefold combination of rapid developments of an exceptional separation technique, of selective mass detection possibilities, and of very mild ionization modes first allowed these progresses. This article shows the CE specificities that need to be well controlled/known, compared to classical and more routinely used liquid chromatography in the light of its coupling to MS. The major trends and developments over the last 15 years and most of the reviews and applications found in ISI Web of science and publisher databases are presented in a tabulated way. The reader can thus rapidly find existing CE-MS analysis techniques in his field of research and application (forensics, environment, bioanalytics, pharmaceutics, and metabolites).

Electrophoresis, Capillary↗

PubMed2003

Insoluble eggshell matrix proteins--their peptide mapping and partial characterization by capillary electrophoresis and high-performance liquid chromatography.

Avian eggshell matrix proteins were studied by two analytical approaches. Peptide mapping was done by trypsin and pepsin followed by collagenase cleavage; analyses were carried out by capillary electrophoresis and reversed-phase high-performance liquid chromatography (HPLC). Comparison of peptide maps obtained by both methods revealed a complex mixture of peptides in the insoluble layers of the eggshell; it was concluded that there are at least three different insoluble protein/peptide layers in the avian eggshell (cuticle, palisade, and mammillary layer). Partial characterization of peptides in each layer was made by HPLC-mass spectrometry analysis. There is an evidence that the eggshell insoluble proteins contain species susceptible to collagenase cleavage, however, the sequences split by this enzyme probably are not those typical for the main triple-helical core of collagenous proteins. It is proposed that the action of collagenase upon eggshell proteins is caused by the side effect of collagenase described previously with synthetic peptides. Some of the proteins present are probably glycosylated. Fatty acid content in the insoluble eggshell layers (after decalcification) was in the range of 2-4% (which reflected both lipid and lipoproteins bound fatty acids). Porphyrin pigments are dominant in the cuticle layer.

Animals↗

PubMed2004

Speciation of protein-bound trace elements by gel electrophoresis and atomic spectrometry.

The metabolism of trace elements, in particular their binding to proteins in biological systems is of great importance in biochemical, toxicological, and pharmacological studies. As a result there has been a sustained interest over the last two decades in the speciation of protein-bound metals. Various analytical approaches have been employed, combining efficient separation of metalloproteins by liquid chromatography or electrophoresis with high-sensitivity elemental detection. Slab-gel electrophoresis (GE) is a key platform for high-resolution protein separation, and has been combined with autoradiography and various atomic spectrometric techniques for in-gel determination of protein-bound metals. Recently, the combination of GE with state-of-the-art inductively coupled plasma-mass spectrometry (ICP-MS), particularly when linked to laser ablation (LA) for direct gel interrogation, has opened up new opportunities for rapid characterization of metalloproteins. The use of GE and atomic spectrometry for the speciation of protein-bound trace elements is reviewed in this paper. Technical requirements for gel electrophoresis/atomic spectrometric measurement are considered in terms of method compatibilities, detection capability and potential usefulness. The literature is also surveyed to illustrate current status and future trends.

Autoradiography↗

PubMed2006

Comparative studies on the analysis of urinary trypsin inhibitor (ulinastatin) preparations.

Urinary trypsin inhibitor (ulinastatin) is a characteristic protein pharmaceutical which contains both glycosaminoglycans and N-linked glycans in its molecule and has been used for treatment of acute pancreatitis. The comparability of ulinastatin preparations of different lots or from different companies was studied by using conventional analytical approaches such as SDS-PAGE, cellulose acetate membrane electrophoresis, and HP size-exclusion chromatography (SEC) and also by using newly developed techniques such as CE and MALDI-TOF MS. The methods using SEC and SDS-PAGE according to The Japanese Pharmacopoeia showed similar molecular masses for two different preparations, and the estimated molecular masses were significantly different from those observed with MALDI-TOF MS. We also showed that the electrophoretic methods using cellulose acetate membrane electrophoresis and CE can be used for comparability assessments of ulinastatin preparations. In addition, we analyzed the unsaturated disaccharides derived from glycosaminoglycan (chondroitin 4-sulfate chain) and N-linked oligosaccharides attached to ulinastatin by CE after releasing them by enzymatic digestion followed by fluorescent labeling with 2-aminoacridone and 2-aminobenzoic acid, respectively. The results indicated that carbohydrate chains are important as markers for comparability assessments of ulinastatin pharmaceutical preparations.

Amino Acid Sequence↗

PubMed1988

Genetic factors influencing apolipoprotein AI and AII levels in a kindred with premature coronary heart disease.

A single 51-member kindred, ascertained on the basis of a normotriglyceridemic proband with depressed high-density lipoprotein cholesterol (HDL-C) and myocardial infarctions at ages 40 and 42, was studied with respect to quantitative variation in HDL-C and apolipoprotein (apo) AI and AII levels. The results of bivariate segregation analysis suggest that the etiology of depressed HDL-C involves one or possibly two major loci: one has a pleiotropic effect on apo AI and apo AII levels and, possibly another one that affects apo AI levels. Both the major loci were characterized as having a dominant allele leading to depression of the respective trait(s). In addition, analysis of the cosegregation of HDL-C and apo AI levels gave evidence of residual nonfamilial factors common to both traits, leading to a positive covariance between them. This could reflect the role of apo AI in the transformation of nascent HDL-C particles into mature ones via its cofactor activity to lecithin cholesterol acyltransferase. The proposed two-locus model represents one possible etiology for the heterogeneous disorder of hypoalphalipoproteinemia. This analysis of a single pedigree does not completely define the genetic mechanism, but it does illustrate a useful new analytic approach.

Apolipoprotein A-I↗

PubMed1989

Affective disorder not linked to HLA.

These analyses focused on the relationship of affective disorders to HLA. The sample of 86 previously unpublished families from Ontario and 10 unpublished pedigrees from Newfoundland, as well as the original Weitkamp et al. [1981] sample of 20 families, the samples provided by NIMH [Goldin et al., 1982] (18 families), and Egeland et al. [1987] (2 large pedigrees), were examined using sib pair methods as well as standard linkage analysis of the full pedigrees. A variety of genetic models were examined. There was no evidence for linkage from any of the samples based on either analytic approach or for any genetic model. Groups of sibling pairs concordant for affective illness, concordant for being well, or discordant for affective illness did not differ in the proportion of genes identical by descent. No group differed significantly from 50%. From the analysis of full pedigrees, linkage to HLA could be excluded to a distance of approximately 20 to 25 centimorgans. There was no evidence for linkage heterogeneity. These results argue against linkage of affective disorder to HLA.

Affective Disorders, Psychotic↗

PubMed1995

Genetic epidemiologic analysis of quantitative phenotypes using Gibbs sampling.

We analyzed two quantitative traits (Q1 and Q2) provided in the 'Common Disease' data set with the aim of detecting both genetic and environmental determinants. We used linear regression for screening measured variables, maximum likelihood segregation and linkage analyses for detecting and localizing unmeasured genes, and Gibbs sampling for joint segregation and linkage analyses with estimation of gene-environment interaction and polygenic effects. For both Q1 and Q2, we successfully detected the unmeasured codominant major gene (MG) that was tightly linked to candidate gene C2. We also detected all of the measured variables used in generating Q1 (age, Q3, candidate gene C5) and Q2 (EF). Although our final models differed slightly from the true data generation models, our multifaceted analytic approach was successful in characterizing the determinants of Q1 and Q2.

Alleles↗

PubMed2001

Life after the screen: making sense of many P-values.

A multiple analytic approach may be useful for analyzing complex traits since different methods extract both similar and distinct, but complementary pieces of information from genome screen data on extended pedigrees. We examined the usefulness of combining p-values both across methods and across adjacent markers, taking into account the observed correlation structure among these p-values. To this end, we employed the recently proposed truncated product method [Zaykin et al., Genet Epidemiol, in press]. It appears that this approach is helpful for visualizing priority regions for follow-up analysis and reducing the number of false-positive linkage signals.

Chromosome Mapping↗

PubMed2001

Common disease analysis using Multivariate Adaptive Regression Splines (MARS): Genetic Analysis Workshop 12 simulated sequence data.

A newly developed modern analytic approach, Multivariate Adaptive Regression Splines (MARS), was used to identify both genetic and non-genetic factors involved in the etiology of a common disease. We tested this method on the simulated data provided by the Genetic Analysis Workshop (GAW) 12 in problem 2 for the isolated population. MARS simultaneously analyzes all inputs, in this case DNA sequence variants and non-genetic data, and selectively prunes away variables contributing insignificantly to fit by internal cross-validation to arrive at a generalizable predictive model of the response. The relevant factors identified, by means of an importance value computed by MARS, were assumed to be associated with risk to the disease. The application of a series of subsequent models identified the quantitative traits and a single major gene contributing directly to risk liability using five sets of 7,000 individuals.

Genetic Predisposition to Disease↗

PubMed2001

Quantitative trait linkage analysis of the liability underlying a common oligogenic disease.

We utilized pedigree discriminant and factor analytic approaches to combine multivariate phenotypic information into a single liability phenotype in the isolate and general populations. We applied two-stage relative-pair quantitative trait linkage analysis to detect genetic contributions to variation in the resulting liability phenotypes. Linkage analysis revealed several regions of suggestive linkage in both the general and isolate populations, the majority of which appear in retrospect to be false positives. A likely explanation is an overall lack of power given that we tested hypotheses in data from only one replicate. However, it may be possible that a construct that ignores affection status when using liability-associated characteristics as indicators of this construct is not the most effective approach in modeling the liability underlying a complex phenotype.

Chromosome Mapping↗

PubMed2005

Cross-cultural effect on the brain revisited: universal structures plus writing system variation.

Recognizing printed words requires the mapping of graphic forms, which vary with writing systems, to linguistic forms, which vary with languages. Using a newly developed meta-analytic approach, aggregated Gaussian-estimated sources (AGES; Chein et al. [2002]: Psychol Behav 77:635-639), we examined the neuroimaging results for word reading within and across writing systems and languages. To find commonalities, we compiled 25 studies in English and other Western European languages that use an alphabetic writing system, 9 studies of native Chinese reading, 5 studies of Japanese Kana (syllabic) reading, and 4 studies of Kanji (morpho-syllabic) reading. Using the AGES approach, we created meta-images within each writing system, isolated reliable foci of activation, and compared findings across writing systems and languages. The results suggest that these writing systems utilize a common network of regions in word processing. Writing systems engage largely the same systems in terms of gross cortical regions, but localization within those regions suggests differences across writing systems. In particular, the region known as the visual word form area (VWFA) shows strikingly consistent localization across tasks and across writing systems. This region in the left mid-fusiform gyrus is critical to word recognition across writing systems and languages.

Brain↗

PubMed2005

Involvement of the inferior frontal junction in cognitive control: meta-analyses of switching and Stroop studies.

There is growing evidence that a specific region in the posterior frontolateral cortex is involved intimately in cognitive control processes. This region, located in the vicinity of the junction of the inferior frontal sulcus and the inferior precentral sulcus, was termed the inferior frontal junction (IFJ). The IFJ was shown to be involved in the updating of task representations and to be activated commonly in a within-subject investigation of a task-switching paradigm, the Stroop task, and a verbal n-back task. Here, we investigate the involvement of the IFJ in cognitive control by employing a meta-analytic approach. Two quantitative meta-analyses of functional magnetic resonance imaging (fMRI) studies were conducted. One meta-analysis included frontal activations from task-switching, set-shifting, and stimulus-response (S-R) reversal studies, the other included frontal activations from color-word Stroop studies. Results showed highly significant clustering of activations in the IFJ in both analyses. These results provide strong evidence for the consistent involvement of the IFJ in both switching and Stroop paradigms. Furthermore, they support our concept of areal specialization in the frontolateral cortex, which posits that it is not only the middorsolateral part that plays an important role in cognitive control, but also the IFJ. Finally, our results demonstrate how quantitative meta-analyses can be used to test hypotheses about the involvement of specific brain regions in cognitive control.

Brain Mapping↗

PubMed2006

Milk, milk products and lactose intake and ovarian cancer risk: a meta-analysis of epidemiological studies.

It has been proposed, on the basis of animal models and ecological studies, that consumption or metabolism of dairy sugar may increase the risk of ovarian cancer. Case-control and cohort studies of the association between lactose and dairy food consumption and ovarian cancer risk, however, have yielded varied findings. We summarized the available literature on this topic using a meta-analytic approach. Random-effects models were used to estimate the summary relative risks (RR(summary)). A linear regression analysis of the natural logarithm of the RR was carried out to assess a possible dose-response relationship between lactose intake and ovarian cancer risk. Eighteen case-control and 3 prospective cohort studies were eligible for inclusion in the meta-analysis. The findings of case-control studies were heterogeneous, and, except for whole milk (RR(summary) for highest vs. lowest category = 1.27, 95% confidence interval [CI] = 0.97-1.68), do not provide evidence of positive associations between dairy food and lactose intakes with risk of ovarian cancer. In contrast, the 3 cohort studies are consistent and show significant positive associations between intakes of total dairy foods, low-fat milk, and lactose and risk of ovarian cancer. The RR(summary) for a daily increase of 10 g in lactose intake (the approximate amount in 1 glass of milk) was 1.13 (95% CI = 1.05-1.22) for cohort studies. In conclusion, prospective cohort studies, but not case-control studies, support the hypothesis that high intakes of dairy foods and lactose may increase the risk of ovarian cancer.

Animals↗

PubMed2007

Associations between serum carotenoids and tocopherols and type-specific HPV persistence: the Ludwig-McGill cohort study.

Although oncogenic HPV infections have been established as the necessary cause of cervical cancer, most HPV infections are transient and rarely progress to cervical lesions. Current research is focused on identifying factors associated with viral persistence and clearance, such as nutritional status. We evaluated the association between serum antioxidant nutrients (retinol, 10 carotenoids and 3 tocopherols) and type-specific HPV persistence over 4 visits among 405 women participating in the Ludwig-McGill cohort study. We measured circulating carotenoids and tocopherol at 4 different clinical visits for each woman. We report the results from different analytic approaches (a case-control approach at both the woman and viral level, and a prospective approach based on persistent events) that examined the association between these micronutrients and type-specific oncogenic and nononcogenic HPV persistence. In the case-control analysis at the viral level, midcirculating levels of alpha-tocopherol were inversely associated with nononcogenic HPV persistent infection (adjusted odds ratio (AOR) = 0.28, 95% CI 0.14-0.57), while high levels were marginally associated (AOR = 0.59, 95% CI 0.28-1.19). Similarly, utilizing generalized estimating equation models, circulating levels of alpha- and delta-tocopherol in the middle or upper tertiles were inversely associated with type-specific nononcogenic HPV persistence (AOR = 0.44, 95% CI 0.19-0.97 and AOR = 0.46, 95% CI 0.19-1.11, respectively). Our study among Brazilian women suggests that serum levels of tocopherols may be protective against nononcogenic HPV persistence. However, we did not find a strong protective effect (as hypothesized) of other serum antioxidant nutrients and type-specific oncogenic HPV persistence measured over 4 clinical visits.

Adult↗

PubMed1986

Yeast pre-messenger RNA splicing efficiency depends on critical spacing requirements between the branch point and 3' splice site.

In the yeast Saccharomyces cerevisiae the 5' and 3' splice junctions and the internal branch acceptor site (TACTAAC box) are highly conserved intron elements. Analyses of mutants have demonstrated the importance of each of these elements in the splicing process. In the present report we show by three different analytical approaches (splicing-dependent beta-galactosidase expression, in vitro splicing assays and in vivo RNA analyses) that at least two of these elements (the TACTAAC and 3' splice signals) also have to fulfill certain spacing requirements to allow efficient splicing to occur. In particular, the spacing of the 3' splice site from the 2'-5' branch site is a critical factor in determining the efficiency for completion of the final reactions of splicing, intron release and exon-exon joining. Whereas insertions within this region have little or no effect on the first reactions in splicing (the 5' cleavage and 2'-5' branch formation), they dramatically affect the efficiency of the final reactions. In contrast, a 15-base deletion between these two sites has no detectable effect on splicing efficiency. We also show that the 5' cleavage and branch formation can take place, albeit inefficiently, in transcripts in which all of the yeast sequences downstream of the branch site have been replaced by Escherichia coli sequences. We conclude from these studies that, in yeast, the 5' and 3' splice sites are recognized independently from one another, but always in conjunction with the TACTAAC signal.

Base Sequence↗

PubMed1996

Are vitamin D receptor polymorphisms associated with bone mineral density? A meta-analysis.

Vitamin D receptor (VDR) polymorphisms have been strongly associated with bone mineral density (BMD) in some studies but not in others. We used a meta-analytic approach to assess quantitatively the association between VDR and BMD and to examine the influence of specific study characteristics (e.g., skeletal site, mean age of subjects, menopausal status) on the reported results. Sixteen papers published in peer-reviewed journals through July 1996 were included. We calculated the mean difference, percent difference, and effect size (mean difference divided by standard deviation), comparing BMD between homozygous genotypes. At the hip, BMD in the BB genotype was lower than in the bb genotype (mean difference, -0.02 g/cm2; percent difference, -2.4% and effect size -0.18; p = 0.032). At the spine, the mean difference was -0.03 g/cm2; percent difference, -2.5%; and effect size, -0.19; p = 0.062. At the distal radius, the VDR effect was estimated as the mean difference, -0.01 g/cm2; percent difference, -1.7%; and effect size, -0.16; p = 0.078. The spine measurements exhibited the greatest between- and within-study variability. The difference in hip BMD between genotypes was larger (i.e., a more negative number) among the younger women and seemed to decrease with increasing age. However, statistical evidence for this trend was weak (p = 0.06). Data from the spine and the radius showed no evidence of a comparable interaction of the VDR effect with age. When we omitted data from the first report of an association between VDR polymorphisms and BMD, our analyses gave similar results, although the overall effect estimates were smaller. In the combined data from 29 study groups, the BB genotype frequency was 17.2, 4.9, and 2.3% in studies of whites, blacks, and Asians, respectively. VDR polymorphisms represent one genetic factor affecting BMD, but further research into the mechanisms, clinical significance, and its relation between other genetic and environmental factors is needed.

Adult↗