CiteULike: jyuh Sommer

Microarray-based DNA resequencing using 3' blocked primers.

Jakub Sram — 2007-12-03T10:16:51-00:00

Anal Biochem (4 November 2007)

To exceed the throughput and accuracy of conventional sequencing technologies, we tested a method (pyrophosphorolysis-activated polymerization [PAP]) of nucleic acid amplification that uses 3' blocked primers (P *s). As proof-of-principle, we resequenced a 20-bp region of the factor IX gene with a microarray of P *s. P *s discriminate 3' end mismatches with ultra-high specificity as well as mismatches along their lengths with high specificity. We correctly identified two wild-type samples as well as all mismatches, including three single-base substitutions, one microdeletion, one microinsertion, and one heterozygous mutation. Despite limitations in the primer purity, the signal/noise ratio between the matched and mismatched P *s sometimes exceeded 1000. Thus, PAP resequencing shows great potential for accurate and high-throughput microarray-based resequencing.

Theory and implementation of an electronic, automated measurement system for images obtained from immunohistochemically stained slides.

G Kayser — 2008-05-10T01:29:46-00:00

Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology, Vol. 28, No. 1. (February 2006), pp. 27-38.

OBJECTIVE: To develop and implement an Internet-based, automated image measurement system for immunohistochemically stained slides including fluorescence images in online and off-line modes. STUDY DESIGN: An image analyzing system was developed that automatically measures digitized images obtained from immunohistochemically stained slides. It is divided into a common server platform and a specific image quantification system based upon DIAS (University of Jena). After registration, the user fills in an input data form and attaches images to be measured. The server periodically transfers the data to the measurement system. The measurement works on dynamic thresholding and active sampling of objects visualized by fluorescence and conventional chromogens. It includes stereologic algorithms, object quantification, syntactic structure analysis and quality assurance. RESULTS: The system has been tested for diaminobenzidene, alkaline phosphatase and fluorescence images (FITC, etc.). The reproducibility and stability of the system are > 98%. The series of successfully measured images comprises > 1,000 images in total in the online and off-line modes. CONCLUSION: An Internet-based automated image measurement system has been developed that offers worldwide access to the major requests for quantification of immunohistochemically stained slides-tissue array analysis, nuclear stains (MIB, hormones), membrane stains (CerbB2), vascularization and fluorescence in situ hybridization.

Renal calcinosis and stone formation in mice lacking osteopontin, Tamm-Horsfall protein, or both

Lan Mo — 2007-11-30T15:24:51-00:00

Am J Physiol Renal Physiol, Vol. 293, No. 6. (1 December 2007), pp. F1935-1943.

Although often supersaturated with mineral salts such as calcium phosphate and calcium oxalate, normal urine possesses an innate ability to keep them from forming harmful crystals. This inhibitory activity has been attributed to the presence of urinary macromolecules, although controversies abound regarding their role, or lack thereof, in preventing renal mineralization. Here, we show that 10% of the mice lacking osteopontin (OPN) and 14.3% of the mice lacking Tamm-Horsfall protein (THP) spontaneously form interstitial deposits of calcium phosphate within the renal papillae, events never seen in wild-type mice. Lack of both proteins causes renal crystallization in 39.3% of the double-null mice. Urinalysis revealed elevated concentrations of urine phosphorus and brushite (calcium phosphate) supersaturation in THP-null and OPN/THP-double null mice, suggesting that impaired phosphorus handling may be linked to interstitial papillary calcinosis in THP- but not in OPN-null mice. In contrast, experimentally induced hyperoxaluria provokes widespread intratubular calcium oxalate crystallization and stone formation in OPN/THP-double null mice, while completely sparing the wild-type controls. Whole urine from OPN-, THP-, or double-null mice all possessed a dramatically reduced ability to inhibit the adhesion of calcium oxalate monohydrate crystals to renal epithelial cells. These data establish OPN and THP as powerful and functionally synergistic inhibitors of calcium phosphate and calcium oxalate crystallization in vivo and suggest that defects in either molecule may contribute to renal calcinosis and stone formation, an exceedingly common condition that afflicts up to 12% males and 5% females. 10.1152/ajprenal.00383.2007

A large-scale validation of dosage analysis by robust dosage-polymerase chain reaction.

VQ Nguyen — 2007-11-02T02:54:56-00:00

Anal Biochem, Vol. 371, No. 1. (1 December 2007), pp. 37-42.

Epidemiological and clinical diagnostic assays benefit from accurate detection of deletions and duplications commonly missed by the conventional strategy of polymerase chain reaction (PCR) amplification and sequencing of individual exons. Robust dosage-PCR (RD-PCR) is a quantitative duplex PCR method that coamplifies a target template and an endogenous internal control (an autosomal and an X-chromosomal segment) for detection of these mutations. In this study, 110 consecutive RD-PCR assays were developed and validated. The average linear regression coefficient between template copy number and product yield and the average coefficient of determination for linear correlation, R(2), were very high: 0.95 and 0.98, respectively. The accuracy of RD-PCR revealed somatic mosaicism for a deletion in the factor 9 gene. Advantages of RD-PCR include (1) high accuracy and consistency, (2) easy calibration of linearity using male and female samples, (3) use of an endogenous internal dosage control to eliminate preparation and manipulation errors, and (4) detection of gene dosage over a wide dynamic range. Deletions and duplications can be easily detected (a 2x decrease or a 1.5x increase in gene dosage). Thus, RD-PCR is a general and accurate method for detecting changes in gene dosage.

Investigating gene environment interaction in complex diseases: increasing power by selective sampling for environmental exposure

MPM Boks — 2007-11-01T09:44:41-00:00

Int. J. Epidemiol. (30 October 2007), dym215.

Background The often limited influence of disease associated alleles on the vulnerability to complex diseases has lead to increased interest in environmental interaction with genotype. However, gene environmental interactions (GEIs) are not easily studied, since high numbers of subjects are required to detect GEI. Methods and results This study provides a potential useful method to increase the power of such studies through selective sampling for environmental exposure. We show that selecting the top and bottom 10% regarding environmental exposure can lead to a 70% reduction in the required number of subjects for genotyping. Conclusion This study demonstrates the potential usefulness of selective sampling in the study of the interplay between genes and environment. The reduction of required subjects can be particularly advantageous in studies where genotyping is extensive, such as in whole genome screens or in studies where phenotyping is expensive. 10.1093/ije/dym215

Collagen type VIII expression in human diabetic nephropathy

Gerth — 2007-10-10T02:59:00-00:00

European Journal of Clinical Investigation, Vol. 37, No. 10. (October 2007), pp. 767-773.

Down-regulation of lysyl oxidase-induced tumorigenic transformation in NRK-49F cells characterized by constitutive activation of ras proto-oncogene.

M Giampuzzi — 2007-08-29T06:39:40-00:00

J Biol Chem, Vol. 276, No. 31. (3 August 2001), pp. 29226-29232.

Several investigations have suggested a putative tumor suppressor role for lysyl oxidase because it is down-regulated in many human and oncogene-induced tumors. To address this issue we down-regulated the enzyme in normal rat kidney fibroblasts by stable transfection of its cDNA in an antisense orientation. The selected clones revealed an absence of lysyl oxidase and dramatic phenotypic changes, interpretable as signs of transformation. The antisense lysyl oxidase clones showed, indeed, loose attachment to the plate and anchorage-independent growth and were highly tumorigenic in nude mice. Moreover, we found an impaired response of the PDGF and IGF-1 receptors to their ligands. In particular, the transformed cells showed a down-regulation of both PDGF receptors and expressed the 105-kDa isoform of the IGF-1 beta receptor, which was not present in the normal control cells. The lack of response to PDGF-BB has been described as a feature of many ras-transformed phenotypes. Therefore, we looked at the status of the p21(ras). Indeed, we found a significantly higher level of active p21(ras) both during steady-state growth and prolonged starvation. Our data reveal new evidence for a tumor suppressor activity of lysyl oxidase, highlighting its particular role in controlling Ras activation and growth factor dependence.

Differences in the modulating potential of advanced glycation end product (AGE) peptides versus AGE proteins.

W Deuther-Conrad — 2007-07-25T08:18:15-00:00

Kidney Int Suppl, Vol. 78 (February 2001)

Differences in the modulating potential of advanced glycation end product (AGE) peptides versus AGE proteins. Advanced glycation end products (AGEs), identified as irreversible products of a complex reaction of carbonyl groups of reducing sugars with free protein amino groups, are characterized by resistance to proteolytic degradation. The incomplete digestion of AGEs results in low molecular weight AGEs accumulating in the blood of diabetic and uremic patients. We hypothesized that the accumulation of these compounds may contribute to the dysfunction and/or degeneration of tubular epithelial cells. Our study examined whether low-molecular-weight AGE peptides and high-molecular-weight AGE proteins affect the functional cellular properties of two tubular epithelial cell lines: immortalized human kidney tubular epithelial (IHKE) and immortalized rat renal proximal tubular cells (IRPTCs). Parameters of cellular damage and growth behavior were cell counting, analysis of the cellular metabolic activity (MTT assay), as well as cellular proliferation (3[H]-thymidine-incorporation). IHKE treated with bovine serum albumin-AGE (BSA-AGE 50) or BSA-AGE-Pep 50 revealed a decrease in cellular metabolic activity as compared with controls after 48 hours of incubation (73 +/- 9% for BSA-AGE 50 and 62 +/- 11% for BSA-AGE-Pep 50 vs. 89 +/- 8% for BSA Co 50). Low molecular weight BSA-AGE-Pep 50 induced a significantly greater cellular damage in IRPTCs as compared with high molecular weight BSA-AGE 50 after 144 hours of incubation (59 +/- 15% for BSA-AGE 50 vs. 31 +/- 13% for BSA-AGE-Pep 50). The decrease in metabolic activity correlated well with a decrease in cellular proliferation. The results suggest a higher toxic potential of low molecular weight AGE peptides compared with high molecular weight AGE proteins in IRPTC and IHKE. This may provide evidence that low molecular weight degradation products of AGE-modified proteins have an important risk potential.

In vitro-prepared advanced glycation end-products and the modulating potential of their low-molecular weight degradation products in IRPTC-A rat proximal-tubular derived kidney epithelial cell line.

W Deuther-Conrad — 2007-07-25T05:10:26-00:00

Cell Mol Biol (Noisy-le-grand), Vol. 47 Online Pub (2001)

Low-molecular advanced glycation end-products (AGEs)-degradation products resulting from a proteolysis of tissue or circulating AGEs represent up to 80% of AGE plasma immunoreactivity. These AGE peptides contribute to the dramatic increase in AGE levels in end-stage renal disease even in the absence of diabetes. Because glomerular filtered AGE-degradation products may accumulate within intracellular compartments of proximal tubular epithelial cells, we investigated whether there is a pathway potentially mediating damaging effects of AGE-degradation products by perturbation of the function of the tubuloepithelium. Proximal tubular-derived rat kidney cells (IRPTC) were incubated with high-molecular AGEs highly modified by incubation of bovine serum albumin (BSA) with glucose for 50 days in vitro, and with low-molecular AGE-degradation products derived from proteolytic cleavage and isolated in the molecular range between 1 and 30 kDa. The proliferation of IRPTC (3H-thymidine incorporation) was reduced to 89+/-1% and 69+/-2% after 24 hr of incubation with BSA-AGE and BSA-AGE-degradation products, respectively. The cell viability of IRPTC was reduced significantly to 59+/-15% and 31+/-13% after 144 hr of incubation with BSA-AGE and BSA-AGE-degradation products, respectively. Conditioned media obtained from IRPTC incubated for 72 hr with BSA-AGE and its degradation products increased the proliferation rate of renal fibroblasts (RFb) to 222+/-24% and 449+/-40%, respectively. Incubation of IRPTC with BSA-AGE-degradation products increased the expression of endothelin-1 (ET-1) mRNA to 210% after 1 hr; the expression of platelet-derived growth factor-B (PDGF-B) mRNA reached 184% after 2 hr. Regarding the toxicity of AGEs to the kidney, low-molecular weight AGE-degradation products possibly form an individual fraction with a comparatively higher toxic potential.