Extended microsatellite analysis in microsatellite stable, MSH2 and MLH1 mutation-negative HNPCC patients: Genetic reclassification and correlation with clinical features

Background: Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant disorder predisposing to predominantly colorectal cancer (CRC) and endometrial cancer frequently due to germline mutations in DNA mismatch repair (MMR) genes, mainly MLH1, MSH2 and also MSH6 in families seen to demonstrate an excess of endometrial cancer. As a consequence, tumors in HNPCC reveal alterations in the length of simple repetitive genomic sequences like poly-A, poly-T, CA or GT repeats (microsatellites) in at least 90% of the cases. Aim of the Study: The study cohort consisted of 25 HNPCC index patients ( 19 Amsterdam positive, 6 Bethesda positive) who revealed a microsatellite stable (MSS) - or low instable (MSI-L) - tumor phenotype with negative mutation analysis for the MMR genes MLH1 and MSH2. An extended marker panel (BAT40, D10S197, D13S153, D18S58, MYCL1) was analyzed for the tumors of these patients with regard to three aspects. First, to reconfirm the MSI-L phenotype found by the standard panel; second, to find minor MSIs which might point towards an MSH6 mutation, and third, to reconfirm the MSS status of hereditary tumors. The reconfirmation of the MSS status of tumors not caused by mutations in the MMR genes should allow one to define another entity of hereditary CRC. Their clinical features were compared with those of 150 patients with sporadic CRCs. Results: In this way, 17 MSS and 8 MSI-L tumors were reclassified as 5 MSS, 18 MSI-L and even 2 MSI-H ( high instability) tumors, the last being seen to demonstrate at least 4 instable markers out of 10. Among all family members, 87 malignancies were documented. The mean age of onset for CRCs was the lowest in the MSI-H-phenotyped patients with 40.5 +/- 4.9 years (vs. 47.0 +/- 14.6 and 49.8 +/- 11.9 years in MSI-L- and MSS-phenotyped patients, respectively). The percentage of CRC was the highest in families with MSS-phenotyped tumors (88%), followed by MSI-L-phenotyped ( 78%) and then by MSI-H-phenotyped (67%) tumors. MSS tumors were preferentially localized in the distal colon supposing a similar biologic behavior like sporadic CRC. MSH6 mutation analysis for the MSI-L and MSI-H patients revealed one truncating mutation for a patient initially with an MSS tumor, which was reclassified as MSI-L by analyzing the extended marker panel. Conclusion: Extended microsatellite analysis serves to evaluate the sensitivity of the reference panel for HNPCC detection and permits phenotype confirmation or upgrading. Additionally, it confirms the MSS status of hereditary CRCs not caused by the common mutations in the MMR genes and provides hints to another entity of hereditary CRC. Copyright (C) 2004 S. Karger AG, Basel

N,P,P-Triisopropyl­phosphinic amide

The title compound, C9H22NOP, was obtained by slow diffusion of oxygen into a toluene solution of iPr2PNHiPr. In the crystal, an inter­molecular N—H⋯O hydrogen bond occurs

Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

For modern biology, precise genome annotations are of prime importance, as they allow the accurate definition of genic regions. We employ state-of-the-art machine learning methods to assay and improve the accuracy of the genome annotation of the nematode Caenorhabditis elegans. The proposed machine learning system is trained to recognize exons and introns on the unspliced mRNA, utilizing recent advances in support vector machines and label sequence learning. In 87% (coding and untranslated regions) and 95% (coding regions only) of all genes tested in several out-of-sample evaluations, our method correctly identified all exons and introns. Notably, only 37% and 50%, respectively, of the presently unconfirmed genes in the C. elegans genome annotation agree with our predictions, thus we hypothesize that a sizable fraction of those genes are not correctly annotated. A retrospective evaluation of the Wormbase WS120 annotation [1] of C. elegans reveals that splice form predictions on unconfirmed genes in WS120 are inaccurate in about 18% of the considered cases, while our predictions deviate from the truth only in 10%–13%. We experimentally analyzed 20 controversial genes on which our system and the annotation disagree, confirming the superiority of our predictions. While our method correctly predicted 75% of those cases, the standard annotation was never completely correct. The accuracy of our system is further corroborated by a comparison with two other recently proposed systems that can be used for splice form prediction: SNAP and ExonHunter. We conclude that the genome annotation of C. elegans and other organisms can be greatly enhanced using modern machine learning technology

SNP identification in unamplified human genomic DNA with gold nanoparticle probes

Single nucleotide polymorphisms (SNPs) comprise the most abundant source of genetic variation in the human genome. SNPs may be linked to genetic predispositions, frank disorders or adverse drug responses, or they may serve as genetic markers in linkage disequilibrium analysis. Thus far, established SNP detection techniques have utilized enzymes to meet the sensitivity and specificity requirements needed to overcome the high complexity of the human genome. Herein, we present for the first time a microarray-based method that allows multiplex SNP genotyping in total human genomic DNA without the need for target amplification or complexity reduction. This direct SNP genotyping methodology requires no enzymes and relies on the high sensitivity of the gold nanoparticle probes. Specificity is derived from two sequential oligonucleotide hybridizations to the target by allele-specific surface-immobilized capture probes and gene-specific oligonucleotide-functionalized gold nanoparticle probes. Reproducible multiplex SNP detection is demonstrated with unamplified human genomic DNA samples representing all possible genotypes for three genes involved in thrombotic disorders. The assay format is simple, rapid and robust pointing to its suitability for multiplex SNP profiling at the ‘point of care’

Third order dielectric susceptibility in a model quantum paraelectric

In the context of perovskite quantum paraelectrics, we study the effects of a quadrupolar interaction $J_q$, in addition to the standard dipolar one $J_d$. We concentrate here on the nonlinear dielectric response $\chi_{P}^{(3)}$, as the main response function sensitive to quadrupolar (in our case antiquadrupolar) interactions. We employ a 3D quantum four-state lattice model and mean-field theory. The results show that inclusion of quadrupolar coupling of moderate strength ($J_q \sim {{1}\over{4}} J_d$) is clearly accompanied by a double change of sign of $\chi_{P}^{(3)}$ from negative to positive, near the quantum temperature $T_Q$ where the quantum paraelectric behaviour sets in. We fit our $\chi_{P}^{(3)}$ to recent experimental data for SrTiO$_3$, where the sign change is identified close to $T_Q \sim 37 K$.Comment: 22 page

Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo

Microarray profiling of zebrafish embryos exposed to a range of environmental toxicants revealed distinct expression profiles for each of the toxicants tested

Tuning of metal-insulator transition of two-dimensional electrons at parylene/SrTiO3_3 interface by electric field

Electrostatic carrier doping using a field-effect-transistor structure is an intriguing approach to explore electronic phases by critical control of carrier concentration. We demonstrate the reversible control of the insulator-metal transition (IMT) in a two dimensional (2D) electron gas at the interface of insulating SrTiO$_3$ single crystals. Superconductivity was observed in a limited number of devices doped far beyond the IMT, which may imply the presence of 2D metal-superconductor transition. This realization of a two-dimensional metallic state on the most widely-used perovskite oxide is the best manifestation of the potential of oxide electronics

HIP JOINT LOAD AND MUSCLE STRESS IN SOCCER INSIDE PASSlNG

Studies investigating the mechanisms of adductor injuries in soccer have concentrated on full effort kicks. Purpose of this study was a kinetic analysis of the inside pass. Using infrared cameras and inverse dynamics, hip joint moments and adductor muscle stress was calculated during the swing phase of the pass. Moments in the transverse plane were nearly as high as in full effort kicks reported previously. Muscle stress in the m. gracilis reached up to 450 kPa. Considering the repetitive nature of inside passes in modern sot; cer, adductor muscles undergo high loads in matches and training. This might contribute to the explanation of the high incidences of adductor injuries. Practitioners should therefore consider the load-recovery-relation even in inside pass training. Specific strength training programs for the adductor and abductor muscle groups should be developed

BASEWECS - Influence of the Baltic Sea and its annual ice coverage on the water and energy budget of the Baltic Sea

BASEWECS is a contribution to the German Climate Research Program DEKLIM. The project started in May 2001 and lasted until December 2004. BASEWECS aimed at the investigation of the influence of the Baltic Sea and its annual ice coverage on the water and energy budget of the BALTEX are