Linking the DNA strand asymmetry to the spatio-temporal replication program. I. About the role of the replication fork polarity in genome evolution

Two key cellular processes, namely transcription and replication, require the opening of the DNA double helix and act differently on the two DNA strands, generating different mutational patterns (mutational asymmetry) that may result, after long evolutionary time, in different nucleotide compositions on the two DNA strands (compositional asymmetry). We elaborate on the simplest model of neutral substitution rates that takes into account the strand asymmetries generated by the transcription and replication processes. Using perturbation theory, we then solve the time evolution of the DNA composition under strand-asymmetric substitution rates. In our minimal model, the compositional and substitutional asymmetries are predicted to decompose into a transcription- and a replication-associated components. The transcription-associated asymmetry increases in magnitude with transcription rate and changes sign with gene orientation while the replication-associated asymmetry is proportional to the replication fork polarity. These results are confirmed experimentally in the human genome, using substitution rates obtained by aligning the human and chimpanzee genomes using macaca and orangutan as outgroups, and replication fork polarity determined in the HeLa cell line as estimated from the derivative of the mean replication timing. When further investigating the dynamics of compositional skew evolution, we show that it is not at equilibrium yet and that its evolution is an extremely slow process with characteristic time scales of several hundred Myrs.

How reliably can paediatric professionals identify pale stool from cholestatic newborns?

BACKGROUND

The success of surgery in infants with hepatobiliary disease is inversely proportional to the age when surgery was performed. Pale stool colour is a major indicator of biliary obstruction. However, simple recognition has been inadequate, resulting in late diagnosis and referral. Objective To assess the skills of healthcare professionals in recognising pale stools.

METHOD

Photographs of normal, acholic and indeterminate infant stools were shown to paediatric professionals who have regular contact with jaundiced babies at three London teaching hospitals. Each stool was classified as 'healthy' or 'suspect'.

RESULTS

One-third of the stools were not correctly identified by physicians and nurses.

CONCLUSION

Experienced professionals often do not recognise stool colour associated with biliary obstruction. The authors propose that stool colour cards similar to those used in Japan and Taiwan may improve early detection of hepatobiliary disease at a minimal cost.

Impact of bias in crown-rump length measurement at first-trimester screening for trisomy 21

OBJECTIVE

To assess the repeatability of crown-rump length (CRL) measurement and examine the effect of its over- and underestimation on first-trimester combined screening.

METHODS

Intra- and interoperator repeatability of CRL measurement at 11-13 weeks of gestation was assessed in 124 cases by two operators. Raw data were transformed into gestational age and intra- and interoperator repeatability was evaluated by within-operator standard deviation (SD) and the SD of differences in measurements between both operators. Modeling techniques were used to assess the impact of CRL measurement error on general population screening and on the operator-specific screening performance. The impact of errors in CRL measurement were investigated by simulating fetal nuchal translucency (NT) measurements and multiple of the median (MoM) values for pregnancy-associated plasma protein A (PAPP-A) and free β-human chorionic gonadotropin (β-hCG) for 500 000 euploid and 500 000 trisomy 21 pregnancies at 12 weeks and 9 weeks of gestation, and adding to or subtracting from each CRL value up to 10 mm and recalculating patient-specific risks.

RESULTS

Within-operator SD of the CRL measurement was 1.27 days of gestation. The SD of the differences in CRL measurement between operators was 1.37 days of gestation. Both intra- and interoperator 95% limits of agreement were around ± 5 mm. In general population-based screening, a CRL measurement error SD of 5 mm accounts for an estimated 5% of the SD of log MoM PAPP-A and less than 1% of the SD of log MoM free β-hCG. Modeling the effect of removing this measurement error on overall screening performance showed a minimal impact. For a risk cut-off of 1 in 100, the benefit in terms of overall screening performance would be an increase in detection rate of about 1% and a reduction in false-positive rate of less than 0.1%. With regard to the operator-specific screening performance, a consistent 5-mm underestimation of CRL reduces the detection rate from 84% to 79% and the false-positive rate from 2.4% to 1.2%. With a consistent 5-mm overestimation the rates would be 88% and 5.6%, respectively.

CONCLUSION

The impact of the interoperator variability in CRL measurement on patient-specific risk needs to be taken into account when interpreting first-trimester screening results. A systematic under- or overestimation of CRL should be avoided.

Inferring where and when replication initiates from genome-wide replication timing data

Based on an analogy between DNA replication and one dimensional nucleation-and-growth processes, various attempts to infer the local initiation rate I(x,t) of DNA replication origins from replication timing data have been developed in the framework of phase transition kinetics theories. These works have all used curve-fit strategies to estimate I(x,t) from genome-wide replication timing data. Here, we show how to invert analytically the Kolmogorov-Johnson-Mehl-Avrami model and extract I(x,t) directly. Tests on both simulated and experimental budding-yeast data confirm the location and firing-time distribution of replication origins.

S3-5: Next Generation Sequencing Reveals Co-Activating Events in the MAPK and P13K/AKT Pathways in Metastatic Triple Negative Breast Cancers

INTRODUCTION: The clinical application of next generation sequencing to comprehensively characterize groups of driving mutations in individual metastatic triple negative breast cancer (mTNBC) genomes has the potential to reveal therapeutically relevant pathway dependencies. Towards this end, we harvested tissue from 14 patients with mTNBC and are conducting deep whole genome and transcriptome sequencing for each case to identify mutations that can guide therapeutic targeting within available phase I/II clinical trials.

METHODS: Metastatic tumor tissue was harvested from 14 mTNBC patients, and 7 samples have undergone total genome and transcriptome sequencing with the others currently underway. We are utilizing the Life Technologies SOLiD® system to sequence germline and tumor DNA to sufficient depth to identify somatic genome alterations including point mutations, indels, and structural events including translocations. Furthermore, RNA-seq is being performed on these tumors, along with a series of age- and ethnicity-matched normal breast controls to perform deep differential expression analysis, isoform expression analysis, and fusion transcript detection. Our team of genome scientists and clinical oncologists are evaluating the sequencing findings and are prioritizing the investigational therapeutic options for each patient.

RESULTS: Our whole genome and transcriptome sequencing study has revealed numerous known and novel mutations in mTNBC. However, all patients’ cancers analyzed to date had alterations that would activate the MAPK pathway, but through various mechanisms in different patients. These include BRAF amplification and overexpression, NF1 homozygous deletion, and consistent IQGAP3 overexpression. Furthermore, all patients’ cancers also harbor mutations that would activate the PI3K/AKT pathway including PTEN homozygous deletion or down-regulation, consistent INPP4B down-regulation, FBXW7 homozygous deletion, and ERAS overexpression. Moreover, although we and others show ERBB4 down-regulation in breast tumors, we are the first to report unique somatic genomic events that significantly alter the ERBB4 locus leading to its loss in the majority (5/7) of our patients’ tumors. Importantly, we are beginning to use these insights to prioritize therapeutic targeting and have observed that one chemotherapy-refractory mTNBC patient, with a high-level BRAF amplification/overexpression along with down-regulation of PTEN and INPP4B, had a major response to combined mek plus akt inhibitors on a phase I study.

CONCLUSIONS: Comprehensive genomic and transcriptomic interrogation of mTNBCs has revealed events supporting co-activation of the MAPK and PI3K/AKT pathways in all the tumors albeit by different mutational mechanisms and supports potential effectiveness of combination therapy in the treatment of mTNBC. We plan to treat these patients with combined mek plus akt inhibitors on a new phase I study beginning in August 2011 to determine the effectiveness of co-inhibition of these pathways based on this frequent genomic context.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S3-5.

Analysis of airway epithelial regeneration and repair following endobronchial brush biopsy in sheep

Understanding the fundamental processes involved in repairing the airway wall following injury is fundamental to understanding the way in which these processes are perturbed during disease pathology. Indeed complex diseases such as asthma and chronic obstructive pulmonary disease (COPD) have at their core evidence of airway wall remodeling processes that play a crucial functional role in these diseases. The authors sought to understand the dynamic cellular events that occur during bronchial airway epithelial repair in sheep. The injury was induced by endobronchial brush biopsy (BBr), a process that causes epithelial débridement and induces a consequential repair process. In addition, the current experimental protocol allowed for the time-dependent changes in airway wall morphology to be studied both within and between animals. The initial débridement was followed by evidence of dedifferentiation in the intact epithelium at the wound margins, followed by proliferation of cells both within the epithelium and in the deeper wall structures, notably in association with the submucosal glands and smooth muscle bundles. Seven days after injury, although the airway wall was thickened at the site of damage, the epithelial layer was intact, with evidence of redifferentiation. These studies, in demonstrating broad agreement with previous studies in small animals, indicate the wider relevance of this system as a comparative model and should provide a solid basis upon which to further characterize the critical cellular and molecular interactions that underlie both effective restitution and pathological repair.

Impact of bias in serum free beta-human chorionic gonadotropin and pregnancy-associated plasma protein-A multiples of the median levels on first-trimester screening for trisomy 21

OBJECTIVE

To examine the effect of bias in median multiples of the median (MoM) levels of pregnancy-associated plasma protein-A (PAPP-A) and free beta-human chorionic gonadotropin (β-hCG) on first-trimester combined screening for trisomy 21.

METHODS

The effects of deviations in the MoM levels of free β-hCG and PAPP-A were investigated by simulating nuchal translucency (NT) at 12 weeks and MoM values for PAPP-A and free β-hCG for 500 000 euploid and 500 000 trisomy 21 pregnancies at 9 and at 12 weeks of gestation. Likelihoods were calculated using the mixture model for NT and the standard Gaussian model for log MoM PAPP-A and free β-hCG values. Deviations in MoM marker levels were simulated by applying percentage changes of 5% to 20% to MoM values. Detection and false-positive rates were calculated with and without adjustments of the maternal serum marker levels by taking the proportion of euploid and aneuploid cases above given thresholds for each maternal age and then taking a weighted average with respect to the maternal age distribution.

RESULTS

With median MoM levels on target, the modeled detection and false-positive rates in combined screening for trisomy 21 at 12 weeks of gestation with a fixed risk cut-off of 1 in 100 were 85% and 2.5%, respectively. For median MoM levels of free β-hCG and PAPP-A between 0.8 and 1.2 MoM, detection rates ranged from 77% to 91%, with corresponding false-positive rates ranging from 1.0% to 6.1%.

CONCLUSION

In first-trimester screening for trisomy 21, biases in the serum marker MoM levels of 10% can increase false-positive rates by over 50%, whilst biases of 20% can more than double false-positive rates.

Characterisation of dissolved organic matter in karst spring waters using intrinsic fluorescence: relationship with infiltration processes

From analysis of spectrophotometric properties of dissolved organic matter (OM) and the hydrochemical responses of some karst springs under different hydrologic conditions, an assessment of the origin and transfer pathway of OM present in karst spring waters, from soil and epikarst toward the spring, has been conducted for three karst aquifers in southern Spain: Alta Cadena, Sierra de Enmedio and Los Tajos. Intrinsic fluorescence (excitation-emission matrices or EEMs), together with major water chemistry (electrical conductivity, temperature, alkalinity, Cl⁻, Mg⁺²) and P(CO₂) along with natural hydrochemical tracers (TOC and NO₃⁻, have been monitored in 19 springs which drain the three karst aquifers examined in this study. The spring water EEM spectra indicate that fulvic acid-like substances, produced in the soil as a consequence of the decomposition of OM, are the dominant fluorophores, although some of the OM appears to originate from in situ microbiological activity but could be indicative of contamination present in recharge waters from livestock. During each recharge event, TOC and NO₃⁻ concentrations increased and variations in fluorescence intensities of peaks attributed to fulvic acid-like compounds were observed. In areas with minimal soil development, spatial and temporal variations in the fluorescence intensity of fulvic acid-like substances and other fluorophores derived from microbiological activity, together with other hydrochemical parameters, provide insights into the hydrogeological functioning of karst aquifers and the infiltration velocity of water from soil and facilitate assessment of contamination vulnerability in these aquifers.

Comparison of heating methods and the use of different tissues for sensory assessment of abnormal odours (boar taint) in pig meat

Five heating methods (microwave, hotwire, boiling at 25 °C and 75 °C and melting) were used to generate cooking odours from backfat of entire male pigs and a 'composite' sample consisting of fat and muscle from the head along with salivary glands. The methods elicited significantly different scores for odours from 4 groups of 10 samples differing in their concentrations and ratios of skatole and androstenone. The odours (pork odour, abnormal odour, skatole odour and androstenone odour) were assessed by 3 experienced assessors. Correlations between skatole and androstenone concentrations and abnormal odour score in backfat were higher for skatole, suggesting it is the more important boar taint compound. In the composite sample, androstenone concentration was much higher than in backfat and androstenone was a more important contributor to boar taint. The microwave, hotwire and boiling (75 °C) methods produced the clearest separation between samples and the microwave method was considered the most suitable for on-line use.

A non-synonymous SNP within membrane metalloendopeptidase-like 1 (MMEL1) is associated with multiple sclerosis

Several single-nucleotide polymorphism (SNP) genome-wide association studies (GWASs) have been completed in multiple sclerosis (MS). Follow-up studies of the variants with the most promising rankings, especially when supplemented by informed candidate gene selection, have proven to be extremely successful. In this study we report the results of a multi-stage replication analysis of the putatively associated SNPs identified in the Wellcome Trust Case Control Consortium non-synonymous SNP (nsSNP) screen. In total, the replication sample consisted of 3444 patients and 2595 controls. A combined analysis of the nsSNP screen and replication data provides evidence implicating a novel additional locus, rs3748816 in membrane metalloendopeptidase-like 1 (MMEL1; odds ratio=1.16, P=3.54 × 10⁻⁶) in MS susceptibility.

Nitrogen fixation associated with sago (Metroxylon sagu) and some implications

AIMS

To determine the presence and contribution of diazotrophic bacteria to nitrogen concentrations in edible starch derived from the sago palm (Metroxylon sagu).

METHODS AND RESULTS

Isolation of diazotrophic bacteria and analysis of nitrogen fixation were conducted on pith, root and sago starch samples. Acetylene reduction showed that five of ten starch samples were fixing nitrogen. Two presumptive nitrogen-fixing bacteria from starch fixed nitrogen in pure culture and five isolates were positive for the nif H gene. Nitrogen concentrations in 51 starch samples were low (37 samples <0·2 g kg(-1); 14 ranging from 0·2 to 2·0 g kg(-1)).

CONCLUSIONS

Nitrogen fixation occurs in sago starch, which undoubtedly plays a role in fermentation ecology. Nitrogen levels are considered too low to be of nutritional benefit and to protect against nutritional-associated illnesses.

SIGNIFICANCE AND IMPACT OF THE STUDY

Sago starch does not add significantly to the protein calorie intake and may be associated with susceptibility to nutritional-associated illness.

Fluorescent properties of organic carbon in cave dripwaters: effects of filtration, temperature and pH

For the first time the specific fluorescent characteristics of organic carbon (OC) in sequentially filtered cave dripwater samples have been studied and the proportions of organic carbon in each size fraction quantified. We examined the effects of pH, temperature and filtration on the fluorescent properties of OC sampled from four drip points in different seasons. Dripwaters were sampled from both normal (pH 7.5-8.5) and hyper-alkaline (pH 9-13) drip points in Poole's Cavern, Buxton, UK, which provides a model system for understanding the effects of pH on the chemical properties of OC. At high-pH values, charge stabilisation of OC is greatly enhanced, resulting in 10-20 times more coarse colloidal and particulate (>100 nm) organic carbon than in lower pH dripwaters; indicating that destabilisation (e.g. charge shielding) of colloidal OC is an important process control on the transmission of OC in cave dripwaters at near-neutral pH. OC fluorescence in high-pH dripwaters exhibited a high degree of pH sensitivity between pH 10 and 12, consistent with substantial changes in the coordination or neighbouring environment of fluorescent acidic functional groups. Inner-filter effects (IFE) associated with the coarse colloidal and particulate fraction of OM mask the true fluorescent signal, so that size fractionation is necessary to obtain a signal which is correlated with the concentration of organic carbon. Fluorescence intensities in the samples studied were best correlated with organic carbon with a dimension <100 nm. These results have important implications for the use of fluorescence as a tracer in hydrogeological studies.