Ectodermal Wnt signaling, cell fate determination, and polarity of the skate gill arch skeleton

The gill skeleton of cartilaginous fishes (sharks, skates, rays, and holocephalans) exhibits a striking anterior-posterior polarity, with a series of fine appendages called branchial rays projecting from the posterior margin of the gill arch cartilages. We previously demonstrated in the skate (Leucoraja erinacea) that branchial rays derive from a posterior domain of pharyngeal arch mesenchyme that is responsive to Sonic hedgehog (Shh) signaling from a distal gill arch epithelial ridge (GAER) signaling centre. However, how branchial ray progenitors are specified exclusively within posterior gill arch mesenchyme is not known. Here, we show that genes encoding several Wnt ligands are expressed in the ectoderm immediately adjacent to the skate GAER, and that these Wnt signals are transduced largely in the anterior arch environment. Using pharmacological manipulation, we show that inhibition of Wnt signalling results in an anterior expansion of Shh signal transduction in developing skate gill arches, and in the formation of ectopic anterior branchial ray cartilages. Our findings demonstrate that ectodermal Wnt signalling contributes to gill arch skeletal polarity in skate by restricting Shh signal transduction and chondrogenesis to the posterior arch environment and highlights the importance of signalling interactions at embryonic tissue boundaries for cell fate determination in vertebrate pharyngeal arches.

Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis

BACKGROUND

Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood.

RESULTS

Here we report a single-cell transcriptomic atlas from Dnmt and Tet mutant mouse embryos during early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos.

CONCLUSIONS

This study provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at a whole organism scale and affords new insights into the regulatory mechanisms of cell fate decisions.

Intrinsic Nature of Spontaneous Magnetic Fields in Superconductors with Time-Reversal Symmetry Breaking

We present a systematic investigation of muon-stopping states in superconductors that reportedly exhibit spontaneous magnetic fields below their transition temperatures due to time-reversal symmetry breaking. These materials include elemental rhenium, several intermetallic systems, and Sr_{2}RuO_{4}. We demonstrate that the presence of the muon leads to only a limited and relatively localized perturbation to the local crystal structure, while any small changes to the electronic structure occur several electron volts below the Fermi energy, leading to only minimal changes in the charge density on ions close to the muon. Our results imply that the muon-induced perturbation alone is unlikely to lead to the observed spontaneous fields in these materials, whose origin is more likely intrinsic to the time-reversal symmetry-broken superconducting state.

Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw

The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral (DV) patterning mechanisms within the developing mandibular, hyoid, and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralizing BMP and endothelin signaling pathways and their effectors, the joint markers nkx3.2 and gdf5 and prochondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, whereas differences in notch signaling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the DV axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.

Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis

Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome of individual oocytes from reproductively young and old mice undergoing natural ovulation. We find reduced complexity as well as increased variance in the transcriptome of oocytes from aged females. This transcriptome heterogeneity is reflected in the identification of discrete sub‐populations. Oocytes with a transcriptome characteristic of immature chromatin configuration (NSN) clustered into two groups: one with reduced developmental competence, as indicated by lower expression of maternal effect genes, and one with a young‐like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post‐transcriptional basis for most age‐related effects on the transcriptome. However, we did find differences in gene body methylation at which there were corresponding changes in gene expression, indicating age‐related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age‐related phenotypes in offspring.

Origin of Magnetic Ordering in a Structurally Perfect Quantum Kagome Antiferromagnet

The ground state of the simple Heisenberg nearest-neighbor quantum kagome antiferromagnetic model is a magnetically disordered spin liquid, yet various perturbations may lead to fundamentally different states. Here we disclose the origin of magnetic ordering in the structurally perfect kagome material YCu_{3}(OH)_{6}Cl_{3}, which is free of the widespread impurity problem. Ab initio calculations and modeling of its magnetic susceptibility reveal that, similar to the archetypal case of herbertsmithite, the nearest-neighbor exchange is by far the dominant isotropic interaction. Dzyaloshinskii-Moriya (DM) anisotropy deduced from electron spin resonance, susceptibility, and specific-heat data is, however, significantly larger than in herbertsmithite. By enhancing spin correlations within kagome planes, this anisotropy is essential for magnetic ordering. Our study isolates the effect of DM anisotropy from other perturbations and unambiguously confirms the predicted phase diagram.

Multi-omics profiling of mouse gastrulation at single-cell resolution

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes1-5. Global epigenetic reprogramming accompanies these changes6-8, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.

Using deterministic record linkage to link ambulance and emergency department data: is it possible without patient identifiers? A case study from the UK

INTRODUCTION

Routine linkage of emergency ambulance records with those from the emergency department is uncommon in the UK. Our study, known as the Pre-Hospital Emergency Department Data Linking Project (PHED Data), aimed to link records of all patients conveyed by a single emergency ambulance service to thirteen emergency departments in the UK from 2012-2016.

OBJECTIVES

We aimed to examine the feasibility and resource requirements of collecting de-identified emergency department patient record data and, using a deterministic matching algorithm, linking it to ambulance service data.

METHODS

We used a learning log to record contacts and activities undertaken by the research team to achieve data linkage. We also conducted semi-structured interviews with information management/governance staff involved in the process.

RESULTS

We found that five steps were required for successful data linkage for each hospital trust. The total time taken to achieve linkage was a mean of 65 weeks. A total of 958,057 emergency department records were obtained and, of these, 81% were linked to a corresponding ambulance record. The match rate varied between hospital trusts (50%-94%). Staff expressed strong enthusiasm for data linkage. Barriers to successful linkage were mainly due to inconsistencies between and within acute trusts in the recording of two ambulance event identifiers (CAD and call sign). Further data cleaning was required on emergency department fields before full analysis could be conducted. Ensuring the data was not re-identifiable limited validation of the matching method.

CONCLUSION

We conclude that deterministic record linkage based on the combination of two event identifiers (CAD and call sign) is possible. There is an appetite for data linkage in healthcare organisations but it is a slow process. Developments in standardising the recording of emergency department data are likely to improve the quality of the resultant linked dataset. This would further increase its value for providing evidence to support improvements in health care delivery.

HIGHLIGHTS

Ambulance records are rarely linked to other datasets; this study looks at the feasibility and resource requirement to use deterministic matching to link ambulance and emergency department data for patients conveyed by ambulance to the emergency department.It is possible to link these data, with an average match rate of 81% across 13 emergency departments and one large ambulance trust.All trusts approached provided match-able data and there was an appetite for data linkage; however, it was a long process taking an average of 65 weeks.We conclude that deterministic matching using no patient identifiers can be used in this setting.

Local magnetism, magnetic order and spin freezing in the 'nonmetallic metal' FeCrAs

We present the results of x-ray scattering and muon-spin relaxation ([Formula: see text]SR) measurements on the iron-pnictide compound FeCrAs. Polarized non-resonant magnetic x-ray scattering results reveal the 120° periodicity expected from the suggested three-fold symmetric, non-collinear antiferromagnetic structure. [Formula: see text]SR measurements indicate a magnetically ordered phase throughout the bulk of the material below [Formula: see text] K. There are signs of fluctuating magnetism in a narrow range of temperatures above [Formula: see text] involving low-energy excitations, while at temperatures well below [Formula: see text] behaviour characteristic of freezing of dynamics is observed, likely reflecting the effect of disorder in our polycrystalline sample. Using density functional theory we propose a distinct muon stopping site in this compound and assess the degree of distortion induced by the implanted muon.

Complex Low Energy Tetrahedral Polymorphs of Group IV Elements from First Principles

The energy landscape of carbon is exceedingly complex, hosting diverse and important metastable phases, including diamond, fullerenes, nanotubes, and graphene. Searching for structures, especially those with large unit cells, in this landscape is challenging. Here we use a combined stochastic search strategy employing two algorithms (ab initio random structure search and random sampling strategy combined with space group and graph theory) to apply connectivity constraints to unit cells containing up to 100 carbon atoms. We uncover three low energy carbon polymorphs (Pbam-32, P6/mmm, and I4[over ¯]3d) with new topologies, containing 32, 36, and 94 atoms in their primitive cells, respectively. Their energies relative to diamond are 96, 131, and 112  meV/atom, respectively, which suggests potential metastability. These three carbon allotropes are mechanically and dynamically stable, insulating carbon crystals with superhard mechanical properties. The I4[over ¯]3d structure possesses a direct band gap of 7.25 eV, which is the widest gap in the carbon allotrope family. Silicon, germanium, and tin versions of Pbam-32, P6/mmm, and I4[over ¯]3d also show energetic, dynamical, and mechanical stability. The computed electronic properties show that they are potential materials for semiconductor and photovoltaic applications.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

Histopathological tumour viability after neoadjuvant chemotherapy influences survival in resected pancreatic cancer: analysis of early outcome data

BACKGROUND

Neoadjuvant therapy is increasingly recognized as an effective strategy prior to pancreatoduodenectomy. We investigate the role of neoadjuvant chemotherapy (NAC) followed by surgery and the predictive role of viable residual tumour cells histopathologically on outcomes.

METHODS

The study population comprised of 195 consecutive patients with pancreatic adenocarcinoma who were treated with either NAC or a surgery-first (SF) strategy. Histopathological viable tumour cells were examined in the NAC patients and clinicopathological factors were correlated with overall survival.

RESULTS

Forty-two patients (22%) were treated with NAC and 153 patients (78%) underwent SF. NAC was associated with higher estimated blood loss during surgery (928 mL versus 615 mL; P = 0.004), fewer (<15) excised lymph nodes (37% versus 17%; P = 0.015) and lower rates of lymphovascular invasion (65% versus 45%; P = 0.044) when compared with SF. Two-year survival of patients undergoing NAC was 63% and 51% in patients undergoing SF (P = 0.048). The 2-year survival of patients who had >65% residual tumour cells was 45% and 90% in patients who had <65% residual tumour cells (P = 0.022). Favourable responders (<65% viable tumour cells) were observed to have shorter operation time (<420 min) (55% versus 13%; P = 0.038), trend towards negative lymph node status (38% versus 10%; P = 0.067) and greater lymph node harvest in node positive patients (≥4 positive lymph nodes) (77% versus 37%; P = 0.045).

CONCLUSION

The improved survival of patients undergoing NAC indicates effective management of micrometastatic disease and is an effective option requiring further investigation. Histopathological viable tumour cells after NAC was a surrogate marker for survival.

A local Fock-exchange potential in Kohn-Sham equations

We derive and employ a local potential to represent the Fock exchange operator in electronic single-particle equations. This local Fock-exchange (LFX) potential is very similar to the exact exchange (EXX) potential in density functional theory (DFT). The practical software implementation of the two potentials (LFX and EXX) yields robust and accurate results for a variety of systems (semiconductors, transition metal oxides) where Hartree-Fock and popular approximations of DFT typically fail. This includes examples traditionally considered qualitatively inaccessible to calculations that omit correlation.

Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity

Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

Induced thiacloprid insensitivity in honeybees (Apis mellifera L.) is associated with up-regulation of detoxification genes

Honey bees, Apis mellifera, are markedly less sensitive to neonicotinoid insecticides containing a cyanoimino pharmacophore than to those with a nitroimino group. Although previous work has suggested that this results from enhanced metabolism of the former by detoxification enzymes, the specific enzyme(s) involved remain to be characterized. In this work, a pretreatment of honey bees with a sublethal dose of thiacloprid resulted in induced insensitivity to the same compound immediately following thiacloprid feeding. A longer pretreatment time resulted in no, or increased, sensitivity. Transcriptome profiling, using microarrays, identified a number of genes encoding detoxification enzymes that were over-expressed significantly in insecticide-treated bees compared with untreated controls. These included five P450s, CYP6BE1, CYP305D1, CYP6AS5, CYP315A1, CYP301A1, and a carboxyl/cholinesterase (CCE) CCE8. Four of these P450s were functionally expressed in Escherichia coli and their ability to metabolize thiacloprid examined by liquid chromatography-mass spectrometry (LC-MS) analysis.

Muon-spin relaxation study of the double perovskite insulators Sr2 BOsO6 (B = Fe, Y, ln)

We present the results of zero-field muon-spin relaxation measurements made on the double perovskite insulators Sr2 BOsO6 (B = Fe,Y, In). Spontaneous muon-spin precession indicative of quasistatic long range magnetic ordering is observed in Sr2FeOsO6 within the AF1 antiferromagnetic phase for temperatures below [Formula: see text] K. Upon cooling below T2≈67 K the oscillations cease to be resolvable owing to the coexistence of the AF1 and AF2 phases, which leads to a broader range of internal magnetic fields. Using density functional calculations we identify a candidate muon stopping site within the unit cell, which dipole field simulations show to be consistent with the proposed magnetic structure. The possibility of incommensurate magnetic ordering is discussed for temperatures below TN = 53 K and 25 K for Sr2YOsO6 and Sr2InOsO6, respectively.

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneously methylated distal regulatory elements and transcription of key pluripotency genes.

Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis

The integrity of chromatin, which provides a dynamic template for all DNA-related processes in eukaryotes, is maintained through replication-dependent and -independent assembly pathways. To address the role of histone deposition in the absence of DNA replication, we deleted the H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is dynamic and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. Our study thus unequivocally shows the importance of continuous histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in a non-replicative system in vivo.

A national survey of parent perspectives on use of patient portals for their children's health care

OBJECTIVES

To assess parents' current utilization and future willingness to use patient portals to interact with their child's health care provider.

METHODS

A cross-sectional survey of a nationally representative sample of US parents was conducted using an established online panel. Bivariate analyses assessed associations between current utilization and future willingness to use patient portals, parental concerns, and demographic variables.

RESULTS

Among the 1,420 parent respondents, 40% did not know whether their child's health practice offers the option of setting up a patient portal for their child. Of the 21% of parents who reported being offered the option of setting up a patient portal for their child, 59% had done so. Among parents who had the option but chose not to set up a patient portal for their child, lack of time and low perceived need were the main reasons cited. Current use and likelihood of future use was highest for viewing lab results and immunization records. The most common concern about patient portals was the security of the child portal system.

CONCLUSIONS

Current use of patient portals by parents is low. Only about half of parents currently using or likely to use a portal perceive value in using portals for certain tasks, which suggests that providers will need to continue traditional communication mechanisms to reach their entire patient population.

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation

Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup.

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An enhanced bisulfite strategy allows genome-wide methylation profiling of zygotes

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Gene bodies constitute a major target of zygotic demethylation and TET3 oxidation

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The impact of TET3 loss is moderate and implicates redundant demethylation pathways

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Protective TET3 activity shields certain CpG islands against methylation buildup

Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer

Background:

Glutathione S-transferase 1 (GSTP1) inactivation is associated with CpG island promoter hypermethylation in the majority of prostate cancers (PCs). This study assessed whether the level of circulating methylated GSTP1 (mGSTP1) in plasma DNA is associated with chemotherapy response and overall survival (OS).

Methods:

Plasma samples were collected prospectively from a Phase I exploratory cohort of 75 men with castrate-resistant PC (CRPC) and a Phase II independent validation cohort (n=51). mGSTP1 levels in free DNA were measured using a sensitive methylation-specific PCR assay.

Results:

The Phase I cohort identified that detectable baseline mGSTP1 DNA was associated with poorer OS (HR, 4.2 95% CI 2.1–8.2; P<0.0001). A decrease in mGSTP1 DNA levels after cycle 1 was associated with a PSA response (P=0.008). In the Phase II cohort, baseline mGSTP1 DNA was a stronger predictor of OS than PSA change after 3 months (P=0.02). Undetectable plasma mGSTP1 after one cycle of chemotherapy was associated with PSA response (P=0.007).

Conclusions:

We identified plasma mGSTP1 DNA as a potential prognostic marker in men with CRPC as well as a potential surrogate therapeutic efficacy marker for chemotherapy and corroborated these findings in an independent Phase II cohort. Prospective Phase III assessment of mGSTP1 levels in plasma DNA is now warranted.

Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer

Background:

Docetaxel is the first-line chemotherapy for castration-resistant prostate cancer (CRPC). However, response rates are ∼50% and determined quite late in the treatment schedule, thus non-responders are subjected to unnecessary toxicity. The potential of circulating microRNAs as early biomarkers of docetaxel response in CRPC patients was investigated in this study.

Methods:

Global microRNA profiling was performed on docetaxel-resistant and sensitive cell lines to identify candidate circulating microRNA biomarkers. Custom Taqman Array MicroRNA cards were used to measure the levels of 46 candidate microRNAs in plasma/serum samples, collected before and after docetaxel treatment, from 97 CRPC patients.

Results:

Fourteen microRNAs were associated with serum prostate-specific antigen (PSA) response or overall survival, according to Mann–Whitney U or log-rank tests. Non-responders to docetaxel and patients with shorter survival generally had high pre-docetaxel levels of miR-200 family members or decreased/unchanged post-docetaxel levels of miR-17 family members. Multivariate Cox regression with bootstrapping validation showed that pre-docetaxel miR-200b levels, post-docetaxel change in miR-20a levels, pre-docetaxel haemoglobin levels and visceral metastasis were independent predictors of overall survival when modelled together.

Conclusions:

Our study suggests that circulating microRNAs are potential early predictors of docetaxel chemotherapy outcome, and warrant further investigation in clinical trials.

Cardiac Troponin T Following Anthracycline Chemotherapy in Children and Adolescents

Cardiac troponin T (CTT) is elevated acutely in animal models of anthracycline cardiotoxicity. We assessed CTT release in children receiving anthracylines using a third generation assay. We measured CTT in 30 children receiving anthracycline chemotherapy. A total of 3 samples were taken from each child: 1) prior to, 2) immediately after and 3) between 24-48 hours after the infusion. The dose range given during the measurements of cardiac troponin T was 15-60 (median 25) mg/m(2) and the previous exposure ranged from 0-300 (median 150) mg/m(2). Not one child had a detectable CTT level at any time. This study shows a lack of acute elevation CTT following anthracycline administration. In this respect it is unlikely that early estimation of CTT using this modern assay will be useful for screening for anthracycline cadiomyopathy. Further studies using a third generation assay, are, however, indicated to determine whether delayed elevation of CTT occurs.

Three-point appraisal of genetic linkage maps

This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8-12 cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped.

The high-pressure electronic structure of the [Ni(ptdt)2] organic molecular conductor

The electronic structure of the single component molecular crystal [Ni(ptdt)(2)] (ptdt = propylenedithiotetrathiafulvalenedithiolate) is determined at ambient and high pressure using density functional theory. The electronic structure of this crystal is found to be of the "crossing bands" type with respect to the dispersion of the HOMO and LUMO, resulting in a small, non-zero density of states at the Fermi energy at ambient pressure, indicating that this crystal is a "poor quality" metal, and is consistent with the crystal's resistivity exhibiting a semiconductor-like temperature dependence. The ambient pressure band structure is found to be predominantly one-dimensional, reflecting enhanced intermolecular interactions along the [100] stacking direction. Our calculations indicate that the band structure becomes two-dimensional at high pressures and reveals the role of shortened intermolecular contacts in this phenomenon. The integrity of the molecular structure is found to be maintained up to at least 22 GPa. The electronic structure is found to exhibit a crossing bands nature up to 22 GPa, where enhanced intermolecular interactions increase the Brillouin zone centre HOMO-LUMO gap from 0.05 eV at ambient pressure to 0.15 eV at 22 GPa; this enhanced HOMO-LUMO interaction ensures that enhancement of a metallic state in this crystal cannot be simply achieved through the application of pressure, but rather requires some rearrangement of the molecular packing. Enhanced HOMO-LUMO interactions result in a small density of states at the Fermi energy for the high pressure window 19.8-22 GPa, and our calculations show that there is no change in the nature of the electronic structure at the Fermi energy for these pressures. We correspondingly find no evidence of an electronic semiconducting-metal insulator transition for these pressures, contrary to recent experimental evidence [Cui et al., J. Am. Chem. Soc. 131, 6358 (2009)].

Mesocosm experiments to assess the transmission of Pandora neoaphidis within simple and mixed field margins and over the crop-margin interface

Although considerable research on the development of agri-environment schemes has focussed on the value of managed field margins as reservoirs for arthropod natural enemies, their potential as reservoirs of entomopathogenic fungi has received less attention. Whether field margins that are most beneficial for arthropod natural enemies are the same as those for entomopathogenic fungi is unknown. Here, within glasshouse mesocosms, we assessed the reproductive success of the aphid-specific entomopathogenic fungus Pandora neoaphidis on aphids in a 'simple margin' containing one plant species and on the same species of aphid in a 'mixed margin' containing seven plant species. These assessments were done in the presence of Aphidius ervi, a hymenopteran parasitoid of aphids regarded as being a key species to conserve in agri-environment schemes in the UK. When only the plants initially infested with aphids were assessed, transmission of P. neoaphidis was significantly greater (p<0.001) in the mixed margin as was parasitisation by A. ervi (p<0.05). However, when all of the plants in the mesocosms were assessed, transmission of P. neoaphidis remained greater in the mixed margin (p<0.05) whereas parasitisation by A. ervi was greater in the simple margin (p<0.05). This difference may be due to aphid dispersal which was greater in the simple margin thereby benefitting the actively foraging parasitoid whereas clustering of aphids in the mixed margin benefited the passively dispersed fungus. In a second mesocosm experiment, the movement of P. neoaphidis over the crop-margin interface was similar to that of A. ervi despite the fungus only being passively dispersed in contrast to the actively foraging parasitoid. The results presented here indicate that, although the optimal plant composition of field margins may differ for P. neoaphidis and A. ervi, both species can co-exist and reproduce in field margins and will move over the crop-margin interface. Managed field margins that benefit both key arthropod and key microbial enemies have potential for enhancing pest control in associated crops.

Association of sirtuin 1 (SIRT1) gene SNPs and transcript expression levels with severe obesity

Recent studies have reported associations of sirtuin 1 (SIRT1) single nucleotide polymorphisms (SNPs) to both obesity and BMI. This study was designed to investigate association between SIRT1 SNPs, SIRT1 gene expression and obesity. Case-control analyses were performed using 1,533 obese subjects (896 adults, BMI >40 kg/m(2) and 637 children, BMI >97th percentile for age and sex) and 1,237 nonobese controls, all French Caucasians. Two SNPs (in high linkage disequilibrium (LD), r(2) = 0.96) were significantly associated with adult obesity, rs33957861 (P value = 0.003, odds ratio (OR) = 0.75, confidence interval (CI) = 0.61-0.92) and rs11599176 (P value: 0.006, OR = 0.74, CI = 0.61-0.90). Expression of SIRT1 mRNA was measured in BMI-discordant siblings from 154 Swedish families. Transcript expression was significantly correlated to BMI in the lean siblings (r(2) = 0.13, P value = 3.36 × 10(-7)) and lower SIRT1 expression was associated with obesity (P value = 1.56 × 10(-35)). There was also an association between four SNPs (rs11599176, rs12413112, rs33957861, and rs35689145) and BMI (P values: 4 × 10(-4), 6 × 10(-4), 4 × 10(-4), and 2 × 10(-3)) with the rare allele associated with a lower BMI. However, no SNP was associated with SIRT1 transcript expression level. In summary, both SNPs and SIRT1 gene expression are associated with severe obesity.

Intraguild interactions between the entomopathogenic fungus Pandora neoaphidis and an aphid predator and parasitoid at the population scale

The interactions that occur between the entomopathogenic fungus Pandora neoaphidis and a predator (Coccinella septempunctata) and a parasitoid (Aphidius ervi) were assessed in microcosm and polytunnel experiments. Transmission of P. neoaphidis to the pea aphid, Acyrthosiphon pisum, was enhanced in the presence of both C. septempunctata and A. ervi in microcosm experiments done under fixed abiotic conditions. In contrast, the reproductive success of A. ervi was reduced in the presence of P. neoaphidis. Despite the increased fungal transmission in the presence of C. septempunctata, there was no additional decrease in the aphid population indicating that P. neoaphidis is functionally redundant in the presence of the coccinellid. In polytunnel experiments the reproductive success of A. ervi was not affected by P. neoaphidis. These results do not support those of the microcosm and may be due to the more natural abiotic conditions in the polytunnel reducing the competitive advantage of the fungus. Microcosms therefore provide an arena in which the interactions between fungal pathogens and other aphid-natural enemies can be assessed however, further assessments at increased spatial scales under more natural abiotic conditions are also required to accurately determine the outcome of these interactions.

Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease

Large chromosomal regions can be suppressed in cancer cells as denoted by hypermethylation of neighbouring CpG islands and downregulation of most genes within the region. We have analysed the extent and prevalence of long-range epigenetic silencing at 2q14.2 (the first and best characterised example of coordinated epigenetic remodelling) and investigated its possible applicability as a non-invasive diagnostic marker of human colorectal cancer using different approaches and biological samples. Hypermethylation of at least one of the CpG islands analysed (EN1, SCTR, INHBB) occurred in most carcinomas (90%), with EN1 methylated in 73 and 40% of carcinomas and adenomas, respectively. Gene suppression was a common phenomenon in all the tumours analysed and affected both methylated and unmethylated genes. Detection of methylated EN1 using bisulfite treatment and melting curve (MC) analysis from stool DNA in patients and controls resulted in a predictive capacity of, 44% sensitivity in positive patients (27% of overall sensitivity) and 97% specificity. We conclude that epigenetic suppression along 2q14.2 is common to most colorectal cancers and the presence of a methylated EN1 CpG island in stool DNA might be used as biomarker of neoplastic disease.

Prevalence of carotid and pulp calcifications: a correlation using digital panoramic radiographs

OBJECTIVE

To compare the prevalence of pulp calcification with that of carotid calcification using digital panoramic dental radiographs.

STUDY DESIGN

Digital panoramic radiographs of patients at a dental oncology clinic were included if (1) the carotid artery bifurcation region was visible bilaterally and (2) the patient had non-restored or minimally restored molars and/or canines. An endodontist evaluated the images for pulpal calcifications in the selected teeth. An oral and maxillofacial radiologist independently evaluated the same images for calcifications in the carotid bifurcation region. Odds-ratio and Pearson chi(2) were used for data analysis. Presence of pulpal calcification was also evaluated as a screening test for the presence of carotid calcification.

RESULTS

A total of 247 panoramic radiographs were evaluated. 32% (n = 80) had pulpal calcifications and 25% (n = 61) had carotid calcifications with 12% (n = 29) having both carotid and pulp calcifications. A significantly higher prevalence of both pulp and carotid calcification was found in subjects older than age 60 years compared to younger age groups. Accuracy of pulpal calcification in screening for carotid calcification was 66.4%.

CONCLUSIONS

Both pulp and carotid calcifications were more prevalent in older individuals. The presence of pulp calcification was not a strong predictor for the presence of carotid calcification.

Effect of seasonal abiotic conditions and field margin habitat on the activity of Pandora neoaphidis inoculum on soil

The ability of the aphid pathogenic fungus Pandora neoaphidis to remain active in the absence of a resting stage through a combination of continuous infection and as conidia deposited on soil was assessed alongside the potential for planted field margins to act as a refuge for the fungus. P. neoaphidis was able to infect the pea aphid, Acyrthosiphon pisum, when maintained under controlled conditions that simulated those that occur seasonally in the UK. Although there was a significant inverse relationship between temperature and time-to-kill, with death occurring after 4.2, 6.9 and 13.6 days when maintained under fluctuating summer, autumn and winter temperatures, respectively, there were no additional statistically significant effects of photoperiod. The activity of inoculum on soil was indirectly assessed by baiting with A. pisum. Under controlled conditions P. neoaphidis remained active on soil and was able to infect aphids for up to 80 days. However, the percentage of aphids that became infected decreased from 76% on day 1 to 11% on day 80. Whereas there was little difference in the activity of conidia that had been maintained at 4 degrees C and 10 degrees C, activity at 18 degrees C was considerably reduced. Under field conditions the activity of inoculum was strongly influenced by season. On day 49 there was little or no activity during spring, summer or winter. However, during autumn a mean proportion of 0.08 aphids still became infected with P. neoaphidis. Margin type did not affect the activity of conidia nor was there a difference in activity between blocks that had regenerated naturally and those that had been planted. These results suggest that P. neoaphidis can infect aphids and remain active on soil under the abiotic conditions that occur seasonally in the UK and that this fungus may be able to persist annually without a resting stage.

Variable levels of carry over on platelet counts < or = 20 x 10(9)/l with the Bayer Advia 120

Accurate platelet counts are essential for the safe management of severe thrombocytopenia (platelet counts < or = 20 x 10(9)/l). The effect of carry over on platelet counting in severe thrombocytopenia was investigated by performing counts before and after saline rinses on three Bayer Advia 120 automated blood counters. Counts were performed in both primary and manual closed tube system modes on two instruments and in manual open tube mode on a third. A total of 194 samples with platelet counts < or = 20 x 10(9)/l were studied. First counts were significantly higher in all groups. The magnitude of the difference varied both by analyser and counting mode. Carry over was minimal with one analyser in primary mode and second counts were on average only 5.5% lower; on a second analyser in manual closed tube system mode second counts were on average 37.7% lower. A first count of > or = 10 x 10(9)/l fell to <10 x 10(9)/l on the second count in 35 of 145 samples (24.1%). In five such samples, all tested on one analyser, the second count was <50% of the value of the first count. Two of 49 (4.1%) first counts of <10 x 10(9)/l increased to > or = 10 x 10(9)/l on repeat. These results show a variable and often potentially clinically important carry-over effect on severely thrombocytopenic samples using the Advia 120.

Nematicidal effects of cysteine proteinases against sedentary plant parasitic nematodes

Cysteine proteinases from the fruit and latex of plants, such as papaya, pineapple and fig, have previously been shown to have substantial anthelmintic efficacy, in vitro and in vivo, against a range of animal parasitic nematodes. In this paper, we describe the in vitro effects of these plant extracts against 2 sedentary plant parasitic nematodes of the genera Meloidogyne and Globodera. All the plant extracts examined caused digestion of the cuticle and decreased the activity of the tested nematodes. The specific inhibitor of cysteine proteinases, E-64, blocked this activity completely, indicating that it was essentially mediated by cysteine proteinases. In vitro, plant cysteine proteinases are active against second-stage juveniles of M. incognita and M. javanica, and some cysteine proteinases also affect the second-stage juveniles of Globodera rostochiensis. It is not known yet whether these plant extracts will interfere with, or prevent invasion of, host plants.

Statistical models to evaluate invertebrate-plant trophic interactions in arable systems

Over the past 40 years there have been marked shifts in arable farmland management that are widely believed to have had a considerable impact on flowering plants and invertebrates and the small mammals and birds that rely upon them. It is not yet possible to predict the dynamics of plants and invertebrates either with past or future changes in farmland management. This study investigates whether a basic invertebrate classification, formed of broad trophic groups, can be used to describe interactions between invertebrates and their resource plants and evaluate management impacts for genetically modified, herbicide-tolerant (GMHT) and conventional herbicide management in both spring- and winter-sown oilseed rape. It is argued that the analyses validate trophic-based approaches for describing the dynamics of invertebrates in farmland and that linear models might be used to describe the changes in invertebrate trophic group abundance in farmland when driven by primary producer abundance or biomass and interactions between invertebrates themselves. The analyses indicate that invertebrate dynamics under GMHT management are not unique, but similar to conventional management occurring over different resource ranges, and that dynamics differed considerably between spring- and winter-sown oilseed rape. Thus, herbicide management was of much lower impact on trophic relationships than sowing date. Results indicate that invertebrate dynamics in oilseed rape are regulated by a combination of top-down and bottom-up trophic processes.

Ecotypes of the model legume Lotus japonicus vary in their interaction phenotypes with the root-knot nematode Meloidogyne incognita

BACKGROUND AND AIMS

Knowledge of host factors affecting plant-nematode interactions is scarce. Here, relevant interaction phenotypes between a nodulating model host, Lotus japonicus, and the endoparasitic root-knot nematode Meloidogyne incognita are assessed via a genetic screen.

METHODS

Within an alpha experimental design, 4-week-old replicate plants from 60 L. japonicus ecotypes were inoculated with 1000 nematodes from a single egg mass population, and evaluated for galling and nematode egg masses 6 weeks after inoculation.

KEY RESULTS

Statistical analysis of data for 57 ecotypes showed that ecotype susceptibilities ranged from 3.5 to 406 galls per root, and correlated strongly (r = 0.8, P < 0.001, log scale) with nematode reproduction (ranging from 0.6 to 34.5 egg masses per root). Some ecotypes, however, showed a significant discrepancy between disease severity and nematode reproduction. Necrosis and developmental malformations were observed in other infected ecotypes.

CONCLUSIONS

The first evidence is provided of significant variability in the interactions between L. japonicus and root-knot nematodes that may have further implications for the genetic dissection and characterization of host pathways involved in nematode parasitism and, possibly, in microbial symbiosis.

Correlation between carotid area calcifications and periodontitis: a retrospective study of digital panoramic radiographic findings in pretreatment cancer patients

OBJECTIVES

The objective of this study was to examine the prevalence of carotid area calcifications retrospectively detected on digital panoramic radiographs of pretreatment cancer subjects, and to correlate the finding of such calcifications with radiographic evidence of periodontal bone loss in the same subjects.

STUDY DESIGN

Digital panoramic radiographs of 201 subjects were evaluated for calcifications projected in the carotid artery bifurcation area as well as for alveolar bone loss as a result of periodontal disease. Inclusion criteria were unobscured carotid artery bifurcation regions bilaterally and sufficient index teeth present with a definable cemento-enamel junction and alveolar crest. Radiographs were independently observed for carotid area calcifications and for periodontal status. Image enhancements permitted for detection of calcifications projected in the carotid area included window/level, inverse, and emboss. Periodontal measurements were made on index teeth using proprietary imaging software and a mouse-driven measurement algorithm. A 3-factor analysis of variance was performed with 3 between-subjects comparisons. Percentage of bone loss was the dependent variable. Independent variables were age, subject sex, and the presence or absence of carotid area calcifications.

RESULTS

Differences measured in percentage of bone loss between sexes were not statistically significant. While bone loss did increase with age, comparison of the mean bone loss of each age category revealed no statistical significance. There was a highly significant correlation between carotid artery area calcifications visible on panoramic radiographs and percent alveolar bone loss. Radiographs showing unilateral and bilateral calcifications had a mean percent bone loss of 24.2% +/- 12.6% and 25.7% +/- 13.0% respectively, compared to those with no calcification at 10.4% +/- 9.9%.

CONCLUSIONS

Nearly 1 in 4 subjects in this study evidenced calcifications projected in the carotid bifurcation region. The finding of such calcifications was significantly related to the calculated percentage of alveolar bone loss.

Effects of genetically modified herbicide-tolerant cropping systems on weed seedbanks in two years of following crops

The Farm Scale Evaluations (FSEs) showed that genetically modified herbicide-tolerant (GMHT) cropping systems could influence farmland biodiversity because of their effects on weed biomass and seed production. Recently published results for winter oilseed rape showed that a switch to GMHT crops significantly affected weed seedbanks for at least 2 years after the crops were sown, potentially causing longer-term effects on other taxa. Here, we seek evidence for similar medium-term effects on weed seedbanks following spring-sown GMHT crops, using newly available data from the FSEs. Weed seedbanks following GMHT maize were significantly higher than following conventional varieties for both the first and second years, while by contrast, seedbanks following GMHT spring oilseed rape were significantly lower over this period. Seedbanks following GMHT beet were smaller than following conventional crops in the first year after the crops had been sown, but this difference was much reduced by the second year for reasons that are not clear. These new data provide important empirical evidence for longer-term effects of GMHT cropping on farmland biodiversity.

Effects of imaging system and exposure on accurate detection of the second mesio-buccal canal in maxillary molar teeth

OBJECTIVES

The objectives of this study were to determine observer ability to detect the second mesio-buccal canal (MB2) in maxillary molars using analog film, CMOS, and photostimulable phosphor x-ray detectors across a wide range of radiation exposures and to determine the optimal exposures for these modalities accurately detecting presence of the MB2.

RESEARCH DESIGN

Using 6 experimental models with 2 maxillary molars in each, images were generated with the 3 detector modalities at nominal x-ray beam angulations of 0 degrees and 10 degrees across a range of radiation exposures. Observers independently assessed presence of the MB2 in images presented in random order. Horizontal root sections were then evaluated to determine true MB2 presence.

RESULTS

For single images at optimal exposures, the correct number of mesiobuccal canals could be identified 55% of the time for CMOS (RVG 6000), 44% of the time for analog x-ray film (InSight), and 39% of the time for photostimulable phosphor (DenOptix). Statistically significant differences were observed between the imaging modalities (chi2 = 23.4, crucial value = 5.99, P < or = .05). RVG 6000 CMOS outperformed both DenOptix photostimulable phosphor (z score = -5.5) and InSight analog direct exposure x-ray film (z score = 4). Exposure affected the rate of accuracy for MB2 detection across the exposure range tested for RVG 6000 and for film, but not to any appreciable degree for DenOptix.

CONCLUSIONS

The CMOS detector (RVG-6000) performed best for evaluating presence of the MB2. This was the only modality to exceed 50% reliability with optimal exposure when single images were considered.

Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries

Two different strategies for molecular analysis of bacterial diversity, 16S rDNA cloning and denaturing gradient gel electrophoresis (DGGE), were combined into a single protocol that took advantage of the best attributes of each: the ability of cloning to package DNA sequence information and the ability of DGGE to display a community profile. In this combined protocol, polymerase chain reaction products from environmental DNA were cloned, and then DGGE was used to screen the clone libraries. Both individual clones and pools of randomly selected clones were analyzed by DGGE, and these migration patterns were compared to the conventional DGGE profile produced directly from environmental DNA. For two simple bacterial communities (biofilm from a humics-fed laboratory reactor and planktonic bacteria filtered from an urban freshwater pond), pools of 35-50 clones produced DGGE profiles that contained most of the bands visible in the conventional DGGE profiles, indicating that the clone pools were adequate for identifying the dominant genotypes. However, DGGE profiles of two different pools of 50 clones from a lawn soil clone library were distinctly different from each other and from the conventional DGGE profile, indicating that this small number of clones poorly represented the bacterial diversity in soil. Individual clones with the same apparent DGGE mobility as prominent bands in the humics reactor community profiles were sequenced from the clone plasmid DNA rather than from bands excised from the gel. Because a longer fragment was cloned (approximately 1500 bp) than was actually analyzed in DGGE (approximately 350 bp), far more sequence information was available using this approach that could have been recovered from an excised gel band. This clone/DGGE protocol permitted rapid analysis of the microbial diversity in the two moderately complex systems, but was limited in its ability to represent the diversity in the soil microbial community. Nonetheless, clone/DGGE is a promising strategy for fractionating diverse microbial communities into manageable subsets consisting of small pools of clones.

Reactivation of latent hepatitis B virus infection with HIV-related immunosuppression

The effect of HIV-related immunosuppression and antiretroviral therapy on the reactivation of latent hepatitis B virus (HBV) infection is unclear. We report four patients with advanced HIV-related immunosuppression and abnormal liver function tests who had evidence of HBV reactivation. Reclearance of hepatitis B occurred in two cases with HIV treatment regimens not containing lamivudine, suggesting that improved immune function may be responsible. In three cases, HBV reactivation was recognized during investigation for abnormal liver function initially attributed to drug toxicity. The possibility of HBV reactivation must be considered in the differential diagnosis of abnormal liver function in cases with advanced HIV.

Effect of fungal infection on the reproductive potential of aphids and their progeny

The effect of infection by Pandora neoaphidis and Beauveria bassiana on the reproductive potential of the pea aphid, Acyrthosiphon pisum, and their progeny was assessed. Infection by either P. neoaphidis or B. bassiana reduced the number of nymphs produced within 24 h of inoculation and over the entire infection period compared to uninfected aphids. However, infection by either P. neoaphidis or B. bassiana for 24 or 72 h did not alter the intrinsic rate of increase of the host aphid's progeny. Therefore, fungal infection appears to have no indirect effects on the fitness of the host's progeny.

Gay priests and other bogeymen

The sexual abuse of boys by priests was at the center of the 2002 scandal in the Roman Catholic Church. This scandal has resurrected the misconception that a link exists between having a homosexual orientation and being at increased risk for being a pedophile or child molester. This paper reviews and debunks the arguments in support of this misconception. Central to these arguments is what might be called the "proportionality argument": that the ratio of homosexuals to heterosexuals among child molesters is higher than the ratio of homosexuals to heterosexuals in the general population. The flaws in the proportionality argument and several other misconceptions are discussed.

Wheat containing snowdrop lectin (GNA) does not affect infection of the cereal aphid Metopolophium dirhodum by the fungal natural enemyPandora neoaphidis

Studies were carried out to determine if susceptibility of the cereal aphid Metopolophium dirhodum to the fungus Pandora neoaphidis was affected by wheat expressing snowdrop lectin (GNA). Aphid infection did not differ significantly between the transgenic GNA and non-transformed lines (91 and 82%, respectively). Fecundity also did not differ between aphids on the two lines, and was ca. 18 nymphs adult(-1). Time to infection was ca. 5 days for M. dirhodum on both lines in two of three assays. Our results indicate that wheat expressing GNA would not compromise the efficacy of P. neoaphidis as a biocontrol agent.

Mutation and methylation analysis of TP53 in adrenal carcinogenesis

AIM

To investigate the role of coding region mutation and promoter hypermethylation of TP53 in adrenocortical cancer formation.

METHODS

Twenty sporadic adrenocortical cancers (ACCs) and five normal adrenal tissue samples were available for analysis. Coding region mutation of TP53 in 20 ACCs was examined by polymerase chain amplification using intronic primers for exons 2-11 and direct sequencing of the product. In 10 ACCs and five normal adrenal tissue specimens, methylation of the 16 CpG sites within the TP53 promoter was examined using bisulphite methylation sequencing.

RESULTS

Coding region mutation in TP53 was demonstrated in 5 of 20 ACCs. There were four mis-sense mutations and one frameshift mutation. Four of 5 patients with a TP53 mutation had metastases at diagnosis or detected soon thereafter and 3 of 4 died of disease within 12 months of surgical resection. No methylation was seen in the TP53 promoter in 10 ACC and the five normal adrenal tissues examined.

CONCLUSION

Coding region mutation in TP53 occurs in 25% of ACCs with a trend toward a poorer prognosis. Promoter methylation of TP53 is not present in ACC as a mechanism for tumour suppressor gene (TSG) inactivation and, therefore, other genes in the 17p13 region are implicated in adrenal carcinogenesis.

Ab initiodynamics study of poly-para-phenylene vinylene

We present an ab initio dynamics investigation within a density-functional perturbation theory framework of the properties of the conjugated polymer poly-para-phenylene vinylene (PPV) in both the isolated chain and crystalline states. The calculated results show that for an isolated chain, most of the vibrational modes correspond to experimentally observed modes in crystalline PPV. However, additional hitherto unidentified modes have been observed in experiment and our calculations on crystalline material have allowed us to assign these. We also present the results of calculations of the polarizability and permittivity tensors of the material, which are in reasonable agreement with the typical values for conjugated polymers. Dynamical Born effective charges [S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001)] are calculated and compared with atomic charges obtained from Mulliken population analysis [M. D. Segall, C. J. Pickard, R. Shah, and M. C. Payne, Mol. Phys. 89, 571 (1996)] and we conclude that effective charges are more appropriate for use in the study of the dynamics of the system. Notable differences are found in the infrared-absorption spectra obtained for the isolated chain and crystalline states, which can be attributed to the differences in the crystalline packing effects, which clearly play a key role in influencing the lattice dynamics of PPV.