Time-resolved, integrated analysis of clonally evolving genomes

Clonal genome evolution is a key feature of asexually reproducing species and human cancer development. While many studies have described the landscapes of clonal genome evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and biological/clinical parameters. Subsequently, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. We then applied this framework to predict the time of speciation of the marbled crayfish, an enigmatic, globally invasive parthenogenetic freshwater crayfish. The results predict that speciation occurred between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze whole-genome sequencing datasets from primary and relapsed glioblastoma, an aggressive brain tumor. The results identified evolutionary subgroups and showed that tumor cell survival could be inferred from genomic data that was generated during the resection of the primary tumor. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.

Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed

Queuosine (Q) is a modified nucleoside at the wobble position of specific tRNAs. In mammals, queuosinylation is facilitated by queuine uptake from the gut microbiota and is introduced into tRNA by the QTRT1-QTRT2 enzyme complex. By establishing a Qtrt1 knockout mouse model, we discovered that the loss of Q-tRNA leads to learning and memory deficits. Ribo-Seq analysis in the hippocampus of Qtrt1-deficient mice revealed not only stalling of ribosomes on Q-decoded codons, but also a global imbalance in translation elongation speed between codons that engage in weak and strong interactions with their cognate anticodons. While Q-dependent molecular and behavioral phenotypes were identified in both sexes, female mice were affected more severely than males. Proteomics analysis confirmed deregulation of synaptogenesis and neuronal morphology. Together, our findings provide a link between tRNA modification and brain functions and reveal an unexpected role of protein synthesis in sex-dependent cognitive performance.

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets

Conventional dimensionality reduction methods like Multidimensional Scaling (MDS) are sensitive to the presence of orthogonal outliers, leading to significant defects in the embedding. We introduce a robust MDS method, called DeCOr-MDS (Detection and Correction of Orthogonal outliers using MDS), based on the geometry and statistics of simplices formed by data points, that allows to detect orthogonal outliers and subsequently reduce dimensionality. We validate our methods using synthetic datasets, and further show how it can be applied to a variety of large real biological datasets, including cancer image cell data, human microbiome project data and single cell RNA sequencing data, to address the task of data cleaning and visualization.

Evaluation of primary care physicians' competence in selective skin tumor triage after short versus long dermoscopy training A randomized non-inferiority trial

BACKGROUND

Although primary care physicians (PCPs) play a key role in skin cancer screening, their skills in detecting malignant tumors is suboptimal.

OBJECTIVES

To determine whether a short dermoscopy e-learning course (4 hours) in skin tumor diagnosis for PCPs is non-inferior to a long course (12 hours) in selective triage of skin lesions. Secondly, to evaluate whether regular refresher training sessions are necessary to maintain the PCPs' skills in the medium term.

METHODS

A randomized 2x2 factorial non-inferiority trial was conducted online over an 8-month period among 233 PCPs including 126 certified general practitioners, 94 PCPs in training, and 13 occupational physicians, all without prior advanced dermoscopy training. Participants were randomized 1:1:1:1 to receive short training and mandatory refreshers (n=58), short training and optional refreshers (n=59), long training and mandatory refreshers (n=58), or long training and optional refreshers (n=58). PCPs' skills were evaluated before training (T0), immediately after training (T1) to test the non-inferiority, and after five months (T2) to evaluate the impact of the refreshers. The primary endpoint was the difference in the change of score after short and long training. The non-inferiority margin was set at -28%.

RESULTS

Among the 233 randomized participants, 216 (93%) completed T1 and 197 (84.5%) completed T2. For short vs. long training, the primary endpoint was 1.392 (95% CI: 0.138; 2.645) in the per-protocol population (P<.001) and 1.016 (95% CI: -0.224; 2.256) in the modified intention-to-treat population (P<.001). After training, the type of refresher showed no impact on the score (P=.840). However, PCPs who completed all refreshers showed the best mean overall score at T2 (P<.001).

CONCLUSIONS

These findings confirm that short dermoscopy e-learning is non-inferior in training PCPs to triage skin lesions compared to long training. After training, regular refreshers are important to maintain the PCPs' acquired skills over time.

Burden of visible [face and hands] skin diseases: Results from a large international survey

BACKGROUND

While numerous surveys over the last decade have evaluated the burden of skin diseases, none have focused on the specific impact of disease-location on the hands and face.

AIM

The purpose of our study was to evaluate the burden of 8 skin diseases on the multidimensional aspects of subjects' daily lives in respect to their location on visible body areas (face or hands) versus non-visible areas.

METHODS

This was a population-based study in a representative sample of the Canadian, Chinese, Italian, Spanish, German and French populations, aged over 18 years using the proportional quota sampling method. All participants were asked (i) to complete a specific questionnaire including socio-demographic characteristics, (ii) to declare if they had a skin disease. All respondents with a skin disease were asked (iii) to specify the respective disease locations (hands, face, body) and (iv) to complete the DLQI questionnaire. Respondents with 8 selected skin diseases were asked (v) to complete a questionnaire evaluating the impact of the skin disease on their daily life, including their professional activity, social relations, emotional and intimate life, leisure, sports activities and perceived stigma.

RESULTS

A total of 13,138 adult participants responded to the questionnaire, of whom 26.2 % (n = 3,450) had skin diseases, and 23.4 % (n = 3,072) reported having one of the 8 selected skin diseases. Fifty-three percent were women and the mean age was 39.6 ± 15.5 years. The QoL was mostly impaired when the visible localization was solely on the hands as compared with the face (38 % had a DLQI > 10 versus 22 % respectively). More subjects with a visible localization on the hands reported felt-stigma, having difficulty falling asleep and felt that their sex life had been affected.

CONCLUSION

Special attention should be given to patients with skin disease on the hands and face as they are at higher risk of social exclusion and lower quality of life.

Analysis of Ribosome Profiling Data

Ribosome profiling methods are based on high-throughput sequencing of ribosome-protected mRNA footprints and allow to study in detail translational changes. Bioinformatic and statistical tools are necessary to analyze sequencing data. Here, we describe our developed methods for a fast and reliable quality control of ribosome profiling data, to efficiently visualize ribosome positions and to estimate ribosome speed in an unbiased way. The methodology described here is applicable to several genetic and environmental conditions including stress and are based on the R package RiboVIEW and calculation of quantitative estimates of local and global translation speed, based on a biophysical model of translation dynamics.

Novel organic semiconductors based on 2-amino-anthracene: Synthesis, charge transport and photo-conductive properties

Anthracene is considered to be a popular choice as a building block for organic semiconductors. The present work is dedicated to the synthesis and characterization of a novel semiconductor (10-OPIA) possessing mesogenic properties, which allows better control over charge transport in the bulk of a material. A novel anthracene-based molecule is characterized for its potential applications: frontier molecular energy levels are studied by optical spectroscopy and cyclic voltammetry and compared to values obtained via ab initio calculations. Thermophysical and mesogenic properties are investigated by optical microscopy and differential scanning calorimetry. Charge transport properties are characterized by means of an OFET device. It is found that this material can be easily aligned and exhibits a field effect hole mobility of 5.22 × 10^-5 cm² V^-1 s^-1 and an ON/OFF ratio of 10⁴ in the device prepared by drop casting. Finally, the photoconductive properties of this novel material are addressed in order to investigate its potential applications for organic phototransistors: it exhibits a large photoconductive gain of >100 and a photo-responsivity of >1 A W^-1.

Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans

Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5 C-methyltransferases have been studied, the impact of the global cytosine-5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5 C in RNA, demonstrating that this modification is non-essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5 C sites in the RNome in vivo. We find that NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5 C34-modified tRNA. This leads to reduced translation efficiency of UUG-rich transcripts and impaired fertility, suggesting a role of m5 C tRNA wobble methylation in the adaptation to higher temperatures.

Impact of acne on the daily life of adult patients: building a self-administered patient questionnaire

BACKGROUND

Acne is a long-lasting disease in adolescents and adults impacting the patient's daily life. Currently, there is no specific questionnaire that assesses its impact in adult patients.

AIM

To build a self-administered questionnaire assessing the impact of acne on the daily life in adult patients.

METHOD

A multidisciplinary working group was created, including 3 experts in healthcare questionnaires and dermatologists specialized in acne. A questionnaire using a standardized methodology for designing self-administered patient questionnaires according to conceptual, development and validation phases was developed. A cultural and linguistic validation into US English was conducted, based on the original French version.

RESULTS

A 14-item questionnaire demonstrating consistency, reproducibility and high reliability was build. The questionnaire significantly correlated with the SF-12 mental and SF-12 physical scores and CADI, indicating good external validity.

CONCLUSION

The present acne burden questionnaire AI-ADL allows the practioner to assess quickly and easily the burden of acne in patients during his daily clinical practice. Moreover, its short format allows patients to express easily and quickly their feelings and to initiate a conversation between the practioner and his patient. Thus, AI-ADL may help to better understand the multidimensional nature of acne, as well as the individual impact on the acne patient's daily life and moreover, it may play a key role in the decision-making process of treatment initiation and involvement of the patient in the management of his acne.

Genome analysis of the monoclonal marbled crayfish reveals genetic separation over a short evolutionary timescale

The marbled crayfish (Procambarus virginalis) represents a very recently evolved parthenogenetic freshwater crayfish species that has invaded diverse habitats in Europe and in Madagascar. However, population genetic analyses have been hindered by the homogeneous genetic structure of the population and the lack of suitable tools for data analysis. We have used whole-genome sequencing to characterize reference specimens from various known wild populations. In parallel, we established a whole-genome sequencing data analysis pipeline for the population genetic analysis of nearly monoclonal genomes. Our results provide evidence for systematic genetic differences between geographically separated populations and illustrate the emerging differentiation of the marbled crayfish genome. We also used mark-recapture population size estimation in combination with genetic data to model the growth pattern of marbled crayfish populations. Our findings uncover evolutionary dynamics in the marbled crayfish genome over a very short evolutionary timescale and identify the rapid growth of marbled crayfish populations as an important factor for ecological monitoring.

Olena Maiakovska et al. provide whole-genome sequencing of the parthenogenetic and invasive marbled crayfish and develop a computational framework for data analysis of monoclonal genomes. These data and methodology allow the authors to demonstrate genetic separation between two populations and provide the first size estimate for a marbled crayfish colony, which they used to model population growth patterns.

Natural History of Perianal Fistulising Lesions in Patients With Elderly-onset Crohn's Disease: A Population-based Study

INTRODUCTION

Most studies of elderly-onset Crohn's disease [CD; diagnosed in patients aged 60 or over] have described a mild course. However, data on the natural history of perianal fistulising CD [pfCD] in this population are scarce. In a population-based cohort study, we described the prevalence, natural history, and treatment of pfCD in patients with elderly-onset CD vs patients with paediatric-onset CD.

METHOD

All patients diagnosed with CD at or after the age of 60 between 1988 and 2006, were included [n = 372]. Logistic regression, Cox models, and a nested case-control method were used to identify factors associated with pfCD.

RESULTS

A total of 34 elderly patients [9% of the 372] had pfCD at diagnosis. After a median follow-up of 6 years (interquartile range [IQR]: 3; 10), 59 patients [16%] had pfCD; the same prevalence [16%] was observed in paediatric-onset patients. At last follow-up, anal incontinence was more frequent in elderly patients with pfCD than in elderly patients without pfCD [22% vs 4%, respectively; p < 10-4]. Rectal CD at diagnosis was associated with pfCD: hazard ratio (95% confidence interval [CI] = 2.8 [1.6-5.0]). Although 37% of the patients received immunosuppressants and 17% received anti-tumour necrosis factor agents, 24% [14 out of 59] had a definitive stoma at last follow-up.

CONCLUSION

During the first 6 years of disease, the prevalence of pfCD was similar in elderly and paediatric patients. Rectal involvement was associated with the appearance of pfCD in elderly-onset patients. Around a quarter of patients with elderly-onset CD will have a stoma. Our results suggest that treatment with biologics should be evaluated in these patients.

RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data

Recently, newly developed ribosome profiling methods based on high-throughput sequencing of ribosome-protected mRNA footprints allow to study genome-wide translational changes in detail. However, computational analysis of the sequencing data still represents a bottleneck for many laboratories. Further, specific pipelines for quality control and statistical analysis of ribosome profiling data, providing high levels of both accuracy and confidence, are currently lacking. In this study, we describe automated bioinformatic and statistical diagnoses to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. We present an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors. We expect our pipeline to allow an optimal use of the wealth of information provided by ribosome profiling experiments.

Queuine links translational control in eukaryotes to a micronutrient from bacteria

In eukaryotes, the wobble position of tRNA with a GUN anticodon is modified to the 7-deaza-guanosine derivative queuosine (Q34), but the original source of Q is bacterial, since Q is synthesized by eubacteria and salvaged by eukaryotes for incorporation into tRNA. Q34 modification stimulates Dnmt2/Pmt1-dependent C38 methylation (m⁵C38) in the tRNA^Asp anticodon loop in Schizosaccharomyces pombe. Here, we show by ribosome profiling in S. pombe that Q modification enhances the translational speed of the C-ending codons for aspartate (GAC) and histidine (CAC) and reduces that of U-ending codons for asparagine (AAU) and tyrosine (UAU), thus equilibrating the genome-wide translation of synonymous Q codons. Furthermore, Q prevents translation errors by suppressing second-position misreading of the glycine codon GGC, but not of wobble misreading. The absence of Q causes reduced translation of mRNAs involved in mitochondrial functions, and accordingly, lack of Q modification causes a mitochondrial defect in S. pombe. We also show that Q-dependent stimulation of Dnmt2 is conserved in mice. Our findings reveal a direct mechanism for the regulation of translational speed and fidelity in eukaryotes by a nutrient originating from bacteria.

Molecular p-doping in organic liquid crystalline semiconductors: influence of the charge transfer complex on the properties of mesophase and bulk charge transport

We explore the molecular nature of doping in organic semiconductors (OSCs) by employing a liquid crystalline organic semiconductor based on phenyl naphthalene as a model. The mesophase nature of composites that include a charge transfer complex (CTC) between the OSC (8-PNP-O12) and an electron acceptor (F4TCNQ) has been investigated by means of differential scanning calorimetry, polarized optical microscopy and X-ray scattering. Optical and vibrational spectroscopies allow us to explore the characteristics and the amount of charge transfer in the CTC and expose some properties that appear only in the complexed state. We have found this system to exhibit partial charge transfer, which manifests itself in all the phase states of the host 8-PNP-O12, as well as in solution. Due to the lowering of molecular symmetry as a result of the charge transfer, one of the previously IR-only vibrational bands of the nitrile group is found to be now active in the Raman spectrum. We have also made an attempt to further investigate the influence of dopant introduction on the bulk hole mobility of 8-PNP-O12. It is found that the presence of the CTC promotes the hole transport in the Smectic B mesophase, however it seems to have a somewhat negative influence in the less ordered smectic A mesophase. This work aims to establish the link between the inevitable change of molecular geometry that occurs on charge transfer with the results obtained by spectroscopic techniques and electronic charge carrier mobility measurements.

Mutations in Cytosine-5 tRNA Methyltransferases Impact Mobile Element Expression and Genome Stability at Specific DNA Repeats

The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5) RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects. In contrast, NSun2 function affected mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicated that tRNA-dependent processes affected mobile element expression and DNA repeat stability. Importantly, further experiments indicated that complex formation with RNA could also contribute to the impact of RCMT function on gene expression control. These results thus uncover a link between tRNA modification enzymes, the expression of repeat DNA, and genomic integrity.

Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases Trm4a and Trm4b in fission yeast

Enzymes of the cytosine-5 RNA methyltransferase Trm4/NSun2 family methylate tRNAs at C48 and C49 in multiple tRNAs, as well as C34 and C40 in selected tRNAs. In contrast to most other organisms, fission yeast Schizosaccharomyces pombe carries two Trm4/NSun2 homologs, Trm4a (SPAC17D4.04) and Trm4b (SPAC23C4.17). Here, we have employed tRNA methylome analysis to determine the dependence of cytosine-5 methylation (m⁵C) tRNA methylation in vivo on the two enzymes. Remarkably, Trm4a is responsible for all C48 methylation, which lies in the tRNA variable loop, as well as for C34 in tRNA^Leu_CAA and tRNA^Pro_CGG, which are at the anticodon wobble position. Conversely, Trm4b methylates C49 and C50, which both lie in the TΨC-stem. Thus, S. pombe show an unusual separation of activities of the NSun2/Trm4 enzymes that are united in a single enzyme in other eukaryotes like humans, mice and Saccharomyces cerevisiae. Furthermore, in vitro activity assays showed that Trm4a displays intron-dependent methylation of C34, whereas Trm4b activity is independent of the intron. The absence of Trm4a, but not Trm4b, causes a mild resistance of S. pombe to calcium chloride.

BisAMP: A web-based pipeline for targeted RNA cytosine-5 methylation analysis

RNA cytosine-5 methylation (m⁵C) has emerged as a key epitranscriptomic mark, which fulfills multiple roles in structural modulation, stress signaling and the regulation of protein translation. Bisulfite sequencing is currently the most accurate and reliable method to detect m⁵C marks at nucleotide resolution. Targeted bisulfite sequencing allows m⁵C detection at single base resolution, by combining the use of tailored primers with bisulfite treatment. A number of computational tools currently exist to analyse m⁵C marks in DNA bisulfite sequencing. However, these methods are not directly applicable to the analysis of RNA m⁵C marks, because DNA analysis focuses on CpG methylation, and because artifactual unconversion and misamplification in RNA can obscure actual methylation signals. We describe a pipeline designed specifically for RNA cytosine-5 methylation analysis in targeted bisulfite sequencing experiments. The pipeline is directly applicable to Illumina MiSeq (or equivalent) sequencing datasets using a web interface (https://bisamp.dkfz.de), and is defined by optimized mapping parameters and the application of tailored filters for the removal of artifacts. We provide examples for the application of this pipeline in the unambiguous detection of m⁵C marks in tRNAs from mouse embryonic stem cells and neuron-differentiated stem cells as well as in 28S rRNA from human fibroblasts. Finally, we also discuss the adaptability of BisAMP to the analysis of DNA methylation. Our pipeline provides an accurate, fast and user-friendly framework for the analysis of cytosine-5 methylation in amplicons from bisulfite-treated RNA.

Queuosine-modified tRNAs confer nutritional control of protein translation

Global protein translation as well as translation at the codon level can be regulated by tRNA modifications. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the diet and gut microbiota. We show here that nutritionally determined Q‐tRNA levels promote Dnmt2‐mediated methylation of tRNA Asp and control translational speed of Q‐decoded codons as well as at near‐cognate codons. Deregulation of translation upon queuine depletion results in unfolded proteins that trigger endoplasmic reticulum stress and activation of the unfolded protein response, both in cultured human cell lines and in germ‐free mice fed with a queuosine‐deficient diet. Taken together, our findings comprehensively resolve the role of this anticodon tRNA modification in the context of native protein translation and describe a novel mechanism that links nutritionally determined modification levels to effective polypeptide synthesis and cellular homeostasis.

Dramatic Increase in Incidence of Ulcerative Colitis and Crohn's Disease (1988-2011): A Population-Based Study of French Adolescents

OBJECTIVES

Few data are available to describe the changes in incidence of pediatric-onset inflammatory bowel disease (IBD). The aim of this study was to describe changes in incidence and phenotypic presentation of pediatric-onset IBD in northern France during a 24-year period.

METHODS

Pediatric-onset IBD (<17 years) was issued from a population-based IBD study in France between 1988 and 2011. Age groups and digestive location were defined according to the Paris classification.

RESULTS

1,350 incident cases were recorded (8.3% of all IBD) including 990 Crohn's disease (CD), 326 ulcerative colitis (UC) and 34 IBD unclassified (IBDU). Median age at diagnosis was similar in CD (14.4 years (Q1=11.8-Q3=16.0)) and UC (14.0 years (11.0-16.0)) and did not change over time. There were significantly more males with CD (females/males=0.82) than UC (females/males=1.25) (P=0.0042). Median time between onset of symptoms and IBD diagnosis was consistently 3 months (1-6). Mean incidence was 4.4/10⁵ for IBD overall (3.2 for CD, 1.1 for UC and 0.1 for IBDU). From 1988-1990 to 2009-2011, a dramatic increase in incidences of both CD and UC were observed in adolescents (10-16 years): for CD from 4.2 to 9.5/10⁵ (+126%; P<0.001) and for UC, from 1.6 to 4.1/10⁵ (+156%; P<0.001). No modification in age or location at diagnosis was observed in either CD or UC.

CONCLUSIONS

In this population-based study, CD and UC incidences increased dramatically in adolescents across a 24-year span, suggesting that one or more strong environmental factors may predispose this population to IBD.

Extra-intestinal Manifestations at Diagnosis in Paediatric- and Elderly-onset Ulcerative Colitis are Associated With a More Severe Disease Outcome: A Population-based Study

BACKGROUND AND AIMS

Data on extra-intestinal manifestations [EIM] and their impact on the disease course of ulcerative colitis [UC] in population-based cohorts are scarce, particularly in paediatric- and elderly-onset UC patients. The aims of this population-based study were to assess: 1] the occurrence of EIM in paediatric- and elderly-onset UC; 2] the factors associated with EIM; and 3] their impact on long-term disease outcome.

METHODS

Paediatric-onset [< 17 years at diagnosis] and elderly-onset UC patients [> 60 years at diagnosis] from a French prospective population-based registry [EPIMAD] were included. Data on EIM and other clinical factors at diagnosis and at maximal follow-up were collected.

RESULTS

In all, 158 paediatric- and 470 elderly-onset patients were included [median age at diagnosis 14.5 and 68.8 years, median follow-up 11.2 and 6.2 years, respectively]. EIM occurred in 8.9% of childhood- and 3% of elderly-onset patients at diagnosis and in 16.7% and 2.2% of individuals during follow-up [p < 0.01], respectively. The most frequent EIM was joint involvement [15.8% of paediatric onset and 2.6% of elderly-onset]. Presence of EIM at diagnosis was associated with more severe disease course [need for immunosuppressants or biologic therapy or colectomy] in both paediatric- and elderly-onset UC (hazard ratio [HR] = 2.0, 95% confidence interval [CI]: 1.0-4.2; and HR = 2.8, 0.9-7.9, respectively). Extensive colitis was another independent risk factor in both age groups.

CONCLUSIONS

Elderly-onset UC patients had lower risk of EIM either at diagnosis or during follow-up than paediatric-onset individuals. EIM at diagnosis predicted more severe disease outcome, including need for immunosuppressive or biologic therapy or surgery, in both paediatric- and elderly-onset UC.

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

Cytosine-5 RNA methylation plays an important role in several biologically and pathologically relevant processes. However, owing to methodological limitations, the transcriptome-wide distribution of this mark has remained largely unknown. We previously established RNA bisulfite sequencing as a method for the analysis of RNA cytosine-5 methylation patterns at single-base resolution. More recently, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. Here, we present a computational approach that integrates tailored filtering and data-driven statistical modeling to eliminate many of the artifacts that are known to be associated with bisulfite sequencing. By using RNAs from mouse embryonic stem cells, we performed a comprehensive methylation analysis of mouse tRNAs, rRNAs, and mRNAs. Our approach identified all known methylation marks in tRNA and two previously unknown but evolutionary conserved marks in 28S rRNA. In addition, mRNAs were found to be very sparsely methylated or not methylated at all. Finally, the tRNA-specific activity of the DNMT2 methyltransferase could be resolved at single-base resolution, which provided important further validation. Our approach can be used to profile cytosine-5 RNA methylation patterns in many experimental contexts and will be important for understanding the function of cytosine-5 RNA methylation in RNA biology and in human disease.

Design of experiments in medical physics: Application to the AAA beam model validation

PURPOSE

The purpose of this study is to evaluate the usefulness of the design of experiments in the analysis of multiparametric problems related to the quality assurance in radiotherapy. The main motivation is to use this statistical method to optimize the quality assurance processes in the validation of beam models.

METHOD

Considering the Varian Eclipse system, eight parameters with several levels were selected: energy, MLC, depth, X, Y₁ and Y₂ jaw dimensions, wedge and wedge jaw. A Taguchi table was used to define 72 validation tests. Measurements were conducted in water using a CC04 on a TrueBeam STx, a TrueBeam Tx, a Trilogy and a 2300IX accelerator matched by the vendor. Dose was computed using the AAA algorithm. The same raw data was used for all accelerators during the beam modelling.

RESULTS

The mean difference between computed and measured doses was 0.1±0.5% for all beams and all accelerators with a maximum difference of 2.4% (under the 3% tolerance level). For all beams, the measured doses were within 0.6% for all accelerators. The energy was found to be an influencing parameter but the deviations observed were smaller than 1% and not considered clinically significant.

CONCLUSION

Designs of experiment can help define the optimal measurement set to validate a beam model. The proposed method can be used to identify the prognostic factors of dose accuracy. The beam models were validated for the 4 accelerators which were found dosimetrically equivalent even though the accelerator characteristics differ.

Allochthonous matter: an important factor shaping the phytoplankton community in the Baltic Sea

It is well-known that nutrients shape phytoplankton communities in marine systems, but in coastal waters allochthonous dissolved organic matter (ADOM) may also be of central importance. We studied how humic substances (proxy of ADOM) and other variables influenced the nutritional strategies, size structure and pigment content of the phytoplankton community along a south-north gradient in the Baltic Sea. During the summer, the proportion of mixotrophs increased gradually from the phosphorus-rich south to the ADOM-rich north, probably due to ADOM-fueled microbes. The opposite trend was observed for autotrophs. The chlorophyll a (Chl a): carbon (C) ratio increased while the levels of photoprotective pigments decreased from south to north, indicating adaptation to the darker humic-rich water in the north. Picocyanobacteria dominated in phosphorus-rich areas while nanoplankton increased in ADOM-rich areas. During the winter-spring the phytoplankton biomass and concentrations of photoprotective pigments were low, and no trends with respect to autotrophs and mixotrophs were observed. Microplankton was the dominant size group in the entire study area. We conclude that changes in the size structure of the phytoplankton community, the Chl a:C ratio and the concentrations of photoprotective pigments are indicative of changes in ADOM, a factor of particular importance in a changing climate.

A comparative study of nematic liquid crystals doped with harvested and non-harvested ferroelectric nanoparticles: phase transitions and dielectric properties

Broadband dielectric spectroscopy is used to determine the dielectric properties and phase transitions of the 4-n-octyl-4′-cyanobiphenyl liquid crystal (8CB) doped with harvested and non-harvested ferroelectric nanoparticles.

Using next-generation DNA sequence data for genetic association tests based on allele counts with and without consideration of zero inflation

The relationship between genetic variability and individual phenotypes is usually investigated by testing for association relying on called genotypes. Allele counts obtained from next-generation sequence data could be used for this purpose too. Genetic association can be examined by treating alternative allele counts (AACs) as the response variable in negative binomial regression. AACs from sequence data often contain an excess of zeros, thus motivating the use of Hurdle and zero-inflated models. Here we examine rough type I error rates and the ability to pick out variants with small probability values for 7 different testing approaches that incorporate AACs as an explanatory or as a response variable. Model comparisons relied on chromosome 3 DNA sequence data from 407 Hispanic participants in the Type 2 Diabetes Genetic Exploration by Next-generation sequencing in Ethnic Samples (T2D-GENES) project 1 with complete information on diastolic blood pressure and related medication. Our results suggest that in the investigation of the relationship between AAC as response variable and individual phenotypes as explanatory variable, Hurdle-negative binomial regression has some advantages. This model showed a good ability to discriminate strongly associated variants and controlled overall type I error rates. However, probability values from Hurdle-negative binomial regression were not obtained for approximately 25 % of the investigated variants because of convergence problems, and the mass of the probability value distribution was concentrated around 1.

Electric field effects on phase transitions in the 8CB liquid crystal doped with ferroelectric nanoparticles

The influence of a low ac electric field on phase transitions is discussed in the case of a nematic liquid crystal 4-n-octyl-4^{'}-cyanobiphenyl (8CB) doped with Sn_{2}P_{2}S_{6} ferroelectric nanoparticles. The phase-transition temperatures obtained from temperature-dependent dielectric measurements were higher than those determined by the calorimetric method. This difference is explained by the presence of the measuring electric field which induces two effects. The first one is the amplification of the interactions between the nanoparticle polarization and the liquid-crystal order parameter. The second one is the field-induced disaggregation or aggregation process at high nanoparticle concentrations.

Allochthonous Carbon--a Major Driver of Bacterioplankton Production in the Subarctic Northern Baltic Sea

Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May-August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60% of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2%. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60%. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.

Distinct localizations and roles of non-muscle myosin II during proplatelet formation and platelet release

BACKGROUND

At the end of maturation, megakaryocytes (MKs) form long cytoplasmic extensions called proplatelets (PPT). Enormous changes in cytoskeletal structures cause PPT to extend further, to re-localize organelles such as mitochondria and to fragment, leading to platelet release. Two non-muscle myosin IIs (NMIIs) are expressed in MKs; however, only NMII-A (MYH9), but not NMII-B (MYH10), is expressed in mature MKs and is implicated in PPT formation.

OBJECTIVES

To provide in vivo evidence on the specific role of NMII-A and IIB in MK PPT formation.

METHODS

We studied two transgenic mouse models in which non-muscle myosin heavy chain (NMHC) II-A was genetically replaced either by II-B or by a chimeric NMHCII that combined the head domain of II-A with the rod and tail domains of II-B.

RESULTS AND CONCLUSIONS

This work demonstrates that the kinetic properties of NM-IIA, depending on the N-terminal domain, render NMII-A the better NMII candidate to control PPT formation. Furthermore, the carboxyl-terminal domain determines myosin II localization in the constriction region of PPT and is responsible for the specific role of NMII in platelet release.

Inherited variability in a master regulator polymorphism (rs4846126) associates with survival in 5-FU treated colorectal cancer patients

BACKGROUND

Treatment with 5-fluorouracil (5-FU) is known to improve survival in many cancers including colorectal cancer. Response to the treatment, overall survival and recurrence show inter-individual variation.

METHODS

In this study we employed a strategy to search eQTL variants influencing the expression of a large number of genes. We identified four single nucleotide polymorphisms, defined as master regulators of transcription, and genotyped them in a set of 218 colorectal cancer patients undergoing adjuvant 5-FU based therapy.

RESULTS

Our results showed that the minor allele variant of the rs4846126 polymorphism was associated with poor overall and progression-free survival. Patients that were homozygous for the variant allele showed an over two fold increased risk of death (HR 2.20 95%CI 1.05-4.60) and progression (HR 2.88, 95% 1.47-5.63). The integration of external information from publicly available gene expression repositories suggested that the rs4846126 polymorphism deserves further investigation. This variant potentially regulates the gene expression of 273 genes with some of them possibly associated to the patient's response to 5-FU treatment or colorectal cancer.

CONCLUSIONS

Present results show that mining of public data repositories in combination with own data can be a fruitful approach to identify markers that affect therapy outcome. In particular, a genetic screen of master regulators may help in order to search for the polymorphisms involved in treatment response in cancer patients.

Practical investigation of the performance of robust logistic regression to predict the genetic risk of hypertension

Logistic regression is usually applied to investigate the association between inherited genetic variants and a binary disease phenotype. A limitation of standard methods used to estimate the parameters of logistic regression models is their strong dependence on a few observations deviating from the majority of the data.

We used data from the Genetic Analysis Workshop 18 to explore the possible benefit of robust logistic regression to estimate the genetic risk of hypertension. The comparison between standard and robust methods relied on the influence of departing hypertension profiles (outliers) on the estimated odds ratios, areas under the receiver operating characteristic curves, and clinical net benefit.

Our results confirmed that single outliers may substantially affect the estimated genotype relative risks. The ranking of variants by probability values was different in standard and in robust logistic regression. For cutoff probabilities between 0.2 and 0.6, the clinical net benefit estimated by leave-one-out cross-validation in the investigated sample was slightly larger under robust regression, but the overall area under the receiver operating characteristic curve was larger for standard logistic regression. The potential advantage of robust statistics in the context of genetic association studies should be investigated in future analyses based on real and simulated data.

Dielectric Relaxation in Nematic and Isotropic Phases of 4-(trans-4'-n-Propylcyclohexyl) isothiocyanatobenzene

The results o f a dielectric relaxation study (in the frequency region from about 1 kHz to 1 GHz) of the liquid crystalline title com pound (C3H7-Cyhx-Ph-NCS , 3-CHBT) in the isotropic and the nematic phase (measurements with electric field parallel to alignment) are presented. The spectra of both phases can be described by two relaxation processes of Debye-type, possibly related to rotation around the long and short molecular axes.