Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"

Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094]

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints

Blood pressure and hypertension in type 1 diabetes mellitus patients with long duration

Type 1 diabetes mellitus (T1DM) has significantly better prognosis which has led to increased cardio-vascular diseases (CVD) prevalence. The detection of CVD risk factors and their treatment become tasks of paramount importance. Among them, high blood pressure (BP) is a target of primary purpose. Aim: to explore the blood pressure values, the prevalence of hypertension (HTN) and its management in patients with T1DM with long duration and without overt CVD, in comparison to matched controls. Participants and methods: totally, 124 patients with T1DM were matched to 59 controls by sex, age and approximate body mass index (BMI). All participants filled in questionnaires with information on demographics, physical activity, life style, concomitant diseases, treatments, presence of complications, etc. Blood samples were taken for laboratory and biomarkers investigation. Blood pressure was measured by investigators twice and the mean of the two measurements was used. HTN was accepted using standard definitions. BP values were compared using t-test. Multiple linear regression models with dependent variable BP measures and age, sex, BMI, presence of T1DM, glycated hemoglobin levels, creatinine levels as independent variables were created. ANOVA method was used to test the interaction of sex and presence of T1DM. Results: The mean age of the participants was 43.47 ± 10.1 years, 54% were males. The mean duration of T1DM was 25.31 ± 8.2 years and the mean HbA1c was 8.42 ± 1.8% for diabetic patients. The mean blood pressure measures in T1DM groups were higher than in controls, both in males and females. The difference reached significance for SBP and pulse pressure (PP). The presence of T1DM independently affected the BP values, after adjusting for major confounders. The mean adjusted differences between T1DM and controls were 8.37 mm Hg for SBP, 4.92 mm Hg for DBP, and 5.19 mm Hg for PP (p < 0.001). HTN was significantly more frequent in T1DM patients than in controls – 54% vs. 27%, p = 0.0001, mainly due to already known hypertension. BP control was insufficient – in only 36% and 13% of the treated hypertensive participants, respectively, for BP < 140/90 and < 130/80 mm Hg. The majority of the patients with HTN were treated with combination therapy, mostly single-pill fixed dosage but 30% of the hypertensive patients with diabetes did not take antihypertensive medications. Inhibitors of the renin-angiotensin system were the preferred class of medications. Conclusions: SBP and PP were significantly higher in middle-aged patients with T1DM with long duration than their control counterparts. The presence of HTN was significantly more common in T1DM. Although treated according to the current recommendations, the control of BP was far from effective. These results show the need for constant screening of patients with T1DM for HTN and other risk factors and for more aggressive antihypertensive treatment to prevent future CVD events

Complementary feeding and overweight in European preschoolers : the ToyBox-study

Complementary feeding (CF) should start between 4-6 months of age to ensure infants' growth but is also linked to childhood obesity. This study aimed to investigate the association of the timing of CF, breastfeeding and overweight in preschool children. Infant-feeding practices were self-reported in 2012 via a validated questionnaire by >7500 parents from six European countries participating in the ToyBox-study. The proportion of children who received breast milk and CF at 4-6 months was 51.2%. There was a positive association between timing of solid food (SF) introduction and duration of breastfeeding, as well as socioeconomic status and a negative association with smoking throughout pregnancy (p = 4 months or were formula-fed. The study did not identify any significant association between the timing of introducing SF and obesity in childhood. It is likely that other factors than timing of SF introduction may have impact on childhood obesity

The effect of a cluster-randomized controlled trial on lifestyle behaviors among families at risk for developing type 2 diabetes across Europe: the Feel4Diabetes-study

Background: This study investigated the effect of the Feel4Diabetes-intervention, a 2-year multilevel intervention, on energy balance-related behaviors among European families at risk for developing type 2 diabetes. Intervention effects on self-reported physical activity, sedentary behavior and eating behaviors were investigated across and within the participating countries: Belgium, Finland, Greece, Spain, Hungary and Bulgaria. Methods: Families were recruited through schools, located in low socio-economic status areas. In total, 4484 families at risk for developing type 2 diabetes were selected using the FINDRISC-questionnaire. Parents’ and children’s energy balance-related behaviors data were collected by questionnaires at three time points (baseline, mid- and post intervention). Families assigned to the intervention group were invited to participate in a 2-year school-, community-, and family-based intervention to promote a healthier lifestyle, including counseling sessions (first intervention year) and text messages (second intervention year). Families assigned to the control group received standard care, including medical check-up results and recommendations and tips regarding a healthy lifestyle. To assess the intervention-effects, Mixed Models were conducted using the R-Package “lmer “with R v3.2. Results: Significant intervention effects were found on a certain number of families’ lifestyle behaviors. Significant favorable intervention effects were detected on parents’ water consumption and consumption of fruit and vegetables, and on children’s consumption of sweets and moderate-to-vigorous physical activity. Analyses by country revealed significant favorable intervention effects on water consumption and on moderate-to-vigorous physical activity in Belgian parents and on fruit and vegetable consumption among Belgian children, on sweets consumption among Spanish parents and children, and on moderate-to-vigorous physical activity among Finnish children. Unfavorable intervention effects were found on the consumption of soft drinks and sugar-containing juices among Hungarian children and parents, while when examining the intervention effects for the overall population and per country, 10 from the 112 investigated outcome variables were improved in the intervention group compared to the control group (9%). Conclusions: The Feel4Diabetes-intervention managed to improve a certain number of targeted lifestyle behaviors while the intervention was not effective on a large number of targeted lifestyle behaviors. The findings of the current study are encouraging, but further research is needed on how we can further improve effectiveness of lifestyle interventions to prevent type 2 diabetes in families at risk. Trial registration: The Feel4Diabetes-study is registered with the clinical trials registry http://clinicaltrials.gov, ID: 643708. © 2021, The Author(s)

Global meta‐analysis of over 50 years of multidisciplinary and international collaborations on transmissible cancers

International audienceAlthough transmissible cancers have, so far, only been documented in three independent animal groups, they not only impact animals that have high economic, environmental and social significance, but they are also one of the most virulent parasitic life forms. Currently known transmissible cancers traverse terrestrial and marine environments, and are predicted to be more widely distributed across animal groups; thus, the implementation of effective collaborative scientific networks is important for combating existing and emerging forms. Here, we quantify how collaborative effort on the three known transmissible cancers has advanced through the formation of collaborative networks among institutions and disciplines. These three cancers occur in bivalves (invertebrates—disseminated neoplasia; DN), Tasmanian devils (vertebrate—marsupial; devil facial tumour disease; DFTD) and dogs (vertebrate—eutherian mammal; canine transmissible venereal tumour; CTVT). Research on CTVT and DN has been conducted since 1876 and 1969, respectively, whereas systematic research on DFTD only started in 2006. Yet, collaborative effort on all three diseases is global, encompassing six major Scopus subject areas. Collaborations steadily increased between 1963 and 2006 for CTVT and DN, with similar acceleration for all three cancers since 2006. Network analyses demonstrated that scientists are organizing themselves into efficient collaborative networks; however, these networks appear to be far stronger for DFTD and DN, possibly due to the recent detection of new strains adding impetus to research and associated publications (enhancing citation trajectories). In particular, global and multidisciplinary collaborations formed almost immediately after DFTD research was initiated, leading to similar research effort and relatively greater research outputs compared to the other two diseases. Therefore, in the event of outbreaks of new lineages of existing transmissible cancers, or the discovery of new transmissible cancers in the future, the rapid formation of international collaborations spanning relevant disciplines is vital for the efficient management of these diseases

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter

Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter DNA. Experimental data suggest that a spontaneous dsDNA strand separation at the transcriptional start site is likely to be a requirement for transcription initiation in several promoters. Here, we use Langevin molecular dynamic simulations based on the Peyrard-Bishop-Dauxois nonlinear model of DNA (PBD LMD) to analyze the strand separation (bubble) dynamics of 80-bp-long promoter DNA sequences. We derive three dynamic criteria, bubble probability, bubble lifetime, and average strand separation, to characterize bubble formation at the transcriptional start sites of eight mammalian gene promoters. We observe that the most stable dsDNA openings do not necessarily coincide with the most probable openings and the highest average strand displacement, underscoring the advantages of proper molecular dynamic simulations. The dynamic profiles of the tested mammalian promoters differ significantly in overall profile and bubble probability, but the transcriptional start site is often distinguished by large (longer than 10 bp) and long-lived transient openings in the double helix. In support of these results are our experimental transcription data demonstrating that an artificial bubble-containing DNA template is transcribed bidirectionally by human RNA polymerase alone in the absence of any other transcription factors

Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis

Summary DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the functional basis for this is unknown. Here, we show that loss-of-function DDX3X mutations are also enriched in MYC-translocated diffuse large B cell lymphoma and reveal functional cooperation between mutant DDX3X and MYC. DDX3X promotes the translation of mRNA encoding components of the core translational machinery, thereby driving global protein synthesis. Loss-of-function DDX3X mutations moderate MYC-driven global protein synthesis, thereby buffering MYC-induced proteotoxic stress during early lymphomagenesis. Established lymphoma cells restore full protein synthetic capacity by aberrant expression of DDX3Y, a Y chromosome homolog, the expression of which is normally restricted to the testis. These findings show that DDX3X loss of function can buffer MYC-driven proteotoxic stress and highlight the capacity of male B cell lymphomas to then compensate for this loss by ectopic DDX3Y expression

Feel4Diabetes healthy diet score: Development and evaluation of clinical validity

Background: The aim of this paper is to present the development of the Feel4Diabetes Healthy Diet Score and to evaluate its clinical validity. Methods: Study population consisted of 3268 adults (63% women) from high diabetes risk families living in 6 European countries. Participants filled in questionnaires at baseline and after 1 year, reflecting the dietary goals of the Feel4Diabetes intervention. Based on these questions the Healthy Diet Score was constructed, consisting of the following components: breakfast, vegetables, fruit and berries, sugary drinks, whole-grain cereals, nuts and seeds, low-fat dairy products, oils and fats, red meat, sweet snacks, salty snacks, and family meals. Maximum score for each component was set based on its estimated relative importance regarding T2DM risk, higher score indicating better quality of diet. Clinical measurements included height, weight, waist circumference, heart rate, blood pressure, and fasting blood sampling, with analyses of glucose, total cholesterol, HDL-cholesterol, LDL-cholesterol, and triglycerides. Analysis of (co) variance was used to compare the Healthy Diet Score and its components between countries and sexes using baseline data, and to test differences in clinical characteristics between score categories, adjusted for age, sex and country. Pearson''s correlations were used to study the association between changes from baseline to year 1 in the Healthy Diet Score and clinical markers. To estimate reproducibility, Pearson''s correlations were studied between baseline and 1 year score, within the control group only. Results: The mean total score was 52.8 ± 12.8 among women and 46.6 ± 12.8 among men (p < 0.001). The total score and its components differed between countries. The change in the Healthy Diet Score was significantly correlated with changes in BMI, waist circumference, and total and LDL cholesterol. The Healthy Diet Score as well as its components at baseline were significantly correlated with the values at year 1, in the control group participants. Conclusion: The Feel4Diabetes Healthy Diet Score is a reproducible method to capture the dietary information collected with the Feel4Diabetes questionnaire and measure the level of and changes in the adherence to the dietary goals of the intervention. It gives a simple parameter that associates with clinical risk factors in a meaningful manner