Comparative assessment of commercially available wound gels in ex vivo human skin reveals major differences in immune response-modulatory effects.

Wound healing is a crucial process for maintaining the function of human skin as a protective barrier to pathogens and other external stress factors. Hydrogels-in combination with antimicrobials-are often used, as moist wound care has been widely accepted as standard therapy. Recently, we reported about immune response-modulatory effects of an octenidine-based hydrogel, however little is known about the mechanism of action of other hydrogels including antiseptic molecules or chlorine-based and chlorine-releasing agents, respectively. The aim of this study was the comparative assessment of commercially available wound gels (octenilin®, Prontosan®, Lavanid®, Betadona®, ActiMaris®, Microdacyn60®, VeriforteTMmed) with regard to their effects on the secretion of distinct cytokines (IL-6, IL-8, IL-10), matrix-metalloproteinases as well as their potential to cause alterations in skin structure and apoptosis. Hence, tape-stripped human ex vivo skin biopsies were treated topically with wound gels and cultured for 48 h. Enzyme-linked immunosorbent assays and an enzyme activity assay of culture supernatants revealed that octenilin® demonstrates significantly broader anti-inflammatory and protease-inhibitory capacities than other wound gels. Further, haematoxylin & eosin as well as caspase-3 staining of treated biopsies showed that octenilin® does not alter skin morphology and shows the least interfering effect on human epidermal cells compared to untreated controls. Overall, this study clearly demonstrates totally different effects for several commercially available hydrogels in our wound model, which gives also new insight into their tissue compatibility and mode of action.

Cardiac biomarkers for risk stratification of arrhythmic death in patients with heart failure and reduced ejection fraction.

Objectives. Patients with heart failure and reduced left ventricular ejection fraction (HFrEF) are prone to ventricular tachyarrhythmias. We tested whether biomarkers C-terminal Endothelin 1 (CT-ET1), midregional pro atrial natriuretic peptide (MR-proANP) and midregional pro adrenomedullin (MR-proADM) might improve risk stratification for arrhythmic death.Methods: This prospective observational study included 160 heart failure patients with ischaemic cardiomyopathy (ICM) or non-ischaemic, dilated cardiomyopathy (DCM) and 30 control patients without heart disease. Primary endpoint was arrhythmic death (ArD) or resuscitated cardiac arrest (resCA).Results: A total of 61 patients died during the median follow-up of 7.0 [5.2-8.4] years. An ArD or resCA was observed in 48 patients. Plasma levels of CT-ET1 (p = 0.002), MR-proANP (p < 0.001) and MR-proADM (p = 0.013) were significantly higher in ICM or DCM patients compared to controls. MR-proANP levels in ICM patients were associated with a significantly increased risk for ArD or resCA (hazard ratio (HR) = 1.42, [95%CI: 1.08-1.85], p = 0.011) in a multivariable Cox regression model. Plasma levels of CT-ET1 (HR = 1.07 [0.98-1.17], p = 0.113) and MR-proADM (HR = 1.80 [0.92-3.55], p = 0.087) were not associated with ArD or resCA in ICM patients. No significant association with ArD or resCA was found in DCM patients. Multivariable Cox regression showed that CT-ET1 (HR = 1.14 [1.07-1.22], p < 0.001), MR-proANP (HR = 1.64 [1.29-2.08], p < 0.001) and MR-pro ADM (HR = 2.06 [1.12-3.77], p = 0.020) were associated with a higher risk for overall mortality.Conclusion: Patients with HFrEF had elevated levels of CT-ET1, MR-proANP and MR-proADM. Plasma levels of MR-proANP are useful as predictor for arrhythmic death in patients with ICM.

A global cloud free pixel- based image composite from Sentinel-2 data.

Large-scale land cover classification from satellite imagery is still a challenge due to the big volume of data to be processed, to persistent cloud-cover in cloud-prone areas as well as seasonal artefacts that affect spatial homogeneity. Sentinel-2 times series from Copernicus Earth Observation program offer a great potential for fine scale land cover mapping thanks to high spatial and temporal resolutions, with a decametric resolution and five-day repeat time. However, the selection of best available scenes, their download together with the requirements in terms of storage and computing resources pose restrictions for large-scale land cover mapping. The dataset presented in this paper corresponds to global cloud-free pixel based composite created from the Sentinel-2 data archive (Level L1C) available in Google Earth Engine for the period January 2017- December 2018. The methodology used for generating the image composite is described and the metadata associated with the 10 m resolution dataset is presented. The data with a total volume of 15 TB is stored on the Big Data platform of the Joint Research Centre. It can be downloaded per UTM grid zone, loaded into GIS clients and displayed easily thanks to pre-computed overviews.

From ear to eye? No effect of transcutaneous vagus nerve stimulation on human pupil dilation: A report of three studies.

Transcutaneous stimulation of the auricular branch of the vagus nerve (tVNS) has been proposed as a treatment for a spectrum of physical and psychological disorders. One of the proposed working mechanisms of tVNS is a modulatory effect on the locus coeruleus - noradrenaline (LC-NA) network. We tested this hypothesis in humans in a series of three studies: one focusing on high trait worriers, and two in healthy populations. In all three studies, we tested whether tVNS increases resting pupil diameter - as an index of LC-NA network activity. Additionally, we tested whether tVNS affects task performance and task-related pupil dilation during an Attentional Blink task. We found no evidence that tVNS increases pupil diameter or task-related pupil dilation in any of the tasks. No consistent effects of tVNS on performance on the attentional blink task were found. Overall, the results of these studies indicate that tVNS does not affect these behavioral and physiological indices of noradrenergic activity.

Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples.

The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.

15 years of the model study course in medicine at the Ruhr University Bochum.

The Faculty of Medicine of the Ruhr University Bochum (RUB) introduced a model study course in medicine (MSM) in the winter semester 2003. For 9 consecutive years, 42 out of 280 first year students at the Ruhr University Bochum had the opportunity to begin their studies in the model study course in medicine. The places were allocated amongst the applicants internally through a raffle. The MSM was consistently problem-, practice- and patient-oriented and largely did away with lectures, broke with the distinction between a pre-clinical and clinical phase and tested basic knowledge in equivalent integrated exams focusing on clinical application. Following a comparative evaluation of the standard degree course (RSM) and the MSM, the faculty merged the two degree courses into the Integrated Reformed Medical Curriculum (IRMC), which has been on offer since 2013 and is characterized by a topic-oriented hybrid curriculum. This article examines experiences relating to the origins, conception and introduction of the MSM.

Evaluation of a 3D-printed total knee arthroplasty using radiostereometric analysis: assessment of highly porous biological fixation of the tibial baseplate and metal-backed patellar component.

AIMS: Our intention was to investigate if the highly porous biological fixation surfaces of a new 3D-printed total knee arthroplasty (TKA) achieved adequate fixation of the tibial and patellar components to the underlying bone. PATIENTS AND METHODS: A total of 29 patients undergoing primary TKA consented to participate in this prospective cohort study. All patients received a highly porous tibial baseplate and metal-backed patella. Patient-reported outcomes measures were recorded and implant migration was assessed using radiostereometric analysis. RESULTS: Patient function significantly improved by three months postoperatively (p < 0.001). Mean difference in maximum total point motion between 12 and 24 months was 0.021 mm (-0.265 to 0.572) for the tibial implant and 0.089 mm (-0.337 to 0.758) for the patellar implant. The rate of tibial and patellar migration was largest over the first six postoperative weeks, with no changes in mean tibia migration occurring after six months, and no changes in mean patellar migration occurring after six weeks. One patellar component showed a rapid rate of migration between 12 and 24 months. CONCLUSION: Biological fixation appears to occur reliably on the highly porous implant surface of the tibial baseplate and metal-backed patellar component. Rapid migration after 12 months was measured for one patellar component. Further investigation is required to assess the long-term stability of the 3D-printed components and to determine if the high-migrating components achieve fixation. Cite this article: Bone Joint J 2019;101-B(7 Supple C):40-47.

The effect of Oncotype DX® on adjuvant chemotherapy treatment decisions in early breast cancer.

INTRODUCTION: The aim of this study was to objectively establish the value of the Oncotype DX® (ODX) gene assay in adjuvant treatment decisions for intermediate risk patients with early, oestrogen receptor positive, human epidermal growth factor receptor 2 negative, lymph node negative breast cancer at a district general hospital. METHODS: All patients who underwent surgery for breast cancer between January 2015 and December 2017 at Queen Elizabeth Hospital in King's Lynn were considered for inclusion in the study. Those who did not meet the criteria for ODX referral were excluded. Patients were divided into two cohorts based on whether they were treated before or after the introduction of ODX testing in this hospital (June 2016): the pre-ODX and post-ODX groups. The primary outcome was the percentage of patients for whom adjuvant chemotherapy (AC) was recommended in each group. RESULTS: Of the 462 patients who underwent surgery during the study period, 43 met the eligibility criteria for ODX testing: 18 in the pre-ODX group and 25 in the post-ODX group. AC was recommended and given to 11 (61%) of the patients in the pre-ODX group. In the post-ODX group, AC was recommended for seven patients with an ODX Recurrence Score® (RS) of >25; this was given to six patients (24%). One patient (with a RS of 26) declined AC. ODX testing led to a significant reduction in the proportion of patients who received AC (p=0.015). CONCLUSIONS: In intermediate risk patients with breast cancer, the results of the ODX gene assay may change the decision for adjuvant treatment. It represents a valuable tool to assist patients' and clinicians' decision making regarding adjuvant chemotherapy.

The effect of transcutaneous vagus nerve stimulation on fear generalization and subsequent fear extinction.

Fear overgeneralization is thought to be one of the cardinal processes underlying anxiety disorders, and a determinant of the onset, maintenance and recurrence of these disorders. Animal studies have shown that stimulating the vagus nerve (VNS) affects neuronal pathways implicated in pattern separation and completion, suggesting it may reduce the generalization of a fear memory to novel situations. In a one-day study, 58 healthy students were subjected to a fear conditioning, fear generalization, and fear extinction paradigm. Participants were randomly assigned to receive either transcutaneous auricular VNS (tVNS; final N = 29) or sham stimulation (final N = 29) during the generalization and extinction phases. tVNS did not affect fear generalization, as reflected by US expectancy ratings and fear potentiated startle responses. However, participants who received tVNS reported lower US expectancy ratings to the CS+ during the extinction phase, possibly reflecting a stronger declarative extinction of fear. No effects of tVNS on fear potentiated startle responses during extinction were found. The pattern of findings regarding extinction of declarative fear suggest a facilitating effect of tVNS.

Transcutaneous vagus nerve stimulation reduces spontaneous but not induced negative thought intrusions in high worriers.

Worrying is a central component of anxiety disorders. We tested whether non-invasive vagus nerve stimulation reduces negative thought intrusions in high worriers. Worry was assessed with a Breathing Focus Task, which consists of a pre-worry period, a worry induction, and a post-worry period. Ninety-seven high worriers were randomly allocated to receive transcutaneous electrical stimulation of the auricular branch of the vagus nerve at the concha (tVNS), or of the earlobe (sham stimulation) throughout the lab session. Participants who received tVNS reported significantly fewer negative thought intrusions during the pre-worry period, but the effects of tVNS after the worry induction were mixed. An exploratory analysis indicated that participants in the tVNS condition were more likely to report negative thought intrusions shortly after the worry induction, but became less likely to do so as the post-worry period went on. No effects of tVNS on RMSSD were observed. These findings provide preliminary indications that tVNS may decrease the occurrence of worrisome thoughts.

Emergency Centre-based paediatric procedural sedation: current practice and challenges in Cape Town

Background: The aims and objectives of this survey of the current practice of doctors working in Emergency Centres (ECs) in the Cape Town metropole was to assess clinical practice and attempt to identify obstacles to the practice of paediatric procedural sedation and analgesia (PPSA). This was considered essential to establish a baseline for quality assurance purposes and improvement. Methods: After institutional ethics approval, a cross-sectional descriptive study was performed in 25 ECs in both private and government sectors in Cape Town. Specific aspects of PPSA practice were analysed after the anonymous completion of a specifically designed questionnaire, by full-time doctors working at each EC. The doctors' grade and training, practice preferences, medication and use of monitoring, and any perceived challenges to performing PPSA were assessed. Results: Sixteen ECs agreed to be part of the study and 62 questionnaires were completed (a 64% response rate). Procedural sedation and analgesia was performed at all the participating ECs, by medical practitioners of varying experience. Doctors' awareness of unit protocols was inconsistent. Common indications were orthopaedic interventions, radiological investigations and surgical procedures. Medications used were similar in the responding units, but dosages varied. Monitoring was poor compared with local and international standards. The obstacles reported predominantly related to a lack of training and formal protocols. Conclusions: This study was the first to evaluate the practice of Emergency Centre paediatric procedural sedation and analgesia practice in a South African setting. The lack of a formal system of training and accreditation, for both doctors and facilities, and the need for institutional and nationwide PPSA guidelines were highlighted

Factors associated with healthy and unhealthy workplace eating behaviours in individuals with overweight/obesity with and without binge eating disorder.

Objective: Most Americans spend an average of 8 hours per day in the workplace. Current understanding of eating behaviours in the workplace and their association with overweight, obesity and binge eating disorder (BED) is limited. Workplace eating behaviours and weight-related self-efficacy were examined in a sample of 98 individuals with overweight or obesity, with or without BED. Design: Participants completed the Weight Efficacy Lifestyle Questionnaire, Work and Social Adjustment Scale, Worker's Perception of Environmental Factors, and a Workplace Questionnaire. Results: Eating unplanned food occurred on average 2.43 times per week (SD = 3.37), and eating unplanned food even when meals were brought from home occurred on average 1.28 times per week (SD = 1.84). Individuals with BED purchased lunch even when they brought food from home significantly more frequently than did individuals without BED. Those with BED also reported significantly poorer work and social adjustment related to binge eating as compared with those without BED. The most significant barriers to healthy eating in the workplace were coworker influence, eating more food in general and more junk food in response to stress, eating unplanned food at work and time constraints. Conclusions: These factors may be important to target in weight-loss treatment to increase individuals' weight loss success. As individuals with BED may be the most vulnerable to eating unplanned foods, clinicians may want to focus on this potential barrier in BED treatment.

Metabolic control of type 1 diabetes in youth with autism spectrum disorder: A multicenter Diabetes-Patienten-Verlaufsdokumentation analysis based on 61 749 patients up to 20 years of age.

BACKGROUND: A paucity of reports in the literature exists concerning the co-existence between autism spectrum disorder (ASD) and type 1 diabetes (T1D). OBJECTIVE: To compare clinical characteristics, diabetes management and metabolic control in youth with T1D and ASD (T1D-ASD) with youth without ASD (T1D-non ASD). METHODS: Using the German/Austrian diabetes patient follow-up registry, this study analyzed aggregated data from the last available year of observation for each patient with T1D, ages 1-20 with consistent data on insulin regimen and glycated hemoglobin (A1C), between January, 2005 and March, 2017. RESULTS: From 61 749 patients, 150 (0.24%) were identified as T1D-ASD. Non-adjusted comparisons showed similar results for mean age at onset and duration of diabetes, but not for gender (male: T1D-ASD: 85.3%; T1D-non ASD: 52.8%; P < .001). Unadjusted comparisons showed no difference for severe hypoglycemia, diabetic ketoacidosis, insulin doses, insulin pump therapy, and body mass index. A statistical difference was observed for A1C (P-value .01) and in the number of blood glucose (SMBG) tests/day (median [interquartile range]: T1D-ASD 6.0 [4.4-7.0]; T1D-non ASD 5.0 [4.4-7.0]; P-value < .001). After adjusting for age, gender, duration of diabetes, and year of observation, only SMBG remained significant (P-value .003). T1D-ASD used psycho-stimulants (15.3% vs 2.2%; P-value < .001), antipsychotics (10.7% vs 0.6%; P-value < .001), and antidepressive medications (3.6% vs 0.7%; P-value < .001) more frequently. CONCLUSION: Metabolic control was similar in the T1D-ASD group compared to T1D-non ASD despite their comorbidity. Awareness of ASD remains important in T1D treatment, as both conditions require long-term multi-disciplinary medical follow-up for optimal outcomes.

Mixed evidence for the potential of non-invasive transcutaneous vagal nerve stimulation to improve the extinction and retention of fear.

Extinction memories are fragile and their formation has been proposed to partially rely on vagus nerve activity. We tested whether stimulating the auricular branch of the vagus (transcutaneous VNS; tVNS) accelerates extinction and reduces spontaneous recovery of fear. Forty-two healthy students participated in a 3-day fear conditioning study, where we tested fear acquisition (day 1), fear extinction (day 2) and the retention of the extinction memory (day 3). During extinction, participants were randomly allocated to receive tVNS or sham stimulation concurrently with each CS presentation. During the acquisition and retention phases, all participants received sham stimulation. Indexes of fear included US-expectancy, startle blink EMG and skin conductance responses. Results showed successful acquisition and extinction of fear in all measures. tVNS facilitated the extinction of declarative fear (US expectancy ratings), but did not promote a stronger retention of the declarative extinction memory. No clear effects of tVNS on extinction and retention of extinction were found for the psychophysiological indexes. The present findings provide tentative indications that tVNS could be a promising tool to improve fear extinction and call for larger scale studies to replicate these effects.

Associations of socioeconomic position in childhood and young adulthood with cardiometabolic risk factors: the Jerusalem Perinatal Family Follow-Up Study.

BACKGROUND: Several stages in the life course have been identified as important to the development of cardiovascular disease. This study aimed to assess the associations of childhood and adulthood socioeconomic position (SEP) and social mobility with cardiometabolic risk factors (CMRs) later in life. METHODS: We conducted follow-up examinations of 1132 offspring, aged 32, within a population-based cohort of all births in Jerusalem from 1974 to 1976. SEP was indicated by parents' occupation and education, and adulthood SEP was based on offspring's occupation and education recorded at age 32. Linear regression models were used to investigate the associations of SEP and social mobility with CMRs. RESULTS: Childhood-occupational SEP was negatively associated with body mass index (BMI; ß=-0.29, p=0.031), fat percentage (fat%; ß=-0.58, p=0.005), insulin (ß=-0.01, p=0.031), triglycerides (ß=-0.02, p=0.024) and low-density lipoprotein cholesterol (LDL-C; ß=-1.91, p=0.015), independent of adulthood SEP. Adulthood-occupational SEP was negatively associated with waist-to-hip ratio (WHR; ß=-0.01, p=0.002), and positively with high-density lipoprotein cholesterol (HDL-C; ß=0.87, p=0.030). Results remained similar after adjustment for smoking and inactivity. Childhood-educational SEP was associated with decreased WHR and LDL-C level (p=0.0002), and adulthood-educational SEP was inversely associated with BMI (p=0.001), waist circumference (p=0.008), WHR (p=0.001) and fat% (p=0.0002) and positively associated with HDL-C (p=0.030). Additionally, social mobility (mainly upward) was shown to have adverse cardiometabolic outcomes. CONCLUSIONS: Both childhood and adulthood SEP contribute independently to CMR. The match-mismatch hypothesis may explain the elevated CMRs among participants experiencing social mobility. Identification of life-course SEP-related aspects that translate into social inequality in cardiovascular risk may facilitate efforts for improving health and for reducing disparities in cardiovascular disease.

Coping with stress in medical students: results of a randomized controlled trial using a mindfulness-based stress prevention training (MediMind) in Germany.

BACKGROUND: High prevalence rates of psychological distress in medical training and later professional life indicate a need for prevention. Different types of intervention were shown to have good effects, but little is known about the relative efficacy of different types of stress management interventions, and methodological limitations have been reported. In order to overcome some of these limitations, the present study aimed at evaluating the effect of a specifically developed mindfulness-based stress prevention training for medical students (MediMind) on measures of distress, coping and psychological morbidity. METHODS: We report on a prospective randomized controlled trial with three study conditions: experimental treatment (MediMind), standard treatment (Autogenic Training) and a control group without treatment. The sample consisted of medical or dental students in the second or eighth semester. They completed self-report questionnaires at baseline, after the training and at one year follow-up. Distress (Trier Inventory for the Assessment of Chronic Stress, TICS) was assessed as the primary outcome and coping (Brief COPE) as a co-primary outcome. Effects on the psychological morbidity (Brief Symptom Inventory, BSI) as a secondary outcome were expected one year after the trainings. RESULTS: Initially, N = 183 students were randomly allocated to the study groups. At one year follow-up N = 80 could be included into the per-protocol analysis: MediMind (n =31), Autogenic Training (n = 32) and control group (n = 17). A selective drop-out for students who suffered more often from psychological symptoms was detected (p = .020). MANCOVA's on TICS and Brief COPE revealed no significant interaction effects. On the BSI, a significant overall interaction effect became apparent (p = .002, η2partial = .382), but post hoc analyses were not significant. Means of the Global Severity Index (BSI) indicated that MediMind may contribute to a decrease in psychological morbidity. CONCLUSION: Due to the high and selective dropout rates, the results cannot be generalized and further research is necessary. Since the participation rate of the trainings was high, a need for further prevention programs is indicated. The study gives important suggestions on further implementation and evaluation of stress prevention in medical schools. TRIAL REGISTRATION: This trial is recorded at German Clinical Trials Register under the number DRKS00005354 (08.11.2013).

Outcome of culture-confirmed isoniazid-resistant rifampicin-susceptible tuberculosis in children.

SETTING: Isoniazid-resistant rifampicin-susceptible (HRRS) tuberculosis (TB) is the most prevalent form of drug-resistant TB globally, and may be a risk factor for poor outcomes, but has been poorly described in children. OBJECTIVE: To characterise the clinical presentation, treatment, and clinical and microbiological outcomes among children with culture-confirmed HRRS TB. DESIGN: Retrospective hospital-based cohort study. RESULTS: Of the 72 children included in the study, the median age was 50.1 months (IQR 21.5-102.5); 42% were male. Forty-four (51%) had a potential source case; only 13 were confirmed HRRS TB. Of 66 tested, 12 (17%) were human immunodeficiency virus (HIV) infected, and 36 (60%) of the 60 with pulmonary TB (PTB) had severe disease. Seventy children had treatment data; the median total duration of treatment was 11.3 months (IQR 9-12.3); 25 (36%) initiated treatment with a three-drug intensive phase; 52 (74%) received a fluoroquinolone. Of 63 children with known outcomes, 55 (88%) had a favourable outcome, 1 died and 3 had treatment failure. Ten had positive follow-up cultures at ⩾2 months after starting treatment. Older age (P = 0.008), previous anti-tuberculosis treatment (P = 0.023) and severe PTB (P = 0.018) were associated with failure to culture-convert at ⩾2 months. CONCLUSIONS: Although overall outcomes were good, prolonged culture positivity and cases of treatment failure emphasise the need for additional attention to the management of children with HRRS TB.

Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators.

The vertebrate heart develops from two distinct lineages of cardiomyocytes that arise from the first and second heart fields (FHF and SHF, respectively). The FHF forms the primitive heart tube, while adding cells from the SHF allows elongation at both poles of the tube. Initially seen as an exclusive characteristic of higher vertebrates, recent work has demonstrated the presence of a distinct FHF and SHF in lower vertebrates, including zebrafish. We found that key transcription factors that regulate septation and chamber formation in higher vertebrates, including Tbx5 and Pitx2, influence relative FHF and SHF contributions to the zebrafish heart tube. To identify molecular modulators of heart field migration, we used microarray-based expression profiling following inhibition of tbx5a and pitx2ab in embryonic zebrafish (Mosimann & Panakova, et al, 2015; GSE70750). Here, we describe in more detail the procedure used to process, prioritize, and analyze the expression data for functional enrichment.

TRANSCRIPTION. Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4.

Pioneer transcription factors initiate cell-fate changes by binding to silent target genes. They are among the first factors to bind key regulatory sites and facilitate chromatin opening. Here, we identify an additional role for pioneer factors. In early Caenorhabditis elegans foregut development, the pioneer factor PHA-4/FoxA binds promoters and recruits RNA polymerase II (Pol II), often in a poised configuration in which Pol II accumulates near transcription start sites. At a later developmental stage, PHA-4 promotes chromatin opening. We found many more genes with poised RNA polymerase than had been observed previously in unstaged embryos, revealing that early embryos accumulate poised Pol II and that poising is dynamic. Our results suggest that Pol II recruitment, in addition to chromatin opening, is an important feature of PHA-4 pioneer factor activity.