ChIP-Chip Designs to Interrogate the Genome of Xenopus Embryos for Transcription Factor Binding and Epigenetic Regulation

Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos. genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5′ ends of genes. These regions truly represent promoters as shown by binding of TBP, a key transcription initiation factor. embryos

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

ABSTRACT Summary: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. Availability and Implementation: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz

Infected pancreatic necrosis: outcomes and clinical predictors of mortality. A post hoc analysis of the MANCTRA-1 international study

: The identification of high-risk patients in the early stages of infected pancreatic necrosis (IPN) is critical, because it could help the clinicians to adopt more effective management strategies. We conducted a post hoc analysis of the MANCTRA-1 international study to assess the association between clinical risk factors and mortality among adult patients with IPN. Univariable and multivariable logistic regression models were used to identify prognostic factors of mortality. We identified 247 consecutive patients with IPN hospitalised between January 2019 and December 2020. History of uncontrolled arterial hypertension (p = 0.032; 95% CI 1.135-15.882; aOR 4.245), qSOFA (p = 0.005; 95% CI 1.359-5.879; aOR 2.828), renal failure (p = 0.022; 95% CI 1.138-5.442; aOR 2.489), and haemodynamic failure (p = 0.018; 95% CI 1.184-5.978; aOR 2.661), were identified as independent predictors of mortality in IPN patients. Cholangitis (p = 0.003; 95% CI 1.598-9.930; aOR 3.983), abdominal compartment syndrome (p = 0.032; 95% CI 1.090-6.967; aOR 2.735), and gastrointestinal/intra-abdominal bleeding (p = 0.009; 95% CI 1.286-5.712; aOR 2.710) were independently associated with the risk of mortality. Upfront open surgical necrosectomy was strongly associated with the risk of mortality (p < 0.001; 95% CI 1.912-7.442; aOR 3.772), whereas endoscopic drainage of pancreatic necrosis (p = 0.018; 95% CI 0.138-0.834; aOR 0.339) and enteral nutrition (p = 0.003; 95% CI 0.143-0.716; aOR 0.320) were found as protective factors. Organ failure, acute cholangitis, and upfront open surgical necrosectomy were the most significant predictors of mortality. Our study confirmed that, even in a subgroup of particularly ill patients such as those with IPN, upfront open surgery should be avoided as much as possible. Study protocol registered in ClinicalTrials.Gov (I.D. Number NCT04747990)

Vztah bilance tekutin k neuromuskularnim porucham u kriticky nemocnych.

Development of severe muscular weakness is a frequent complication in critically ill septic patients. It is associated with prolonged length of stay and increased morbidity and mortality. The pathogenesis of neuromuscular (NM) failure in not known so far. One of common characteristics of critical illness is the positive fluid balance and generalized edema as a consequence of septic capillary leakage. The aim of this study is to test the hypothesis that generalized soft tissue edema may cause damage to NM structures which would result in subsequent skeletal muscle weakness. We found relationships between markers of NM failure and signs of multiple organ dysfunction. There was no correlation between the NM function and fluid balance. Experimentally we did not find any clinically relevant increase of intramuscular pressure during massive fluid accumulation. The decrease in compound muscle action potentials can not be explained by increased intramuscular pressure, but more likely by presence of sepsis on itself. We did not find any data to support the original hypothesis that NM failure in critically ill may be a consequence of massive fluid accumulation. Our results suggest that NM dysfunction is more likely to be regarded as a part of multiorgan failure.Available from STL Prague, CZ / NTK - National Technical LibrarySIGLECZCzech Republi

On the Importance of Combined Scratch/Acoustic Emission Test Evaluation: SiC and SiCN Thin Films Case Study

The scratch test, as probably the most widespread technique for assessment of the adhesive/cohesive properties of a film–substrate system, fully depends on reliable evaluation based on assessment of critical loads for systems’ failures. Traditionally used evaluation methods (depth change record and visual observation) may sometimes give misleading conclusions about the failure dynamics, especially in the case of opaque films. Therefore, there is a need for another independent evaluation technique with the potential to complete the existing approaches. The nondestructive method of acoustic emission, which detects the elastic waves emitted during film cracking and delamination, can be regarded as a convenient candidate for such a role even at nano/micro scale. The strength of the combination of microscopic observation of the residual groove and depth change record with the acoustic emission detection system proved to be a robust and reliable approach in analyzing adhesion/cohesion properties of thin films. The dynamics of the gradual damage taking place during the nano/micro scratch test revealed by the combined approach is presented for SiC and SiCN thin films. Comparison of critical load values clearly reflects the higher ability of the AE approach in detecting the initial material failure compared to the visual observation

The Impact of Glucose-Based or Lipid-Based Total Parenteral Nutrition on the Free Fatty Acids Profile in Critically Ill Patients

Introduction: Our study aim was to assess how the macronutrient intake during total parenteral nutrition (TPN) modulates plasma total free fatty acids (FFAs) levels and individual fatty acids in critically ill patients. Method: Adult patients aged 18–80, admitted to the intensive care unit (ICU), who were indicated for TPN, with an expected duration of more than three days, were included in the study. Isoenergetic and isonitrogenous TPN solutions were given with a major non-protein energy source, which was glucose (group G) or glucose and lipid emulsions (Smof lipid; group L). Blood samples were collected on days 0, 1, 3, 6, 9, 14, and 28. Results: A significant decrease (p < 0.001) in total FFAs occurred in both groups with a bigger decrease in group G (p < 0.001) from day 0 (0.41 ± 0.19 mmol∙L−1) to day 28 (0.10 ± 0.07 mmol∙L−1). Increased palmitooleic acid and decreased linoleic and docosahexaenoic acids, with a trend of increased mead acid to arachidonic acid ratio, on day 28 were observed in group G in comparison with group L. Group G had an insignificant increase in leptin with no differences in the concentrations of vitamin E, triacylglycerides, and plasminogen activator inhibitor-1. Conclusion: Decreased plasma FFA in critically ill patients who receive TPN may result from increased insulin sensitivity with a better effect in group G, owing to higher insulin and glucose dosing and no lipid emulsions. It is advisable to include a lipid emulsion at the latest from three weeks of TPN to prevent essential fatty acid deficiency