ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets

Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering is routinely applied to gene expression data, there is a lack of appropriate general methodology for clustering of sequence-level genomic and epigenomic data, e.g. ChIP-based data. We here introduce a general methodology for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. By defining appropriate feature extraction approaches and similarity measures, we allow biologically meaningful clustering to be performed for genomic tracks using standard clustering algorithms. An implementation of the methodology is provided through a tool, ClusTrack, which allows fine-tuned clustering analyses to be specified through a web-based interface. We apply our methods to the clustering of occupancy of the H3K4me1 histone modification in samples from a range of different cell types. The majority of samples form meaningful subclusters, confirming that the definitions of features and similarity capture biological, rather than technical, variation between the genomic tracks. Input data and results are available, and can be reproduced, through a Galaxy Pages document at http://hyperbrowser.uio.no/hb/u/hb-superuser/p/clustrack. The clustering functionality is available as a Galaxy tool, under the menu option "Specialized analyzis of tracks", and the submenu option "Cluster tracks based on genome level similarity", at the Genomic HyperBrowser server: http://hyperbrowser.uio.no/hb/.     

Correction to: Who is the ocean? Preface to the future seas 2030 special issue

Reviews in Fish Biology and Fisheries - A correction to this paper has been published: https://doi.org/10.1007/s11160-021-09657-9     

Regional myocardial work by strain Doppler echocardiography and LV pressure: a new method for quantifying myocardial function

There is a need for better methods to quantify regional myocardial function. In the present study, we investigated the feasibility of quantifying regional function in terms of a segmental myocardial work index as derived from strain Doppler echocardiography (SDE) and invasive pressure. In 10 anesthetized dogs, we measured left ventricular (LV) pressure by micromanometer and myocardial longitudinal strains by SDE and sonomicrometry. The regional myocardial work index (RMWI) was calculated as the area of the pressure-strain loop. As a reference method for strain, we used sonomicrometry. By convention, the loop area was assigned a positive sign when the pressure-strain coordinates rotated counterclockwise. Measurements were done at baseline and during volume loading and left anterior descending coronary artery (LAD) occlusion, respectively. There was a good correlation between RMWI calculated from strain by SDE and strain by sonomicrometry (y = 0.73x + 0.21, r = 0.82, P < 0.01). Volume loading caused an increase in RMWI from 1.3 +/- 0.2 to 2.2 +/- 0.1 kJ/m3 (P < 0.05) by SDE and from 1.5 +/- 0.3 to 2.7 +/- 0.3 kJ/m3 (P = 0.066) by sonomicrometry. Short-term ischemia (1 min) caused a decrease in RMWI from 1.3 +/- 0.2 to 0.3 +/- 0.04 kJ/m3 (P < 0.05) and from 1.3 +/- 0.3 to 0.5 +/- 0.2 kJ/m3 (P < 0.05) by SDE and sonomicrometry, respectively. In the nonischemic ventricle and during short-term ischemia, the pressure-strain loops rotated counterclockwise, consistent with actively contracting segments. Long-term ischemia (3 h), however, caused the pressure-strain loop to rotate clockwise, consistent with entirely passive segments, and the loop areas became negative, -0.2 +/- 0.1 and -0.1 +/- 0.03 kJ/m3 (P < 0.05) by SDE and sonomicrometry, respectively. A RMWI can be estimated by SDE in combination with LV pressure. Furthermore, the orientation of the loop can be used to assess whether the segment is active or passive.     

Interaction between left ventricular wall motion and intraventricular flow propagation in acute and chronic ischemia

Myocardial ischemia has been associated with left ventricular (LV) postsystolic shortening. The combination of tissue Doppler imaging and high frame-rate acquisition of two-dimensional color flow makes it possible to study the interaction between LV wall motion and intraventricular flow propagation. The aim of this study was to examine in a clinical model the impact that acute myocardial ischemia and prior myocardial infarct might have on LV flow patterns and to explain the underlying mechanisms from the tissue Doppler data. LV flow propagation and tissue velocities during early diastole were studied in 18 healthy individuals, 17 patients with prior anterior myocardial infarct, and 16 patients before and during percutaneous coronary intervention (PCI) of the left anterior descending artery. Normal individuals had intraventricular flow propagation toward the apex during isovolumic relaxation. During this early diastolic time phase, myocardial velocities measured at mid- and apical septal segment were directed away from the apex. Before PCI, patients without myocardial infarction had similar findings as in normal individuals. In contrast, each patient with either prior myocardial infarction or PCI-induced acute ischemia had flow propagation opposite to normal individuals, and tissue velocities reversed toward the apex during early diastole. Reversal of early diastolic LV flow propagation in acute and chronic anterior myocardial ischemia reflects postsystolic shortening in the dyskinetic apical and septal myocardial segments.     

Antibacterial activity of marine-derived fungi

A total of 227 marine isolates of ubiqituous fungi were cultivated on different media and the secondary metabolite content of the extracts (ethyl acetate/chloroform/methanol 3 : 2 : 1) characterized by HPLC. The fungi were secured from animals, plants and sediments of Venezuelan waters (0–10 m) including mangroves and lagoonal areas. The extracts were tested for antibacterial activity. A total of 7 were active towards Vibrio parahaemolyticus and 55 towards Staphylococcus aureus, representing 18 different fungal species from 8 ascomycetous genera. For 61 strains of Penicillium citrinum antibacterial activity correlated well with content of secondary metabolites as measured by HPLC. Thirteen isolates of Penicillium steckii produced very similar profiles of secondary metabolites and 6 of these had activity against either V. parahaemolyticus or S. aureus or both. This revised version was published online in June 2006 with corrections to the Cover Date.     

Empowering her guardians to nurture our Ocean’s future

Reviews in Fish Biology and Fisheries - Coastal Indigenous and Traditional communities are starting to see changes to their lives from climate change, whether this is from species range changes or...     

Body configuration as a predictor of mortality: comparison of five anthropometric measures in a 12 year follow-up of the Norwegian HUNT 2 study

Background

Distribution of body fat is more important than the amount of fat as a prognostic factor for life expectancy. Despite that, body mass index (BMI) still holds its status as the most used indicator of obesity in clinical work.

Methods

We assessed the association of five different anthropometric measures with mortality in general and cardiovascular disease (CVD) mortality in particular using Cox proportional hazards models. Predictive properties were compared by computing integrated discrimination improvement and net reclassification improvement for two different prediction models. The measures studied were BMI, waist circumference, hip circumference, waist-to-hip ratio (WHR), and waist-to-height ratio (WHtR). The study population was a prospective cohort of 62,223 Norwegians, age 20–79, followed up for mortality from 1995–1997 to the end of 2008 (mean follow-up 12.0 years) in the Nord-Trøndelag Health Study (HUNT 2).

Results

After adjusting for age, smoking and physical activity WHR and WHtR were found to be the strongest predictors of death. Hazard ratios (HRs) for CVD mortality per increase in WHR of one standard deviation were 1.23 for men and 1.27 for women. For WHtR, these HRs were 1.24 for men and 1.23 for women. WHR offered the greatest integrated discrimination improvement to the prediction models studied, followed by WHtR and waist circumference. Hip circumference was in strong inverse association with mortality when adjusting for waist circumference. In all analyses, BMI had weaker association with mortality than three of the other four measures studied.

Conclusions

Our study adds further knowledge to the evidence that BMI is not the most appropriate measure of obesity in everyday clinical practice. WHR can reliably be measured and is as easy to calculate as BMI and is currently better documented than WHtR. It appears reasonable to recommend WHR as the primary measure of body composition and obesity.     

Unguisin C,a GABA-containing cyclic peptide from the fungus Emericella unguis

Besides the known unguisins A and B, a new cyclic heptapeptide, unguisin C, containing a GABA-derived moiety in the ring, was isolated from the fungus Emericella unguis. The structure was determined by 1D and 2D NMR techniques. Marfey's method was used to determine the absolute stereochemistry. Precursor-directed biosynthesis of the unguisins was performed by supplementation of the culture medium with amino acids (L-Ala, L-Ser, L-Phe and L-Leu). A related cyclic heptapeptide, unguisin D, was detected by HPLC and characterized by sequence analysis using LC-QITMS.     

Cyclin-Dependent Kinase Suppression by WEE1 Kinase Protects the Genome through Control of Replication Initiation and Nucleotide Consumption

Activation of oncogenes or inhibition of WEE1 kinase deregulates cyclin-dependent kinase (CDK) activity and leads to replication stress; however, the underlying mechanism is not understood. We now show that elevation of CDK activity by inhibition of WEE1 kinase rapidly increases initiation of replication. This leads to nucleotide shortage and reduces replication fork speed, which is followed by SLX4/MUS81-mediated DNA double-strand breakage. Fork speed is normalized and DNA double-strand break (DSB) formation is suppressed when CDT1, a key factor for replication initiation, is depleted. Furthermore, addition of nucleosides counteracts the effects of unscheduled CDK activity on fork speed and DNA DSB formation. Finally, we show that WEE1 regulates the ionizing radiation (IR)-induced S-phase checkpoint, consistent with its role in control of replication initiation. In conclusion, these results suggest that deregulated CDK activity, such as that occurring following inhibition of WEE1 kinase or activation of oncogenes, induces replication stress and loss of genomic integrity through increased firing of replication origins and subsequent nucleotide shortage.     

Unguisin C, a GABA-containing cyclic peptide from the fungus Emericella unguis

Besides the known unguisins A and B, a new cyclic heptapeptide, unguisin C, containing a GABA-derived moiety in the ring, was isolated from the fungus Emericella unguis. The structure was determined by 1D and 2D NMR techniques. Marfey's method was used to determine the absolute stereochemistry. Precursor-directed biosynthesis of the unguisins was performed by supplementation of the culture medium with amino acids ( -Ala, -Ser, -Phe and -Leu). A related cyclic heptapeptide, unguisin D, was detected by HPLC and characterized by sequence analysis using LC-QITMS.