Statistical modeling for selecting housekeeper genes

There is a need for statistical methods to identify genes that have minimal variation in expression across a variety of experimental conditions. These 'housekeeper' genes are widely employed as controls for quantification of test genes using gel analysis and real-time RT-PCR. Using real-time quantitative RT-PCR, we analyzed 80 primary breast tumors for variation in expression of six putative housekeeper genes (MRPL19 (mitochondrial ribosomal protein L19), PSMC4 (proteasome (prosome, macropain) 26S subunit, ATPase, 4), SF3A1 (splicing factor 3a, subunit 1, 120 kDa), PUM1 (pumilio homolog 1 (Drosophila)), ACTB (actin, beta) and GAPD (glyceraldehyde-3-phosphate dehydrogenase)). We present appropriate models for selecting the best housekeepers to normalize quantitative data within a given tissue type (for example, breast cancer) and across different types of tissue samples

Genome sequences of human coronavirus OC43 and NL63, associated with respiratory infections in Kilifi, Kenya

Coding-complete genomes of two human coronavirus OC43 strains and one NL63 strain were obtained by metagenomic sequencing of clinical samples collected in 2017 and 2018 in Kilifi, Kenya. Maximum likelihood phylogenies showed that the OC43 strains were genetically dissimilar and that the NL63 strain was closely related to NL63 genotype B viruses. [Abstract copyright: Copyright © 2019 Kamau et al.

Evolution monitoring of a solution-mining cavern in salt : identifying and analysing early-warning signals prior to collapse

International audienceRisk management of underground cavities requires a good working knowledge of accidental phenomena like subsidence or large-scale collapse. This was the context when the opportunity was taken to instrument a large size in use saline cavern, so as to test various auscultation techniques available under controlled conditions. A microseismic monitoring network coupled to a surface measurement system was installed to improve our knowledge of the mechanisms that initiate and govern the evolution of the cavern up to its collapse. After a stationary period combined with partial depressurization tests conducted in 2005 and 2007, the cavern appears to have entered into its final evolution phase, and this probably since early 2008. This results in continuous and highly sustained microseismic activity as well as the occurrence of a number of microseismic episodes localized around the cavern roof. The localization of the microseismic events, for some of these episodes, is closely correlated to the quasi-dynamic brine pressure variations and to the evolutions of the roof depth measured at observation boreholes. The microseismic activity turns out to be more precise when it comes to the evolution affecting the mine cavern than the movement measurements taken on the surface or sub-surface

Correction: Statistical modeling for selecting housekeeper genes

A correction to Statistical modeling for selecting housekeeper genes by Aniko Szabo, Charles M Perou, Mehmet Karaca, Laurent Perreard, John F Quackenbush, and Philip S Bernard. Genome Biology 2004, 5:R5

A Serpin shapes the extracellular environment to prevent influenza A virus maturation

Interferon-stimulated genes (ISGs) act in concert to provide a tight barrier against viruses. Recent studies have shed light on the contribution of individual ISG effectors to the antiviral state, but most have examined those acting on early, intracellular stages of the viral life cycle. Here, we applied an image-based screen to identify ISGs inhibiting late stages of influenza A virus (IAV) infection. We unraveled a directly antiviral function for the gene SERPINE1, encoding plasminogen activator inhibitor 1 (PAI-1). By targeting extracellular airway proteases, PAI-1 inhibits IAV glycoprotein cleavage, thereby reducing infectivity of progeny viruses. This was biologically relevant for IAV restriction in vivo. Further, partial PAI-1 deficiency, attributable to a polymorphism in human SERPINE1, conferred increased susceptibility to IAV in vitro. Together, our findings reveal that manipulating the extracellular environment to inhibit the last step in a virus life cycle is an important mechanism of the antiviral response

Somatotyping of Division I Athletes

Somatotyping has previously examined athletes\u27 genetic morphology. Categorization of somatotyping can be utilized in athletes for specialized, adaptive sports performance. PURPOSE: The purpose of this study was to report somatotyping differences (ectomorph, mesomorph, and endomorph) in selected Division I athletes. METHOD: 39 male football athletes and seven female softball Division I athletes were recruited for this investigation. Height (m), weight (kg), waist-to-hip ratio (cm), and a 4-site skinfold measurement was collected. Skinfold locations were recorded from the triceps (mm), subscapular (mm), supraspinal (mm), and the medial calf (mm). Biepicondylar breadth measures of the humerus (cm), and the femur (cm) were recorded at a respective 90°. Additionally, the girth of the subject’s dominant upper arm (cm) and dominant calf (cm) were recorded. All measurement locations were taken from the Heath-Carter Anthropometric protocol, respectfully. The Heath Carter Somatotype Worksheet consists of a rating scale that is based on a 3-component categorization. All measures are considered when calculating a participant\u27s score. Scores between .5 and 2.5 are low, 3 to 5 are moderate, 5.5 to 7 are high and anything over a 7.5 is considered very high. The first component calculated scores of endomorphy, the second calculated mesomorphy scores, and the last component calculated ectomorph scores. Using these measurements, equations are used to determine a participant’s score to a specific somatotype. The athletes\u27 numbers were then processed and plotted on a 2-D graph plotting the somatotype (X= ectomorph-endomorph, Y=2 x mesomorphy- (endomorphy+ectomorph)). RESULTS: There was a clear indication that somatotyping had variety based on sports and position specialization in football athletes. Football athletes consisted of 6 endomorphs, 30 mesomorphs, and 3 ectomorphs, while softball athletes consisted of 7 meso-endomorphs. CONCLUSION: Due to the anthropometric position differences in male football athletes there was a considerable amount of variety and lack of specificity, while the female softball athletes consisted of a lesser variety in anthropometric measures

Vessel Segmentation on Computed Tomography Angiography

International audienceThis short paper describes our contribution in the research aimed at model based vessel segmentation on CTA. Although each partner was involved in a main subject among what follows, the contribution is a joint effort of all the partners, as a result of regular visits in France and Israel, as well as between partners in each country. The French Hospital Partner in Lyon provided a large set of CTA studies, including sets with two studies performed on each patient and about 20 studies suitable for work on other aspects of cardiac vessel segmentation

High spatial resolution T-ReCS mid-infrared imaging of Luminous Infrared Galaxies

We present diffraction-limited (FWHM ~ 0.3arcsec) Gemini/T-ReCS mid-infrared (MIR: N-band or narrow-band at 8.7micron) imaging of four Luminous Infrared Galaxies (LIRGs) drawn from a representative local sample. The MIR emission in the central few kpc is strikingly similar to that traced by Pa-alpha, and generally consists of bright nuclear emission and several compact circumnuclear and/or extranuclear HII regions. The central MIR emission is dominated by these powerful HII regions, consistent with the majority of AGN in this local sample of LIRGs contributing a minor part of the MIR emission. The luminous circumnuclear HII regions detected in LIRGs follow the extrapolation of the 8micron vs. Pa-alpha relation found for M51 HII knots. The integrated central 3-7kpc of galaxies, however, present elevated 8micron/Pa-alpha ratios with respect to individual HII regions, similar to the integrated values for star-forming galaxies. Our results show that the diffuse 8micron emission, not directly related to the ionizing stellar population, can be as luminous as that from the resolved HII regions. Therefore, calibrations of the star formation rate for distant galaxies should be based on the integrated 8micron emission of nearby galaxies, not that of the HII regions alone.Comment: Accepted for publication in Astrophysical Journal Letters. Paper with high resolution Fig.1 can be found at http://damir.iem.csic.es/extragalactic/publications/publications.htm