VisGenome: visualization of single and comparative genome representations

VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser

Enhanced relativistic-electron beam collimation using two consecutive laser pulses

The double laser pulse approach to relativistic electron beam (REB) collimation has been investigated at the LULI-ELFIE facility. In this scheme, the magnetic field generated by the first laser-driven REB is used to guide a second delayed REB. We show how electron beam collimation can be controlled by properly adjusting laser parameters. By changing the ratio of focus size and the delay time between the two pulses we found a maximum of electron beam collimation clearly dependent on the focal spot size ratio of the two laser pulses and related to the magnetic field dynamics. Cu-K alpha and CTR imaging diagnostics were implemented to evaluate the collimation effects on the respectively low energy ( MeV) components of the REB

Gender, media, and mixed martial arts in Poland: the case of Joanna Jędrzejczyk

Recent growth in the media visibility of female combat sport athletes has offered a compelling site for research on gender and sport media, as women in deeply masculinized sports have been increasingly placed in the public spotlight. While scholars in the Anglophone West have offered analyses of the media framing of this phenomenon, little work has been done outside these cultural contexts. Thus, in this paper we offer a qualitative exploration of how Joanna Jędrzejczyk, a Polish champion of the Ultimate Fighting Championship, has been represented in Polish media. Our findings reveal a relatively de-gendered, widely celebratory account, primarily framed by nationalistic discourse–findings we ascribe to both the particularities of the sport of mixed martial arts as well as the historic nature of Jędrzejczyk’s success

Preliminary studies of sediments from the Dobczyce drinking water reservoir

The analysis of river and lake sediments indicates that the physical, chemical, biochemical and geochemical processes that influence the fate of toxic compounds and elements in sediments are numerous and complex (for example: sorption - desorption, oxidation - reduction, ion-exchange, biological activity). Due to the above-mentioned general statement, only a long term and complex research programme can lead to satisfactory answers to the questions relating to possible changes of water and environmental quality in the future. The aim of our study consisted in physical and chemical characterisation of sediments in in-depth profiles taken from the Dobczyce reservoir in southern Poland that is a main source of drinking water for the city of Kraków. Due to morphological reasons, 7 layers of sediment samples were distinguished from the ground level to about 90 cm below (total thickness of the sediments in the sampling site). Analysis of grain size distribution and application of x-ray diffraction method, enabled mineralogical description of sediments. The use of proton-induced x-ray emission (PIXE) and atomic absorption spectrometry (AAS) revealed elemental composition of the samples (Al, P, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn). Concentrations of natural 40K and artificial 137Cs radionuclides were determined by the use of gamma spectrometry. The following facts were established: 1) the oldest (deepest) and newest, recently deposited layers of sediments are similar in their physical and chemical properties. It means that the inflow of contaminants and biogenic compounds to the reservoir has changed little since it was constructed and filled with water; 2) the severe flood in 1997 changed significantly sediment composition and, in fact, led to purification of sediments in the Dobczyce reservoir

Characterization of the c.190T>C missense mutation in BRCA1 codon 64 (Cys64Arg).

In the Milan area (Northern Italy), we identified a family characterized by a high prevalence of ovarian and breast cancer cases (5 out of 6 subjects, over 3 generations), and a predominant prevalence of ovarian lesions (4 out of 5 patients). Analysis of BRCA1 and BRCA2 genes allowed the identification of the missense c.190T>C mutation in codon 64 (Cys64Arg) of BRCA1. The aims of the present investigation were to characterize the functional implications of the c.190T>C mutation at the molecular level, and to search whether additional polymorphisms might be linked to the peculiar phenotypic features observed in the Italian pedigree. Molecular modelling studies suggested that substitution of the cysteine 64 with an arginine likely disrupts the architecture of the BRCA1 RING finger domain, responsible for the interaction with BARD1, essential for the tumor-suppressor activity of the BRCA1-BARD1 complex. By splicing site information analysis, exonic splicing enhancer site characterization, and analysis of transcript fragment length and sequence, we showed that the c.190T>C mutation was able to modulate the splicing of exon 5 in a fashion opposite to the c.190T>G transversion, responsible for the functionally-related Cys64Gly amino acid substitution. Genotyping of BRCA1 and BRCA2 in the Italian family revealed the presence of two significant polymorphisms: the cancer-associated c.2612C>T SNP in BRCA1, and the c.-26G>A SNP in the BRCA2 gene, acting as an ovarian cancer risk modifier in carriers of deleterious BRCA1 mutations. Analysis of these SNPs in a genotypically-unrelated Polish family, characterized by prevalent breast neoplasms in carriers of the c.190T>C mutation, revealed a genetic profile consistent with the hypothetic role of both polymorphisms

Stress-induced traps in multilayered structures

The trap parameters of defects in Si/CaF2 multilayered structures were determined from the analysis of optical charging spectroscopy measurements. Two kinds of maxima were observed. Some of them were rather broad, corresponding to "normal" traps, while the others, very sharp, were attributed to stress-induced traps. A procedure of optimal linear smoothing the noisy experimental data has been developed and applied. This procedure is based on finding the minimal value of the relative error with respect to the value of the smoothing window. In order to obtain a better accuracy for the description of the trapping-detrapping process, a Gaussian temperature dependence of the capture crosssections characterizing the stress-induced traps was introduced. Both the normal and the stress-induced traps have been characterized, including some previously considered as only noise features.Comment: 37 pages, 9 figure

Comparison of three methods of DNA extraction from human bones with different degrees of degradation

There is a necessity for deceased identification as a result of many accidents and sometimes bones are the only accessible source of DNA. So far, a universal method that allows for extraction of DNA from materials at different stages of degradation does not exist. The aims of this study were: the comparison of three methods of DNA extraction from bones with different degree of degradation and an evaluation of the usefulness of these methods in forensic genetics. The efficiency of DNA extraction, the degree of extract contamination by polymerase chain reaction (PCR) inhibitors and the possibility of determining the STR loci profile were especially being compared. Nuclear DNA from bones at different states of degradation was isolated using three methods: classical, organic phenol–chloroform extraction, DNA extraction from crystal aggregates and extraction by total demineralisation. Total demineralisation is the best method for most cases of DNA extraction from bones, although it does not provide pure DNA. DNA extraction from aggregates removes inhibitors much better and is also a good method of choice when identity determination of exhumed remains is necessary. In the case of not buried bones (remains found outside) total demineralisation or phenol–chloroform protocols are more efficient for successful DNA extraction