Náklon výtahové šachty bunkru Skutina

The measurement of deformations of the elevator shaft in the Skutina fortress between the 2nd floor and the depth of 33 m below the surface took place in 2009. These measurements showed that, in addition to the tides, the diurnal thermoelastic wave deforms the body of the bunker, particularly in the NS direction. The amplitude of this deformation depends mainly on the cloudiness (opposite to the irradiance). Morning and evening deformation curves depend mainly on the time of sunrise and the geometry of the body of the bunker (irradiance of the bunker walls) and less of the outside temperature.V roce 2009 probíhalo v bunkru Skutina měření deformace výtahové šachty od druhého nadzemního podlaží bunkru do hloubky cca 33 m pod povrch. Tato měření ukázala, že kromě slapů se na deformaci tělesa bunkru podílí celodenní termoelastická vlna, zejména ve směru S-J. Amplituda této deformace závisí zejména na oblačnosti (protiklad osvitu). Ranní a večerní obraty deformační křivky jsou závislé zejména na době východu Slunce a na geometrii tělesa bunkru (osvitu stěn bunkru) a méně na venkovní teplotě

Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

<p>Abstract</p> <p>Background</p> <p>Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (<it>Pisum sativum</it>).</p> <p>Results</p> <p>Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in <it>M. truncatula</it>.</p> <p>Conclusion</p> <p>We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data provide a starting point for further investigations of legume plant genomes based on their global comparative analysis and for the development of more sophisticated approaches for data mining.</p

Early results of micro-deformation measurements in Magdalena Jama (Slovenia) by a vertical static pendulum

Vertical static pendulums have been installed in mines or caves in Central Europe since 2007. Two-dimensional optical measurement of the tilt of a rock mass and continuous fully digital on-line evaluation of results makes possible the detection of a small tilt of the surroundings with a resolution of tens of nanoradians or the deformation of the surroundings in the horizontal plane with resolution of hundreds of nanometres. The paper describes the measurement device and the first results of the measurements in Magdalena Jama, which is part of the Postojna Cave System (Slovenia). The correlation of deformation between distant stations shows the existence of stress variations that are not only of local origin (high floods, local seismicity, and aseismic deformations). The stress field has a wider, and not only regional, character with effects that can be observed very far from the origin

Analysis and Parameter Identification of Automatic Cannon Carriages

Experimental procedures for the research of vibrations in automatic weapons mounted on combat vehicles is introduced. Experiment preparation procedures, experience and examples of evaluation of measured results in direct fire from a tracked combat vehicle are explained on BMP-2 IFV example. The result is the movements of the turret and the hull of a combat vehicle in single shot firing, and short and long burst firing. In addition to time domain analysis, methods of correlation and spectral analysis are used. Live firing experiments are complemented by laboratory experiments and are used to determine model parameters for calculations such as stiffness and damping in the suspensions of the hull, elevation parts, clearance in the elevating gear, and the natural vibration frequency of the hull and elevation parts

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

BACKGROUND: Silene latifolia is a dioecious [corrected] plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. METHODOLOGY/PRINCIPAL FINDINGS: We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. CONCLUSIONS/SIGNIFICANCE: This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight

<p>Abstract</p> <p>Background</p> <p>Late blight is the most serious potato disease world-wide. The most effective and environmentally sound way for controlling late blight is to incorporate natural resistance into potato cultivars. Several late blight resistance genes have been cloned recently. However, there is almost no information available about the resistance pathways mediated by any of those genes.</p> <p>Results</p> <p>We previously cloned a late blight resistance gene, <it>RB</it>, from a diploid wild potato species <it>Solanum bulbocastanum</it>. Transgenic potato lines containing a single <it>RB </it>gene showed a rate-limiting resistance against all known races of <it>Phytophthora infestans</it>, the late blight pathogen. To better understand the <it>RB</it>-mediated resistance we silenced the potato <it>Rar1 </it>and <it>Sgt1 </it>genes that have been implicated in mediating disease resistance responses against various plant pathogens and pests. The <it>Rar1 </it>and <it>Sgt1 </it>genes of a <it>RB</it>-containing potato clone were silenced using a RNA interference (RNAi)-based approach. All of the silenced potato plants displayed phenotypically normal growth. The late blight resistance of the <it>Rar1 </it>and <it>Sgt1 </it>silenced lines were evaluated by a traditional greenhouse inoculation method and quantified using a GFP-tagged <it>P. infestans </it>strain. The resistance of the <it>Rar1</it>-silenced plants was not affected. However, silencing of the <it>Sgt1 </it>gene abolished the <it>RB</it>-mediated resistance.</p> <p>Conclusion</p> <p>Our study shows that silencing of the <it>Sgt1 </it>gene in potato does not result in lethality. However, the <it>Sgt1 </it>gene is essential for the <it>RB</it>-mediated late blight resistance. In contrast, the <it>Rar1 </it>gene is not required for <it>RB</it>-mediated resistance. These results provide additional evidence for the universal role of the <it>Sgt1 </it>gene in various <it>R </it>gene-mediated plant defense responses.</p

A Computational Workflow for Interdisciplinary Deep Learning Projects utilizing bwHPC Infrastructure

Deep neural networks have the capability to solve complex tasks through accurate function approximation. The process from submitting domain data and defining process requirements to analyzed data consists of multiple steps, disallowing a simplistic straightforward procedure. It follows that one of the core questions is: how does an application development process facilitating interaction between data scientists and domain experts look like? Practically, two connected challenges need to be addressed. Firstly, it requires a solution for handling large amounts of domain-specific data. Secondly, when dealing with complex deep neural networks, it is essential to find a concept of how model training can be designed in an computationally efficient manner. While tailored solutions for addressing these challenges in interdisciplinary deep learning projects exist, a comprehensive and structured approach is missing. Hence, we present a computational workflow to enhance these kinds of projects concerning data handling, integration of cluster computing resources such as bwHPC infrastructure, and development processes. We exemplify our proposal by means of a biomedical image analysis project

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

Impact of Angiogenesis- and Hypoxia-Associated Polymorphisms on Tumor Recurrence in Patients with Hepatocellular Carcinoma Undergoing Surgical Resection

Simple Summary: Hepatocellular carcinoma remains a leading cause of cancer-related death and the most common primary hepatic malignancy in the Western hemisphere. Previous research found that angiogenesis-related cytokines and elevated levels of interleukin 8 and vascular endothelial growth factor (VEGF) shorten the expected time of survival. Moreover, factors of tumor angiogenesis- and hypoxia-driven signaling pathways are already associated with worse outcome in disease-free survival in several tumor entities. Our study investigates the prognosis of hepatocellular carcinoma patients based on a selection of ten different single-nucleotide polymorphisms from angiogenesis, carcinogenesis, and hypoxia pathways. Our study with 127 patients found supporting evidence that polymorphisms in angiogenesis-associated pathways corelate with disease-free survival and clinical outcome in patients with hepatocellular carcinoma. Abstract: Tumor angiogenesis plays a pivotal role in hepatocellular carcinoma (HCC) biology. Identifying molecular prognostic markers is critical to further improve treatment selection in these patients. The present study analyzed a subset of 10 germline polymorphisms involved in tumor angiogenesis pathways and their impact on prognosis in HCC patients undergoing partial hepatectomy in a curative intent. Formalin-fixed paraffin-embedded (FFPE) tissues were obtained from 127 HCC patients at a German primary care hospital. Genomic DNA was extracted, and genotyping was carried out using polymerase chain reaction (PCR)-restriction fragment length polymorphism-based protocols. Polymorphisms in interleukin-8 (IL-8) (rs4073; p = 0.047, log-rank test) and vascular endothelial growth factor (VEGF C + 936T) (rs3025039; p = 0.045, log-rank test) were significantly associated with disease-free survival (DFS). After adjusting for covariates in the multivariable model, IL-8 T-251A (rs4073) (adjusted p = 0.010) and a combination of "high-expression" variants of rs4073 and rs3025039 (adjusted p = 0.034) remained significantly associated with DFS. High-expression variants of IL-8 T-251A may serve as an independent molecular marker of prognosis in patients undergoing surgical resection for HCC. Assessment of the patients' individual genetic risks may help to identify patient subgroups at high risk for recurrence following curative-intent surgery