Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

<p>Abstract</p> <p>Background</p> <p>Alternative splicing expands transcriptome diversity and plays an important role in regulation of gene expression. Previous studies focus on the regulation of a single cassette exon, but recent experiments indicate that multiple cassette exons within a gene may interact with each other. This interaction can increase the potential to generate various transcripts and adds an extra layer of complexity to gene regulation. Several cases of exon interaction have been discovered. However, the extent to which the cassette exons coordinate with each other remains unknown.</p> <p>Results</p> <p>Based on EST data, we employed a metric of correlation coefficients to describe the interaction between two adjacent cassette exons and then categorized these exon pairs into three different groups by their interaction (correlation) patterns. Sequence analysis demonstrates that strongly-correlated groups are more conserved and contain a higher proportion of pairs with reading frame preservation in a combinatorial manner. Multiple genome comparison further indicates that different groups of correlated pairs have different evolutionary courses: (1) The vast majority of positively-correlated pairs are old, (2) most of the weakly-correlated pairs are relatively young, and (3) negatively-correlated pairs are a mixture of old and young events.</p> <p>Conclusion</p> <p>We performed a large-scale analysis of interactions between adjacent cassette exons. Compared with weakly-correlated pairs, the strongly-correlated pairs, including both the positively and negatively correlated ones, show more evidence that they are under delicate splicing control and tend to be functionally important. Additionally, the positively-correlated pairs bear strong resemblance to constitutive exons, which suggests that they may evolve from ancient constitutive exons, while negatively and weakly correlated pairs are more likely to contain newly emerging exons.</p

A Spontaneous Fatp4/Scl27a4 Splice Site Mutation in a New Murine Model for Congenital Ichthyosis

Congenital ichthyoses are life-threatening conditions in humans. We describe here the identification and molecular characterization of a novel recessive mutation in mice that results in newborn lethality with severe congenital lamellar ichthyosis. Mutant newborns have a taut, shiny, non-expandable epidermis that resembles cornified manifestations of autosomal-recessive congenital ichthyosis in humans. The skin is stretched so tightly that the newborn mice are immobilized. The genetic defect was mapped to a region near the proximal end of chromosome 2 by SNP analysis, suggesting Fatp4/Slc27a4 as a candidate gene. FATP4 mutations in humans cause ichthyosis prematurity syndrome (IPS), and mutations of Fatp4 in mice have previously been found to cause a phenotype that resembles human congenital ichthyoses. Characterization of the Fatp4 cDNA revealed a fusion of exon 8 to exon 10, with deletion of exon 9. Genomic sequencing identified an A to T mutation in the splice donor sequence at the 3′-end of exon 9. Loss of exon 9 results in a frame shift mutation upstream from the conserved very long-chain acyl-CoA synthase (VLACS) domain. Histological studies revealed that the mutant mice have defects in keratinocyte differentiation, along with hyperproliferation of the stratum basale of the epidermis, a hyperkeratotic stratum corneum, and reduced numbers of secondary hair follicles. Since Fatp4 protein is present primarily at the stratum granulosum and the stratum spinosum, the hyperproliferation and the alterations in hair follicle induction suggest that very long chain fatty acids, in addition to being required for normal cornification, may influence signals from the stratum corneum to the basal cells that help to orchestrate normal skin differentiation

Data Release of the AST3-2 Automatic Survey from Dome A, Antarctica

AST3-2 is the second of the three Antarctic Survey Telescopes, aimed at wide-field time-domain optical astronomy. It is located at Dome A, Antarctica, which is by many measures the best optical astronomy site on the Earth's surface. Here we present the data from the AST3-2 automatic survey in 2016 and the photometry results. The median 5$\sigma$ limiting magnitude in $i$-band is 17.8 mag and the light curve precision is 4 mmag for bright stars. The data release includes photometry for over 7~million stars, from which over 3,500 variable stars were detected, with 70 of them newly discovered. We classify these new variables into different types by combining their light curve features with stellar properties from surveys such as StarHorse.Comment: 16 pages, 20 figures, accepted for publication in MNRA

Individual Professional Practice in the Company

Import 23/08/2017Cílem této bakalářské práce je popsat absolvování odborné praxe ve firmě HS Interactive s.r.o. Praxe byla zaměřena na vývoj mobilní aplikace pro operační systém Android. Aplikace je mobilním klientem pro sociální síť MatchToMe. V úvodu popisuji důvody, které vedly k výběru odborné praxe. Dále se věnuji úkolům, které mi byly zadány s jejich implementací a postupem řešení problémů, které se objevily při vývoji. Závěr práce je věnován zhodnocení získaných zkušeností a dosažených výsledků.Purpose of this bachelor thesis is to describe a professional practice in company HS Interactive s.r.o. Practice was focused on the development of mobile application for the operating system Android. The application is a mobile client for social network MatchToMe. In the introduction I describe reasons that led to the selection of professional practice. Then I describe tasks that I have been awarded with their implementations and process of solution issues that have emerged during development. The conclusion of thesis is dedicated to the evaluation of the experience gained and the results achieved.440 - Katedra telekomunikační technikyvýborn

Exoplanets in the Antarctic Sky I. The first data release of AST3-II (CHESPA) and new found variables within the southern CVZ of TESS

Located at Dome A, the highest point of the Antarctic plateau, the Chinese Kunlun station is considered to be one of the best ground-based photometric sites because of its extremely cold, dry, and stable atmosphere. A target can be monitored from there for over 40 days without diurnal interruption during a polar winter. This makes Kunlun station a perfect site to search for short-period transiting exoplanets. Since 2008, an observatory has existed at Kunlun station, and three telescopes are working there. Using these telescopes, the AST3 project has been carried out over the last 6 yr with a search for transiting exoplanets as one of its key programs (CHESPA). In the austral winters of 2016 and 2017, a set of target fields in the southern continuous viewing zone (CVZ) of TESS were monitored by the AST3-II telescope. In this paper, we introduce the CHESPA and present the first data release containing photometry of 26,578 bright stars (m(i) <= 15). The best photometric precision at the optimum magnitude for the survey is around 2 mmag. To demonstrate the data quality, we also present a catalog of 221 variables with a brightness variation greater than 5 mmag from the 2016 data. Among these variables, 179 are newly identified periodic variables not listed in the AAVSO database (https://www.aavso.org/), and 67 are listed in the Candidate Target List. These variables will require careful attention to avoid false-positive signals when searching for transiting exoplanets. Dozens of new transiting exoplanet candidates will be released in a subsequent paper

Exoplanets in the Antarctic Sky. II. 116 Transiting Exoplanet Candidates Found by AST3-II (CHESPA) within the Southern CVZ of TESS

We report first results from the CHinese Exoplanet Searching Program from Antarctica (CHESPA)-a wide-field high-resolution photometric survey for transiting exoplanets carried out using telescopes of the AST3 (Antarctic Survey Telescopes times 3) project. There are now three telescopes (AST3-I, AST3-II, and CSTAR-II) operating at Dome A-the highest point on the Antarctic Plateau-in a fully automatic and remote mode to exploit the superb observing conditions of the site, and its long and uninterrupted polar nights. The search for transiting exoplanets is one of the key projects for AST3. During the austral winters of 2016 and 2017 we used the AST3-II telescope to survey a set of target fields near the southern ecliptic pole, falling within the continuous viewing zone of the TESS mission. The first data release of the 2016 data, including images, catalogs, and light curves of 26,578 bright stars (7.5 <= m(i) <= 15), was presented in Zhang et al. The best precision, as measured by the rms of the light curves at the optimum magnitude of the survey (m(i) = 10), is around 2 mmag. We detect 222 objects with plausible transit signals from these data, 116 of which are plausible transiting exoplanet candidates according to their stellar properties as given by the TESS Input Catalog, Gaia DR2, and TESS-HERMES spectroscopy. With the first data release from TESS expected in late 2018, this candidate list will be timely for improving the rejection of potential false-positives

Thermocapillary migration mechanism of molten silicon droplets on horizontal solid surfaces

Abstract Effective lubrication under extreme conditions such as high temperature is of considerable importance to ensure the reliability of a mechanical system. New lubricants that can endure high temperatures should be studied and employed as alternatives to traditional oil-based lubricant. In this paper, a thermocapillary model of a silicone-oil droplet is developed by solving the Navier–Stokes and energy equations to obtain the flow, pressure, and temperature fields. This is accomplished using a conservative microfluidic two-phase flow level set method designed to track the interface between two immiscible fluids. The numerical simulation accuracy is examined by comparing the numerical results with experimental results obtained for a silicone-oil droplet. Hence, the movement and deformation of molten silicon droplets on graphite and corundum are numerically simulated. The results show that a temperature gradient causes a tension gradient on the droplet surface, which in turn creates a thermocapillary vortex. As the vortex develops, the droplet migrates to the low-temperature zone. In the initial stage, the molten silicon droplet on the corundum substrate forms two opposite vortex cells, whereas two pairs of opposite vortices are formed in the silicone fluid on the graphite substrate. Multiple vortex cells gradually develop into a single vortex cell, and the migration velocity tends to be stable. The greater the basal temperature gradient, the stronger the internal thermocapillary convection of the molten silicon droplet has, which yields higher speeds

Modeling and Analysis of Novel Horizontal Ribbon Growth of Silicon Crystal

We present a novel horizontal ribbon growth (HRG) process and a theoretical analysis of this method. Assuming that the existence of the meniscus is defined by diffuse growth, we determine analytically the thickness and height of the meniscus and an explicit expression for the performance of meniscus under different conditions. We then calculate the thermal profile in melt part, as well as the conditions under which the undercooling is sufficient around the solidification point. We find that diffuse growth is more sensitive to small initial thickness, and find the minimum length of the melt part to obtain undercooling. Finally, we calculate the change rule of solidification position by a variational approach, as well as the stability of the process under different conditions. We also give an expression to the instability of past HRG methods

Simulating the horizontal growth process of silicon ribbon

In this paper, we present a solidification growth model that primarily describes the principal components of horizontal ribbon growth process, but also discusses the interaction between fluid flow and heat transfer, crystallization dynamics, and the effects of oxygen impurity distribution in melts, particularly with respect to the morphology of the interface. The effects of the jet cooling rate, pulling speed, and transfer coefficient on solute transport were studied. The results showed that a higher jet velocity produces a sharper temperature gradient at the interface and a stronger Marangoni effect, facilitates solute transport in the silicon melt, and promotes higher oxygen concentration in crystal. The stronger Marangoni convection causes more rapid oxygen transfer in the silicon melt and a higher oxygen concentration. Solidification front increases the downward flow velocity of the eddy current as the pulling speed is increased; this leads to a decrease in solute concentration at the interface. An increase in the downward flow of the vortex confluence facilitates the reduction of solute concentration in the crystal. An increase in the upward flow of the vortex confluence will increase the concentration in the crystal. The oxygen concentration is concentrated at the top and bottom of the silicon ribbon