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Where splicing joins chromatin

Jarmila Hnilicová, David Staněk
2011 Nucleus  
Staněk; Email: Submitted: 03/09/11; Revised: 04/18/11; Accepted: 04/19/11 DOI: 10.4161/nucl.2.3.15876 et al. which indicates a presence of additional regulatory signals. 7 Table  ...  Projects in David Stanek's lab are supported by grants from the Czech Science Foundation (P305/10/0424) and from the Academy of Sciences of the Czech Republic (KAN200520801, AV0Z50520514).  ... 
doi:10.4161/nucl.2.3.15876 pmid:21818411 pmcid:PMC3149878 fatcat:pzob7wqorjde7bsenkpy7uoolu

Cajal bodies and snRNPs - friends with benefits

David Staněk
2016 RNA Biology  
ORCID David Stan ek Figure 2 . SnRNP biogenesis is closely controlled along the maturation pathway.  ... 
doi:10.1080/15476286.2016.1231359 pmid:27627834 pmcid:PMC5519240 fatcat:majow525c5fw3e7vb7gdcro2ye

Coilin: The first 25 years

Martin Machyna, Karla M Neugebauer, David Staněk
2015 RNA Biology  
Funding David Stanek was supported by a Fulbright scholar fellowship, the Academy of Sciences of the Czech Republic (RVO68378050) and the Czech Science Foundation (P305/12/G034).  ... 
doi:10.1080/15476286.2015.1034923 pmid:25970135 pmcid:PMC4615369 fatcat:eewhxsy3xnfuzdvcdkyhwgijca

Retinaldehyde cyclodextrin complex for topical skin therapy

David Peter, John Stanek, Shyam Gupta
2016 Global Dermatology  
Retinaldehyde (retinal) has been identified as having superior topical activity, unrivaled topical bioavailability, and is less irritating than most other vitamin A derivatives. However, it has not received its deserved market attention possibly due to formulation-related issues. A novel compound, Retinaldehyde γ-Cyclodextrin Complex (RCC), has been developed to address the principal issues preventing retinaldehyde to enter the marketplace. Gene expression data of RCC have shown certain unique
more » ... kin care attributes that are not present in retinaldehyde, including significantly less topical irritation.
doi:10.15761/god.1000161 fatcat:xxsk5bajwvhbvpnuzbo7ntwof4

Mutations in spliceosomal proteins and retina degeneration

Šárka Růžičková, David Staněk
2016 RNA Biology  
A majority of human genes contain non-coding intervening sequencesintrons that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases
more » ... re caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations. KEYWORDS Retinitis pigmentosa; snRNP; splicing Small nuclear ribonucleoprotein particles Spliceosomal snRNPs are complex particles consisting of small nuclear RNA (snRNA), a heptameric ring of Sm or Like-Sm (LSm) proteins and 1-13 proteins that are specific for each snRNP. Five major and four minor snRNPs have been described and named according to their snRNA composition. The major snRNPs are U1, U2, U4, U5 and U6 and the minor snRNPs are U11, U12, U4atac and U6atac. The U5 snRNP is common to both major and minor splicing pathways. The most accepted view of spliceosome formation is a stepwise assembly model, which has been supported by numerous
doi:10.1080/15476286.2016.1191735 pmid:27302685 pmcid:PMC5449078 fatcat:se5grromiffbfohvfwhmnyc2g4

Mold Cavity Roughness vs. Flow of Polymer

Michal Stanek, Miroslav Manas, David Manas, Martin Zatloukal
2009 AIP Conference Proceedings  
Injection molding represents such a way of polymer processing that requires injection of polymer melt into the mold cavity with very high injection rate. The fluidity of polymers is affected by many parameters (mold design, melt temperature, injection rate and pressure). The main objective of this paper is the study of influence of surface roughness of mold cavity of the polymer melts flow. Evaluation of set of data obtained by experiments where the testing conditions were widely changed shows
more » ... hat quality of cavity surface affects on the length of flow.
doi:10.1063/1.3203288 fatcat:jinzassslvfyrkczn6gp6d2zni

Rapid Purification of Endotoxin-Free RTX Toxins

Ondrej Stanek, Jiri Masin, Radim Osicka, David Jurnecka, Adriana Osickova, Peter Sebo
2019 Toxins  
Cytolytic leukotoxins of the repeat in toxin (RTX) family are large proteins excreted by gram-negative bacterial pathogens through the type 1 secretion system (T1SS). Due to low yields and poor stability in cultures of the original pathogens, it is useful to purify recombinant fatty-acylated RTX cytolysins from inclusion bodies produced in E. coli. Such preparations are, however, typically contaminated by high amounts of E. coli lipopolysaccharide (LPS or endotoxin). We report a simple
more » ... for purification of large amounts of biologically active and endotoxin-free RTX toxins. It is based on the common feature of RTX cytolysins that are T1SS-excreted as unfolded polypeptides and fold into a biologically active toxin only upon binding of calcium ions outside of the bacterial cell. Mimicking this process, the RTX proteins are solubilized from inclusion bodies with buffered 8 M urea, bound onto a suitable chromatographic medium under denaturing conditions and the contaminating LPS is removed through extensive on-column washes with buffers containing 6 to 8 M urea and 1% Triton X-100 or Triton X-114. Extensive on-column rinsing with 8 M urea buffer removes residual detergent and the eluted highly active RTX protein preparations then contain only trace amounts of LPS. The procedure is exemplified using four prototypic RTX cytolysins, the Bordetella pertussis CyaA and the hemolysins of Escherichia coli (HlyA), Kingella kingae (RtxA), and Actinobacillus pleuropneumoniae (ApxIA).
doi:10.3390/toxins11060336 pmid:31212877 pmcid:PMC6628407 fatcat:rvdtfygomzh3dhe2isadtuia4y

Sequences of Groups, Hypergroups and Automata of Linear Ordinary Differential Operators

Jan Chvalina, Michal Novák, Bedřich Smetana, David Staněk
2021 Mathematics  
The main objective of our paper is to focus on the study of sequences (finite or countable) of groups and hypergroups of linear differential operators of decreasing orders. By using a suitable ordering or preordering of groups linear differential operators we construct hypercompositional structures of linear differential operators. Moreover, we construct actions of groups of differential operators on rings of polynomials of one real variable including diagrams of actions–considered as special
more » ... tomata. Finally, we obtain sequences of hypergroups and automata. The examples, we choose to explain our theoretical results with, fall within the theory of artificial neurons and infinite cyclic groups.
doi:10.3390/math9040319 fatcat:2h3st7jf65cxlnk7snjyebmzm4

Histone Deacetylase Activity Modulates Alternative Splicing

Jarmila Hnilicová, Samira Hozeifi, Eva Dušková, Jaroslav Icha, Tereza Tománková, David Staněk, Juan Valcarcel
2011 PLoS ONE  
Acknowledgments We thank Reinhard Lührmann, David Drechsel, Ina Poser, Tony Hyman, Karla Neugebauer, Douglas Black, Pavel Draber, Marta Miaczynska and Konstantinos Anastassiadis for gifts of reagents.  ...  and Genetics, Germany), anti-tubulin antibody was kindly provided by Pavel Draber (Institute of Molecular Genetics ASCR, Prague, Czech Republic), goat anti-GFP antibody used for ChIP was received from David  ... 
doi:10.1371/journal.pone.0016727 pmid:21311748 pmcid:PMC3032741 fatcat:xdjb2dad2vc4tea5z7idph2kke

Binding-Linked Protonation of a DNA Minor-Groove Agent

Binh Nguyen, Jaroslav Stanek, W. David Wilson
2006 Biophysical Journal  
The energetics for binding of a diphenyl diamidine antitrypanosomal agent CGP 40215A to DNA have been studied by spectroscopy, isothermal titration calorimetry, and surface plasmon resonance biosensor methods. Both amidines are positively charged under experimental conditions, but the linking group for the two phenyl amidines has a pK a of 6.3 that is susceptible to a protonation process. Spectroscopic studies indicate an increase of 2.7 pK a units in the linking group when the compound binds
more » ... an A/T minor-groove site. Calorimetric titrations in different buffers and pH conditions support the protonlinkage process and are in a good agreement with spectroscopic titrations. The two methods established a proton-uptake profile as a function of pH. The exothermic enthalpy of complex formation varies with different pH conditions. The observed binding enthalpy increases as a function of temperature indicating a negative heat capacity change that is typical for DNA minor-groove binders. Solvent accessible surface area calculations suggest that surface burial accounts for about one-half of the observed intrinsic negative heat capacity change. Biosensor and calorimetric experiments indicate that the binding affinities vary with pH values and salt concentrations due to protonation and electrostatic interactions. The surface plasmon resonance binding studies indicate that the charge density per phosphate in DNA hairpins is smaller than that in polymers. Energetic contributions from different factors were also estimated for the ligand/DNA complex.
doi:10.1529/biophysj.105.071381 pmid:16299076 pmcid:PMC1367283 fatcat:2x2ant7vtrhpppnsfevept3u4u

SATB1 undergoes isoform-specific phase transitions in T cells [article]

Tomas Zelenka, Petros Tzerpos, Giorgos Panagopoulos, Konstantinos Tsolis, Dionysios-Alexandros Papamatheakis, Vassilis M. Papadakis, David Stanek, Charalampos Spilianakis
2021 bioRxiv   pre-print
The long SATB1-specific antisera were produced by Davids Biotechnologie upon immunization of New Zealand rabbits with the GKGESRGVFLPSLLTPAPWPHAA peptide (corresponding to the extra peptide identified  ...  The membrane was incubated with antibodies against the long isoform of SATB1 (1:200; Davids Biotechnologie, custom-made), all isoforms of SATB1 (1:50; Santa Cruz Biotechnology, sc-5990) and beta Actin  ... 
doi:10.1101/2021.08.11.455932 fatcat:mgfhd5eybbcdffrndrfq7zoqbm

Pontin is localized in nucleolar fibrillar centers

Zuzana Cvačková, Kai F. Albring, Karel Koberna, Anna Ligasová, Otmar Huber, Ivan Raška, David Staněk
2008 Chromosoma  
Rabbit anti-SART3 antibodies (Stanek et al. 2003) were used as nucleoplasmic markers.  ... 
doi:10.1007/s00412-008-0170-8 pmid:18548265 pmcid:PMC2564108 fatcat:p3hmz7kj6rdg7onxw7djkr5him

Nanohardness of Electron Beam Irradiated HDPE

David Manas, Martin Ovsik, Miroslav Manas, Michal Stanek, Karel Kocman, Martin Bednarik, Vojtech Senkerik
2014 Advanced Materials Research  
Micromechanical changes in the surface layer of High-density polyethylene HDPE modified by beta radiation were measured by instrumented test of nanohardness. The specimens were prepared by injection technology and subjected to radiation doses of 0, 132, 165, 198 kGy. Measurements of nanohardness showed considerable changes of behavior of surface layer in middle as well as high radiation doses with higher values of indentation hardness and stiffness.
doi:10.4028/ fatcat:rd7apy2ngnctjhfrug4yb6xqsm

CRE promoter sites modulate alternative splicing via p300-mediated histone acetylation

Eva Dušková, Jarmila Hnilicová, David Staněk
2014 RNA Biology  
Genetics, academy of sciences of the czech republic, prague, czech republic; 2 Faculty of science, charles University in prague, prague, czech republic; 3 Institute of Microbiology, academy of sciences of the czech republic, prague, czech republic;
doi:10.4161/rna.29441 pmid:25019513 pmcid:PMC4179961 fatcat:6pgorbkw3ja5vdo4pyxzbnshti

The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze

David Staněk, Karla M. Neugebauer
2006 Chromosoma  
2004; Stanek et al. 2003) .  ...  Instead, the U6 snRNP is targeted to CBs through the HAT domain of SART3 (Stanek et al. 2003) .  ... 
doi:10.1007/s00412-006-0056-6 pmid:16575476 fatcat:kxwxpcym4vfepd3q6hajrqzirq
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