Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs

Sawyer, Eric M.,Barta, Cody,Clemente, Romina,Conn, Michel,Davis, Clif,Doyle, Catherine,Gearing, Mary,Ho-Shing, Olivia,Mooney, Alyndria,Morton, Jerrad,Punjabi, Shamita,Schnoor, Ashley,Sun, Siya,Suresh, Korean Society for Bioinformatics 2012 Interdisciplinary Bio Central (IBC) Vol.4 No.3

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

Luminescence and scintillation properties of Lu₃Al₅O₁₂ nanoceramics sintered by SPS method

Pejchal, Jan,Babin, Vladimir,Beitlerova, Alena,Kucerkova, Romana,Panek, Dalibor,Barta, Jan,Cuba, Vaclav,Yamaji, Akihiro,Kurosawa, Shunsuke,Mihokova, Eva,Ito, Akihiko,Goto, Takashi,Nikl, Martin,Yoshika Elsevier 2016 Optical Materials Vol.53 No.-

<P><B>Abstract</B></P> <P>Ce-doped lutetium aluminum garnet Lu<SUB>3</SUB>Al<SUB>5</SUB>O<SUB>12</SUB> (LuAG) nanoceramics were fabricated at 1600°C and 1700°C by spark-plasma sintering (SPS) method from nano-powders prepared by radiation synthesis. Both undoped and Ce-doped LuAG ceramic samples were also prepared from the nano-powders at 1700°C with significantly increased pre-heating rate. The backscattered electron images revealed large amount of pores in all the Ce-doped samples causing their significant opacity. On the other hand, very large grains and no pores were revealed in the undoped sample, which was the only transparent one. The radioluminescence measurements revealed superior overall scintillation efficiency of the samples sintered at the temperature 1700°C, and their defect emission in the UV region was ascribed to oxygen-vacancy-related defects such as F<SUP>+</SUP> centers. The photoluminescence decay of the defect emission was characterized by an extremely fast decay time of a few nanoseconds. Influence of sintering procedure and subsequent annealing on the luminescence and scintillation properties is discussed.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Ce-doped scintillation nanoceramics were prepared by a Spark-Plasma-Sintering method. </LI> <LI> High overall scintillation efficiency was found. </LI> <LI> For samples prepared with slower pre-heating, scintillation efficiency can be increased by annealing. </LI> <LI> Higher sintering temperatures and slower pre-heating stages positively influence scintillation efficiency. </LI> </UL> </P>

An inactivating mutation in intestinal cell kinase, <i>ICK</i>, impairs hedgehog signalling and causes short rib-polydactyly syndrome

Paige Taylor, S.,Kunova Bosakova, Michaela,Varecha, Miroslav,Balek, Lukas,Barta, Tomas,Trantirek, Lukas,Jelinkova, Iva,Duran, Ivan,Vesela, Iva,Forlenza, Kimberly N.,Martin, Jorge H.,Hampl, Ales,Bamsha IRL Press 2016 Human molecular genetics Vol.25 No.18

<P>Mutations in several genes affecting cilia function cause SRPS, revealing a role for cilia function in skeletal development. To identify additional SRPS genes and discover novel ciliary molecules required for normal skeletogenesis, we performed exome sequencing in a cohort of patients and identified homozygosity for a missense mutation, p. E80K, in Intestinal Cell Kinase, ICK, in one SRPS family. The p. E80K mutation abolished serine/threonine kinase activity, resulting in altered ICK subcellular and ciliary localization, increased cilia length, aberrant cartilage growth plate structure, defective Hedgehog and altered ERK signalling. These data identify ICK as an SRPS-associated gene and reveal that abnormalities in signalling pathways contribute to defective skeletogenesis.</P>

Neutron and Gamma Spectra Measurement and Calculations Using Different Data Libraries on Nickel Benchmark Assembly

B. Jansky,Z. Turzik,E. Novak,M. Svadlenkova,M. Barta,L. A. Trykov,A. I. Blokhin 한국물리학회 2011 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.59 No.23

The leakage neutron and gamma spectra measurements have been done on benchmark spherical assembly-nickel sphere with diameter of 50 cm. The Cf-252 neutron sources with different emissions were placed into the centre of nickel sphere. The proton recoil method was used for neutron spectra measurement using stilbene crystals and hydrogen proportional counters. The neutron energy range of spectrometer was from 0.02 to 17 MeV. The gamma pulse shape discrimination method has been applied in stilbene measurements. The gamma energy range of spectrometer was from 0.1 to 10 MeV. The fine structure of gamma spectrum was measured by HPGe spectrometer. The experimental data were compared to results of transport calculations based on different evaluated nuclear data libraries (ENDF/B-VII.0, JENDL-3.3, JEFF-3.1.1, TENDL-2009). The continuous energy Monte Carlo transport calculation code MCNP-4C was employed for the calculations. Main observed differences between experiments and transport calculations are discussed.

Fibroblast growth factor receptor influences primary cilium length through an interaction with intestinal cell kinase

Kunova Bosakova, Michaela,Nita, Alexandru,Gregor, Tomas,Varecha, Miroslav,Gudernova, Iva,Fafilek, Bohumil,Barta, Tomas,Basheer, Neha,Abraham, Sara P.,Balek, Lukas,Tomanova, Marketa,Fialova Kucerova, J National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.10

<▼1><P><B>Significance</B></P><P>A properly functioning primary cilium is prerequisite for both normal development and aging of all ciliated organisms, including humans. In vertebrates, the signaling of Hedgehog family morphogens depends entirely on primary cilium. Recently, we reported that fibroblast growth factors (FGF) signaling interacts with that of Hedgehog, and that this is a consequence of FGF regulating length of the cilium and speed of processes that happen therein. In this report, we provide a molecular mechanism of such interaction, identifying intestinal cell kinase as a mediator of the FGF-induced changes in the ciliary morphology and function. This expands our understanding how FGF signaling regulates intracellular processes, and how aberrant FGF signaling contributes to diseases, such as achondroplasia and cancer.</P></▼1><▼2><P>Vertebrate primary cilium is a Hedgehog signaling center but the extent of its involvement in other signaling systems is less well understood. This report delineates a mechanism by which fibroblast growth factor (FGF) controls primary cilia. Employing proteomic approaches to characterize proteins associated with the FGF-receptor, FGFR3, we identified the serine/threonine kinase intestinal cell kinase (ICK) as an FGFR interactor. ICK is involved in ciliogenesis and participates in control of ciliary length. FGF signaling partially abolished ICK’s kinase activity, through FGFR-mediated ICK phosphorylation at conserved residue Tyr15, which interfered with optimal ATP binding. Activation of the FGF signaling pathway affected both primary cilia length and function in a manner consistent with cilia effects caused by inhibition of ICK activity. Moreover, knockdown and knockout of ICK rescued the FGF-mediated effect on cilia. We provide conclusive evidence that FGF signaling controls cilia via interaction with ICK.</P></▼2>