Difference between revisions of "Stusti 2018"

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= Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas =
 
= Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas =
  
−
==  What makes RNA such a special molecule – specific chemical and structural features of RNA ==
+
==  What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl ==
 
<pubmed>  21930584</pubmed>
 
<pubmed>  21930584</pubmed>
  
−
== RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair ==
+
== RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner ==
 
<pubmed>  24219496 8156586 28979293 26109351</pubmed>
 
<pubmed>  24219496 8156586 28979293 26109351</pubmed>
  
−
== Ribozymes (catalytically active RNAs) (Intro)==
+
== Ribozymes (catalytically active RNAs: Christian Thielscher) ==
−
<pubmed>  21930582</pubmed>
+
<pubmed>  21930582 22454536 14730013 10554775 21930585 6297745</pubmed>
  
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== The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology ==
+
== The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz ==
 
<pubmed> 18292779 21930591 25500179</pubmed>
 
<pubmed> 18292779 21930591 25500179</pubmed>
  
−
== The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity ==
+
== The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider ==
 
<pubmed>  24452469,26682498 25798239 </pubmed>
 
<pubmed>  24452469,26682498 25798239 </pubmed>
  
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== Protein independent ribozymes – about Hammerhead,  Varkud satellite,  hairpin ribozyme & Co ==
+
== Riboregulation and virulence, targeting by antibiotics: Theresia Eisele ==
−
<pubmed> 22454536 14730013 10554775 21930585 6297745</pubmed>
 
−
 
 
−
== RNA-based second messengers ==
 
−
<pubmed> 28420751    25616065 25682701    25869574 26280533</pubmed>
 
−
 
 
−
== Riboregulation and virulence, targeting by antibiotics ==
 
 
<pubmed>27651123      26416753
 
<pubmed>27651123      26416753
 
   27120414   27672192  28434876  28529506 28886688</pubmed>   
 
   27120414   27672192  28434876  28529506 28886688</pubmed>   
−
 
−
== Riboswitches ==
 
−
<pubmed>    27607554      26655897   28121427      29618088 25794618    25794617 25848023    24769284 25571850   25964329   26118534 26494285 28206750  28375729    28396576    28541183    28455443   29537923      27798597 29135333  29420816  28611182</pubmed>
 
  
 
== Riboswitch modeling: Mark Sinzger ==
 
== Riboswitch modeling: Mark Sinzger ==
 
<pubmed>19381267 28591515 27378291</pubmed>
 
<pubmed>19381267 28591515 27378291</pubmed>
  
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== Protein- or tRNA-controlled RNA switches ==
+
== RNA thermometers: Jana Horlacher ==
−
<pubmed>25959893        24816551 25583497</pubmed>
 
−
 
 
−
== RNA thermometers ==
 
 
<pubmed>25477380 27060146 </pubmed>
 
<pubmed>25477380 27060146 </pubmed>
 
   
 
   
−
== The RNA world and evolution ==
+
== The RNA world and evolution: Roman Doll ==
 
<pubmed>      25109990 25385129    25734234 25739364    26439358 17540026 29031737      28657884  19117371</pubmed>  
 
<pubmed>      25109990 25385129    25734234 25739364    26439358 17540026 29031737      28657884  19117371</pubmed>  
  
−
== RNA modification ==
+
== RNA modification: Jan Michel Göring ==
 
<pubmed>      26189113    26832457  27375676
 
<pubmed>      26189113    26832457  27375676
 
     28264529 28624569</pubmed>
 
     28264529 28624569</pubmed>
  
−
== RNA degradation/processing ==
+
== RNA degradation/processing: Lena Kricsfalussy-Hrabar ==
 
<pubmed>      26096689  28202538    19239894 </pubmed>  
 
<pubmed>      26096689  28202538    19239894 </pubmed>  
  
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== Regulation by non-coding RNA ==
+
== Regulation by non-coding RNA: Maxin Drömer ==
 
  <pubmed>        18981470      24667238 </pubmed>
 
  <pubmed>        18981470      24667238 </pubmed>
  
−
== RNA dependent DNA Polymerases - from telomerase to retroviruses==
+
== RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel==
 
<pubmed>      18972389 26830230     28141967 </pubmed>  
 
<pubmed>      18972389 26830230     28141967 </pubmed>  
  
−
== RNA dependent RNA Polymerases – the RNA replicase ==
+
== CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier ==
−
<pubmed>          29439438     18268843 9878607 </pubmed>
 
−
 
 
−
== CRISPR/Cas: Science – the bacterial “immune” system ==
 
 
<pubmed>      29358495      29169146 28375731</pubmed>
 
<pubmed>      29358495      29169146 28375731</pubmed>
  
−
== CRISPR/Cas: Application and groundbreaking  perspectives ==
+
== CRISPR/Cas: Application and groundbreaking  perspectives: Johann Liebeton ==
 
<pubmed>    26771484 </pubmed>  
 
<pubmed>    26771484 </pubmed>  
  
−
== The mysterious function and role of 6S-RNA and pRNA in bacteria ==
+
== Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol ==
−
<pubmed>    24786589  17383220 24742053 23457253</pubmed>
 
−
 
 
−
== Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer ==
 
 
<pubmed>    22016848 26186290 21957054 23166520 21930591</pubmed>  
 
<pubmed>    22016848 26186290 21957054 23166520 21930591</pubmed>  
  
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== Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways ==
 
== Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways ==
 
<pubmed>  17627883 19943183  </pubmed>
 
<pubmed>  17627883 19943183  </pubmed>
 +
 +
== RNA-based second messengers: Jörg Stülke ==
 +
<pubmed> 28420751    25616065 25682701    25869574 26280533</pubmed>
 +
 +
== Riboswitches: Jörg Stülke ==
 +
<pubmed>    27607554      26655897   28121427      29618088 25794618    25794617 25848023    24769284 25571850   25964329 25959893        24816551 25583497  26118534 26494285 28206750  28375729    28396576    28541183    28455443   29537923      27798597 29135333  29420816  28611182</pubmed>
 +
 +
== RNA dependent RNA Polymerases – the RNA replicase ==
 +
<pubmed>          29439438     18268843 9878607 </pubmed>
 +
 +
== The mysterious function and role of 6S-RNA and pRNA in bacteria ==
 +
<pubmed>    24786589  17383220 24742053 23457253</pubmed>

Revision as of 18:52, 20 July 2018

Contents

Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas

What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl


RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner


Ribozymes (catalytically active RNAs: Christian Thielscher)


The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz

Meredith Root-Bernstein, Robert Root-Bernstein
The ribosome as a missing link in the evolution of life.
J Theor Biol: 2015, 367;130-158
[PubMed:25500179] [WorldCat.org] [DOI] (I p)

Ingo Wohlgemuth, Corinna Pohl, Joerg Mittelstaet, Andrey L Konevega, Marina V Rodnina
Evolutionary optimization of speed and accuracy of decoding on the ribosome.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2979-86
[PubMed:21930591] [WorldCat.org] [DOI] (I p)

Thomas A Steitz
A structural understanding of the dynamic ribosome machine.
Nat Rev Mol Cell Biol: 2008, 9(3);242-53
[PubMed:18292779] [WorldCat.org] [DOI] (I p)


The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider


Riboregulation and virulence, targeting by antibiotics: Theresia Eisele


Riboswitch modeling: Mark Sinzger

Christopher Schneider, Leo Bronstein, Jascha Diemer, Heinz Koeppl, Beatrix Suess
ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data.
ACS Synth Biol: 2017, 6(7);1211-1224
[PubMed:28591515] [WorldCat.org] [DOI] (I p)

Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini
SwiSpot: modeling riboswitches by spotting out switching sequences.
Bioinformatics: 2016, 32(21);3252-3259
[PubMed:27378291] [WorldCat.org] [DOI] (I p)

Chase L Beisel, Christina D Smolke
Design principles for riboswitch function.
PLoS Comput Biol: 2009, 5(4);e1000363
[PubMed:19381267] [WorldCat.org] [DOI] (I p)


RNA thermometers: Jana Horlacher


The RNA world and evolution: Roman Doll


RNA modification: Jan Michel Göring


RNA degradation/processing: Lena Kricsfalussy-Hrabar


Regulation by non-coding RNA: Maxin Drömer


RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel


CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier


CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton


Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol

Tessa E F Quax, Nico J Claassens, Dieter Söll, John van der Oost
Codon Bias as a Means to Fine-Tune Gene Expression.
Mol Cell: 2015, 59(2);149-61
[PubMed:26186290] [WorldCat.org] [DOI] (I p)

Sibah Alkatib, Lars B Scharff, Marcelo Rogalski, Tobias T Fleischmann, Annemarie Matthes, Stefanie Seeger, Mark A Schöttler, Stephanie Ruf, Ralph Bock
The contributions of wobbling and superwobbling to the reading of the genetic code.
PLoS Genet: 2012, 8(11);e1003076
[PubMed:23166520] [WorldCat.org] [DOI] (I p)

Tamir Tuller
Codon bias, tRNA pools and horizontal gene transfer.
Mob Genet Elements: 2011, 1(1);75-77
[PubMed:22016848] [WorldCat.org] [DOI] (P p)

Richard Giegé, Frank Jühling, Joern Pütz, Peter Stadler, Claude Sauter, Catherine Florentz
Structure of transfer RNAs: similarity and variability.
Wiley Interdiscip Rev RNA: 2012, 3(1);37-61
[PubMed:21957054] [WorldCat.org] [DOI] (I p)

Ingo Wohlgemuth, Corinna Pohl, Joerg Mittelstaet, Andrey L Konevega, Marina V Rodnina
Evolutionary optimization of speed and accuracy of decoding on the ribosome.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2979-86
[PubMed:21930591] [WorldCat.org] [DOI] (I p)


Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)

Shahnaz Haque, Lorna W Harries
Circular RNAs (circRNAs) in Health and Disease.
Genes (Basel): 2017, 8(12);
[PubMed:29182528] [WorldCat.org] [DOI] (P e)

Feng Liu
Enhancer-derived RNA: A Primer.
Genomics Proteomics Bioinformatics: 2017, 15(3);196-200
[PubMed:28533025] [WorldCat.org] [DOI] (I p)

Kuei-Yang Hsiao, H Sunny Sun, Shaw-Jenq Tsai
Circular RNA - New member of noncoding RNA with novel functions.
Exp Biol Med (Maywood): 2017, 242(11);1136-1141
[PubMed:28485684] [WorldCat.org] [DOI] (I p)

Yiwen Fang, Melissa J Fullwood
Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer.
Genomics Proteomics Bioinformatics: 2016, 14(1);42-54
[PubMed:26883671] [WorldCat.org] [DOI] (I p)

Tae-Kyung Kim, Martin Hemberg, Jesse M Gray
Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers.
Cold Spring Harb Perspect Biol: 2015, 7(1);a018622
[PubMed:25561718] [WorldCat.org] [DOI] (I e)

Kevin C Wang, Howard Y Chang
Molecular mechanisms of long noncoding RNAs.
Mol Cell: 2011, 43(6);904-14
[PubMed:21925379] [WorldCat.org] [DOI] (I p)


Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways


RNA-based second messengers: Jörg Stülke


Riboswitches: Jörg Stülke


RNA dependent RNA Polymerases – the RNA replicase


The mysterious function and role of 6S-RNA and pRNA in bacteria

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