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"Transfers"
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Spectral Properties of Ruelle Transfer Operators for Regular Gibbs Measures and Decay of Correlations for Contact Anosov Flows
In this work we study strong spectral properties of Ruelle transfer operators related to a large family of Gibbs measures for contact
Anosov flows. The ultimate aim is to establish exponential decay of correlations for Hölder observables with respect to a very general
class of Gibbs measures. The approach invented in 1997 by Dolgopyat in “On decay of correlations in Anosov flows” and further developed
in Stoyanov (2011) is substantially refined here, allowing to deal with much more general situations than before, although we still
restrict ourselves to the uniformly hyperbolic case. A rather general procedure is established which produces the desired estimates
whenever the Gibbs measure admits a Pesin set with exponentially small tails, that is a Pesin set whose preimages along the flow have
measures decaying exponentially fast. We call such Gibbs measures regular. Recent results in Gouëzel and Stoyanov (2019) prove existence
of such Pesin sets for hyperbolic diffeomorphisms and flows for a large variety of Gibbs measures determined by Hölder continuous
potentials. The strong spectral estimates for Ruelle operators and well-established techniques lead to exponential decay of correlations
for Hölder continuous observables, as well as to some other consequences such as: (a) existence of a non-zero analytic continuation of
the Ruelle zeta function with a pole at the entropy in a vertical strip containing the entropy in its interior; (b) a Prime Orbit
Theorem with an exponentially small error.
eBook
Monstrous anger of the guns : how the global arms trade is ruining the world and what we can do about it
We are seeing injustices caused by war and occupation unfold in real-time via social media, and we are speaking out in our millions against these horrors. Yet, from Gaza to Ukraine, the bombs continue to fall. We must understand why this is happening if we are to end it. 'Monstrous Anger of the Guns' lays bare the dark and deceitful world of the global arms trade, which, often funded in our name, is a business that counts its profits in trillions and its losses in human lives. Leading activists and campaigners connect the dots, showing how notions of citizenship, democracy and trust in governments are misguided, and how we can fight back by building mass movements, using direct action and legal justice to end the flow of weapons and the environmental and human devastation they bring.
Book
The quenching of the fluorescence of carbon dots: A review on mechanisms and applications
Carbon dots (CDs) possess unique optical properties such as tunable photoluminescence (PL) and excitation dependent multicolor emission. The quenching and recovery of the fluorescence of CDs can be utilized for detecting analytes. The PL mechanisms of CDs have been discussed in previous articles, but the quenching mechanisms of CDs have not been summarized so far. Quenching mechanisms include static quenching, dynamic quenching, Förster resonance energy transfer (FRET), photoinduced electron transfer (PET), surface energy transfer (SET), Dexter energy transfer (DET) and inner filter effect (IFE). Following an introduction, the review (with 88 refs.) first summarizes the various kinds of quenching mechanisms of CDs (including static quenching, dynamic quenching, FRET, PET and IFE), the principles of these quenching mechanisms, and the methods of distinguishing these quenching mechanisms. This is followed by an overview on applications of the various quenching mechanisms in detection and imaging.
Graphical abstract
Schematic representation of the quenching mechanisms of carbon dots (CDs) which include static quenching, dynamic quenching, Förster resonance energy transfer (FRET), photoinduced electron transfer(PET), surface energy transfer (SET), Dexter energy transfer (DET) and inner filter effect (IFE). All these effects can be used to detect and image analytes.
Journal Article
Ribosome-dependent activation of stringent control
The structure of a bacterial ribosome–RelA complex reveals that RelA, a protein recruited to the ribosome in the case of scarce amino acids, binds in a different location to translation factors, and that this binding event suppresses auto-inhibition to activate synthesis of the (p)ppGpp secondary messenger, thus initiating stringent control.
How the starved ribosome exerts control
When bacteria are starved of nutrients, they initiate a program known as stringent response, or stringent control, in which the transcriptional pattern responds to the changing metabolic needs. In the case of amino acid starvation, which causes ribosome stalling, RelA protein is recruited to the ribosome. Venki Ramakrishnan and colleagues have solved the cryo-electron microscopy structure of a bacterial ribosome–RelA complex to understand how amino acid deficiency is detected. They find that RelA binds in a location different from that used by translation factors, and that this binding event releases an inhibitory state of RelA that normally prevents synthesis of the (p)ppGpp secondary messenger. This messenger initiates the stringent response.
In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation
1
,
2
that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns
3
. In general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated
4
. Amino acid starvation is sensed by depletion of the aminoacylated tRNA pools
5
, and this results in accumulation of ribosomes stalled with non-aminoacylated (uncharged) tRNA in the ribosomal A site
6
,
7
. RelA is recruited to stalled ribosomes and activated to synthesize a hyperphosphorylated guanosine analogue, (p)ppGpp
8
, which acts as a pleiotropic secondary messenger. However, structural information about how RelA recognizes stalled ribosomes and discriminates against aminoacylated tRNAs is missing. Here we present the cryo-electron microscopy structure of RelA bound to the bacterial ribosome stalled with uncharged tRNA. The structure reveals that RelA utilizes a distinct binding site compared to the translational factors, with a multi-domain architecture that wraps around a highly distorted A-site tRNA. The TGS (ThrRS, GTPase and SpoT) domain of RelA binds the CCA tail to orient the free 3′ hydroxyl group of the terminal adenosine towards a β-strand, such that an aminoacylated tRNA at this position would be sterically precluded. The structure supports a model in which association of RelA with the ribosome suppresses auto-inhibition to activate synthesis of (p)ppGpp and initiate the stringent response. Since stringent control is responsible for the survival of pathogenic bacteria under stress conditions, and contributes to chronic infections and antibiotic tolerance, RelA represents a good target for the development of novel antibacterial therapeutics.
Journal Article
Ser/Leu-swapped cell-free translation system constructed with natural/in vitro transcribed-hybrid tRNA set
The Ser/Leu-swapped genetic code can act as a genetic firewall, mitigating biohazard risks arising from horizontal gene transfer in genetically modified organisms. Our prior work demonstrated the orthogonality of this swapped code to the standard genetic code using a cell-free translation system comprised of 21 in vitro transcribed tRNAs. In this study, to advance this system for protein engineering, we introduce a natural
/
in vitro transcribed-hybrid tRNA set. This set combines natural tRNAs from
Escherichia coli
(excluding Ser, Leu, and Tyr) and in vitro transcribed tRNAs, encompassing anticodon-swapped tRNA
Ser
GAG
and tRNA
Leu
GGA
. This approach reduces the number of in vitro transcribed tRNAs required from 21 to only 4. In this optimized system, the production of a model protein, superfolder green fluorescent protein, increases to 3.5-fold. With this hybrid tRNA set, the Ser/Leu-swapped cell-free translation system will stand as a potent tool for protein production with reduced biohazard concerns in future biological endeavors.
The use of orthogonal genetic code can help to prevent the escape of hazardous genes through horizontal gene transfer. Here, the authors develop a cell-free translation system with the Ser/Leu-swapped genetic code using a hybrid tRNA set and show its application in enhancing the production of superfolder GFP.
Journal Article
tRNA Actively Shuttles between the Nucleus and Cytosol in Yeast
Previous evidence suggested that transfer RNAs (tRNAs) cross the nuclear envelope to the cytosol only once after maturing in the nucleus. We now present evidence for nuclear import of tRNAs in yeast. Several export mutants accumulate mature tRNAs in the nucleus even in the absence of transcription. Import requires energy but not the Ran cycle. These results indicate that tRNAs shuttle between the nucleus and cytosol.
Journal Article