scholarly journals Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Jiacheng Zhang ◽  
Bhaskar Chetnani ◽  
Eric D Cormack ◽  
Dulce Alonso ◽  
Wei Liu ◽  
...  
Keyword(s):  
Second Step ◽  
Regulatory Rna ◽  
Structural Elements ◽  
Acid Biosynthesis ◽  
Site Specific ◽  
T Box ◽  
Set Up ◽  
Cognate Trna ◽  
Trna Binding ◽  
Different Parts

T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3’ NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and suggest such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand.

scholarly journals Two-step binding kinetics of tRNAGly by the glyQS T-box riboswitch and its regulation by T-box structural elements

2018 ◽  
Author(s):  
Jiacheng Zhang ◽  
Bhaskar Chetnani ◽  
Eric D. Cormack ◽  
Wei Liu ◽  
Alfonso Mondragón ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Regulatory Rna ◽  
Structural Elements ◽  
T Box ◽  
Loop Region ◽  
Rna Elements ◽  
Set Up ◽  
Trna Binding

ABSTRACTT-box riboswitches are cis-regulatory RNA elements that regulate mRNAs encoding for aminoacyl tRNA synthetases or proteins involved in amino acid biosynthesis and transport. Rather than using small molecules as their ligands, as do most riboswitches, T-box riboswitches uniquely bind tRNA and sense their aminoacylated state. Whereas the anticodon and elbow regions of the tRNA interact with Stem I, located in the 5’ portion of the T-box, sensing of the aminoacylation state involves direct binding of the NCCA sequence at the tRNA 3’ end to the anti-terminator sequence located in the 3’ portion of the T-box. However, the kinetic trajectory that describes how each of these interactions are established temporally during tRNA binding remains unclear. Using singlemolecule fluorescence resonance energy transfer (smFRET), we demonstrate that tRNA binds to the riboswitch in a two-step process, first with anticodon recognition followed by NCCA binding, with the second step accompanied by an inward motion of the 3’ portion of the T-box riboswitch relative to Stem I. By using site-specific mutants, we further show that the T-loop region of the T-box significantly contributes to the first binding step, and that the K-turn region of the T-box influences both binding steps, but with a more dramatic effect on the second binding step. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches and highlight the important roles of several T-box structural elements in regulating each binding step.SIGNIFICANCEBacteria commonly use riboswitches, cis-regulatory RNA elements, to regulate the transcription or translation of the mRNAs upon sensing signals. Unlike small molecule binding riboswitches, T-box riboswitches bind tRNA and sense their aminoacylated state. T-box modular structural elements that recognize different parts of a tRNA have been identified, however, how each of these interactions is established temporally during tRNA binding remains unclear. Our study reveals that tRNA binds to the riboswitch in a two-step mechanism, with anticodon recognition first, followed by binding to the NCCA sequence at the 3’ end of the tRNA with concomitant conformational changes in the T-box. Our results also highlight the importance of the modular structural elements of the T-box in each of the binding steps.

scholarly journals TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs

2020 ◽  
Author(s):  
Jorge A. Marchand ◽  
Merrick D. Pierson Smela ◽  
Thomas H. H. Jordan ◽  
Kamesh Narasimhan ◽  
George M. Church
Keyword(s):  
De Novo ◽  
Bacterial Species ◽  
Large Family ◽  
T Box ◽  
Gram Positive Bacteria ◽  
Binding Partners ◽  
Open Access Database ◽  
Feature Sequence ◽  
Cognate Trna ◽  
Trna Binding

AbstractT-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-boxes is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches and de novo prediction of binding specificities requires advance knowledge of computational tools to annotate riboswitch secondary structure features. Here we present T-box annotation Database (TBDB,https://tbdb.io), an open-access database with a collection of 23,497 T-box sequences, spanning the major phyla of 3,621 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory target. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

scholarly journals IN-PLACE ANALYSIS OF OFFSHORE JACKET PLATFORM FOR DIFFERENT WAVE DIRECTIONS

2020 ◽  
Vol 4 (5) ◽  
pp. 16-25
Author(s):  
MIRZA AAMIR BAIG ◽  
UMER MAQBOOL
Keyword(s):  
Extreme Point ◽  
Oil And Gas ◽  
Structural Elements ◽  
Great Care ◽  
Dynamic Reaction ◽  
Ecological Conditions ◽  
Offshore Jacket Platform ◽  
Space Technique ◽  
Fixed Base ◽  
Set Up

Offshore jacket platforms are subjected to variety of forces during their life period. To resists all kinds of forces, the structural elements should be designed properly to have safety and economy. In order to fulfil this purpose, the structure should be analyzed with great care. As the improvement of oil and gas moves into more profound water, in any case, taller stages with longer periods are fabricated that react all the more powerfully to extraordinary waves. Expectation of the dynamic reaction of such structures in extraordinary ocean states is in this way an essential plan thought. Standard waves have all their vitality lumped at a couple of particular frequencies and can, in this manner, cause wrong powerful enhancements, particularly if these frequencies happen to be near the regular frequencies of the structure. In any case, waves in the ocean are exceptionally sporadic and can be best depicted as directional range, which indicates the appropriation of wave vitality as for recurrence and heading, and is most appropriate for the examination of structure in recurrence space technique. For this situation the nonlinear drag is linearized and utilized in the Morison's condition. This guess is proper for the littler, operational sort waves considered in weariness counts, in light of the fact that the powers because of these waves are overwhelmed by the direct idleness part. Various kinds of investigations related with the coat stage ought to be performed to figure the reaction of the structure and measurement the components of the structure. Here an endeavor has been made to complete various examinations to comprehend the dynamic conduct of coat stages subject to different stacking conditions in various ecological conditions. Coat set up investigation was performed, both static and dynamic hypothetically fixed base stage. With the ongoing imaginative thoughts of investigation utilizing programming, it is presently simpler for the seaward architects to do disentangled and sensible assessment of the static operational and extreme point of confinement state qualities of format or coat stages, which are exposed to different ecological conditions. The essential auxiliary parts of coat type seaward structures including topsides, coat, heaps and the encompassing soil are viewed as utilizing SACS programming various types of investigations identified with coat stage according to API code prerequisite.

Formation of Part Families for Shared Setups Generation in Sheet Metal Bending

1998 ◽  
Author(s):  
Satyandra K. Gupta
Keyword(s):  
Sheet Metal ◽  
Cost Effective ◽  
Second Step ◽  
Setup Planning ◽  
Planning Techniques ◽  
Individual Part ◽  
Part Families ◽  
Different Types ◽  
Sheet Metal Bending ◽  
Different Parts

Abstract Sheet metal bending press-brakes can be setup to produce more than one type of parts without requiring a setup change. To exploit this flexibility, we need setup planning techniques to generate press-brake setups that can be shared among many different parts. In this paper, we describe an algorithm which partitions a given set of parts into setup compatible part families which can be produced on the same setup. Our algorithm is based on a two step approach. The first step is to identify setup constraints for each individual part. The second step is to form setup-compatible part families based on the compatibility of setup constraints. We expect that by producing many different types of parts on the same setup, we can significantly reduce the required number of setups and enable cost effective small batch manufacturing.

A New Framework for Interpreting Contact Rock Art

2017 ◽  
Author(s):  
Claire Smith ◽  
Jordan Ralph ◽  
Kylie Lower ◽  
Jennifer McKinnon ◽  
Matthew Ebbs ◽  
...  
Keyword(s):  
Rock Art ◽  
South Australia ◽  
Analytical Framework ◽  
Site Specific ◽  
Specific Contact ◽  
Temporal Succession ◽  
Insight Into ◽  
Different Parts ◽  
New Framework

This chapter addresses the challenge of seeing beyond the motif. Based on a case study in the Mid North of South Australia, this chapter presents a new analytical framework for analyzing style in rock art and using stylistic characteristics to identify authorship. The framework can be customized to different sites and/or regions to provide more nuanced understandings of specific contact trajectories. The results of this study suggest that innovation in contact rock art initially occurs in a single aspect of style and that a sequencing of innovations may be able to provide a temporal succession for contact motifs. The wider value of this framework is that it provides a basis for developing regional or site-specific models of style that may help researchers obtain greater insight into the authorship of contact rock art in different parts of the world.

scholarly journals Two-step approach for pressure oscillations prediction in gas turbine combustion chambers

2017 ◽  
Vol 9 (4) ◽  
pp. 424-437 ◽  
Author(s):  
Dmytro Iurashev ◽  
Giovanni Campa ◽  
Vyacheslav V Anisimov ◽  
Ezio Cosatto
Keyword(s):  
Transfer Function ◽  
Gas Turbine ◽  
Gas Turbines ◽  
Navier Stokes ◽  
Second Step ◽  
Combustion Instabilities ◽  
Combustion Chambers ◽  
Step Method ◽  
Pressure Oscillations ◽  
Set Up

Currently, gas turbine manufacturers frequently face the problem of strong acoustic combustion-driven oscillations inside combustion chambers. These combustion instabilities can cause extensive wear and sometimes even catastrophic damage of combustion hardware. This requires prevention of combustion instabilities, which, in turn, requires reliable and fast predictive tools. We have developed a two-step method to find a set of operating parameters under which gas turbines can be operated without going into self-excited pressure oscillations. As the first step, an unsteady Reynolds-averaged Navier–Stokes simulation with the flame speed closure model implemented in the OpenFOAM® environment is performed to obtain the flame transfer function of the combustion set-up. As the second step time-domain simulations employing low-order network model implemented in Simulink® are executed. In this work, we apply the proposed method to the Beschaufelter RingSpalt test rig developed at the Technische Universität München. The sensitivity of thermoacoustic stability to the length of a combustion chamber, flame position, gain and phase of flame transfer function and outlet reflection coefficient are studied.

Towards a General Theory of Reduction. Part III: Cross-Categorical Reduction

Dialogue ◽  
1981 ◽  
Vol 20 (3) ◽  
pp. 496-529 ◽  
Author(s):  
C.A. Hooker
Keyword(s):  
Nervous System ◽  
Prima Facie ◽  
The Other ◽  
Mental Function ◽  
Physical Processes ◽  
Monetary System ◽  
State Association ◽  
Set Up ◽  
The One ◽  
Different Parts

Any theory of reduction that goes only so far as carried in Parts I and II ([165], [166]) does only half the job. Prima facie at least, there are cases of would-be reduction which seem torn between two conflicting intuitions. On the one side there is a strong intuition that reduction is involved, and a strongly retentive reduction at that. On the other side it seems that the concepts at one level cross-classify those at the other level, so that there is no way to identify properties at one level with those at the other. There is evidence to suggest that there will be no unique mental state/neural state association that can be set up, because, e.g., many different parts of the nervous system are all capable of taking over ‘control’ of the one mental function. And it is alleged that infinitely many, worse: indefinitely many, different bio-chemo-physical states could correspond to the economic property ‘has a monetary system of economic exchange’; and similarly for the property ‘has just won a game of tennis’. Yet one doesn't want an economic system or a game of tennis to be some ghostly addition to the actual bio-chemo-physical processes and events involved (cf. Rudner [188]). Similarly one hopes that neurophysiology allied with the rest of natural science will render human experience and behaviour explicable.

Chondroitin - application in the treatment of degenerative joint disease

2016 ◽  
Vol 18 (6) ◽  
pp. 621-628 ◽  
Author(s):  
Wiesław Tomaszewski
Keyword(s):  
Molecular Level ◽  
Proteolytic Enzymes ◽  
Chondroitin Sulphate ◽  
Cartilage Degradation ◽  
Degenerative Joint Disease ◽  
Joint Disease ◽  
Chondrocyte Apoptosis ◽  
Structural Elements ◽  
Acid Biosynthesis ◽  
Physiological Processes

Chondroitin is an organic compound, belonging to the group of glycosaminoglycans. In the treatment of degenerative joint disease, aka osteoarthritis, chondroitin sulphate is applied as a medicine or a dietary supplement. The biological importance of chondroitin sulphate has been already largely determined. The newest data on glycobiology research suggest that proteoglycans, as well as their complex polysaccharide macroparticles not only are the structural elements, but also they participate in multiple metabolic processes at a molecular level as well as in the physiological processes, regulating this type of mechanisms. The preparations applied in the treatment of degenerative joint disease, containing chondroitin sulphate, are attributed numerous therapeutic and chondroprotective properties including stabilizing synthesis processes and cartilage degradation through stimulation and inhibition of chondrocyte apoptosis (production of the elements of the intracellular substance and osteocyte stimulation), an increased proteoglycan and hyaluronic acid biosynthesis, inhibition of the activity of proteolytic enzymes and hyaluronidase, reduction of inflammatory mediators (prostaglandins and leukotrienes) and a decreased collagen II degradation. Based on the results of the multidirectional research available in the newest source literature, the analysis of the therapeutic efficacy and safety of chondroitin application in the treatment of degenerative joint disease was conducted.

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