Translational Coordinates Research Articles

MRNA localization and thylakoid protein biogenesis in the filamentous heterocyst-forming cyanobacterium Anabaena sp. PCC 7120.

Heterocyst-forming cyanobacteria such as Anabaena (Nostoc) sp. PCC 7120 exhibit extensive remodeling of their thylakoid membranes during heterocyst differentiation. Here we investigate the sites of translation of thylakoid membrane proteins in Anabaena vegetative cells and developing heterocysts, using mRNA fluorescent in situ hybridization (FISH) to detect the location of specific mRNA species. We probed mRNAs encoding reaction center core components and the heterocyst-specific terminal oxidases Cox2 and Cox3. As in unicellular cyanobacteria, the mRNAs encoding membrane-integral thylakoid proteins are concentrated in patches at the inner face of the thylakoid membrane system, adjacent to the central cytoplasm. These patches mark the putative sites of translation and membrane insertion of these proteins. Oxidase activity in mature heterocysts is concentrated in the specialized "honeycomb" regions of the thylakoid membranes close to the cell poles. However, cox2 and cox3 mRNAs remain evenly distributed over the inner face of the thylakoids, implying that oxidase proteins migrate extensively after translation to reach their destination in the honeycomb membranes. The RNA-binding protein RbpG is the closest Anabaena homolog of Rbp3 in the unicellular cyanobacterium Synechocystis sp. PCC 6803, which we previously showed to be crucial for the correct location of photosynthetic mRNAs. An rbpG null mutant shows decreased cellular levels of photosynthetic mRNAs and photosynthetic complexes, coupled with perturbations to thylakoid membrane organization and lower efficiency of the Photosystem II repair cycle. This suggests that the chaperoning of photosynthetic mRNAs by RbpG is important for the correct coordination of thylakoid protein translation and assembly.IMPORTANCECyanobacteria have a complex thylakoid membrane system which is the site of the photosynthetic light reactions as well as most of the respiratory activity in the cell. Protein targeting to the thylakoids and the spatial organization of thylakoid protein biogenesis remain poorly understood. Further complexity is found in some filamentous cyanobacteria that produce heterocysts, specialized nitrogen-fixing cells in which the thylakoid membranes undergo extensive remodeling. Here we probe mRNA locations to reveal thylakoid translation sites in a heterocyst-forming cyanobacterium. We identify an RNA-binding protein important for the correct co-ordination of thylakoid protein translation and assembly, and we demonstrate the effectiveness of mRNA fluorescent in situ hybridization (FISH) as a way to probe cell-specific gene expression in multicellular cyanobacteria.

A multi-loudspeaker binaural room impulse response dataset with high-resolution translational and rotational head coordinates in a listening room

A multi-loudspeaker binaural room impulse response dataset with high-resolution translational and rotational head coordinates in a listening room

Elevating plant immunity by translational regulation of a rice WRKY transcription factor.

Plants have intricate mechanisms that tailor their defence responses to pathogens. WRKY transcription factors play a pivotal role in plant immunity by regulating various defence signalling pathways. Many WRKY genes are transcriptionally activated upon pathogen attack, but how their functions are regulated after transcription remains elusive. Here, we show that OsWRKY7 functions as a crucial positive regulator of rice basal immunity against Xanthomonas oryzae pv. oryzae (Xoo). The activity of OsWRKY7 was regulated at both translational and post-translational levels. Two translational products of OsWRKY7 were generated by alternative initiation. The full-length OsWRKY7 protein is normally degraded by the ubiquitin-proteasome system but was accumulated following elicitor or pathogen treatment, whereas the alternate product initiated from the downstream in-frame start codon was stable. Both the full and alternate OsWRKY7 proteins have transcriptional activities in yeast and rice cells, and overexpression of each form enhanced resistance to Xoo infection. Furthermore, disruption of the main AUG inrice increased the endogenous translation of the alternate stabilized form of OsWRKY7 and enhanced bacterial blight resistance. This study provides insights into the coordination of alternative translation and protein stability in the regulation of plant growth and basal defence mediated by the OsWRKY7 transcription factor, and also suggests a promising strategy to breed disease-resistant rice by translation initiation control.

Orbit-attitude-structure coupled modelling method in local translational coordinate frame for multibody systems

The absolute coordinate-based (ACB) method, including absolute nodal coordinate formulation and natural coordinate formulation, is a widely-used dynamic modelling method for multibody systems. However, the problem of accuracy loss would arise when multi-scale motions are described in the same global coordinate system, such as large-scale orbital motions, small-scale attitude motions and structural vibrations, and micro-scale contact/collision. To address this problem, an ACB method in local translational coordinate system is proposed such that the large-scale orbital motions can be separated from other smaller-scale motions. The dynamic equations are derived by the Hamilton's equations and the Kronecker product. The validity of the proposed method is studied using an orbit-attitude coupled model of an orbiting rigid plate. It is found that the attitude errors of the original ACB method increase as time step size decreases. The reason for this counterintuitive phenomenon is that more serious accuracy loss is encountered for smaller time step size. In addition, more iterations are required for the original ACB method to obtain the prescribed tolerable error in each time step due to accuracy loss. In comparison, the proposed method is more accurate and efficient in numerical simulations. Finally, the proposed method is applied to the orbit-attitude-structure coupled simulation of a space robotic system.

Mitochondrial microproteins: critical regulators of protein import, energy production, stress response pathways, and programmed cell death.

Mitochondria rely upon the coordination of protein import, protein translation, and proper functioning of oxidative phosphorylation (OXPHOS) complexes I-V to sustain the activities of life for an organism. Each process is dependent upon the function of profoundly large protein complexes found in the mitochondria [translocase of the outer mitochondrial membrane (TOMM) complex, translocase of the inner mitochondrial membrane (TIMM) complex, OXPHOS complexes, mitoribosomes]. These massive protein complexes, in some instances more than one megadalton, are built up from numerous protein subunits of varying sizes, including many proteins that are ≤100-150 amino acids. However, these small proteins, termed microproteins, not only act as cogs in large molecular machines but also have important steps in inhibiting or promoting the intrinsic pathway of apoptosis, coordinate responses to cellular stress, and even act as hormones. This review focuses on microproteins that occupy the mitochondria and are critical for its function. Although the microprotein field is relatively new, researchers have long recognized the existence of these mitochondrial proteins as critical components of virtually all aspects of mitochondrial biology. Thus, recent studies estimating that hundreds of new microproteins of unknown function exist and are missing from current genome annotations suggests that the mitochondrial "microproteome" is a rich area for future biological investigation.

A comprehensive methodology to obtain electrical analogues of linear mechanical systems

Electrical analogues of linear mechanical systems have traditionally been obtained using a set of rules that can potentially be tedious when applied to complex systems. In addition, such rules do not cover all the possibilities of mechanical systems including rotational and translational generalized coordinates. The present work establishes a comprehensive and systematic methodology for obtaining the electrical analogue of any mechanical system modelled by rigid bodies, springs, and dampers. The method is simple and straightforward. First, the dynamic equations of the mechanical system are derived into matrix form. These equations are then translated to the electrical domain by means of the electromechanical analogy and, finally, the electrical circuit is obtained by direct inspection of the matrices. In addition, the method can deal with a combination of translational and rotational coordinates in the definition of the mechanical model. To support the proposed method, and beyond the planar vehicle models found in the literature, the electrical analogue of a linear 3D 7-DOF full car model is presented in this work.

Supramolecular complexes involved in the coordination of transcription and translation.

Single particle cryo-electron microscopy (cryo-EM) allows us to obtain structural information of increasingly complex and dynamic assemblies. The molecular machines, which carry out gene expression, have been studied in isolation but are often organized in supramolecular complexes to coordinate their functions and regulate each other. Furthermore, new functions emerge as a consequence of this organization, which cannot be easily predicted from structures of the individual machineries. A prominent example is the translation of prokaryotic messenger RNAs by the ribosome, which initiates while they are still being transcribed by RNA polymerase (RNAP). The pioneering ribosome can approach RNAP, forming a supramolecular complex known as the expressome. We previously obtained a series of cryo-EM structures representing decoupled, coupled and collided expressome states, which allowed us to propose roles for coupling of RNAP and the ribosome and provided a framework for studies on the coordination of transcription and translation in bacteria. However, mutual coordination is not restricted to the elongation phase of translation because RNAP can also stimulate translation initiation. We used in vitro single-molecule fluorescence methods and cryo-EM to investigate how translation initiation can be promoted by RNAP. RNAP accelerates binding of the 30S ribosomal subunit to mRNA and this requires ribosomal protein S1 (bS1). The structure of a ribosome-RNAP complex revealed RNAP and bS1 can cooperatively deliver the nascent mRNA for Shine-Dalgarno (SD) duplex formation. Additional structural models showed a reorientation of the SD duplex accompanies the transition from the docking of an mRNA to its accommodation in the decoding center. Thus, transcription-translation coupling can initiate by direct contact between gene expression complexes through bS1.

Stages of sight translation: Evidence from eye movements

AbstractThe aim of the study was to investigate the coordination of source text comprehension and translation in a sight translation task. The study also sought to determine whether translation strategies influence sight translation performance. Two groups of conference interpreters—professionals and trainees—sight translated English sentences into Polish while their eye movements and performance were monitored. Translation demands were manipulated by the use of either high- or low-frequency critical words in the sentences. Translation experience had no effect on first-pass viewing durations, but experts used shorter re-view durations than trainees (especially in the low-frequency condition). Professionals translated more accurately and with less pausing than trainees. Translation in the high-frequency condition was more accurate and had shorter pauses than in the low-frequency condition. Critical word translation accuracy increased with the translation onset latency (TOL) for individual sentences, and pause durations were relatively short when TOLs were either relatively short or long. Together, these findings indicate that, in sight translation, the initial phase of normal reading for comprehension is followed by phases in which reading and translation co-occur, and that translation strategy and translation performance are linked.

Rotordynamics of an accelerating rotor supported on aerodynamic journal bearings

Aerodynamic bearings are being employed in several high-speed micro-turbomachines, where frequent acceleration/deceleration of the rotor is common. Keeping the whirl amplitude of the rotor within acceptable limits is a must for the safety of the rotor-bearing system. This paper presents, for the first time, the dynamics of an accelerating rotor supported on Aerodynamic Journal Bearings. Due to unbalance, the rotordynamics between the spin and translational coordinates get nonlinearly coupled. The paper utilizes these equations to plan suitable acceleration-schedules to limit the whirl amplitude and frequency as low as possible. It is found that the acceleration should be scheduled in at least three regimes: the first with the maximum torque, the second with the minimum torque, and the last with an intermediate torque.

The Coordination of Local Translation, Membranous Organelle Trafficking, and Synaptic Plasticity in Neurons.

Neurons are highly complex polarized cells, displaying an extraordinary degree of spatial compartmentalization. At presynaptic and postsynaptic sites, far from the cell body, local protein synthesis is utilized to continually modify the synaptic proteome, enabling rapid changes in protein production to support synaptic function. Synapses undergo diverse forms of plasticity, resulting in long-term, persistent changes in synapse strength, which are paramount for learning, memory, and cognition. It is now well-established that local translation of numerous synaptic proteins is essential for many forms of synaptic plasticity, and much work has gone into deciphering the strategies that neurons use to regulate activity-dependent protein synthesis. Recent studies have pointed to a coordination of the local mRNA translation required for synaptic plasticity and the trafficking of membranous organelles in neurons. This includes the co-trafficking of RNAs to their site of action using endosome/lysosome “transports,” the regulation of activity-dependent translation at synapses, and the role of mitochondria in fueling synaptic translation. Here, we review our current understanding of these mechanisms that impact local translation during synaptic plasticity, providing an overview of these novel and nuanced regulatory processes involving membranous organelles in neurons.

Dynamics of defects around anisotropic particles in nematic liquid crystals under shear.

Nematic multiparticle collision dynamics is used to simulate disclination ring defects around spherocylinders suspended in a liquid crystal. A solvent-solute interaction potential is integrated over a short-time scale by an auxiliary molecular dynamics procedure that updates the translational and angular coordinates of the spherocylinders. For suspended particles with length in the range ∼(60,160)nm and a fixed aspect ratio, this method is able to simulate static defects reported previously in the literature. It also simulates orientation fluctuations of the elongated colloids that exhibit a broad distribution and a slow relaxation rate. Finally, a nematic host driven from equilibrium by shear flow is simulated, and the consequent dynamic behavior of the colloid-defect pair is studied. Defects under shear present significant structural transformations from chairlike disclination rings to extended defects that cover most of the cylindrical surface of the colloid. This effect results from the hydrodynamic torque on the nematic field caused by the distorted flow around the spherocylinder, and it is present for small Reynolds and Ericksen numbers of order unity.

A strategic initiative to facilitate knowledge translation research in rehabilitation

BackgroundWhile there is a growing body of literature supporting clinical decision-making for rehabilitation professionals, suboptimal use of evidence-based practices in that field persists. A strategic initiative that ensures the relevance of the research and its implementation in the context of rehabilitation could 1) help improve the coordination of knowledge translation (KT) research and 2) enhance the delivery of evidence-based rehabilitation services offered to patients with physical disabilities. This paper describes the process and methods used to develop a KT strategic initiative aimed at building capacity and coordinating KT research in physical rehabilitation and its strategic plan; it also reports the initial applications of the strategic plan implementation.MethodsWe used a 3-phase process consisting of an online environmental scan to identify the extent of KT research activities in physical rehabilitation in Quebec, Canada. Data from the environmental scan was used to develop a strategic plan that structures KT research in physical rehabilitation. Seven external KT experts in health science reviewed the strategic plan for consistency and applicability.ResultsSixty-four KT researchers were identified and classified according to the extent of their level of involvement in KT. Ninety-six research projects meeting eligibility criteria were funded by eight of the fourteen agencies and organizations searched. To address the identified gaps, a 5-year strategic plan was developed, containing a mission, a vision, four main goals, nine strategies and forty-two actions.ConclusionSuch initiatives can help guide researchers and relevant key stakeholders, to structure, organize and advance KT research in the field of rehabilitation. The strategies are being implemented progressively to meet the strategic initiative’s mission and ultimately enhance users’ rehabilitation services.

Abstract IA12: Coordination of mRNA processing, translation, and metabolism by mTORC1

Abstract The mTOR complex 1 (mTORC1)–S6 protein kinase (S6K1) signaling pathway has evolved to sense and respond to changes in growth factor and hormone-dependent signaling, cellular energy status, nutrient availability, and surrounding oxygen concentrations. A major mechanism through which mTOR regulates downstream processes is via the coordinated regulation of gene expression, mRNA biogenesis, protein synthesis, and protein degradation. I will discuss our studies linking mTORC1/S6K1 to mRNA processing, metabolism, and cancer progression. Citation Format: John Blenis, Gina Lee, Sungyun Cho, Yuxiang Zheng, Cholsoon Jang, Lew Cantley, Joshua Rabinowitz, Noah Dephoure. Coordination of mRNA processing, translation, and metabolism by mTORC1 [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr IA12.

Geometrical interpretation of the pilot wave theory and manifestation of spinor fields

Abstract Using the hydrodynamical formalism of quantum mechanics for a Schrödinger spinning particle developed by Takabayashi, Vigier, and followers, which involves vortical flows, we propose a new geometrical interpretation of the pilot wave theory. The spinor wave in this interpretation represents an objectively real field, and the evolution of a material particle controlled by the wave is a manifestation of the geometry of space. We assume this field to have a geometrical nature, basing on the idea that the intrinsic angular momentum, the spin, modifies the geometry of the space, which becomes a manifold, represented as a vector bundle with a base formed by the translational coordinates and time, and the fiber of the bundle, specified at each point by the field of a tetrad $e^a_{\mu}$, forms from bilinear combinations of the spinor wave function. It has been shown that the spin vector rotates following the geodesic of the space with torsion, and the particle moves according to the geometrized guidance equation. This fact explains the self-action of the spinning particle. We show that the curvature and torsion of the spin vector line is determined by the space torsion of the absolute parallelism geometry.

The Importance of Protein Phosphorylation for Signaling and Metabolism in Response to Diel Light Cycling and Nutrient Availability in a Marine Diatom

Diatoms are major contributors to global primary production and their populations in the modern oceans are affected by availability of iron, nitrogen, phosphate, silica, and other trace metals, vitamins, and infochemicals. However, little is known about the role of phosphorylation in diatoms and its role in regulation and signaling. We report a total of 2759 phosphorylation sites on 1502 proteins detected in Phaeodactylum tricornutum. Conditionally phosphorylated peptides were detected at low iron (n = 108), during the diel cycle (n = 149), and due to nitrogen availability (n = 137). Through a multi-omic comparison of transcript, protein, phosphorylation, and protein homology, we identify numerous proteins and key cellular processes that are likely under control of phospho-regulation. We show that phosphorylation regulates: (1) carbon retrenchment and reallocation during growth under low iron, (2) carbon flux towards lipid biosynthesis after the lights turn on, (3) coordination of transcription and translation over the diel cycle and (4) in response to nitrogen depletion. We also uncover phosphorylation sites for proteins that play major roles in diatom Fe sensing and utilization, including flavodoxin and phytotransferrin (ISIP2A), as well as identify phospho-regulated stress proteins and kinases. These findings provide much needed insight into the roles of protein phosphorylation in diel cycling and nutrient sensing in diatoms.

Articles of Significant Interest in This Issue

Unique peptide sequences often direct protein localization to specific cellular sites. However, on-site translation of mRNAs also provides an efficient means of subcellular protein localization. Katsafanas and Moss (e01671-19) found that on-site translation occurred for the poxvirus mRNA that encodes the 150-kDa A-type inclusion (ATI) protein, which forms large inclusion bodies that sequester viral particles. Nascent peptides anchored ATI mRNA at the inclusions, permitting multiple rounds of translation and thereby preventing premature protein aggregation and trapping of virions at transcription sites. These findings shed light on the coordination of transcription, translation, and virion assembly during the poxvirus life cycle.

A Role for the Ribosome-Associated Complex in Activation of the IRE1 Branch of UPR

The ubiquitous ribosome-associated complex (RAC) is a chaperone that spans ribosomes, making contact near both the polypeptide exit tunnel and the decoding center, a position prime for coordination of translation and folding. Loss of RAC results in growth defects and sensitization to translational stress. The mechanism of RAC in responding to specific stresses remains obscure. Data presented here uncover an essential function of mammalian RAC in the unfolded protein response (UPR), coupling the inositol-requiring protein 1α (IRE1α) branch to translation. Knockdown of RAC sensitizes mammalian cells to ER stress by selectively interfering with IRE1α activation. Higher-order oligomerization of IRE1α kinase/endoribonuclease and accurate ribosome stalling of Xbp1 mRNA, as required for IRE1α mediated Xbp1 mRNA splicing activity, depends upon RAC. These results reveal a surveillance function for RAC on the ribosomes: modulating IRE1α clustering and the fitness of Xbp1 mRNA splicing in coordination with translation.

A coarse-grained deep neural network model for liquid water

We introduce a coarse-grained deep neural network (CG-DNN) model for liquid water that utilizes 50 rotational and translational invariant coordinates and is trained exclusively against energies of ∼30 000 bulk water configurations. Our CG-DNN potential accurately predicts both the energies and the molecular forces of water, within 0.9 meV/molecule and 54 meV/Å of a reference (coarse-grained bond-order potential) model. The CG-DNN water model also provides good prediction of several structural, thermodynamic, and temperature dependent properties of liquid water, with values close to those obtained from the reference model. More importantly, CG-DNN captures the well-known density anomaly of liquid water observed in experiments. Our work lays the groundwork for a scheme where existing empirical water models can be utilized to develop a fully flexible neural network framework that can subsequently be trained against sparse data from high-fidelity albeit expensive beyond-DFT calculations.

A formulation for the dynamic analysis of multibody systems using non‐redundant unified local velocity coordinates

AbstractIn this paper, we present a formulation for the dynamic analysis of multibody systems using non‐redundant unified local velocity coordinates. The motivation for the present work is the result of an earlier investigation of unified local velocity coordinates of Holzinger et al. [1]. The equations of motion presented by the authors allow the description of the rigid body motion in space by local, purely translational velocity coordinates. However, the earlier investigations are limited to the description of the spatial motion of a free rigid body. Therefore, constraints are incorporated in the present paper.

The equations of motion for a rigid body using non-redundant unified local velocity coordinates

A novel formulation for the description of spatial rigid body motion using six non-redundant, homogeneous local velocity coordinates is presented. In contrast to common practice, the formulation proposed here does not distinguish between a translational and rotational motion in the sense that only translational velocity coordinates are used to describe the spatial motion of a rigid body. We obtain these new velocity coordinates by using the body-fixed translational velocity vectors of six properly selected points on the rigid body. These vectors are projected into six local directions and thus give six scalar velocities. Importantly, the equations of motion are derived without the aid of the rotation matrix or the angular velocity vector. The position coordinates and orientation of the body are obtained using the exponential map on the special Euclidean group mathit{SE}(3). Furthermore, we introduce the appropriate inverse tangent operator on mathit{SE}(3) in order to be able to solve the incremental motion vector differential equation. In addition, we present a modified version of a recently introduced a fourth-order Runge–Kutta Lie-group time integration scheme such that it can be used directly in our formulation. To demonstrate the applicability of our approach, we simulate the unstable rotation of a rigid body.