Slow Translation Research Articles

Real-time bioluminescent imaging of spatiotemporal variation of microbial retention during transport through porous media under variably saturated flow conditions

This study investigated the transport and retention of bioluminescent Escherichia coli strain 652T7 under different pore water velocities (8.7 cm h−1 and 13.0 cm h−1) and pore water saturations (85% and 100%) utilizing a non-invasive, real-time bioluminescent imaging technique. Under saturated flow conditions, the concentrations of retained bioluminescent E. coli 652T7 decreased exponentially with distance from the source at the lower velocity but decreased non-exponentially at the higher velocity. Under unsaturated flow conditions, pore water velocity had no significant effect on bacterial breakthrough concentration; however, the concentrations of retained cells were maximal at a significant distance from the source (non-monotonic). The distance from source of the maximum concentration increased from 2.4-cm at 1.05 pore volumes to 4.3-cm at 3.15 pore volumes, indicating slow translation of bacterial down-gradient under unsaturated flow conditions. That conditions were modestly unfavorable to attachment at the solid-water interface (SWI) was indicated by deposition rate coefficients being greater (by a factor of four) for simulations versus experiments, and by significant repulsive barriers to attachment at both the SWI (260 kT) and the air–water interface (AWI, fully repulsive). The inferred slow translation under unsaturated flow conditions therefore reflects either accumulation without arrest in the secondary minimum at the SWI and/or capillary interaction at the AWI. This non-invasive bioluminescence method yielded real-time quantitative observation of bacterial distribution from source and demonstrated contrasting transport behaviors previously obtained solely via more laborious methods with limited spatio-temporal observation.

Dynamic history of the inner core constrained by seismic anisotropy

Progressive crystallization of Earth’s inner core drives convection in the outer core and magnetic field generation. Determining the rate and pattern of inner-core growth is thus crucial to understanding the evolution of the geodynamo. The growth history of the inner core is probably recorded in the distribution and strength of its seismic anisotropy, which arises from deformation texturing constrained by conditions at the inner-core solid–fluid boundary. Here we show from analysis of seismic body wave travel times that the strength of seismic anisotropy increases with depth within the inner core, and the strongest anisotropy is offset from Earth’s rotation axis. Then, using geodynamic growth models and mineral physics calculations, we simulate the development of inner-core anisotropy in a self-consistent manner. From this we find that an inner core composed of hexagonally close-packed iron–nickel alloy, deformed by a combination of preferential equatorial growth and slow translation, can match the seismic observations without requiring hemispheres with sharp boundaries. Our model of inner-core growth history is compatible with external constraints from outer-core dynamics, and supports arguments for a relatively young inner core (~0.5–1.5 Ga) and a viscosity >1018 Pa s. The inner core underwent preferential equatorial growth and translation after nucleation ~0.5–1.5 billion years ago, according to an analysis of its seismic anisotropy and self-consistent geodynamic simulations.

Polyamines are Required for tRNA Anticodon Modification in Escherichia coli

Biogenic polyamines are natural aliphatic polycations formed from amino acids by biochemical pathways that are highly conserved from bacteria to humans. Their cellular concentrations are carefully regulated and dysregulation causes severe cell growth defects. Polyamines have high affinity for nucleic acids and are known to interact with mRNA, tRNA and rRNA to stimulate the translational machinery, but the exact molecular mechanism(s) for this stimulus is still unknown. Here we exploit that Escherichia coli is viable in the absence of polyamines, including the universally conserved putrescine and spermidine. Using global macromolecule labelling approaches we find that ribosome efficiency is reduced by 50–70% in the absence of polyamines and this reduction is caused by slow translation elongation speed. The low efficiency causes rRNA and multiple tRNA species to be overproduced in the absence of polyamines, suggesting an impact on the feedback regulation of stable RNA transcription. Importantly, we find that polyamine deficiency affects both tRNA levels and tRNA modification patterns. Specifically, a large fraction of tRNAhis, tRNAtyr and tRNAasn lack the queuosine modification in the anticodon “wobble” base, which can be reversed by addition of polyamines to the growth medium. In conclusion, we demonstrate that polyamines are needed for modification of specific tRNA, possibly by facilitating the interaction with modification enzymes.

Relationships Between the Typhoon‐Induced Wind and Waves in the Northern South China Sea

AbstractWind‐wave interactions have been broadly investigated for their great implications on air‐sea momentum transfer, whereas our knowledge on those forced by typhoons (hurricanes) is still limited. Accordingly, relationships between wind and wave characteristics were analyzed using observations on the northern South China Sea during four typhoons. An empirical wind‐wave model was proposed for typhoon‐induced wind seas which exhibits satisfactory skills in predicting significant wave heights (). Meanwhile, typhoon‐forced wind‐wave relation was investigated using the wave growth function. By delineating the relationship between the dimensionless and peak wave period scaled with 10 m and friction wind velocities, simplified functions for the growing and steady wind seas were proposed, respectively. However, great misalignment could occur owing to the contamination of swells resulting from the typhoon's slow translation speed, as well as the extremely short or long radial distance from typhoon centers, indicating the necessity of considering typhoon structures in screening swell influences.

Identification of conserved slow codons that are important for protein expression and function

ABSTRAST Due to the redundancy of the genetic code most amino acids are encoded by several ‘synonymous‘ codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the ‘preferred’ codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively. However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. ‘slow’) codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure. Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with ‘fast’ ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function. This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.

Modulation of Typhoon-Induced Sea Surface Cooling by Preexisting Eddies in the South China Sea

The interactions between mesoscale eddies and typhoons are important for understanding the oceanic environment, but large variance is identified in each case because of the complex underlying dynamics. Fifteen-year datasets of typhoon tracks and eddy tracks in the South China Sea (SCS) are employed to comprehensively determine the influence of preexisting eddies on typhoon-induced sea surface cooling (SSC). Typhoons with high wind speeds and slow translation speeds induce large SSC in summer and autumn, when more than 80% of typhoons occur during a year. The relative locations of typhoons and eddies are used to classify their distributions, and four groups are identified, with typhoons traversing to the left or right of cyclonic or anticyclonic eddies. Generally, cyclonic eddies (CEs) located to the right of a typhoon track can result in a large cooling core, but anticyclonic eddies (AEs) can interrupt the cooling band along the right side of typhoon tracks. The recovery from typhoon-induced SSC takes longer than 15 days, though preexisting AEs can induce a rapid rebound after reaching the minimum sea surface temperature (SST). In addition, the dependence of SSCs on a typhoon’s features, such as wind speed and translation speed, are amplified (reduced) by CEs (AEs). The enhancement of typhoon-induced local SSC by CEs is counterbalanced by the suppression of SSC by AEs; thus, the overall impacts of CEs and AEs on typhoon-induced local SSC are relatively weak in the SCS.

Real-time measurements of aminoglycoside effects on protein synthesis in live cells

The spread of antibiotic resistance is turning many of the currently used antibiotics less effective against common infections. To address this public health challenge, it is critical to enhance our understanding of the mechanisms of action of these compounds. Aminoglycoside drugs bind the bacterial ribosome, and decades of results from in vitro biochemical and structural approaches suggest that these drugs disrupt protein synthesis by inhibiting the ribosome's translocation on the messenger RNA, as well as by inducing miscoding errors. So far, however, we have sparse information about the dynamic effects of these compounds on protein synthesis inside the cell. In the present study, we measured the effect of the aminoglycosides apramycin, gentamicin, and paromomycin on ongoing protein synthesis directly in live Escherichia coli cells by tracking the binding of dye-labeled transfer RNAs to ribosomes. Our results suggest that the drugs slow down translation elongation two- to fourfold in general, and the number of elongation cycles per initiation event seems to decrease to the same extent. Hence, our results imply that none of the drugs used in this study cause severe inhibition of translocation.

The Molecular Origins of the Influence of Translation-Elongation Kinetics on the Specific Activity of Enzymes

Synonymous codon substitutions, which change the mRNA sequence but not the protein sequence, have been found to affect co-translational folding and post-translational structure of some proteins due to their impact on translation elongation speed. For example, the specific activities of chloramphenicol acetyltransferase III (CAT-III) and Firefly luciferase (LUC) have been found to change due to synonymous codon substitutions. In this study, we use multi-scale modeling to investigate how synonymous mutations lead to changes in the kinetics and structural ensemble of enzymes that alter their specific activities for relatively long time scales. We simulated the synthesis of the enzymes CAT-III, DDLB and DHFR on the ribosome under fast and slow translation schedules, arising from synonymous mRNA variants, followed by post-translational simulations off the ribosome. The specific activity of each protein mutant was then estimated in silico. Our simulation model recapitulates the experimental trends of CAT-III specific activity changes and identifies a reduced activity of the slow-synthesizing DDLB mutant. For the misfolding-prone proteins CAT-III and DDLB, we identified diverse near-native-like, soluble misfolded kinetic traps with topological entanglements formed near the active site, which could establish a memory of the co-translational structural divergence arising from the different translation speeds that persists in the post-translational folding process and causes the altered enzymatic activity. The fast-folding protein DHFR without kinetic traps has no memory of co-translational structural divergence persisting in the post-translation and hence no altered function could be observed in synonymous mutants. We conclude that synonymous mutations lead to populations shifts that can promote the formation of entangled, near-native like structures that are kinetic traps with reduced functionality, but are native enough to bypass the proteostasis quality control systems of the cell.

Composite of Typhoon‐Induced Sea Surface Temperature and Chlorophyll‐a Responses in the South China Sea

AbstractSixteen years of data on typhoons in the South China Sea (SCS) are used to investigate their impacts on sea surface temperature (SST) and chlorophyll‐a (Chl‐a). The time series of SST and Chl‐a before and after typhoons are composited for all typhoon locations to assess their responses. Decreases in SST and increases in Chl‐a occur after 73% and 70% of the typhoons, respectively, with overall averaged changes equal to −0.42 ± 0.015°C and 0.056 ± 0.003 log10 mg/m3, respectively. The largest responses are found near the typhoon center, and the extent of changes in these parameters decreases linearly with distance. The SST responds rapidly, starting to drop 2 days ahead of the typhoon passage and continuing to drop until 2 days after its passage. On the other hand, the Chl‐a increases after the typhoon passage, remaining high for 5 days before beginning to return to the initial conditions. Large (weak) changes are associated with typhoons that have high (low) wind speeds and slow (fast) translation speeds. This is especially true for SST, whereas some typhoons with slow translation speeds are characterized by increases in Chl‐a, mostly occurring near the coast. The largest SST and Chl‐a changes induced by a single typhoon are found in the upwelling region off Vietnam. The study offers a comprehensive quantitative analysis that describes the general pattern of SST and Chl‐a responses to typhoons in the SCS.

Disome and Trisome Profiling Reveal Genome-wide Targets of Ribosome Quality Control

The ribosome-associated protein quality control (RQC) system that resolves stalled translation events is activated when ribosomes collide and form disome, trisome, or higher-order complexes. However, it is unclear whether this system distinguishes collision complexes formed on defective mRNAs from those with functional roles on endogenous transcripts. Here, we performed disome and trisome footprint profiling in yeast and found collisions were enriched on diverse sequence motifs known to slow translation. When 60S recycling was inhibited, disomes accumulated at stop codons and could move into the 3' UTR to reinitiate translation. The ubiquitin ligase and RQC factor Hel2/ZNF598 generally recognized collisions but did not induce degradation of endogenous transcripts. However, loss of Hel2 triggered the integrated stress response, via phosphorylation of eIF2α, thus linking these pathways. Our results suggest that Hel2 has a role in sensing ribosome collisions on endogenous mRNAs, and such events may be important for cellular homeostasis.

Analysis of computational codon usage models and their association with translationally slow codons.

Improved computational modeling of protein translation rates, including better prediction of where translational slowdowns along an mRNA sequence may occur, is critical for understanding co-translational folding. Because codons within a synonymous codon group are translated at different rates, many computational translation models rely on analyzing synonymous codons. Some models rely on genome-wide codon usage bias (CUB), believing that globally rare and common codons are the most informative of slow and fast translation, respectively. Others use the CUB observed only in highly expressed genes, which should be under selective pressure to be translated efficiently (and whose CUB may therefore be more indicative of translation rates). No prior work has analyzed these models for their ability to predict translational slowdowns. Here, we evaluate five models for their association with slowly translated positions as denoted by two independent ribosome footprint (RFP) count experiments from S. cerevisiae, because RFP data is often considered as a "ground truth" for translation rates across mRNA sequences. We show that all five considered models strongly associate with the RFP data and therefore have potential for estimating translational slowdowns. However, we also show that there is a weak correlation between RFP counts for the same genes originating from independent experiments, even when their experimental conditions are similar. This raises concerns about the efficacy of using current RFP experimental data for estimating translation rates and highlights a potential advantage of using computational models to understand translation rates instead.

The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels.

During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. Using a global model of translation that included aaRS recharging, Gln4p depletion was simulated, confirming slowed translation. Modelling also revealed that Gln4p depletion causes negative feedback that matches translational demand for Gln-tRNAGln to aaRS recharging capacity. This maintains normal charged tRNAGln levels despite Gln4p depletion, confirmed experimentally using tRNA Northern blotting. Model analysis resolves the paradox that Gln4p depletion triggers a GCN4 response, despite maintenance of tRNAGln charging levels, revealing that normally, the aaRS population can sequester free, uncharged tRNAs during aminoacylation. Gln4p depletion reduces this sequestration capacity, allowing uncharged tRNAGln to interact with Gcn2 kinase. The study sheds new light on mutant aaRS disease aetiologies, and explains how aaRS sequestration of uncharged tRNAs can prevent GCN4 activation under non-starvation conditions.

Adopting evidence-based guidelines for acute stroke care: barriers and enablers for health professionals.

An evidence summary based on the systematic review: Baatiema L, Otim ME, Mnatzaganian G, de-Graft Aikins A, Coombes J, Somerset S. Health professionals' views on the barriers and enablers to evidence-based practice for acute stroke care: a systematic review. Implement Sci. 2017;12:74. 10.1186/s13012-017-0599-3 Evidence-based practice is the keystone of clinical practice, policy and management. Despite this, a knowledge-to-practice gap still exists, and it is estimated to take 17 years for evidence to be translated into clinical practice. The reasons for slow translation in acute stroke care are not completely understood.

High‐Speed Large‐Field Multifocal Illumination Fluorescence Microscopy

AbstractScanning optical microscopy techniques are commonly restricted to a sub‐millimeter field‐of‐view (FOV) or otherwise employ slow mechanical translation, limiting their applicability for imaging fast biological dynamics occurring over large areas. A rapid scanning large‐field multifocal illumination (LMI) fluorescence microscopy technique is devised based on a beam‐splitting grating and an acousto‐optic deflector synchronized with a high‐speed camera to attain real‐time fluorescence microscopy over a centimeter‐scale FOV. Owing to its large depth of focus, the approach allows noninvasive visualization of perfusion across the entire mouse cerebral cortex, not achievable with conventional wide‐field fluorescence microscopy methods. The new concept can readily be incorporated into conventional wide‐field microscopes to mitigate image blur due to tissue scattering and attain optimal trade‐off between spatial resolution and FOV. It further establishes a bridge between conventional wide‐field macroscopy and laser scanning confocal microscopy, thus it is anticipated to find broad applicability in functional neuroimaging, in vivo cell tracking, and other applications looking at large‐scale fluorescent‐based biodynamics.

Rapid Decay of Slowly Moving Typhoon Soulik (2018) due to Interactions With the Strongly Stratified Northern East China Sea

AbstractTyphoon Soulik decayed rapidly via two‐way interaction with the northern East China Sea, the extratropical shelf region, before landing on the Korean Peninsula on 23 August 2018. In the northern East China Sea, where the water column is strongly stratified with warm surface and cold subsurface waters, a large cold wake emerged with intense sea surface cooling, which is primarily caused by vertical mixing in the water column. This abrupt sea surface cooling rapidly increased the downward enthalpy flux, mostly in the form of latent heat flux. The slow translation speed of Typhoon Soulik and strong thermal stratification in the region transferred its energy into the ocean, as the typhoon had a long residence time over the wake, and consequently led to rapid decay with energy loss to typhoon intensity ratio of −4.4 ± 1.0 hPa (kJ cm−2)−1.

Schlafen12 Reduces the Aggressiveness of Triple Negative Breast Cancer through Post-Transcriptional Regulation of ZEB1 That Drives Stem Cell Differentiation.

Schlafen12 (SLFN12) promotes human intestinal and prostatic epithelial differentiation. We sought to determine whether SLFN12 reduces triple-negative breast cancer (TNBC) aggressiveness. We validated bioinformatics analyses of publicly available databases by staining human TNBC. After virally overexpressing or siRNA-reducing SLFN12 in TNBC cell lines, we measured proliferation by CCK-8 assay, invasion into basement-membrane-coated pores, mRNA by q-RT-PCR and protein by Western blotting. Flow cytometry assessed proliferation and stem cell marker expression, and sorted CD44+/CD24- cells. Stemness was also assessed by mammosphere formation, and translation by click-it-AHA chemistry. SLFN12 expression was lower in TNBC tumors and correlated with survival. SLFN12 overexpression reduced TNBC MDA-MB-231, BT549, and Hs578T proliferation. In MDA-MB-231 cells, AdSLFN12 reduced invasion, promoted cell cycle arrest, increased E-cadherin promoter activity, mRNA, and protein, and reduced vimentin expression and protein. SLFN12 knockdown increased vimentin. AdSLFN12 reduced the proportion of MDA-MB-231 CD44+CD24- cells, with parallel differentiation changes. SLFN12 overexpression reduced MDA-MB-231 mammosphere formation. SLFN12 overexpression decreased ZEB1 and Slug protein despite increased ZEB1 and Slug mRNA in all three lines. SLFN12 overexpression accelerated MDA-MB-231 ZEB1 proteasomal degradation and slowed ZEB1 translation. SLFN12 knockdown increased ZEB1 protein. Coexpressing ZEB1 attenuated the SLFN12 effect on E-cadherin mRNA and proliferation in all three lines. SLFN12 may reduce TNBC aggressiveness and improve survival in part by a post-transcriptional decrease in ZEB1 that promotes TNBC cancer stem cell differentiation.

Review of empirical and emerging breeding methods and tools for yam (Dioscorea spp.) improvement: Status and prospects

AbstractYam (Dioscorea spp.) is an important tuber crop with tremendous potential as a functional food in the tropics and subtropics. However, the crop has not shown progressive productivity gain over decades due to various production constraints. This paper reviews the progress achieved in empirical breeding endeavours and the development, status and application of emerging breeding tools and technologies to translate genetic gains in yam improvement. Significant progress has been made in yam genetic improvement over the years which has led to the identification and development of several improved clones and sources of variability for various economically important traits. Substantial efforts have also been made to develop diverse molecular markers, transcriptome and metabolome profiles of crucial traits, trait mapping and generate reference genome sequences of the key species. However, there seems to be a slow translation of research improvements into widespread applications. These advances and the integration of empirical and emerging methods and technologies into the breeding process will enhance yam breeding efforts and ensure the quick delivery of improved varieties that possess superior agronomic and quality traits.

Dynamic and thermodynamic upper-ocean response to the passage of Bay of Bengal cyclones 'Phailin' and 'Hudhud': a study using a coupled modelling system.

Understanding the upper-ocean response to tropical cyclones (TCs) in terms of sea surface temperature (SST) cooling is of prime importance in the prediction of TC intensity. However, the magnitude of cooling during the passage of TC varies depending on storm characteristics and pre-existing upper-ocean conditions such as the presence of ocean eddy and upper-ocean stratification. The present study investigates the upper-ocean response to two post-monsoon Bay of Bengal (BoB) cyclones, Phailin (October 2013) and Hudhud (October 2014), those followed almost a similar track, in association with pre-existing oceanic conditions using a fully coupled ocean-atmosphere modelling system. The spatial structure and temporal evolution of SST cooling induced by the two cyclones and the physical processes governing the cooling are examined. Analysis shows that the intensity of Phailin is significantly reduced when it encountered the regime of lower tropical cyclone heat potential (TCHP) associated with pre-existing cold core eddy (CCE). Intense upwelling with an average of 0.6 m/h is observed over CCE that resulted in strong temperature tendency of - 4.2 °C prior to landfall. Though average TCHP in the generation region of Hudhud was 50 kJ/cm2, the storm drew sufficient energy from the underlying ocean due to its slow translation speed. Presence of shallow thermocline over extended region and weaker upper-ocean stratification enhanced SST cooling over a larger region after passage of the TC Hudhud. Finally, the present study brings in clarity that the upper-ocean condition and the relative position of the mesoscale oceanic features to the storm track are responsible for the intensification of the TC and the recovery of the ocean surface.

Proteostasis collapse is a driver of cell aging and death

What molecular processes drive cell aging and death? Here, we model how proteostasis-i.e., the folding, chaperoning, and maintenance of protein function-collapses with age from slowed translation and cumulative oxidative damage. Irreparably damaged proteins accumulate with age, increasingly distracting the chaperones from folding the healthy proteins the cell needs. The tipping point to death occurs when replenishing good proteins no longer keeps up with depletion from misfolding, aggregation, and damage. The model agrees with experiments in the worm Caenorhabditis elegans that show the following: Life span shortens nonlinearly with increased temperature or added oxidant concentration, and life span increases in mutants having more chaperones or proteasomes. It predicts observed increases in cellular oxidative damage with age and provides a mechanism for the Gompertz-like rise in mortality observed in humans and other organisms. Overall, the model shows how the instability of proteins sets the rate at which damage accumulates with age and upends a cell's normal proteostasis balance.

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a 1,000 ORFs in exponentially growing wild-type yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and transfer RNA (tRNA) adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein (RP) genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared with other transcripts with equally high ribosome densities.