Degeneracy in the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, has an important role in regulating protein expression, but substantial ...uncertainty exists concerning the details of this phenomenon. Here we analyse the sequence features influencing protein expression levels in 6,348 experiments using bacteriophage T7 polymerase to synthesize messenger RNA in Escherichia coli. Logistic regression yields a new codon-influence metric that correlates only weakly with genomic codon-usage frequency, but strongly with global physiological protein concentrations and also mRNA concentrations and lifetimes in vivo. Overall, the codon content influences protein expression more strongly than mRNA-folding parameters, although the latter dominate in the initial ~16 codons. Genes redesigned based on our analyses are transcribed with unaltered efficiency but translated with higher efficiency in vitro. The less efficiently translated native sequences show greatly reduced mRNA levels in vivo. Our results suggest that codon content modulates a kinetic competition between protein elongation and mRNA degradation that is a central feature of the physiology and also possibly the regulation of translation in E. coli.
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KISLJ, NUK, SBMB, UL, UM, UPUK
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of ...many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts (“zooxanthellae”) that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and rich diversity within the zooxanthella genus Symbiodinium. Despite decades of reporting on the significance of this diversity, the formal systematics of these eukaryotic microbes have not kept pace, and a major revision is long overdue. With the consideration of molecular, morphological, physiological, and ecological data, we propose that evolutionarily divergent Symbiodinium “clades” are equivalent to genera in the family Symbiodiniaceae, and we provide formal descriptions for seven of them. Additionally, we recalibrate the molecular clock for the group and amend the date for the earliest diversification of this family to the middle of the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive radiation of analogs to modern shallow-water stony corals during the Jurassic Period and connects the rise of these symbiotic dinoflagellates with the emergence and evolutionary success of reef-building corals. This improved framework acknowledges the Symbiodiniaceae’s long evolutionary history while filling a pronounced taxonomic gap. Its adoption will facilitate scientific dialog and future research on the physiology, ecology, and evolution of these important micro-algae.
•The micro-algal genus Symbiodinium is split into multiple genera•Seven of these genera are formally described based on genetics and ecology•Dinoflagellates in the family Symbiodiniaceae originated in the Jurassic Period•Symbiodiniaceae diversification coincided with the radiation of reef-building corals
Symbiodinium are micro-algal symbionts of reef-building corals. LaJeunesse et al. report new estimates from molecular dating, indicating that corals and Symbiodinium originated and diversified together ∼140–200 mya. Divergent Symbiodinium “clades” are now partitioned into multiple genera, better reflecting their long evolutionary history.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Detailed photoionization and radiative acceleration of self-similar magnetocentrifugal accretion disk winds are explored. First, a general-purpose hybrid magnetocentrifugal and radiatively driven ...wind model is defined. Solutions are then examined to determine how radiative acceleration modifies magnetocentrifugal winds and how those winds can influence radiative driving in active galactic nuclei. For the models studied here, both radiative acceleration by bound-free ("continuum driving") and bound-bound ("line driving") processes are found to be important, although magnetic driving dominates the mass outflow rate for the Eddington ratios studied (L/L sub(Edd) = 0.001-0.1). The solutions show that shielding by a magnetocentrifugal wind can increase the efficiency of a radiatively driven wind, and also that within a magnetocentrifugal wind, radiative acceleration is sensitive to both the column in the shield, the column of the wind, and the initial density at the base of the wind.
Nine dogs with hemophilia A were treated with adeno-associated viral (AAV) gene therapy and followed for up to 10 years. Administration of AAV8 or AAV9 vectors expressing canine factor VIII ...(AAV-cFVIII) corrected the FVIII deficiency to 1.9-11.3% of normal FVIII levels. In two of nine dogs, levels of FVIII activity increased gradually starting about 4 years after treatment. None of the dogs showed evidence of tumors or altered liver function. Analysis of integration sites in liver samples from six treated dogs identified 1,741 unique AAV integration events in genomic DNA and expanded cell clones in five dogs, with 44% of the integrations near genes involved in cell growth. All recovered integrated vectors were partially deleted and/or rearranged. Our data suggest that the increase in FVIII protein expression in two dogs may have been due to clonal expansion of cells harboring integrated vectors. These results support the clinical development of liver-directed AAV gene therapy for hemophilia A, while emphasizing the importance of long-term monitoring for potential genotoxicity.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
We apply a wind model, driven by combined cosmic-ray and thermal-gas pressure, to the Milky Way, and show that the observed Galactic diffuse soft X-ray emission can be better explained by a wind than ...by previous static gas models. We find that cosmic-ray pressure is essential to driving the observed wind. Having thus defined a "best-fit" model for a Galactic wind, we explore variations in the base parameters and show how the wind's properties vary with changes in gas pressure, cosmic-ray pressure, and density. We demonstrate the importance of cosmic rays in launching winds, and the effect cosmic rays have on wind dynamics. In addition, this model adds support to the hypothesis of Breltschwerdt and collaborators that such a wind may help to explain the relatively small gradient observed in y-ray emission as a function of galactocentric radius.
Objective To quantify the dose-response associations between total physical activity and risk of breast cancer, colon cancer, diabetes, ischemic heart disease, and ischemic stroke ...events.Design Systematic review and Bayesian dose-response meta-analysis.Data sources PubMed and Embase from 1980 to 27 February 2016, and references from relevant systematic reviews. Data from the Study on Global AGEing and Adult Health conducted in China, Ghana, India, Mexico, Russia, and South Africa from 2007 to 2010 and the US National Health and Nutrition Examination Surveys from 1999 to 2011 were used to map domain specific physical activity (reported in included studies) to total activity.Eligibility criteria for selecting studies Prospective cohort studies examining the associations between physical activity (any domain) and at least one of the five diseases studied.Results 174 articles were identified: 35 for breast cancer, 19 for colon cancer, 55 for diabetes, 43 for ischemic heart disease, and 26 for ischemic stroke (some articles included multiple outcomes). Although higher levels of total physical activity were significantly associated with lower risk for all outcomes, major gains occurred at lower levels of activity (up to 3000-4000 metabolic equivalent (MET) minutes/week). For example, individuals with a total activity level of 600 MET minutes/week (the minimum recommended level) had a 2% lower risk of diabetes compared with those reporting no physical activity. An increase from 600 to 3600 MET minutes/week reduced the risk by an additional 19%. The same amount of increase yielded much smaller returns at higher levels of activity: an increase of total activity from 9000 to 12 000 MET minutes/week reduced the risk of diabetes by only 0.6%. Compared with insufficiently active individuals (total activity <600 MET minutes/week), the risk reduction for those in the highly active category (≥8000 MET minutes/week) was 14% (relative risk 0.863, 95% uncertainty interval 0.829 to 0.900) for breast cancer; 21% (0.789, 0.735 to 0.850) for colon cancer; 28% (0.722, 0.678 to 0.768) for diabetes; 25% (0.754, 0.704 to 0.809) for ischemic heart disease; and 26% (0.736, 0.659 to 0.811) for ischemic stroke.Conclusions People who achieve total physical activity levels several times higher than the current recommended minimum level have a significant reduction in the risk of the five diseases studied. More studies with detailed quantification of total physical activity will help to find more precise relative risk estimates for different levels of activity.
Cancer immunotherapy based on genetically redirecting T cells has been used successfully to treat B cell malignancies
. In this strategy, the T cell genome is modified by integration of viral vectors ...or transposons encoding chimaeric antigen receptors (CARs) that direct tumour cell killing. However, this approach is often limited by the extent of expansion and persistence of CAR T cells
. Here we report mechanistic insights from studies of a patient with chronic lymphocytic leukaemia treated with CAR T cells targeting the CD19 protein. Following infusion of CAR T cells, anti-tumour activity was evident in the peripheral blood, lymph nodes and bone marrow; this activity was accompanied by complete remission. Unexpectedly, at the peak of the response, 94% of CAR T cells originated from a single clone in which lentiviral vector-mediated insertion of the CAR transgene disrupted the methylcytosine dioxygenase TET2 gene. Further analysis revealed a hypomorphic mutation in this patient's second TET2 allele. TET2-disrupted CAR T cells exhibited an epigenetic profile consistent with altered T cell differentiation and, at the peak of expansion, displayed a central memory phenotype. Experimental knockdown of TET2 recapitulated the potency-enhancing effect of TET2 dysfunction in this patient's CAR T cells. These findings suggest that the progeny of a single CAR T cell induced leukaemia remission and that TET2 modification may be useful for improving immunotherapies.
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Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, ...and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
We study the change in cosmic-ray pressure, the change in cosmic-ray density, and the level of cosmic-ray-induced heating via Alfven-wave damping when cosmic rays move from a hot ionized plasma to a ...cool cloud embedded in that plasma. The general analysis method outlined here can apply to diffuse clouds in either the ionized interstellar medium or in galactic winds. We introduce a general-purpose model of cosmic-ray diffusion building upon the hydrodynamic approximation for cosmic rays (from McKenzie & Volk and Breitschwerdt and collaborators). Our improved method self-consistently derives the cosmic-ray flux and diffusivity under the assumption that the streaming instability is the dominant mechanism for setting the cosmic-ray flux and diffusion. We find that, as expected, cosmic rays do not couple to gas within cool clouds (cosmic rays exert no forces inside of cool clouds), that the cosmic-ray density does not increase within clouds (it may decrease slightly in general, and decrease by an order of magnitude in some cases), and that cosmic-ray heating (via Alfven-wave damping and not collisional effects as for ~10 MeV cosmic rays) is only important under the conditions of relatively strong (10 Delta *mG) magnetic fields or high cosmic-ray pressure (~10--11 erg cm--3).
AbstractObjectiveTo assess the relation between autocratisation—substantial decreases in democratic traits (free and fair elections, freedom of civil and political association, and freedom of ...expression)—and countries’ population health outcomes and progress toward universal health coverage (UHC).DesignSynthetic control analysis.Setting and country selectionGlobal sample of countries for all years from 1989 to 2019, split into two categories: 17 treatment countries that started autocratising during 2000 to 2010, and 119 control countries that never autocratised from 1989 to 2019. The treatment countries comprised low and middle income nations and represent all world regions except North America and western Europe. A weighted combination of control countries was used to construct synthetic controls for each treatment country. This statistical method is especially well suited to population level studies when random assignment is infeasible and sufficiently similar comparators are not available. The method was originally developed in economics and political science to assess the impact of policies and events, and it is now increasingly used in epidemiology.Main outcome measuresHIV-free life expectancy at age 5 years, UHC effective coverage index (0-100 point scale), and out-of-pocket spending on health per capita. All outcome variables are for the period 1989 to 2019.ResultsAutocratising countries underperformed for all three outcome variables in the 10 years after the onset of autocratisation, despite some improvements in life expectancy, UHC effective coverage index, and out-of-pocket spending on health. On average, HIV-free life expectancy at age 5 years increased by 2.2% (from 64.7 to 66.1 years) during the 10 years after the onset of autocratisation. This study estimated that it would have increased by 3.5% (95% confidence interval 3.3% to 3.6%, P<0.001) (from 64.7 to 66.9 years) in the absence of autocratisation. On average, the UHC effective coverage index increased by 11.9% (from 42.5 to 47.6 points) during the 10 years after the onset of autocratisation. This study estimated that it would have increased by 20.2% (95% confidence interval 19.6% to 21.2%, P<0.001) (from 42.5 to 51.1 points) in the absence of autocratisation. Finally, on average, out-of-pocket spending on health per capita increased by 10.0% (from $4.00 (£3.1; €3.4) to $4.4, log transformed) during the 10 years after the onset of autocratisation. This study estimated that it would have increased by only 4.4% (95% confidence interval 3.9% to 4.6%, P<0.001) (from $4.0 to $4.2, log transformed) in the absence of autocratisation.ConclusionsAutocratising countries had worse than estimated life expectancy, effective health service coverage, and levels of out-of-pocket spending on health. These results suggest that the noticeable increase in the number of countries that are experiencing democratic erosion in recent years is hindering population health gains and progress toward UHC. Global health institutions will need to adjust their policy recommendations and activities to obtain the best possible results in those countries with a diminishing democratic incentive to provide quality healthcare to populations.
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