GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

Integrating genome-scale sequence, expression, structural and protein interaction data from E. coli we establish an interaction between chaperone (GroEL) dependency and optimal codon usage.Highly expressed sporadic substrates of GroEL employ more optimal codons than expected, show enrichment for optimal codons at structurally sensitive sites and greater conservation of codon optimality under conditions of relaxed purifying selection.We suggest that highly expressed genes cannot routinely utilize GroEL for error control so that codon usage has evolved to provide complementary error limitation, whereas obligate GroEL substrates experience relaxed selection on codon usage.Our results support a critical role of misfolding prevention in gene evolution

Investigation of fundamental ultrasonic propagation characteristics in NDT of electron beam melting additive manufactured samples

New approaches for efficient NDT inspection of modern additively manufactured metallic components are required urgently to qualify and validate the next generation of metallic parts across a range of industries. Ultrasonic testing is a fundamental component of NDT for such additive manufacturing processes. This work studies the ultrasonic propagation characteristics of EBM manufactured sample coupons in Alloy 718 material. Fundamental longitudinal and shear wave velocity measurements are experimentally measured in 3 orthogonal build directions of the sample coupons. Results show a dependency of the ultrasonic velocities and the build direction. The measured velocities are further verified in a phased array measurement showing successful results that highlights the potential of continued studies with synthetic apertures techniques

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Determinants of translation efficiency and accuracy

A given protein sequence can be encoded by an astronomical number of alternative nucleotide sequences. Recent research has revealed that this flexibility provides evolution with multiple ways to tune the efficiency and fidelity of protein translation and folding

The promise and pitfalls of the internet for cognitive behavioral therapy

Internet-administered cognitive behavior therapy is a promising new way to deliver psychological treatment. There are an increasing number of controlled trials in various fields such as anxiety disorders, mood disorders and health conditions such as headache and insomnia. Among the advantages for the field of cognitive behavior therapy is the dissemination of the treatment, being able to access treatment from a distance, and possibilities to tailor the interventions. To date, studies in which large effects have been obtained have included patient support from a clinician. Recent trials suggest that this support may come from non-clinicians and that therapist effects are minimal. Since studies also suggest that internet-delivered cognitive behavior therapy can be equally effective as face-to-face cognitive behavior therapy, this is a finding that may have implications for CBT practitioners. However, there are other aspects to consider for implementation, as while clinicians may hold positive attitudes towards internet-delivered CBT a recent study suggested that patients are more skeptical and may prefer face-to-face treatment. In the present work, I argue that internet-delivered CBT may help to increase adherence to treatment protocols, that training can be facilitated by means of internet support, and that research on internet interventions can lead to new insights regarding what happens in regular CBT. Moreover, I conclude that internet-delivered CBT works best when support is provided, leaving an important role for clinicians who can incorporate internet treatment in their services. However, I also warn against disseminating internet-delivered CBT to patients for whom it is not suitable, and that clinical skills may suffer if clinicians are trained and practice mainly using the internet

Inactivation of SAM-methyltransferase is the mechanism of attenuation of a historic louse borne typhus vaccine strain

Louse borne typhus (also called epidemic typhus) was one of man's major scourges, and epidemics of the disease can be reignited when social, economic, or political systems are disrupted. The fear of a bioterrorist attack using the etiologic agent of typhus, Rickettsia prowazekii, was a reality. An attenuated typhus vaccine, R. prowazekii Madrid E strain, was observed to revert to virulence as demonstrated by isolation of the virulent revertant Evir strain from animals which were inoculated with Madrid E strain. The mechanism of the mutation in R. prowazekii that affects the virulence of the vaccine was not known. We sequenced the genome of the virulent revertant Evir strain and compared its genome sequence with the genome sequences of its parental strain, Madrid E. We found that only a single nucleotide in the entire genome was different between the vaccine strain Madrid E and its virulent revertant strain Evir. The mutation is a single nucleotide insertion in the methyltransferase gene (also known as PR028) in the vaccine strain that inactivated the gene. We also confirmed that the vaccine strain E did not cause fever in guinea pigs and the virulent revertant strain Evir caused fever in guinea pigs. We concluded that a single nucleotide insertion in the methyltransferase gene of R. prowazekii attenuated the R. prowazekii vaccine strain E. This suggested that an irreversible insertion or deletion mutation in the methyl transferase gene of R. prowazekii is required for Madrid E to be considered a safe vaccine

Meta-analysis of breast cancer mortality benefit and overdiagnosis adjusted for adherence: improving information on the effects of attending screening mammography

Background: Women require information about the impact of regularly attending screening mammography on breast cancer mortality and overdiagnosis to make informed decisions. To provide this information we aimed to meta-analyse randomised controlled trials adjusted for adherence to the trial protocol. Methods: Nine screening mammography trials used in the Independent UK Breast Screening Report were selected. Extending an existing approach to adjust intention-to-treat (ITT) estimates for less than 100% adherence rates, we conducted a random-effects meta-analysis. This produced a combined deattenuated prevented fraction and a combined deattenuated percentage risk of overdiagnosis. Results: In women aged 39–75 years invited to screen, the prevented fraction of breast cancer mortality at 13-year follow-up was 0.22 (95% CI 0.15–0.28) and it increased to 0.30 (95% CI 0.18–0.42) with deattenuation. In women aged 40–69 years invited to screen, the ITT percentage risk of overdiagnosis during the screening period was 19.0% (95% CI 15.2–22.7%), deattenuation increased this to 29.7% (95% CI 17.8–41.5%). Conclusions: Adjustment for nonadherence increased the size of the mortality benefit and risk of overdiagnosis by up to 50%. These estimates are more appropriate when developing quantitative information to support individual decisions about attending screening mammography

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

The therapeutic and research potentials of oligonucleotides (ONs) have been hampered in part by their inability to effectively escape endosomal compartments to reach their cytosolic and nuclear targets. Splice-switching ONs (SSOs) can be used with endosomolytic small molecule compounds to increase functional delivery. So far, development of these compounds has been hindered by a lack of high-resolution methods that can correlate SSO trafficking with SSO activity. Here we present in-depth characterization of two novel endosomolytic compounds by using a combination of microscopic and functional assays with high spatiotemporal resolution. This system allows the visualization of SSO trafficking, evaluation of endosomal membrane rupture, and quantitates SSO functional activity on a protein level in the presence of endosomolytic compounds. We confirm that the leakage of SSO into the cytosol occurs in parallel with the physical engorgement of LAMP1-positive late endosomes and lysosomes. We conclude that the new compounds interfere with SSO trafficking to the LAMP1-positive endosomal compartments while inducing endosomal membrane rupture and concurrent ON escape into the cytosol. The efficacy of these compounds advocates their use as novel, potent, and quick-acting transfection reagents for antisense ONs