Coupling and competition between ferroelectricity, magnetism, strain, and oxygen vacancies in AMnO₃ perovskites

We use first-principles calculations based on density functional theory to investigate the interplay between oxygen vacancies, A-site cation size/tolerance factor, epitaxial strain, ferroelectricity, and magnetism in the perovskite manganite series, AMnO3 (A = Ca2+, Sr2+, Ba2+). We find that, as expected, increasing the volume through either chemical pressure or tensile strain generally lowers the formation energy of neutral oxygen vacancies consistent with their established tendency to expand the lattice. Increased volume also favors polar distortions, both because competing rotations of the oxygen octahedra are suppressed and because Coulomb repulsion associated with cation off-centering is reduced. Interestingly, the presence of ferroelectric polarization favors ferromagnetic (FM) over antiferromagnetic (AFM) ordering due to suppressed AFM superexchange as the polar distortion bends the Mn–O–Mn bond angles away from the optimal 180°. Intriguingly, we find that polar distortions compete with the formation of oxygen vacancies, which have a higher formation energy in the polar phases; conversely the presence of oxygen vacancies suppresses the onset of polarization. In contrast, oxygen vacancy formation energies are lower for FM than AFM orderings of the same structure type. Our findings suggest a rich and complex phase diagram, in which defect chemistry, polarization, structure, and magnetism can be modified using chemical potential, stress or pressure, and electric or magnetic fields

Origin of ferroelectric polarization in tetragonal tungsten-bronze-type oxides

The origin of ferroelectric polarization in tetragonal tungsten-bronze- (TTB-) type oxide strontium barium niobate (SBN) is investigated using first-principles density functional calculations. We study in particular the relationship between the polarization and the cation and vacancy ordering on alkali-earth metal lattice sites. Lattice dynamical calculations for paraelectric structures demonstrate that all cation configurations that can be accommodated in a 1×1×2 supercell result in a single unstable polar phonon, composed primarily of relative Nb-O displacements along the polar axis, as their dominant instability. The majority of the configurations also have a second octahedral tilt-mode instability which couples weakly to the polar mode. The existence of the tilt mode is strongly dependent on the local cation ordering, consistent with the fact that it is not found experimentally. Our results suggest that ferroelectricity in the SBN system is driven by a conventional second-order Jahn-Teller mechanism caused by the d 0 Nb 5 + cations, and demonstrate the strong influence of the size of Sr and Ba on the lattice distortions associated with polarization and octahedral tilting. Finally, we suggest a mechanism for the relaxor behavior in Sr-rich SBN based on Sr displacement inside pentagonal channels in the TTB structure

Global quantification of mammalian gene expression control

Gene expression is a multistep process that involves the transcription, translation and turnover of messenger RNAs and proteins. Although it is one of the most fundamental processes of life, the entire cascade has never been quantified on a genome-wide scale. Here we simultaneously measured absolute mRNA and protein abundance and turnover by parallel metabolic pulse labelling for more than 5,000 genes in mammalian cells. Whereas mRNA and protein levels correlated better than previously thought, corresponding half-lives showed no correlation. Using a quantitative model we have obtained the first genome-scale prediction of synthesis rates of mRNAs and proteins. We find that the cellular abundance of proteins is predominantly controlled at the level of translation. Genes with similar combinations of mRNA and protein stability shared functional properties, indicating that half-lives evolved under energetic and dynamic constraints. Quantitative information about all stages of gene expression provides a rich resource and helps to provide a greater understanding of the underlying design principles

Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells

In this work we have described the translatome of two mammalian cell lines, NIH3T3 and Jurkat, by scoring the relative polysome association of ∼10,000 mRNA under normal and ER stress conditions. We have found that translation efficiencies of mRNA correlated poorly with transcript abundance, although a general tendency was observed so that the highest translation efficiencies were found in abundant mRNA. Despite the differences found between mouse (NIH3T3) and human (Jurkat) cells, both cell types share a common translatome composed by ∼800–900 mRNA that encode proteins involved in basic cellular functions. Upon stress, an extensive remodeling in translatomes was observed so that translation of ∼50% of mRNA was inhibited in both cell types, this effect being more dramatic for those mRNA that accounted for most of the cell translation. Interestingly, we found two subsets comprising 1000–1500 mRNA whose translation resisted or was induced by stress. Translation arrest resistant class includes many mRNA encoding aminoacyl tRNA synthetases, ATPases and enzymes involved in DNA replication and stress response such as BiP. This class of mRNA is characterized by high translation rates in both control and stress conditions. Translation inducible class includes mRNA whose translation was relieved after stress, showing a high enrichment in early response transcription factors of bZIP and zinc finger C2H2 classes. Unlike yeast, a general coordination between changes in translation and transcription upon stress (potentiation) was not observed in mammalian cells. Among the different features of mRNA analyzed, we found a relevant association of translation efficiency with the presence of upstream ATG in the 5′UTR and with the length of coding sequence of mRNA, and a looser association with other parameters such as the length and the G+C content of 5′UTR. A model for translatome remodeling during the acute phase of stress response in mammalian cells is proposed

Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear

We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions, integrating miRNA, transcriptome and proteome profiles and advanced in silico analysis using the FAME algorithm. Since miRNAs play a crucial role in the inner ear, demonstrated by the discovery of mutations in a miRNA leading to human and mouse deafness, we applied this approach to microdissected auditory and vestibular sensory epithelia. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. Functionally important miRNAs were determined by searching for enriched or depleted targets in the transcript and protein datasets with an expression consistent with the dogma of miRNA regulation. Importantly, quite a few of the targets were detected only in the protein datasets, attributable to regulation by translational suppression. We identified and experimentally validated the regulation of PSIP1-P75, a transcriptional co-activator previously unknown in the inner ear, by miR-135b, in vestibular hair cells. Our findings suggest that miR-135b serves as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells

MicroRNAs Differentially Expressed in Postnatal Aortic Development Downregulate Elastin via 3′ UTR and Coding-Sequence Binding Sites

Elastin production is characteristically turned off during the maturation of elastin-rich organs such as the aorta. MicroRNAs (miRNAs) are small regulatory RNAs that down-regulate target mRNAs by binding to miRNA regulatory elements (MREs) typically located in the 3′ UTR. Here we show a striking up-regulation of miR-29 and miR-15 family miRNAs during murine aortic development with commensurate down-regulation of targets including elastin and other extracellular matrix (ECM) genes. There were a total of 14 MREs for miR-29 in the coding sequences (CDS) and 3′ UTR of elastin, which was highly significant, and up to 22 miR-29 MREs were found in the CDS of multiple ECM genes including several collagens. This overrepresentation was conserved throughout mammalian evolution. Luciferase reporter assays showed synergistic effects of miR-29 and miR-15 family miRNAs on 3′ UTR and coding-sequence elastin constructs. Our results demonstrate that multiple miR-29 and miR-15 family MREs are characteristic for some ECM genes and suggest that miR-29 and miR-15 family miRNAs are involved in the down-regulation of elastin in the adult aorta

Trastuzumab without chemotherapy in the adjuvant treatment of breast cancer: subgroup results from a large observational study

Abstract Background The topic of trastuzumab therapy without chemotherapy in early breast cancer (EBC) has been repeatedly discussed at international consensus meetings, but is compromised by the lack of solid evidence from clinical studies. Methods An observational study database of patients with EBC receiving trastuzumab-containing (neo)adjuvant therapy was screened to identify those patients who did not receive cytostatic agents. Results Of 3935 patients, 232 (6%) were identified who received no chemotherapy, being characterized by older age, worse performance status, and/or less aggressive histology. Relapse-free survival in this cohort was 84% (95% confidence interval [CI] 78–89%) at 3 years and 80% (95% CI 74–87%) at 5 years. However, these rates were significantly worse than those in the group of patients who received chemotherapy (hazard ratio 1.49; 95% CI 1.06–2.09; P = 0.022). A similar pattern was observed for overall survival, with marginally non-significant inferiority in the group receiving no chemotherapy (hazard ratio 1.56; 95% CI 1.00–2.44; P = 0.052). Survival rates in patients receiving no chemotherapy were 93% (95% CI 88–97%) and 87% (95% CI 81–93%) at 3 and 5 years, respectively. These findings were confirmed by a propensity score analysis accounting for selection bias. Conclusions Trastuzumab plus chemotherapy should remain the preferred option in all patients with HER2-positive EBC with an indication for adjuvant treatment. However, a limited proportion of patients will need an alternative treatment approach, either because of contraindications or the patient’s preference. In these selected patients, trastuzumab monotherapy, eventually combined with endocrine agents, might be a reasonable option offering favorable long-term outcomes by addressing the high-risk profile associated with HER2-positive disease