The electronic structure of La1−x_{1-x}Srx_{x}MnO3_{3} thin films and its TcT_c dependence as studied by angle-resolved photoemission

We present angle-resolved photoemission spectroscopy results for thin films of the three-dimensional manganese perovskite La$_{1-x}$Sr$_{x}$MnO$_{3}$. We show that the transition temperature ($T_c$) from the paramagnetic insulating to ferromagnetic metallic state is closely related to details of the electronic structure, particularly to the spectral weight at the ${\bf k}$-point, where the sharpest step at the Fermi level was observed. We found that this ${\bf k}$-point is the same for all the samples, despite their different $T_c$. The change of $T_c$ is discussed in terms of kinetic energy optimization. Our ARPES results suggest that the change of the electronic structure for the samples having different transition temperatures is different from the rigid band shift.Comment: Accepted by Journal of Physics: Condensed Matte

Pulsed laser deposition of atomically flat La1-xSrxMnO3 thin films using a novel target geometry

A new ablation target geometry is presented that was used to produce thin films of La1-xSrxMnO3 grown heteroepitaxially on SrTiO3 by pulsed reactive crossed-beam laser ablation. The films were grown in order to perform angle-resolved photoelectron spectroscopy, which demands that the surface be atomically flat. In situ and ex situ analysis shows that this condition was met, even after depositing to a thickness of over 100n

Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation

Enzymes in heteromeric, allosterically regulated complexes catalyze a rich array of chemical reactions. Separating the subunits of such complexes, however, often severely attenuates their catalytic activities, because they can no longer be activated by their protein partners. We used directed evolution to explore allosteric regulation as a source of latent catalytic potential using the β-subunit of tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of its native αββα complex, TrpB efficiently produces tryptophan and tryptophan analogs; activity drops considerably when it is used as a stand-alone catalyst without the α-subunit. Kinetic, spectroscopic, and X-ray crystallographic data show that this lost activity can be recovered by mutations that reproduce the effects of complexation with the α-subunit. The engineered PfTrpB is a powerful platform for production of Trp analogs and for further directed evolution to expand substrate and reaction scope

Synthesis of β-Branched Tryptophan Analogues Using an Engineered Subunit of Tryptophan Synthase

We report that l-threonine may substitute for l-serine in the β-substitution reaction of an engineered subunit of tryptophan synthase from Pyrococcus furiosus, yielding (2S,3S)-β-methyltryptophan (β-MeTrp) in a single step. The trace activity of the wild-type β-subunit on this substrate was enhanced more than 1000-fold by directed evolution. Structural and spectroscopic data indicate that this increase is correlated with stabilization of the electrophilic aminoacrylate intermediate. The engineered biocatalyst also reacts with a variety of indole analogues and thiophenol for diastereoselective C–C, C–N, and C–S bond-forming reactions. This new activity circumvents the 3-enzyme pathway that produces β-MeTrp in nature and offers a simple and expandable route to preparing derivatives of this valuable building block

Effect of microstructural evolution on magnetic properties of Ni thin films

Copyright © Indian Academy of Sciences.The magnetic properties of Ni thin films, in the range 20–500 nm, at the crystalline-nanocrystalline interface are reported. The effect of thickness, substrate and substrate temperature has been studied. For the films deposited at ambient temperatures on borosilicate glass substrates, the crystallite size, coercive field and magnetization energy density first increase and achieve a maximum at a critical value of thickness and decrease thereafter. At a thickness of 50 nm, the films deposited at ambient temperature onto borosilicate glass, MgO and silicon do not exhibit long-range order but are magnetic as is evident from the non-zero coercive field and magnetization energy. Phase contrast microscopy revealed that the grain sizes increase from a value of 30–50 nm at ambient temperature to 120–150 nm at 503 K and remain approximately constant in this range up to 593 K. The existence of grain boundary walls of width 30–50 nm is demonstrated using phase contrast images. The grain boundary area also stagnates at higher substrate temperature. There is pronounced shape anisotropy as evidenced by the increased aspect ratio of the grains as a function of substrate temperature. Nickel thin films of 50 nm show the absence of long-range crystalline order at ambient temperature growth conditions and a preferred [111] orientation at higher substrate temperatures. Thin films are found to be thermally relaxed at elevated deposition temperature and having large compressive strain at ambient temperature. This transition from nanocrystalline to crystalline order causes a peak in the coercive field in the region of transition as a function of thickness and substrate temperature. The saturation magnetization on the other hand increases with increase in substrate temperature.University Grants Commission for Centre of Advanced Studies in Physic

Large differences in regional precipitation change between a first and second 2 K of global warming

For adaptation and mitigation planning, stakeholders need reliable information about regional precipitation changes under different emissions scenarios and for different time periods. A significant amount of current planning effort assumes that each K of global warming produces roughly the same regional climate change. Here using 25 climate models, we compare precipitation responses with three 2 K intervals of global ensemble mean warming: a fast and a slower route to a first 2 K above pre-industrial levels, and the end-of-century difference between high-emission and mitigation scenarios. We show that, although the two routes to a first 2 K give very similar precipitation changes, a second 2 K produces quite a different response. In particular, the balance of physical mechanisms responsible for climate model uncertainty is different for a first and a second 2 K of warming. The results are consistent with a significant influence from nonlinear physical mechanisms, but aerosol and land-use effects may be important regionally

Split & mix assembly of DNA libraries for ultrahigh throughput on-bead screening of functional proteins.

Site-saturation libraries reduce protein screening effort in directed evolution campaigns by focusing on a limited number of rationally chosen residues. However, uneven library synthesis efficiency leads to amino acid bias, remedied at high cost by expensive custom synthesis of oligonucleotides, or through use of proprietary library synthesis platforms. To address these shortcomings, we have devised a method where DNA libraries are constructed on the surface of microbeads by ligating dsDNA fragments onto growing, surface-immobilised DNA, in iterative split-and-mix cycles. This method-termed SpliMLiB for Split-and-Mix Library on Beads-was applied towards the directed evolution of an anti-IgE Affibody (ZIgE), generating a 160,000-membered, 4-site, saturation library on the surface of 8 million monoclonal beads. Deep sequencing confirmed excellent library balance (5.1% ± 0.77 per amino acid) and coverage (99.3%). As SpliMLiB beads are monoclonal, they were amenable to direct functional screening in water-in-oil emulsion droplets with cell-free expression. A FACS-based sorting of the library beads allowed recovery of hits improved in Kd over wild-type ZIgE by up to 3.5-fold, while a consensus mutant of the best hits provided a 10-fold improvement. With SpliMLiB, directed evolution workflows are accelerated by integrating high-quality DNA library generation with an ultra-high throughput protein screening platform.ERC, EU H202

ESD Reviews: Model dependence in multi-model climate ensembles: weighting, sub-selection and out-of-sample testing

The rationale for using multi-model ensembles in climate change projections and impacts research is often based on the expectation that different models constitute independent estimates; therefore, a range of models allows a better characterisation of the uncertainties in the representation of the climate system than a single model. However, it is known that research groups share literature, ideas for representations of processes, parameterisations, evaluation data sets and even sections of model code. Thus, nominally different models might have similar biases because of similarities in the way they represent a subset of processes, or even be near-duplicates of others, weakening the assumption that they constitute independent estimates. If there are near-replicates of some models, then treating all models equally is likely to bias the inferences made using these ensembles. The challenge is to establish the degree to which this might be true for any given application. While this issue is recognised by many in the community, quantifying and accounting for model dependence in anything other than an ad-hoc way is challenging. Here we present a synthesis of the range of disparate attempts to define, quantify and address model dependence in multi-model climate ensembles in a common conceptual framework, and provide guidance on how users can test the efficacy of approaches that move beyond the equally weighted ensemble. In the upcoming Coupled Model Intercomparison Project phase 6 (CMIP6), several new models that are closely related to existing models are anticipated, as well as large ensembles from some models. We argue that quantitatively accounting for dependence in addition to model performance, and thoroughly testing the effectiveness of the approach used will be key to a sound interpretation of the CMIP ensembles in future scientific studies.</p

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

Over the past decade, it has become clear that mammalian genomes encode thousands of long non-coding RNAs (lncRNAs), many of which are now implicated in diverse biological processes. Recent work studying the molecular mechanisms of several key examples — including Xist, which orchestrates X chromosome inactivation — has provided new insights into how lncRNAs can control cellular functions by acting in the nucleus. Here we discuss emerging mechanistic insights into how lncRNAs can regulate gene expression by coordinating regulatory proteins, localizing to target loci and shaping three-dimensional (3D) nuclear organization. We explore these principles to highlight biological challenges in gene regulation, in which lncRNAs are well-suited to perform roles that cannot be carried out by DNA elements or protein regulators alone, such as acting as spatial amplifiers of regulatory signals in the nucleus

Low back pain patients with Modic type 1 changes exhibit distinct bacterial and non-bacterial subtypes

OBJECTIVES: Modic type 1 changes (MC1) are vertebral endplate bone marrow (BM) lesions observed on magnetic resonance images in sub-populations of chronic low back pain (CLBP) patients. The etiopathogenesis remains unknown and treatments that modify the underlying pathomechanisms do not exist. We hypothesized that two biological MC1 subtypes exist: a bacterial and a non-bacterial. This would have important implications for developing treatments targeting the underlying pathomechanisms. METHODS: Intervertebral disc (IVD) samples adjacent to MC1 (n ​= ​34) and control (n ​= ​11) vertebrae were collected from patients undergoing spinal fusion. Cutibacterium acnes (C.acnes) genome copy numbers (GCNs) were quantified in IVD tissues with 16S qPCR, transcriptomic signatures and cytokine profiles were determined in MC1 and control BM by RNA sequencing and immunoassay. Finally, we assessed if C.acnes GCNs are associated with blood plasma cytokines. RESULTS: IVD tissues from control levels had 870) C.acnes GCNs. MC1 patients with "high" C.acnes GCNs had upregulated innate immune cell signatures (neutrophil, macrophage/monocyte) and pro-inflammatory cytokines related to neutrophil and macrophage/monocyte function in the BM, consistent with a host defense against bacterium. MC1 patients with "low" C.acnes GCNs had increased adaptive immune cell signatures (T-and B-cell) in the BM and elevated IL-13 blood plasma levels. CONCLUSION: Our study provides the first evidence for the existence of bacterial (C.acnes "high") and non-bacterial (C.acnes "low") subtypes in MC1 patients with CLBP. This supports the need for different treatment strategies