Genome re-annotation and DNA motif identification in Brassicaceae species

The DNA sequence analysis field has experienced a paradigm shift caused by the drastic reduction in the sequencing cost and time. With the availability of several reference genome assemblies, understanding of structural and functional aspects of genomes has started growing. Annotating a reference genome is the first and very crucial step that ensures its efficient usability to serve as a community resource. Unlike coding regions, non–coding regions do not translate into proteins but still play a central role in development and physiology of an organism by regulating gene expression. Identification and annotation of these regions are only initial steps, equally interesting and even more rewarding is to decipher the interplay between these two components of a genome. Identification of cis-regulatory elements (CREs), the functional components of the non-coding genome, is paramount to our understanding regarding the gene expression regulation. The role of CREs in regulating rhythmic (diurnal) expression of thousands of genes has been reported in several plants species (including Arabidopsis thaliana) but still only a few CREs have been reported so far. In the first project, using extensive RNA-sequencing data, I substantially improved the annotation and usability of a Brassicaceae species, Arabidopsis lyrata. Gene model coordinates for over 90% genes are corrected, with improved UTRs (untranslated regions) annotation. Over 2,000 genes are now annotated as transposable element (TE)-related genes and around 8% annotated with alternate transcripts. With hundreds of cases of gene-merge and gene-split, improved annotation also corrects coding space of the genome. Experimentally validated data for several such cases strongly supported updated annotation, highlighting the importance of employing species-specific RNA-sequencing data for genome annotation. In the second project, I compared time-series transcriptomics data for two Brassicaceae species, Arabidopsis thaliana and Arabis alpina. Around 30% genes were found under the control of diurnal regulation in both species. An interesting finding regarding phase-shift of the circadian clock genes and their direct targets was also observed. Gene Ontology term enrichment analysis suggested that diurnal genes associated to carbohydrate metabolism are the most affected by this phase shift while light-signaling associated genes are the least affected. I also demonstrated the usefulness of Phylogenetic shadowing to identify enriched CREs in the diurnal genes. Using several recently assembled Brassicaceae genomes, I analyzed the conservation patterns in promoters of orthologous diurnal genes. In total, I identified 54 and 45 DNA motifs for Arabidopsis thaliana and Arabis alpina respectively. Over 65% motifs were found common for both species including previously reported six motifs. Based on recently published open chromatin data, around 30% of the DNA motifs revealed protected sites from an endonuclease (DNase I), indicating their potential role as protein-binding sites. Several phase-specific co-occurring DNA motifs pairs were found conserved in both species, including previously known Evening Element (EE) and ABA Response Element Like (ABREL) pair, underlining the broad conservation of cis-regulation of diurnal expression

Recent Admixture in an Indian Population of African Ancestry

053907Quantum Matter and Optic

Dense plasma irradiated platinum with improved spin Hall effect

The impurity incorporation in host high-spin orbit coupling materials like platinum has shown improved charge-to-spin conversion by modifying the up-spin and down-spin electron trajectories by bending or skewing them in opposite directions. This enables efficient generation, manipulation, and transport of spin currents. In this study, we irradiate the platinum with non-focus dense plasma to incorporate the oxygen ion species. We systematically analyze the spin Hall angle of the oxygen plasma irradiated Pt films using spin torque ferromagnetic resonance. Our results demonstrate a 2.4 times enhancement in the spin Hall effect after plasma treatment of Pt as compared to pristine Pt. This improvement is attributed to the introduction of disorder and defects in the Pt lattice, which enhances the spin-orbit coupling and leads to more efficient charge-to-spin conversion without breaking the spin-orbit torque symmetries. Our findings offer a new method of dense plasma-based modification of material for the development of advanced spintronic devices based on Pt and other heavy metals

Facet controlled anisotropic magnons in Y<inf>3</inf>Fe<inf>5</inf>O<inf>12</inf> thin films

Directional specific control on the generation and propagation of magnons is essential for designing future magnon-based logic and memory devices for low power computing. The epitaxy of the ferromagnetic thin film is expected to facilitate anisotropic linewidths, which depend on the crystal cut and the orientation of the thin film. Here, we have shown the growth-induced magneto-crystalline anisotropy in 40 nm epitaxial yttrium iron garnet (YIG) thin films, which facilitate cubic and uniaxial in-plane anisotropy in the resonance field and linewidth using ferromagnetic resonance measurements. The growth-induced cubic and non-cubic anisotropy in epitaxial YIG thin films are explained using the short-range ordering of the Fe3þ cation pairs in octahedral and tetrahedral sublattices with respect to the crystal growth directions. This site-preferred directional anisotropy enables an anisotropic magnon–magnon interaction and opens an avenue to precisely control the propagation of magnonic current for spin-transfer logics using YIG-based magnonic technology

Magnetoimpedance of Epitaxial Y3Fe5O12 (001) Thin Film in Low-Frequency Regime

The atomically flat interface of the Y3Fe5O12 (YIG) thin film and the Gd3Ga5O12 (GGG) substrate plays a vital role in obtaining the magnetization dynamics of YIG below and above the anisotropy field. Here, magnetoimpedance (MI) is used to investigate the magnetization dynamics in fully epitaxial 45 nm YIG thin films grown on the GGG (001) substrates using a copper strip coil in the MHz–GHz frequency region. The resistance (R) and reactance (X), which are components of impedance (Z), allow us to probe the absorptive and dispersive components of the dynamic permeability, whereas a conventional spectrometer only measures the field derivative of the power absorbed. The distinct excitation modes arising from the resonance in the uniform and dragged magnetization states of YIG are respectively observed above and below the anisotropy field. The magnetodynamics clearly shows the visible dichotomy between two resonant fields below and above the anisotropy field and its motion as a function of the direction of the applied magnetic field. A low value of a damping factor of ∼4.7 – 6.1 × 10–4 is estimated for uniform excitation mode with an anisotropy field of 65 ± 2 Oe. Investigation of below and above anisotropy field-dependent magnetodynamics in the low-frequency mode can be useful in designing the YIG-based resonators, oscillators, filters, and magnonic devices

Nonstoichiometric FePt Nanoclusters for Heated Dot Magnetic Recording Media

Heated dot magnetic recording (HDMR) provides a path to increase the areal density of magnetic recording media beyond 4 Tb/in2. HDMR-based recording media requires ultrasmall, noninteracting, and thermally stable magnetic dots with high perpendicular anisotropy. We have synthesized nonstoichiometric Fe60Pt40 nanoclusters with and without a Pt buffer layer on silicon substrates, which shows a reduction in chemical ordering temperatures. The Fe60Pt40 nanoclusters retain the hard magnetic phase up to 1023 K with the coercive field of 1.3 Tesla due to the Pt element compensation from the buffer layer. This compensation of Pt was confirmed through X-ray diffraction (XRD) investigations where two distinct phases of Fe3Pt and FePt3 are observed at elevated annealing temperatures. Micromagnetic simulations were performed to understand the effect of magnetic anisotropy, dipolar interaction, and exchange coupling between the soft magnetic Fe3Pt and hard magnetic FePt. The results imply that nonstoichiometric Fe60Pt40 with the Pt buffer layer facilitates low chemical ordering temperatures retaining the high perpendicular anisotropy with minimal noninteracting behavior, suitable for HDMR

Enhanced Spin Hall Effect in S-Implanted Pt

High efficiency of charge–spin interconversion in spin Hall materials is a prime necessity to apprehend intriguing functionalities of spin–orbit torque for magnetization switching, auto-oscillations, and domain wall motion in energy-efficient and high-speed spintronic devices. To this end, innovations in fabricating advanced materials that possess not only large charge–spin conversion efficiency but also viable electrical and spin Hall conductivity are of importance. Here, a new spin Hall material designed by implanting low energy 12 keV sulfur ions in heavy metal Pt, named as Pt(S), is reported that demonstrates eight times higher conversion efficiency as compared to pristine Pt. The figure of merit, spin Hall angle (θSH), up to θPt(S)SH of 0.502 together with considerable electrical conductivity σPt(S)xx of 1.65 × 10 6 Ω–1 m–1 is achieved. The spin Hall conductivity σPt(S)SH increases with increasing σPt(S)xx, as σPt(S)SH∝σPt(S)1.7xx, implying an intrinsic mechanism in a dirty metal conduction regime. A comparatively large σPt(S)SH of 8.32 × 10 5 (ℏ/2e) Ω–1 m–1 among the reported heavy-metals-based alloys can be useful for developing next-generation spintronic devices using spin–orbit torque

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

This document is the Accepted Manuscript version, made available in accordance to Springer Nature Terms of reuse of archived manuscripts.Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 .Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.Peer reviewe