Functionally conserved enhancers with divergent sequences in distant vertebrates

Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identical n-mers (n ≥ 7) identified in the zebrafish, mouse, and human sequences of the five syntenic CNS were examined for the presence of transcription factor binding motifs; only motifs with E-value E ≤ 0.1 are shown. (XLSX 15 kb

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.

Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples. We show that lncRNA-based profiling categorizes breast tumours by their known molecular subtypes in breast cancer. We identify a cohort of breast cancer-associated and oestrogen-regulated lncRNAs, and investigate the role of the top prioritized oestrogen receptor (ER)-regulated lncRNA, DSCAM-AS1. We demonstrate that DSCAM-AS1 mediates tumour progression and tamoxifen resistance and identify hnRNPL as an interacting protein involved in the mechanism of DSCAM-AS1 action. By highlighting the role of DSCAM-AS1 in breast cancer biology and treatment resistance, this study provides insight into the potential clinical implications of lncRNAs in breast cancer

Spontaneous symmetry breaking of an optical polarization state in a polarization-selective nonlinear reson

We exploit polarization self-rotation (PSR) in atomic rubidium vapor to observe spontaneous symmetry breaking and bistability of polarization patterns. We pump the vapor cell with horizontally polarized light while the vertical polarization, which is initially in the vacuum state, is resonated in a ring cavity. Microscopic field fluctuations in this mode experience cumulative gain due to the compound action of amplification due to the self-rotation and feedback through the resonator, eventually acquiring a macroscopic magnitude akin to an optical parametric oscillator. The randomness of these fluctuations results in a bistable, random macroscopic polarization pattern at the output. We propose utilizing this mechanism to simulate an Ising-like interaction between multiple spatial modes and as a basis for a fully optical coherent Ising machine (CIM)

Plastic Response of a 2D Lennard-Jones amorphous solid: Detailed analysis of the local rearrangements at very slow strain-rate

We analyze in details the atomistic response of a model amorphous material submitted to plastic shear in the athermal, quasistatic limit. After a linear stress-strain behavior, the system undergoes a noisy plastic flow. We show that the plastic flow is spatially heterogeneous. Two kinds of plastic events occur in the system: quadrupolar localized rearrangements, and shear bands. The analysis of the individual motion of a particle shows also two regimes: a hyper-diffusive regime followed by a diffusive regime, even at zero temperature

Multiple whole genome alignments and novel biomedical applications at the VISTA portal

The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing users to study the regions of their interest without having to manually download the individual sequences. Here we describe various algorithmic and functional improvements implemented in the VISTA portal over the last 2 years. The VISTA Portal is accessible at http://genome.lbl.gov/vista

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Constitutivism

A brief explanation and overview of constitutivism

Extensive parallelism in protein evolution

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years