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"Kyle, J."
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Characterizing cis-regulatory elements using single-cell epigenomics
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.In this Review, Preissl, Gaulton and Ren discuss single-cell epigenomic methods and data analysis tools, their readiness for profiling cis-regulatory elements in human tissues and the insight they can provide into dynamic, context-specific gene regulation.
Journal Article
Shape-directed rotation of homogeneous micromotors via catalytic self-electrophoresis
The pursuit of chemically-powered colloidal machines requires individual components that perform different motions within a common environment. Such motions can be tailored by controlling the shape and/or composition of catalytic microparticles; however, the ability to design particle motions remains limited by incomplete understanding of the relevant propulsion mechanism(s). Here, we demonstrate that platinum microparticles move spontaneously in solutions of hydrogen peroxide and that their motions can be rationally designed by controlling particle shape. Nanofabricated particles with
n
-fold rotational symmetry rotate steadily with speed and direction specified by the type and extent of shape asymmetry. The observed relationships between particle shape and motion provide evidence for a self-electrophoretic propulsion mechanism, whereby anodic oxidation and cathodic reduction occur at different rates at different locations on the particle surface. We develop a mathematical model that explains how particle shape impacts the relevant electrocatalytic reactions and the resulting electrokinetic flows that drive particle motion.
Self-propelled motors operating at the micro- or nanoscale can be powered by catalytic reactions and show appealing potential in robotic applications. Brooks et al. describe how the motions of platinum spinners in hydrogen peroxide solutions can be rationally designed by controlling particle shape.
Journal Article
Nightwing. Volume 1, Traps and trapezes
Dick Grayson, Batman's former ward, must now embrace his destiny alone as the high-flyer Nightwing. Haly's Circus, where Dick grew up and performed under the big top, returns to Gotham City, bringing with it murder, mystery and superhuman mayhem.
Book
Directed propulsion of spherical particles along three dimensional helical trajectories
Active colloids are a class of microparticles that ‘swim’ through fluids by breaking the symmetry of the force distribution on their surfaces. Our ability to direct these particles along complex trajectories in three-dimensional (3D) space requires strategies to encode the desired forces and torques at the single particle level. Here, we show that spherical colloids with metal patches of low symmetry self-propel along non-linear 3D trajectories when powered remotely by an alternating current (AC) electric field. In particular, particles with triangular patches of approximate mirror symmetry trace helical paths along the axis of the field. We demonstrate that the speed and shape of the particle’s trajectory can be tuned by the applied field strength and the patch geometry. We show that helical motion can enhance particle transport through porous materials with implications for the design of microrobots that can navigate complex environments.
The development of functional microrobots calls for new strategies to design locomotion facilitating navigation through complex environments. Here, Lee et al. show how to realize and program helical motion in three dimensions using patchy microspheres under an alternating current electric field.
Journal Article
Eukaryotic microalgae as hosts for light‑driven heterologous isoprenoid production
Isoprenoids, also known as terpenes or terpenoids, are the largest class of natural chemicals, with a vast diversity of structures and biological roles. Some have high-value in human-use applications, although may be found in their native contexts in low abundance or be difficult to extract and purify. Heterologous production of isoprenoid compounds in heterotrophic microbial hosts such as bacteria or yeasts has been an active area of research for some time and is now a mature technology. Eukaryotic microalgae represent sustainable alternatives to these hosts for biotechnological production processes as their cultivation can be driven by light and freely available CO₂ as a carbon source. Their photosynthetic lifestyles require metabolic architectures structured towards the generation of associated isoprenoids (carotenoids, phytol) which participate in photon capture, energy dissipation, and electron transfer. Eukaryotic microalgae should, therefore, contain inherently high capacities for the generation of heterologous isoprenoid products. Although engineering strategies in eukaryotic microalgae have lagged behind the more genetically tractable bacteria and yeasts, recent advances in algal engineering concepts have demonstrated prominent examples of light-driven heterologous isoprenoid production from these photosynthetic hosts. This work seeks to provide practical insights into the choice of eukaryotic microalgae as biotechnological chassis. Recent reports of advances in algal engineering for heterologous isoprenoid production are highlighted as encouraging examples that promote their expanded use as sustainable green-cell factories. Current state of the art, limitations, and future challenges are also discussed.
Journal Article
The fifth Beatle : the Brian Epstein story
Tells the story of Brian Epstein, the discoverer and manager of the Beatles, in graphic novel format that also includes memorabilia, sketches, and alternate covers, highlighting his struggle against a society that reviled his homosexuality, Judaism, and Liverpool upbringing.
Book
Introns mediate post-transcriptional enhancement of nuclear gene expression in the green microalga Chlamydomonas reinhardtii
Efficient nuclear transgene expression in the green microalga Chlamydomonas reinhardtii is generally hindered by low transcription rates. Introns can increase transcript abundance by a process called Intron-Mediated Enhancement (IME) in this alga and has been broadly observed in other eukaryotes. However, the mechanisms of IME in microalgae are poorly understood. Here, we identified 33 native introns from highly expressed genes in C. reinhardtii selected from transcriptome studies as well as 13 non-native introns. We investigated their IME capacities and probed the mechanism of action by modification of splice sites, internal sequence motifs, and position within transgenes. Several introns were found to elicit strong IME and found to be broadly applicable in different expression constructs. We determined that IME in C. reinhardtii exclusively occurs from introns within transcribed ORFs regardless of the promoter and is not induced by traditional enhancers of transcription. Our results elucidate some mechanistic details of IME in C. reinhardtii, which are similar to those observed in higher plants yet underly distinctly different induction processes. Our findings narrow the focus of targets responsible for algal IME and provides evidence that introns are underestimated regulators of C. reinhardtii nuclear gene expression.
Journal Article