Applications of a Rayleigh-Taylor model to direct-drive laser fusion.

This paper presents a simple physics-based model for the interpretation of key metrics in laser direct drive. The only input parameters required are target scale, in-flight aspect ratio, and beam-to-target radius, and the importance of each has been quantified with a tailored set of cryogenic implosion experiments. These analyses lead to compact and accurate predictions of the fusion yield and areal density as a function of hydrodynamic stability, and they suggest new ways to take advantage of direct drive.

Intein-based thermoregulated meganucleases for containment of genetic material.

Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures.

Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials.

Metagenomic sequences represent an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of conjugative systems purely from metagenomic sequences requires the identification of suitable candidate systems as starting scaffolds for DNA synthesis. Here, we developed a bioinformatics approach that searches through the metagenomic "trash bin" for genes associated with conjugative systems present on contigs that are typically excluded from common metagenomic analysis pipelines.

A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets.

The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models struggle with accurate predictions and do not generalize well, possibly because the underlying datasets used to train the models do not accurately measure SpCas9/sgRNA activity and cannot distinguish on-target cleavage from toxicity. Here, we solve this problem by using a two-plasmid positive selection system to generate high-quality data that more accurately reports on SpCas9/sgRNA cleavage and that separates activity from toxicity.

Noncanonical functions of Ku may underlie essentiality in human cells.

The Ku70/80 heterodimer is a key player in non-homologous end-joining DNA repair but is involved in other cellular functions like telomere regulation and maintenance, in which Ku's role is not fully characterized. It was previously reported that knockout of Ku80 in a human cell line results in lethality, but the underlying cause of Ku essentiality in human cells has yet to be fully explored. Here, we established conditional Ku70 knockout cells using CRISPR/Cas9 editing to study the essentiality of Ku70 function.

Inverse Bremsstrahlung Absorption.

Inverse bremsstrahlung absorption was measured based on transmission through a finite-length plasma that was thoroughly characterized using spatially resolved Thomson scattering. Expected absorption was then calculated using the diagnosed plasma conditions while varying the absorption model components. To match data, it is necessary to account for (i) the Langdon effect; (ii) laser-frequency (rather than plasma-frequency) dependence in the Coulomb logarithm, as is typical of bremsstrahlung theories but not transport theories; and (iii) a correction due to ion screening.

Metabolically-targeted dCas9 expression in bacteria.

The ability to restrict gene expression to a relevant bacterial species in a complex microbiome is an unsolved problem. In the context of the human microbiome, one desirable target metabolic activity are glucuronide-utilization enzymes (GUS) that are implicated in the toxic re-activation of glucuronidated compounds in the human gastrointestinal (GI) tract, including the chemotherapeutic drug irinotecan. Here, we take advantage of the variable distribution of GUS enzymes in bacteria as a means to distinguish between bacteria with GUS activity, and re-purpose the glucuronide-responsive GusR transcription factor as a biosensor to regulate dCas9 expression in response to glucuronide inducers.

Scattered-light uniformity imager for diagnosing laser absorption asymmetries on OMEGA.

Light scattered from a target is the most-direct measurement for diagnosing laser absorption in a direct-drive implosion. Observations from OMEGA implosions show much larger scattered-light asymmetries than predictions. A new instrument has been developed to absolutely measure the scattered-light intensity and nonuniformity for the purpose of diagnosing the asymmetry.

Direct Measurement of the Return Current Instability in a Laser-Produced Plasma.

Measurements were made of the return current instability growth rate, demonstrating its concurrence with nonlocal transport. Thomson scattering was used to measure a maximum growth rate of 5.1×10^{9}  Hz, which was 3 times less than classical Spitzer-Härm theory predicts.

3D Simulations Capture the Persistent Low-Mode Asymmetries Evident in Laser-Direct-Drive Implosions on OMEGA.

Spherical implosions in inertial confinement fusion are inherently sensitive to perturbations that may arise from experimental constraints and errors. Control and mitigation of low-mode (long wavelength) perturbations is a key milestone to improving implosion performances. We present the first 3D radiation-hydrodynamic simulations of directly driven inertial confinement fusion implosions with an inline package for polarized crossed-beam energy transfer.

Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi.

Fungi are nature's recyclers, allowing for ecological nutrient cycling and, in turn, the continuation of life on Earth. Some fungi inhabit the human microbiome where they can provide health benefits, while others are opportunistic pathogens that can cause disease. Yeasts, members of the fungal kingdom, have been domesticated by humans for the production of beer, bread, and, recently, medicine and chemicals.

Telomere-to-telomere genome assembly of .

is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for .

Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics.

The worldwide COVID-19 pandemic caused by the SARS-CoV-2 betacoronavirus has highlighted the need for a synthetic biology approach to create reliable and scalable sources of viral antigen for uses in diagnostics, therapeutics and basic biomedical research. Here, we adapt plasmid-based systems in the eukaryotic microalgae Phaeodactylum tricornutum to develop an inducible overexpression system for SARS-CoV-2 proteins. Limiting phosphate and iron in growth media induced expression of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from the P.

Conjugation-Based Genome Engineering in .

has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based DNA transfer method from to , allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers.

Nonuniform Absorption and Scattered Light in Direct-Drive Implosions Driven by Polarization Smoothing.

Laser-direct-drive symmetric implosions on OMEGA illuminate a target with 60 laser beams and are designed to produce spherical implosions. Each beam is smoothed using orthogonal polarizations obtained by passing the laser beams through distributed polarization rotators (DPRs). Observations of light scattered from OMEGA implosions do not show the expected symmetry and have much larger variation than standard predictions.

Direct Measurements of DT Fuel Preheat from Hot Electrons in Direct-Drive Inertial Confinement Fusion.

Hot electrons generated by laser-plasma instabilities degrade the performance of laser-fusion implosions by preheating the DT fuel and reducing core compression. The hot-electron energy deposition in the DT fuel has been directly measured for the first time by comparing the hard x-ray signals between DT-layered and mass-equivalent ablator-only implosions. The electron energy deposition profile in the fuel is inferred through dedicated experiments using Cu-doped payloads of varying thickness.

Unabsorbed light beamlets for diagnosing coronal density profiles and absorption nonuniformity in direct-drive implosions on OMEGA.

Laser light scattered from a target is the most-direct measurement for diagnosing laser absorption in a direct-drive implosion. The 3ω gated optical imager beamlets diagnostic images unabsorbed light from all 60 OMEGA beams as distinct "beamlet" spots for each beam. The implosion can be diagnosed using the position and intensity of these beamlets.

Cloning of Mitochondrial Genome in and .

Algae are attractive organisms for biotechnology applications such as the production of biofuels, medicines, and other high-value compounds due to their genetic diversity, varied physical characteristics, and metabolic processes. As new species are being domesticated, rapid nuclear and organelle genome engineering methods need to be developed or optimized. To that end, we have previously demonstrated that the mitochondrial genome of microalgae can be cloned and engineered in and .

Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing.

The model diatom Phaeodactylum tricornutum is an attractive candidate for synthetic biology applications. Development of auxotrophic strains of P. tricornutum would provide alternative selective markers to commonly used antibiotic resistance genes.

Anomalous Absorption by the Two-Plasmon Decay Instability.

Radiation-hydrodynamic simulations of directly driven fusion experiments at the Omega Laser Facility predict absorption accurately when targets are driven at low overlapped laser intensity. Discrepancies appear at increased intensity, however, with higher-than-expected laser absorption on target. Strong correlations with signatures of the two-plasmon decay (TPD) instability-including half-harmonic and hard-x-ray emission-indicate that TPD is responsible for this anomalous absorption.

Trans-Kingdom Conjugation within Solid Media from to .

Conjugation is a bacterial mechanism for DNA transfer from a donor cell to a wide range of recipients, including both prokaryotic and eukaryotic cells. In contrast to conventional DNA delivery techniques, such as electroporation and chemical transformation, conjugation eliminates the need for DNA extraction, thereby preventing DNA damage during isolation. While most established conjugation protocols allow for DNA transfer in liquid media or on a solid surface, we developed a procedure for conjugation within solid media.

Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease.

Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein-DNA covariation.