Negative DNA supercoiling induces genome-wide Cas9 off-target activity.

CRISPR-Cas9 is a powerful gene-editing technology; however, off-target activity remains an important consideration for therapeutic applications. We have previously shown that force-stretching DNA induces off-target activity and hypothesized that distortions of the DNA topology in vivo, such as negative DNA supercoiling, could reduce Cas9 specificity. Using single-molecule optical-tweezers, we demonstrate that negative supercoiling λ-DNA induces sequence-specific Cas9 off-target binding at multiple sites, even at low forces.

CRISPR/Cas9 On- and Off-Target Activity Using Correlative Force and Fluorescence Single-Molecule Microscopy.

The discovery of CRISPR/Cas9 as an easily programmable endonuclease heralds a new era of genetic manipulation. With this comes the prospect of novel gene therapy approaches, and the potential to cure previously untreatable genetic diseases. However, reports of spurious off-target editing by CRISPR/Cas9 pose a significant hurdle to realizing this potential.

Gastral Drumming in Vespula germanica (Hymenoptera: Vespidae): Vibrational Communication at Night Suggests Additional Roles in Colony Organization.

Gastral drumming (GD) is a type of vibrational communication that has been reported in several species of yellowjackets and hornets. Despite early claims that it acts as a hunger signal, a more recent study found evidence that it acts as a nest-based food-recruitment signal, the first reported for eusocial wasps. Early studies also claimed, without supporting data, that it is produced most often in the early morning hours when the sun rises.

DNA stretching induces Cas9 off-target activity.

CRISPR/Cas9 is a powerful genome-editing tool, but spurious off-target edits present a barrier to therapeutic applications. To understand how CRISPR/Cas9 discriminates between on-targets and off-targets, we have developed a single-molecule assay combining optical tweezers with fluorescence to monitor binding to λ-DNA. At low forces, the Streptococcus pyogenes Cas9 complex binds and cleaves DNA specifically.

Gastral drumming: a nest-based food-recruitment signal in a social wasp.

Many social insect species produce signals that either recruit foragers to a specific food source or simply activate more nestmates to become foragers. Both are means of enhancing resource exploitation by increasing the number of individuals devoted to gathering profitable resources. Gastral drumming (GD) has been documented in several species of yellowjackets and hornets (Vespidae: Vespinae).

Tunable single-mode coupled-cavity laser in a standard InP photonics platform.

We present a wavelength tunable, coupled-cavity laser in a standard indium phosphide multiproject wafer shuttle which did not support distributed feedback gratings. The single-mode operation was enabled by reflections from slots in the laser cavity. The wavelength of the laser emission was tunable over 20 nm near a wavelength of 1560 nm via the currents applied to each section of the laser.

Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes.

Cytidine deaminases are single stranded DNA mutators diversifying antibodies and restricting viral infection. Improper access to the genome leads to translocations and mutations in B cells and contributes to the mutation landscape in cancer, such as kataegis. It remains unclear how deaminases access double stranded genomes and whether off-target mutations favor certain loci, although transcription and opportunistic access during DNA repair are thought to play a role.

Polarization rotator-splitters and controllers in a Si3N4-on-SOI integrated photonics platform.

We demonstrate novel polarization management devices in a custom-designed silicon nitride (Si(3)N(4)) on silicon-on-insulator (SOI) integrated photonics platform. In the platform, Si(3)N(4) waveguides are defined atop silicon waveguides. A broadband polarization rotator-splitter using a TM0-TE1 mode converter in a composite Si(3)N(4)-silicon waveguide is demonstrated.

Wide bandwidth and high coupling efficiency Si3N4-on-SOI dual-level grating coupler.

We propose and experimentally demonstrate fiber-to-chip grating couplers with aligned silicon nitride (Si(3)N(4)) and silicon (Si) grating teeth for wide bandwidths and high coupling efficiencies without the use of bottom reflectors. The measured 1-dB bandwidth is a record 80 nm, and the measured peak coupling efficiency is -1.3 dB, which is competitive with the best Si-only grating couplers.

Polarization rotator-splitters in standard active silicon photonics platforms.

We demonstrate various silicon-on-insulator polarization management structures based on a polarization rotator-splitter that uses a bi-level taper TM0-TE1 mode converter. The designs are fully compatible with standard active silicon photonics platforms with no new levels required and were implemented in the IME baseline and IME-OpSIS silicon photonics processes. We demonstrate a polarization rotator-splitter with polarization crosstalk < -13 dB over a bandwidth of 50 nm.

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.

Breast cancer genomes have revealed a novel form of mutation showers (kataegis) in which multiple same-strand substitutions at C:G pairs spaced one to several hundred nucleotides apart are clustered over kilobase-sized regions, often associated with sites of DNA rearrangement. We show kataegis can result from AID/APOBEC-catalysed cytidine deamination in the vicinity of DNA breaks, likely through action on single-stranded DNA exposed during resection. Cancer-like kataegis can be recapitulated by expression of AID/APOBEC family deaminases in yeast where it largely depends on uracil excision, which generates an abasic site for strand breakage.

Gender differences in health-related quality of life among cannabis users: results from the National Epidemiologic Survey on Alcohol and Related Conditions.

Background: Cannabis is the most widely used illicit substance worldwide. The aim of the present study was to assess self-reported Quality of Life (QoL) among cannabis users in a large representative sample.

Methods: We analyzed data from the National Epidemiological Survey of Alcohol and Related Conditions (NESARC, n=43,093).

Combining best evidence: a novel method to calculate the alcohol-attributable fraction and its variance for injury mortality.

Background: The alcohol-attributable fraction for injury mortality is defined as the proportion of fatal injury that would disappear if consumption went to zero. Estimating this fraction has previously been based on a simplistic view of drinking and associated risk. This paper develops a new way to calculate the alcohol-attributable fraction for injury based on different dimensions of drinking, mortality data, experimental data, survey research, new risk scenarios, and by incorporating different distributions of consumption within populations.

Alcohol under the radar: do we have policy options regarding unrecorded alcohol?

Background: According to the World Health Organization, the public health impact of illicit alcohol and informally produced alcohol should be reduced. This paper summarizes and evaluates the evidence base about policy and intervention options regarding unrecorded alcohol consumption.

Methods: A systematic review of the literature using electronic databases.

Yellowjackets use nest-based cues to differentially exploit higher-quality resources.

While foraging, social insects encounter a dynamic array of food resources of varying quality and profitability. Because food acquisition influences colony growth and fitness, natural selection can be expected to favor colonies that allocate their overall foraging effort so as to maximize their intake of high-quality nutrients. Social wasps lack recruitment communication, but previous studies of vespine wasps have shown that olfactory cues influence foraging decisions.

The cues have it; nest-based, cue-mediated recruitment to carbohydrate resources in a swarm-founding social wasp.

This study explores whether or not foragers of the Neotropical swarm-founding wasp Polybia occidentalis use nest-based recruitment to direct colony mates to carbohydrate resources. Recruitment allows social insect colonies to rapidly exploit ephemeral resources, an ability especially advantageous to species such as P. occidentalis, which store nectar and prey in their nests.

Alcohol as a risk factor for type 2 diabetes: A systematic review and meta-analysis.

Objective: To clarify the dose-response relationship between alcohol consumption and type 2 diabetes.

Research Design And Methods: A systematic computer-assisted and hand search was conducted to identify relevant articles with longitudinal design and quantitative measurement of alcohol consumption. Adjustment was made for the sick-quitter effect.

Model studies of beta-scission ring-opening reactions of cyclohexyloxy radicals: application to thermal rearrangements of dispiro-1,2,4-trioxanes.

A DFT study of model cyclohexyloxy radicals (8a-c, 9) show that (a) the presence of an adjacent oxygen atom, and (b) alpha-substituents on the cyclohexyl ring, particularly methoxy, accelerate the rate of beta-scission ring-opening reactions. Consistent with theoretical results, thermolysis of the methoxy-substituted dispiro-1,2,4-trioxane 10 afforded the structurally novel, 14-membered macrocyclic keto lactone 11 as the major isolable product.

Radiation-induced apoptosis in MOLT-4 cells requires de novo protein synthesis independent of de novo RNA synthesis.

We investigated the effects of inhibition of de novo RNA and protein synthesis in ionizing radiation (IR)-induced apoptosis in the human T cell line MOLT-4. We observed that pretreatment with cycloheximide inhibited IR-induced apoptosis. However, pretreatment with actinomycin D did not inhibit apoptosis induced by IR.