Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.

Topoisomerase 1 (Top1) incises DNA containing ribonucleotides to generate complex DNA lesions that are resolved by APE2 (Apn2 in yeast). How Apn2 engages and processes this DNA damage is unclear. Here, we report X-ray crystal structures and biochemical analysis of Apn2-DNA complexes to demonstrate how Apn2 frays and cleaves 3' DNA termini via a wedging mechanism that facilitates 1-6 nucleotide endonucleolytic cleavages. APN2 deletion and DNA-wedge mutant Saccharomyces cerevisiae strains display mutator phenotypes, cell growth defects, and sensitivity to genotoxic stress in a ribonucleotide excision repair (RER)-defective background harboring a high density of Top1-incised ribonucleotides. Our data implicate a wedge-and-cut mechanism underpinning the broad-specificity Apn2 nuclease activity that mitigates mutagenic and genome instability phenotypes caused by Top1 incision at genomic ribonucleotides incorporated by DNA polymerase epsilon.

Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques.

Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.

Zac1 and the Imprinted Gene Network program juvenile NAFLD in response to maternal metabolic syndrome.

BACKGROUND AND AIMS: Within the next decade, NAFLD is predicted to become the most prevalent cause of childhood liver failure in developed countries. Predisposition to juvenile NAFLD can be programmed during early life in response to maternal metabolic syndrome (MetS), but the underlying mechanisms are poorly understood. We hypothesized that imprinted genes, defined by expression from a single parental allele, play a key role in maternal MetS-induced NAFLD, due to their susceptibility to environmental stressors and their functions in liver homeostasis. We aimed to test this hypothesis and determine the critical periods of susceptibility to maternal MetS. APPROACH AND RESULTS: We established a mouse model to compare the effects of MetS during prenatal and postnatal development on NAFLD. Postnatal but not prenatal MetS exposure is associated with histological, biochemical, and molecular signatures of hepatic steatosis and fibrosis in juvenile mice. Using RNA sequencing, we show that the Imprinted Gene Network (IGN), including its regulator Zac1, is up-regulated and overrepresented among differentially expressed genes, consistent with a role in maternal MetS-induced NAFLD. In support of this, activation of the IGN in cultured hepatoma cells by overexpressing Zac1 is sufficient to induce signatures of profibrogenic transformation. Using chromatin immunoprecipitation, we demonstrate that Zac1 binds the TGF-ß1 and COL6A2 promoters, forming a direct pathway between imprinted genes and well-characterized pathophysiological mechanisms of NAFLD. Finally, we show that hepatocyte-specific overexpression of Zac1 is sufficient to drive fibrosis in vivo. CONCLUSIONS: Our findings identify a pathway linking maternal MetS exposure during postnatal development to the programming of juvenile NAFLD, and provide support for the hypothesis that imprinted genes play a central role in metabolic disease programming.

Josephson junction infrared single-photon detector.

Josephson junctions are superconducting devices used as high-sensitivity magnetometers and voltage amplifiers as well as the basis of high-performance cryogenic computers and superconducting quantum computers. Although device performance can be degraded by the generation of quasiparticles formed from broken Cooper pairs, this phenomenon also opens opportunities to sensitively detect electromagnetic radiation. We demonstrate single near-infrared photon detection by coupling photons to the localized surface plasmons of a graphene-based Josephson junction. Using the photon-induced switching statistics of the current-biased device, we reveal the critical role of quasiparticles generated by the absorbed photon in the detection mechanism. The photon sensitivity will enable a high-speed, low-power optical interconnect for future superconducting computing architectures.

Graphene-based Josephson junction microwave bolometer.

Sensitive microwave detectors are essential in radioastronomy1, dark-matter axion searches2 and superconducting quantum information science3,4. The conventional strategy to obtain higher-sensitivity bolometry is the nanofabrication of ever smaller devices to augment the thermal response5-7. However, it is difficult to obtain efficient photon coupling and to maintain the material properties in a device with a large surface-to-volume ratio owing to surface contamination. Here we present an ultimately thin bolometric sensor based on monolayer graphene. To utilize the minute electronic specific heat and thermal conductivity of graphene, we develop a superconductor-graphene-superconductor Josephson junction8-13 bolometer embedded in a microwave resonator with a resonance frequency of 7.9 gigahertz and over 99 per cent coupling efficiency. The dependence of the Josephson switching current on the operating temperature, charge density, input power and frequency shows a noise-equivalent power of 7 × 10-19 watts per square-root hertz, which corresponds to an energy resolution of a single 32-gigahertz photon14, reaching the fundamental limit imposed by intrinsic thermal fluctuations at 0.19 kelvin. Our results establish that two-dimensional materials could enable the development of bolometers with the highest sensitivity allowed by the laws of thermodynamics.

Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain.

Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.

Reliability of FORCE COMBAT™: A Canadian army fitness objective.

OBJECTIVES: The Canadian Army fitness objective is FORCE COMBAT™. This consists of a 5km march (35kg) between 50-60min, and the annual FORCE physical employment standard as a circuit without the usual 5min rest intervals (FORCE circuit) in full fighting order (25kg). The objective of this research was to determine the number of practice attempts required to establish reliability of FORCE COMBAT™. Additionally, this study aims to identify the minimal detectable change once reliability is established. DESIGN: The study used a within participant design. METHODS: 33 Canadian Army members were divided into two groups. Group 1 performed four maximum effort attempts of FORCE COMBAT™ completely. Group 2 performed only the FORCE circuit component, not the loaded march. On the fifth trial, the tasks of the groups were switched. Variability within and between trials of the FORCE circuit of FORCE COMBAT™ were analysed based on six statistical factors of reliability. RESULTS: Four statistical factors indicated that one maximal effort practice attempt of FORCE COMBAT™ is required, as reflected in the variability of performance between trials 1 and 2. The minimum detectable change, highlighting inherent measurement error of the test was 89.18s with 95% confidence. CONCLUSIONS: Results suggest that Canadian Army members should complete one FORCE COMBAT™ in completion at maximal effort, before formal assessment. Further, members performing within 89s of the recommended completion time, on FORCE COMBAT™ should be offered a re-attempt (in its entirety).

Fast thermal relaxation in cavity-coupled graphene bolometers with a Johnson noise read-out.

High sensitivity, fast response time and strong light absorption are the most important metrics for infrared sensing and imaging. The trade-off between these characteristics remains the primary challenge in bolometry. Graphene with its unique combination of a record small electronic heat capacity and a weak electron-phonon coupling has emerged as a sensitive bolometric medium that allows for high intrinsic bandwidths1-3. Moreover, the material's light absorption can be enhanced to near unity by integration into photonic structures. Here, we introduce an integrated hot-electron bolometer based on Johnson noise readout of electrons in ultra-clean hexagonal-boron-nitride-encapsulated graphene, which is critically coupled to incident radiation through a photonic nanocavity with Q = 900. The device operates at telecom wavelengths and shows an enhanced bolometric response at charge neutrality. At 5 K, we obtain a noise equivalent power of about 10 pW Hz-1/2, a record fast thermal relaxation time, <35 ps, and an improved light absorption. However the device can operate even above 300 K with reduced sensitivity. We work out the performance mechanisms and limits of the graphene bolometer and give important insights towards the potential development of practical applications.

Ultrahigh-Capacity Lithium-Oxygen Batteries Enabled by Dry-Pressed Holey Graphene Air Cathodes.

Lithium-oxygen (Li-O2) batteries have the highest theoretical energy density of all the Li-based energy storage systems, but many challenges prevent them from practical use. A major obstacle is the sluggish performance of the air cathode, where both oxygen reduction (discharge) and oxygen evolution (charge) reactions occur. Recently, there have been significant advances in the development of graphene-based air cathode materials with a large surface area and catalytically active for both oxygen reduction and evolution reactions, especially with additional catalysts or dopants. However, most studies reported so far have examined air cathodes with a limited areal mass loading rarely exceeding 1 mg/cm2. Despite the high gravimetric capacity values achieved, the actual (areal) capacities of those batteries were far from sufficient for practical applications. Here, we present the fabrication, performance, and mechanistic investigations of high-mass-loading (up to 10 mg/cm2) graphene-based air electrodes for high-performance Li-O2 batteries. Such air electrodes could be easily prepared within minutes under solvent-free and binder-free conditions by compression-molding holey graphene materials because of their unique dry compressibility associated with in-plane holes on the graphene sheet. Li-O2 batteries with high air cathode mass loadings thus prepared exhibited excellent gravimetric capacity as well as ultrahigh areal capacity (as high as ∼40 mAh/cm2). The batteries were also cycled at a high curtailing areal capacity (2 mAh/cm2) and showed a better cycling stability for ultrathick cathodes than their thinner counterparts. Detailed post-mortem analyses of the electrodes clearly revealed the battery failure mechanisms under both primary and secondary modes, arising from the oxygen diffusion blockage and the catalytic site deactivation, respectively. These results strongly suggest that the dry-pressed holey graphene electrodes are a highly viable architectural platform for high-capacity, high-performance air cathodes in Li-O2 batteries of practical significance.

Dry-Processed, Binder-Free Holey Graphene Electrodes for Supercapacitors with Ultrahigh Areal Loadings.

For commercial applications, the need for smaller footprint energy storage devices requires more energy to be stored per unit area. Carbon nanomaterials, especially graphene, have been studied as supercapacitor electrodes and can achieve high gravimetric capacities affording high gravimetric energy densities. However, most nanocarbon-based electrodes exhibit a significant decrease in their areal capacitances when scaled to the high mass loadings typically used in commercially available cells (∼10 mg/cm2). One of the reasons for this behavior is that the additional surface area in thick electrodes is not readily accessible by electrolyte ions due to the large tortuosity. Furthermore, the fabrication of such electrodes often involves complicated processes that limit the potential for mass production. Here, holey graphene electrodes for supercapacitors that are scalable in both production and areal capacitance are presented. The lateral surface porosity on the graphene sheets was created using a facile single-step air oxidation method, and the resultant holey graphene was compacted under ambient conditions into mechanically robust monolithic shapes that can be directly used as binder-free electrodes. In comparison, pristine graphene discs under similar binder-free compression molding conditions were extremely brittle and thus not deemed useful for electrode applications. The coin cell supercapacitors, based on these holey graphene electrodes exhibited small variations in gravimetric capacitance over a wide range of areal mass loadings (∼1-30 mg/cm2) at current densities as high as 30 mA/cm2, resulting in the near-linear increase of the areal capacitance (F/cm2) with the mass loading. The prospects of the presented method for facile binder-free ultrathick graphene electrode fabrication are discussed.

A centric/non-centric impact protocol and finite element model methodology for the evaluation of American football helmets to evaluate risk of concussion.

American football reports high incidences of head injuries, in particular, concussion. Research has described concussion as primarily a rotation dominant injury affecting the diffuse areas of brain tissue. Current standards do not measure how helmets manage rotational acceleration or how acceleration loading curves influence brain deformation from an impact and thus are missing important information in terms of how concussions occur. The purpose of this study was to investigate a proposed three-dimensional impact protocol for use in evaluating football helmets. The dynamic responses resulting from centric and non-centric impact conditions were examined to ascertain the influence they have on brain deformations in different functional regions of the brain that are linked to concussive symptoms. A centric and non-centric protocol was used to impact an American football helmet; the resulting dynamic response data was used in conjunction with a three-dimensional finite element analysis of the human brain to calculate brain tissue deformation. The direction of impact created unique loading conditions, resulting in peaks in different regions of the brain associated with concussive symptoms. The linear and rotational accelerations were not predictive of the brain deformation metrics used in this study. In conclusion, the test protocol used in this study revealed that impact conditions influences the region of loading in functional regions of brain tissue that are associated with the symptoms of concussion. The protocol also demonstrated that using brain deformation metrics may be more appropriate when evaluating risk of concussion than using dynamic response data alone.