Active DNA damage eviction by HLTF stimulates nucleotide excision repair.

Nucleotide excision repair (NER) counteracts the onset of cancer and aging by removing helix-distorting DNA lesions via a "cut-and-patch"-type reaction. The regulatory mechanisms that drive NER through its successive damage recognition, verification, incision, and gap restoration reaction steps remain elusive. Here, we show that the RAD5-related translocase HLTF facilitates repair through active eviction of incised damaged DNA together with associated repair proteins. Our data show a dual-incision-dependent recruitment of HLTF to the NER incision complex, which is mediated by HLTF's HIRAN domain that binds 3'-OH single-stranded DNA ends. HLTF's translocase motor subsequently promotes the dissociation of the stably damage-bound incision complex together with the incised oligonucleotide, allowing for an efficient PCNA loading and initiation of repair synthesis. Our findings uncover HLTF as an important NER factor that actively evicts DNA damage, thereby providing additional quality control by coordinating the transition between the excision and DNA synthesis steps to safeguard genome integrity.

R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.

R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.

TREX1 degrades the 3' end of the small DNA oligonucleotide products of nucleotide excision repair in human cells.

The nucleotide excision repair (NER) machinery removes UV photoproducts from DNA in the form of small, excised damage-containing DNA oligonucleotides (sedDNAs) ∼30 nt in length. How cells process and degrade these byproducts of DNA repair is not known. Using a small scale RNA interference screen in UV-irradiated human cells, we identified TREX1 as a major regulator of sedDNA abundance. Knockdown of TREX1 increased the level of sedDNAs containing the two major UV photoproducts and their association with the NER proteins TFIIH and RPA. Overexpression of wild-type but not nuclease-inactive TREX1 significantly diminished sedDNA levels, and studies with purified recombinant TREX1 showed that the enzyme efficiently degrades DNA located 3' of the UV photoproduct in the sedDNA. Knockdown or overexpression of TREX1 did not impact the overall rate of UV photoproduct removal from genomic DNA or cell survival, which indicates that TREX1 function in sedDNA degradation does not impact NER efficiency. Taken together, these results indicate a previously unknown role for TREX1 in promoting the degradation of the sedDNA products of the repair reaction. Because TREX1 mutations and inefficient DNA degradation impact inflammatory and immune signaling pathways, the regulation of sedDNA degradation by TREX1 may contribute to photosensitive skin disorders.

Enhancement of refractive index sensing for an infrared plasmonic metamaterial absorber with a nanogap.

An infrared plasmonic metamaterial absorber with a nanogap was numerically and experimentally investigated as a refractive index sensor. We experimentally demonstrated large enhancements of both sensitivity (approximately 1091 nm/refractive index unit) and figure of merit (FOM*; approximately 273) owing to the nanogap formation in the metamaterial absorber to achieve perfect absorption (99%). The refractive index sensing platform was fabricated by producible nanoimprint lithography and isotropic dry etching processes to have a large area and low cost while providing a practical solution for high-performance plasmonic biosensors.

Preparation of multilayer periodic nanopatterned WO3-based photoanode by reverse nanoimprinting for water splitting.

Photoelectrochemical (PEC) water splitting has been studied extensively as an environmentally friendly technology for hydrogen production using solar energy. WO3is considered a promising semiconducting material for photoanodes due to its high electron mobility, good hole diffusion length, and chemical stability. Periodic nanostructures of WO3have been investigated for enhancing the PEC performance of WO3-based photoanodes. In this study, facile fabrication of periodic nanostructures of WO3was achieved using reverse nanoimprint lithography, and the multilayer stacking of nanopatterned WO3film was also confirmed. The multilayer nanopatterned WO3films were used as photoanodes for PEC water splitting. The performance of the fabricated photoanode in PEC was 2 times higher than that of planar WO3film due to its higher light absorbance and lower charge transfer resistance.

Multi-Domain Convolutional Neural Networks for Lower-Limb Motor Imagery Using Dry vs. Wet Electrodes.

Motor imagery (MI) brain-computer interfaces (BCIs) have been used for a wide variety of applications due to their intuitive matching between the user's intentions and the performance of tasks. Applying dry electroencephalography (EEG) electrodes to MI BCI applications can resolve many constraints and achieve practicality. In this study, we propose a multi-domain convolutional neural networks (MD-CNN) model that learns subject-specific and electrode-dependent EEG features using a multi-domain structure to improve the classification accuracy of dry electrode MI BCIs. The proposed MD-CNN model is composed of learning layers for three domain representations (time, spatial, and phase). We first evaluated the proposed MD-CNN model using a public dataset to confirm 78.96% classification accuracy for multi-class classification (chance level accuracy: 30%). After that, 10 healthy subjects participated and performed three classes of MI tasks related to lower-limb movement (gait, sitting down, and resting) over two sessions (dry and wet electrodes). Consequently, the proposed MD-CNN model achieved the highest classification accuracy (dry: 58.44%; wet: 58.66%; chance level accuracy: 43.33%) with a three-class classifier and the lowest difference in accuracy between the two electrode types (0.22%, d = 0.0292) compared with the conventional classifiers (FBCSP, EEGNet, ShallowConvNet, and DeepConvNet) that used only a single domain. We expect that the proposed MD-CNN model could be applied for developing robust MI BCI systems with dry electrodes.

Dual nanotransfer printing for complementary plasmonic biosensors.

One of the main challenges in the widespread utilization of localized plasmon resonance-based biosensors is the fabrication of large-area and low-cost plasmonic nanostructures. In this work, we fabricated large-area and low-cost complementary plasmonic biosensors such as nanohole and nanodisk arrays using dual nanotransfer printing (NTP) with a single metal deposition and a single reusable mold. The suspended nanohole arrays and the suspended nanodisk arrays were fabricated using the subsequent dry etching process. We confirmed a maximum enhancement in bulk sensitivity in experiments and simulations by controlling the vertical and lateral etching depths of the dielectric layer underneath the gold (Au) nanohole and nanodisk arrays. Furthermore, we show that the surface sensitivity evaluated by atomic layer deposition of aluminum oxide increased because appropriate vertical and lateral etching depths allow the target analyte to access the additional near-field formed at the bottom of the Au nanostructure. The dual NTP method provides a practical solution for the realization of large-area and low-cost label-free plasmonic biosensing systems, with a reduction in complexity and cost of the fabrication process of complementary plasmonic structures and metasurfaces.

Development of an inverse distance weighted active infrared stealth scheme using the repulsive particle swarm optimization algorithm.

Treatments for detection by infrared (IR) signals are higher than for other signals such as radar or sonar because an object detected by the IR sensor cannot easily recognize its detection status. Recently, research for actively reducing IR signal has been conducted to control the IR signal by adjusting the surface temperature of the object. In this paper, we propose an active IR stealth algorithm to synchronize IR signals from the object and the background around the object. The proposed method includes the repulsive particle swarm optimization statistical optimization algorithm to estimate the IR stealth surface temperature, which will result in a synchronization between the IR signals from the object and the surrounding background by setting the inverse distance weighted contrast radiant intensity (CRI) equal to zero. We tested the IR stealth performance in mid wavelength infrared (MWIR) and long wavelength infrared (LWIR) bands for a test plate located at three different positions on a forest scene to verify the proposed method. Our results show that the inverse distance weighted active IR stealth technique proposed in this study is proved to be an effective method for reducing the contrast radiant intensity between the object and background up to 32% as compared to the previous method using the CRI determined as the simple signal difference between the object and the background.

An Integrated Approach for Analysis of the DNA Damage Response in Mammalian Cells: NUCLEOTIDE EXCISION REPAIR, DNA DAMAGE CHECKPOINT, AND APOPTOSIS.

DNA damage by UV and UV-mimetic agents elicits a set of inter-related responses in mammalian cells, including DNA repair, DNA damage checkpoints, and apoptosis. Conventionally, these responses are analyzed separately using different methodologies. Here we describe a unified approach that is capable of quantifying all three responses in parallel using lysates from the same population of cells. We show that a highly sensitive in vivo excision repair assay is capable of detecting nucleotide excision repair of a wide spectrum of DNA lesions (UV damage, chemical carcinogens, and chemotherapeutic drugs) within minutes of damage induction. This method therefore allows for a real-time measure of nucleotide excision repair activity that can be monitored in conjunction with other components of the DNA damage response, including DNA damage checkpoint and apoptotic signaling. This approach therefore provides a convenient and reliable platform for simultaneously examining multiple aspects of the DNA damage response in a single population of cells that can be applied for a diverse array of carcinogenic and chemotherapeutic agents.

Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells.

The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo.

DNA repair synthesis and ligation affect the processing of excised oligonucleotides generated by human nucleotide excision repair.

Ultraviolet (UV) photoproducts are removed from genomic DNA by dual incisions in humans in the form of 24- to 32-nucleotide-long oligomers (canonical 30-mers) by the nucleotide excision repair system. How the small, excised, damage-containing DNA oligonucleotides (sedDNAs) are processed in cells following the dual incision event is not known. Here, we demonstrate that sedDNAs are localized to the nucleus in two biochemically distinct forms, which include chromatin-associated, transcription factor II H-bound complexes and more readily solubilized, RPA-bound complexes. Because the nuclear mobility and repair functions of transcription factor II H and RPA are influenced by post-incision gap-filling events, we examined how DNA repair synthesis and DNA ligation affect sedDNA processing. We found that although these gap filling activities are not essential for the dual incision/sedDNA generation event per se, the inhibition of DNA repair synthesis and ligation is associated with a decrease in UV photoproduct removal rate and an accumulation of RPA-sedDNA complexes in the cell. These findings indicate that sedDNA processing and association with repair proteins following the dual incisions may be tightly coordinated with gap filling during nucleotide excision repair in vivo.

Rapid Low-Temperature 3D Integration of Silicon Nanowires on Flexible Substrates.

The vertical integration of 1D nanostructures onto the 2D substrates has the potential to offer significant performance gains to flexible electronic devices due to high integration density, large surface area, and improved light absorption and trapping. A simple, rapid, and low temperature transfer bonding method has been developed for this purpose. Ultrasonic vibration is used to achieve a low temperature bonding within a few seconds, resulting in a polymer-matrix-free, electrically conducting vertical assembly of silicon nanowires (SiNWs) with a graphene/PET substrate. The microscopic structure, and mechanical and electrical characteristics of the interface between the transferred SiNW array and graphene layer are subsequently investigated, revealing that this creates a mechanically robust and electrically Ohmic contact. This newly developed ultrasonic transfer bonding technique is also found to be readily adaptable for diverse substrates of both metal and polymer. It is therefore considered as a valuable technique for integrating 1D vertical nanostructures onto the 2D flexible substrates for flexible photovoltaics, energy storage, and water splitting systems.

A facile patterning of silver nanowires using a magnetic printing method.

Patterning of metal nanowires (NWs) is vital for the fabrication of NW-based, high-performance devices such as sensors, transparent conducting electrodes, and optoelectronics. However, the majority of existing patterning methods require complex and expensive technologies. For this reason, we report for the first time a facile and quick patterning method of silver (Ag) NWs using a magnetic printing method. We successfully demonstrated a patterned AgNW grid structure ona flexible substrate as transparent electrodes. The flexible AgNW grid electrode exhibited optical and electrical properties comparable to those of commercial transparent conducting electrodes.We believe our work will be broadly applicable to other NW-based devices such as sensors,energy storage devices, meta devices, nanoscale electronics, and optoelectronics.

Nucleotide excision repair in human cells: fate of the excised oligonucleotide carrying DNA damage in vivo.

Nucleotide excision repair is the sole mechanism for removing the major UV photoproducts from genomic DNA in human cells. In vitro with human cell-free extract or purified excision repair factors, the damage is removed from naked DNA or nucleosomes in the form of 24- to 32-nucleotide-long oligomers (nominal 30-mer) by dual incisions. Whether the DNA damage is removed from chromatin in vivo in a similar manner and what the fate of the excised oligomer was has not been known previously. Here, we demonstrate that dual incisions occur in vivo identical to the in vitro reaction. Further, we show that transcription-coupled repair, which operates in the absence of the XPC protein, also generates the nominal 30-mer in UV-irradiated XP-C mutant cells. Finally, we report that the excised 30-mer is released from the chromatin in complex with the repair factors TFIIH and XPG. Taken together, our results show the congruence of in vivo and in vitro data on nucleotide excision repair in humans.

High-durable AgNi nanomesh film for a transparent conducting electrode.

Uniform metal nanomesh structures are promising candidates that may replace of indium-tin oxide (ITO) in transparent conducting electrodes (TCEs). However, the durability of the uniform metal mesh has not yet been studied. For this reason, a comparative analysis of the durability of TCEs based on pure Ag and AgNi nanomesh, which are fabricated by using simple transfer printing, is performed. The AgNi nanomesh shows high long-term stability to oxidation, heat, and chemicals compared with that of pure Ag nanomesh. This is because of nickel in the AgNi nanomesh. Furthermore, the AgNi nanomesh shows strong adhesion to a transparent substrate and good stability after repeated bending.

Determination of phosphorus impurity that directly affects quantification of microbial genomic DNA using inductively coupled plasma optical emission spectrometry.

We prepared genomic DNA from human placenta, Escherichia coli, and Bacillus subtilis using various DNA extraction methods and quantified the genomic DNA using ultraviolet (UV) spectrophotometry, capillary electrophoresis (CE), and inductively coupled plasma optical emission spectrometry (ICP-OES). Application of ICP-OES unexpectedly led to a serious overestimation of phosphorus in B. subtilis genomic DNA prepared using cetyltrimethyl ammonium bromide (CTAB). Further investigations using reversed-phase high-performance liquid chromatography (RP-HPLC), ultra-performance liquid chromatography electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS), and (31)P nuclear magnetic resonance (NMR) identified the phosphorus impurity as lipoteichoic acid (LTA).

Design of High-Payload Ascorbyl Palmitate Nanosuspensions for Enhanced Skin Delivery.

A high-payload ascorbyl palmitate (AP) nanosuspension (NS) was designed to improve skin delivery following topical application. The AP-loaded NS systems were prepared using the bead-milling technique, and softly thickened into NS-loaded gel (NS-G) using hydrophilic polymers. The optimized NS-G system consisted of up to 75 mg/mL of AP, 0.5% w/v of polyoxyl-40 hydrogenated castor oil (Kolliphor® RH40) as the suspending agent, and 1.0% w/v of sodium carboxymethyl cellulose (Na.CMC 700 K) as the thickening agent, in citrate buffer (pH 4.5). The NS-G system was embodied as follows: long and flaky nanocrystals, 493.2 nm in size, -48.7 mV in zeta potential, and 2.3 cP of viscosity with a shear rate of 100 s-1. Both NS and NS-G provided rapid dissolution of the poorly water-soluble antioxidant, which was comparable to that of the microemulsion gel (ME-G) containing AP in solubilized form. In an ex vivo skin absorption study using the Franz diffusion cell mounted on porcine skin, NS-G exhibited faster absorption in skin, providing approximately 4, 3, and 1.4 times larger accumulation than that of ME-G at 3, 6, and 12 h, respectively. Therefore, the high-payload NS makes it a promising platform for skin delivery of the lipid derivative of ascorbic acid.

Highly sensitive and label-free protein immunoassay-based biosensor comprising infrared metamaterial absorber inducing strong coupling.

A mid-infrared label-free immunoassay-based biosensor is an effective device to help identify and quantify biomolecules. This biosensor employs a surface-enhanced infrared absorption spectroscopy, which is a highly potent sensing technique for detecting minute quantities of analytes. In this study, a biosensor was constructed using a metamaterial absorber, which facilitated strong coupling effects. For maximum coupling effect, it is necessary to enhance the near-field intensity and the spatial and spectral overlap between the optical cavity resonance and the vibrational mode of the analyte. Due to significant peak splitting, conventional baseline correction methods fail to adequately analyze such a coupling system. Therefore, we employed a coupled harmonic oscillation model to analyze the spectral distortion resulting from the peak splitting induced by the strong coupling effect. The proposed biosensor with a thrombin-binding aptamer-based immunoassay could achieve a limit of detection of 267.4 pM, paving the way for more efficient protein detection in clinical practice.

The effect of sintering temperature on the microstructure and electrical performance of sol-gel-deposited SnInZnO thin film transistors.

We reported the capability of the SnInZnO (TIZO) film, fabricated using the sol-gel process, to act as a channel layer for printed electronics. We varied the sintering temperature to examine the potential of both the material and the process for application at low processing temperatures. The structure of the film sintered at 300 degrees C consisted of amorphous phase and the nanocrystalline structure began to appear locally at 400 degrees C. With increasing sintering temperature, the ratio of the crystalline structure was increased. In addition, the saturation mobility (mu sat) and off current were increased, the I(on)/I(off) was decreased, and the threshold voltage was shifted in the negative direction by increasing the sintering temperature (mu sat of 11.91 cm2 V(-1) s(-1) and 0.11 cm2 V(-1) s(-1) for the 700 degrees C- and 300 degrees C-sintered samples, respectively). This study could encourage in developing cost-effective TIZO TFTs with robust performances.