Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain.

The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.

Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain.

The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.

Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB.

Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae (Sven), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of σA (σA4) of the σA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σA4 housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Finally, we compare the architecture of the WhiA/B σA-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.

Longitudinal change of reticular pseudodrusen area in ultrawide-field imaging.

This study aimed to investigate the longitudinal change in the reticular pseudodrusen (RPD) area in the fundus and its association with late age-related macular degeneration (AMD). 91 RPD eyes (55 patients; age 67.9 ± 7.3 years) with > 5 years' follow-up (6.8 ± 0.9 years) from a single medical center were enrolled. Ultrawide-field photography images were analyzed using the concentric rings method, and the RPD area was semi-quantitatively classified according to the affected segment number into central, intermediate, and extensive types. Correlations of longitudinal changes in the RPD area and late AMD risk were investigated. RPD area increased significantly during the follow-up (p < 0.001). The increase rate correlated with age (r = 0.207; p = 0.048), RPD area at first visit (r = - 0.222; p = 0.035), and the decrease rate of subfoveal choroidal thickness (SFCT) (r = 0.217; p = 0.039). Many central (18/49, 36.7%) and intermediate (15/23, 65.2%) types switched to the more advanced type during the follow-up. Macular neovascularization and geographic atrophy developed in 12.3% and 18.7% of patients by 7 years. Late AMD incidence was significantly higher in eyes with large than in those with small RPD areas (p = 0.002). Larger RPD area at baseline, faster increase in RPD area, thinner SFCT, rapid decrease in SFCT, and the presence of late AMD on fellow eye were associated with late AMD. All RPD areas progressively increase over time. The regular assessment of RPD area may help to predict late AMD risk in RPD eyes.

Chromosome Damage in Relation to Recent Radiation Exposure and Radiation Quality in Nuclear Power Plant Workers.

Ionizing radiation is a well-known carcinogen that causes genomic instability. However, the biological and carcinogenetic effects of occupational radiation exposure at low doses have not been extensively studied. The aim of this study was to assess chromosomal instability in power plant workers exposed to occupational radiation at low doses in South Korea. Chromosomal aberrations in the lymphocytes of 201 nuclear power plant workers and 59 sex-matched controls were measured. Chromosomal aberrations in the lymphocytes of 201 nuclear power plant workers (mean age: 41.4 ± 10.0 years) and 59 sex-matched controls (mean age: 47.2 ± 6.0 years) were measured. A total of 500 metaphases for each subject were scored randomly. The means of recent 1.5-year, recent 5.5-year, and cumulative exposed radiation doses among workers were 8.22 ± 7.0 mSv, 30.7 ± 22.0 mSv, and 158.8 ± 86.1 mSv, respectively. The frequency of chromosome-type and chromatid-type aberrations was significantly higher in workers than that in the control group (p < 0.001), and the frequency of chromosome-type aberrations among workers increased in a radiation dose-dependent manner (τ = 0.16, p = 0.005). Poisson regression analyses revealed that chromosome-type aberrations were significantly associated with recent 1.5-year dose after adjusting for confounding variables such as age, smoking, and alcohol intake, even when only the exposed worker was considered. Frequency of multi-aberrant cells (two or more chromosome aberrations within a cell) increased according to cumulative neutron exposure. Our study demonstrates that chromosome damage can be induced in nuclear power plant workers occupationally exposed to ionizing radiation at low doses below the occupational permissible dose limit. Furthermore, an increase in multi-aberrant cells may provide evidence for chronic neutron exposure in nuclear power plant workers. This study was performed to obtain baseline data for a surveillance program of workers occupationally exposed to ionizing radiation long-term.

EN-FACE IMAGING OF ATYPICAL EPIRETINAL TISSUE IN LAMELLAR MACULAR HOLE.

PURPOSE: To elucidate the significance of en-face optical coherence tomography imaging of atypical epiretinal tissue (AET) in the lamellar macular hole (LMH). METHODS: This study involved 29 eyes of 29 patients who underwent surgical treatment for LMH with AET. Best-corrected visual acuity, metamorphopsia assessment (M-score), and optical coherence tomography were evaluated before and 6 months after surgery. The novel en-face optical coherence tomography parameters, such as the area of AET and hyperreflective fringe, were correlated with clinical factors before and after LMH surgery. RESULTS: Preoperatively, hyperreflective fringe was noted in 25 (86.2%) patients. The splitting of the inner retina, disruption of the ellipsoid zone, the extent of foveal cavitation, symptom duration, and change in best-corrected visual acuity were correlated with the area of AET (all P < 0.05). Multivariate regression analysis revealed that a larger area of AET was associated with longer symptom duration and less improvement in postoperative vision (all P < 0.05). CONCLUSION: The area of AET may represent the chronicity of LMH and is significantly associated with visual outcomes after LMH surgery. This novel en-face optical coherence tomography parameter can be used as a predictive factor for surgical outcomes in LMH with AET.

Metabolites with SARS-CoV-2 Inhibitory Activity Identified from Human Microbiome Commensals.

The COVID-19 pandemic has highlighted the need to identify additional antiviral small molecules to complement existing therapies. Although increasing evidence suggests that metabolites produced by the human microbiome have diverse biological activities, their antiviral properties remain poorly explored. Using a cell-based SARS-CoV-2 infection assay, we screened culture broth extracts from a collection of phylogenetically diverse human-associated bacteria for the production of small molecules with antiviral activity. Bioassay-guided fractionation uncovered three bacterial metabolites capable of inhibiting SARS-CoV-2 infection. This included the nucleoside analogue N6-(Δ2-isopentenyl)adenosine, the 5-hydroxytryptamine receptor agonist tryptamine, and the pyrazine 2,5-bis(3-indolylmethyl)pyrazine. The most potent of these, N6-(Δ2-isopentenyl)adenosine, had a 50% inhibitory concentration (IC50) of 2 µM. These natural antiviral compounds exhibit structural and functional similarities to synthetic drugs that have been clinically examined for use against COVID-19. Our discovery of structurally diverse metabolites with anti-SARS-CoV-2 activity from screening a small fraction of the bacteria reported to be associated with the human microbiome suggests that continued exploration of phylogenetically diverse human-associated bacteria is likely to uncover additional small molecules that inhibit SARS-CoV-2 as well as other viral infections. IMPORTANCE The continued prevalence of COVID-19 and the emergence of new variants has once again put the spotlight on the need for the identification of SARS-CoV-2 antivirals. The human microbiome produces an array of small molecules with bioactivities (e.g., host receptor ligands), but its ability to produce antiviral small molecules is relatively underexplored. Here, using a cell-based screening platform, we describe the isolation of three microbiome-derived metabolites that are able to prevent SARS-CoV-2 infection in vitro. These molecules display structural similarities to synthetic drugs that have been explored for the treatment of COVID-19, and these results suggest that the microbiome may be a fruitful source of the discovery of small molecules with antiviral activities.

Photoenzymatic Synthesis of α-Tertiary Amines by Engineered Flavin-Dependent "Ene"-Reductases.

α-Tertiary amines are a common motif in pharmaceutically important molecules but are challenging to prepare using asymmetric catalysis. Here, we demonstrate engineered flavin-dependent 'ene'-reductases (EREDs) can catalyze radical additions into oximes to prepare this motif. Two different EREDs were evolved into competent catalysts for this transformation with high levels of stereoselectivity. Mechanistic studies indicate that the oxime contributes to the enzyme templated charge-transfer complex formed between the substrate and cofactor. These products can be further derivatized to prepare a variety of motifs, highlighting the versatility of ERED photoenzymatic catalysis for organic synthesis.

Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.

Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA-protein cross-linking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3' segment of the product RNA generated by backtracking extrudes through the RdRp nucleoside triphosphate (NTP) entry tunnel, that a mismatched nucleotide at the product RNA 3' end frays and enters the NTP entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.

Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.

Backtracking, the reverse motion of the transcriptase enzyme on the nucleic acid template, is a universal regulatory feature of transcription in cellular organisms but its role in viruses is not established. Here we present evidence that backtracking extends into the viral realm, where backtracking by the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) may aid viral transcription and replication. Structures of SARS-CoV-2 RdRp bound to the essential nsp13 helicase and RNA suggested the helicase facilitates backtracking. We use cryo-electron microscopy, RNA-protein crosslinking, and unbiased molecular dynamics simulations to characterize SARS-CoV-2 RdRp backtracking. The results establish that the single-stranded 3'-segment of the product-RNA generated by backtracking extrudes through the RdRp NTP-entry tunnel, that a mismatched nucleotide at the product-RNA 3'-end frays and enters the NTP-entry tunnel to initiate backtracking, and that nsp13 stimulates RdRp backtracking. Backtracking may aid proofreading, a crucial process for SARS-CoV-2 resistance against antivirals.

Medial Epicanthoplasty: What Works and What Does Not.

Blepharoplasty is the most frequently performed cosmetic surgical procedure in Asia. The epicanthal fold, which is common in Asians, is characterized by a curved skin fold that partially hides the caruncle and lacrimal lake. The epicanthal fold may cause weakening of the esthetic appearance after blepharoplasty. It makes the palpebral fissure height narrower and the length shorter horizontally. Blepharoplasty with epicanthoplasty can enhance the esthetic appearance, but no gold standard surgical technique has been established for epicanthoplasty. Surgeons can choose the surgical technique according to their preference and the patient's characteristics. A carefully designed and fine surgical technique, especially with the use of loupes and tension-free skin closure with the thinnest needle, is required to avoid scarring.

Controlled Segmentation of Metal Nanowire Array by Block Copolymer Lithography and Reversible Ion Loading.

Spatial arrangement of 1D nanomaterials may offer enormous opportunities for advanced electronics and photonics. Moreover, morphological complexity and chemical diversity in the nanoscale components may lead to unique properties that are hardly anticipated in randomly distributed homogeneous nanostructures. Here, controlled chemical segmentation of metal nanowire arrays using block copolymer lithography and subsequent reversible metal ion loading are demonstrated. To impose chemical heterogeneity in the nanowires generated by block copolymer lithography, reversible ion loading method highly specific for one particular polymer block is introduced. Reversibility of the metal ion loading enables area-selective localized replacement of metal ions in the self-assembled patterns and creates segmented metal nanowire arrays with different metallic components. Further integration of this method with shear aligning process produces high aligned segmented metal nanowire array with desired local chemical compositions.

Highly tunable refractive index visible-light metasurface from block copolymer self-assembly.

The refractive index of natural transparent materials is limited to 2-3 throughout the visible wavelength range. Wider controllability of the refractive index is desired for novel optical applications such as nanoimaging and integrated photonics. We report that metamaterials consisting of period and symmetry-tunable self-assembled nanopatterns can provide a controllable refractive index medium for a broad wavelength range, including the visible region. Our approach exploits the independent control of permeability and permittivity with nanoscale objects smaller than the skin depth. The precise manipulation of the interobject distance in block copolymer nanopatterns via pattern shrinkage increased the effective refractive index up to 5.10. The effective refractive index remains above 3.0 over more than 1,000 nm wavelength bandwidth. Spatially graded and anisotropic refractive indices are also obtained with the design of transitional and rotational symmetry modification.

Mitochondrial ATP synthase activity is impaired by suppressed O-GlcNAcylation in Alzheimer's disease.

Glycosylation with O-linked ß-N-acetylglucosamine (O-GlcNAc) is one of the protein glycosylations affecting various intracellular events. However, the role of O-GlcNAcylation in neurodegenerative diseases such as Alzheimer's disease (AD) is poorly understood. Mitochondrial adenosine 5'-triphosphate (ATP) synthase is a multiprotein complex that synthesizes ATP from ADP and Pi. Here, we found that ATP synthase subunit α (ATP5A) was O-GlcNAcylated at Thr432 and ATP5A O-GlcNAcylation was decreased in the brains of AD patients and transgenic mouse model, as well as Aß-treated cells. Indeed, Aß bound to ATP synthase directly and reduced the O-GlcNAcylation of ATP5A by inhibition of direct interaction between ATP5A and mitochondrial O-GlcNAc transferase, resulting in decreased ATP production and ATPase activity. Furthermore, treatment of O-GlcNAcase inhibitor rescued the Aß-induced impairment in ATP production and ATPase activity. These results indicate that Aß-mediated reduction of ATP synthase activity in AD pathology results from direct binding between Aß and ATP synthase and inhibition of O-GlcNAcylation of Thr432 residue on ATP5A.

Direct Observation of a Carbon Filament in Water-Resistant Organic Memory.

The memory for the Internet of Things (IoT) requires versatile characteristics such as flexibility, wearability, and stability in outdoor environments. Resistive random access memory (RRAM) to harness a simple structure and organic material with good flexibility can be an attractive candidate for IoT memory. However, its solution-oriented process and unclear switching mechanism are critical problems. Here we demonstrate iCVD polymer-intercalated RRAM (i-RRAM). i-RRAM exhibits robust flexibility and versatile wearability on any substrate. Stable operation of i-RRAM, even in water, is demonstrated, which is the first experimental presentation of water-resistant organic memory without any waterproof protection package. Moreover, the direct observation of a carbon filament is also reported for the first time using transmission electron microscopy, which puts an end to the controversy surrounding the switching mechanism. Therefore, reproducibility is feasible through comprehensive modeling. Furthermore, a carbon filament is superior to a metal filament in terms of the design window and selection of the electrode material. These results suggest an alternative to solve the critical issues of organic RRAM and an optimized memory type suitable for the IoT era.

Directed self-assembly of cylinder-forming diblock copolymers on sparse chemical patterns.

Using both theory and experiment, we investigate the possibility of creating perfectly ordered block copolymer nanostructures on sparsely patterned substrates. Our study focuses on scrutinizing the appropriate pattern conditions to avoid undesired morphologies or defects when depositing cylinder-forming AB diblock copolymer thin films on the substrates which are mostly neutral with periodic stripe regions preferring the minority domain. By systematically exploring the parameter space using self-consistent field theory (SCFT), the optimal conditions for target phases are determined, and the effects of the chemical pattern period and the block copolymer film thickness on the target phase stability are also studied. Furthermore, as a sample experimental system, almost perfectly aligned polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymers are demonstrated. After the pattern transfer process, highly ordered Al nanodot arrays following the initial vertically aligned cylinder pattern are created. This systematic study demonstrates the ability to control the structure and the position of nanopatterns on sparse chemical patterns.

A bivalent conjugate vaccine containing PspA families 1 and 2 has the potential to protect against a wide range of Streptococcus pneumoniae strains and Salmonella Typhi.

Previously we showed that conjugation of pneumococcal surface protein A (PspA) to Vi capsular polysaccharide from Salmonella Typhi enhanced the anti-PspA response without the need to add adjuvant. In the current study conjugates consisting of the α helical regions of PspA families 1 or 2 bound to Vi were used to vaccinate mice to test their ability to protect against a lethal intravenous challenge of a range of various strains of Streptococcus pneumoniae. Conjugate vaccine containing PspA family 1 provided good protection from PspA family 1 challenge strains but offered very little protection against PspA family 2 challenge strains. Similarly, PspA family 2 conjugates provided good protection from PspA family 2 challenge strains and poor protection against PspA family 1 challenge strains. This observation was supported by the low levels of cross-reactivity of PspA antibodies seen in ELISA plates coated with the heterologous PspA family. Cytokine profiles showed a mixed Th1/Th2 response to Vi and the Vi-PspA conjugates. IgG subclass analysis of the anti-Vi response showed a shift from predominantly IgG2a/3 to IgG1 after conjugation to PspA was consistent with other polysaccharide conjugate vaccines. The results demonstrate that conjugation of the α helical region of PspA to Vi enhances its capacity to induce a protective immune response and that a vaccine based on the α helical region of PspA should contain PspA from both families 1 and 2 to achieve broad cross-protection.

Radiation-induced changes in DNA methylation and their relationship to chromosome aberrations in nuclear power plant workers.

PURPOSE: We investigated the association between occupational radiation exposure and DNA methylation changes in nuclear power plant workers. We also evaluated whether radiation- induced DNA methylation alterations are associated with chromosome aberrations. MATERIALS AND METHODS: The study population included 170 radiation-exposed workers and 30 controls. We measured global, long interspersed nuclear element-1 (LINE-1), and satellite 2 methylation levels in blood leukocyte DNA. The analysis of chromosome aberrations was performed on peripheral lymphocytes. RESULTS: Global DNA methylation levels were lower in radiation-exposed workers than in controls. The methylation levels were negatively associated with the recent 1.5-year radiation dose in a multiple linear regression model (ß = - 0.0088, p ≤ 0.001); the levels increased proportionally with the total cumulative dose in radiation-exposed workers. LINE-1 methylation levels were higher in radiation-exposed workers than in controls and were significantly associated with the total cumulative radiation dose in a multiple linear regression model (ß = - 0.031, p = 0.035). Global DNA methylation levels were also correlated with chromosome aberrations among workers. Workers with low global methylation levels had a higher frequency of chromosome aberrations than did subjects with high global methylation levels. CONCLUSION: Occupational exposure to low-dose radiation could affect DNA methylation levels, and the radiation-induced DNA methylation alterations may be associated with chromosome aberrations.

Nanodomain swelling block copolymer lithography for morphology tunable metal nanopatterning.

Ordered metal nanopatterns are crucial requirements for electronics, magnetics, catalysts, photonics, and so on. Despite considerable progress in the synthetic route to metal nanostructures, highly ordered metal nanopatterning over a large-area is still challenging. Nanodomain swelling block copolymer lithography is presented as a general route to the systematic morphology tuning of metal nanopatterns from amphiphilic diblock copolymer self-assembly. Selective swelling of hydrophilic nanocylinder domains in amphiphilic block copolymer films during metal precursor loading and subsequent oxygen based etching generates diverse shapes of metal nanopatterns, including hexagonal nanoring array and hexagonal nanomesh and double line array in addition to common nanodot and nanowire arrays. Solvent annealing condition of block copolymer templates, selective swelling of hydrophilic cylinder nanodomains, block copolymer template thickness, and oxygen based etching methods are the decisive parameters for systematic morphology evolution. The plasmonic properties of ordered Au nanopatterns are characterized and analyzed with finite differential time domain calculation. This approach offers unprecedented opportunity for diverse metal nanopatterns from commonly used diblock copolymer self-assembly.

Enhanced cytotoxic and genotoxic effects of gadolinium following ELF-EMF irradiation in human lymphocytes.

There are many studies of Gd nephrotoxicity and neurotoxicity, whereas research on cyto- and genotoxicity in normal human lymphocytes is scarce. It is important to investigate the effect of extremely low-frequency electromagnetic fields (ELF-EMF) on Gd toxicity, as patients are co-exposed to Gd and ELF-EMF generated by MRI scanners. We investigated the cytotoxicity and genotoixcity of Gd and the possible enhancing effect of ELF-EMF on Gd toxicity in cultured human lymphocytes by performing a micronuclei (MN) assay, trypan blue dye exclusion, single cell gel electrophoresis, and apoptosis analyses using flow cytometry. Isolated lymphocytes were exposed to 0.2-1.2 mM of Gd only or in combination with a 60-Hz ELF-EMF of 0.8-mT field strength. Exposing human lymphocytes to Gd resulted in a concentration- and time-dependent decrease in cell viability and an increase in MN frequency, single strand DNA breakage, apoptotic cell death, and ROS production. ELF-EMF (0.8 mT) exposure also increased cell death, MN frequency, olive tail moment, and apoptosis induced by Gd treatment alone. These results suggest that Gd induces DNA damage and apoptotic cell death in human lymphocytes and that ELF-EMF enhances the cytotoxicity and genotoxicity of Gd.