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Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting preferred orientations on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.

Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.

Abstract Aims Plasma volume status (PVS), a measure of plasma volume, has been evaluated as a prognostic marker for chronic heart failure. Although the prognostic value of PVS has been reported, its significance in patients with acute decompensated heart failure (ADHF) admitted to the cardiovascular intensive care unit (CICU) remains unclear. In this study, we examined the relationship between PVS and long‐term mortality in patients with ADHF admitted to the CICU. Methods Between January 2018 and December 2020, 363 consecutive patients with ADHF were admitted to the Nippon Medical School Hospital CICU. Of the 363 patients, 206 (mean age, 74.9 ± 12.9 years; men, 64.6%) were enrolled in this study. Patients who received red blood cell transfusions, underwent dialysis, were discharged from the CICU or died in the hospital were excluded from the study. We measured the PVS of the patients at admission, transfer to the general ward (GW) and discharge using the Kaplan–Hakim formula. The patients were assigned to four groups according to the quartiles of their PVS measured at each of the three abovementioned timepoints. We examined the association between PVS and all‐cause mortality during the observation period (1134 days). The primary endpoint of this study was all‐cause mortality. Results The Kaplan–Meier analysis showed that the high PVS group had a significantly higher mortality rate at admission, transfer to the GW and discharge than the other groups (log‐rank test: P = 0.016, P = 0.005 and P

The accumulation of a disease-specific isoform of prion protein (PrPSc) and histopathological lesions, such as neuronal loss, are unevenly distributed in the brains of humans and animals affected with prion diseases. This distribution varies depending on the diseases and/or the combinations of prion strain and experimental animal. The brain region-dependent distribution of PrPSc and neuropathological lesions suggests a neuronal cell-type-dependent prion propagation and vulnerability to prion infection. However, the underlying mechanism is largely unknown. In this study, we provided evidence that the prion 22L strain propagates more efficiently in excitatory neurons than inhibitory neurons and that excitatory neurons in the thalamus are vulnerable to prion infection. PrPSc accumulation was less intense in the striatum, where GABAergic inhibitory neurons predominate, compared to the cerebral cortex and thalamus, where glutamatergic excitatory neurons are predominant, in mice intracerebrally or intraperitoneally inoculated with the 22L strain. PrPSc stains were observed along the needle track after stereotaxic injection into the striatum, whereas they were also observed away from the needle track in the thalamus. Consistent with inefficient prion propagation in the striatum, the 22L prion propagated more efficiently in glutamatergic neurons than GABAergic neurons in primary neuronal cultures. RNAscope in situ hybridization revealed a decrease in Vglut1- and Vglut2-expressing neurons in the ventral posterolateral nuclei of the thalamus in 22L strain-infected mice, whereas no decrease in Vgat-expressing neurons was observed in the adjacent reticular nucleus, mainly composed of Vgat-expressing interneurons. The excitatory neuron-prone prion propagation and excitatory neuronal loss in 22L strain-infected mice shed light on the neuropathological mechanism of prion diseases.

Abstract Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.

Abstract Background Interferon-α (IFN-α) exerts an anti-tumor effect at least through induction of apoptosis in a variety of types including B lymphoma cells. We recently found that IFN-α induced a sustained activation of c-Jun NH2-terminal kinase1 (JNK1), which is implicated in activation of the tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) promoter. In the present study, we explored upstream component(s) of the prolonged IFN-α-initiated activation of JNK1. Results IFN-α caused activation of PKC-δ in Daudi B lymphoma cells and myeloma U266 cells, as detected by Western blotting using a monoclonal antibody specific for the phosphorylated form of PKC-δ. The dominant-negative form of mutant PKC-δ (dnPKC-δ) reduced the IFN-α-induced JNK1 activation, TRAIL promoter activity, loss of mitochondrial membrane potential (ΔΨm), and increase in propidium iodide (PI) positive cells. The IFN-α-induced activation of JNK1 and the TRAIL promoter was also attenuated by the PKC-δ inhibitor rottlerin. Moreover, a constitutively active form of mutant PKC-δ enhanced the IFN-α-induced TRAIL promoter activity and loss of ΔΨm in Daudi B lymphoma cells. In addition, IFN-α-induced Ser727 phosphorylation of Stat1 was also abrogated by dnPKC-δ. Conclusions IFN-α induced JNK1 activation via PKC-δ, leading to upregulation of TRAIL. The interaction of the consequent enhanced TRAIL expression with TRAIL-receptor results in a loss of ΔΨm and increase in PI positive cells. The IFN-α-induced apoptotic events may also be affected by the Ser727-Stat1 induced by PKC-δ-mediated signaling component(s).

Urban air pollution poses a significant threat to human health, with metropolitan areas particularly affected due to high emissions from human activities. Particulate matter (PMx) is among the most harmful pollutants to human health, being composed of a complex mixture of substances related to severe pulmonary conditions. Urban green spaces play a vital role in mitigating air pollution by capturing PMx, and it is essential to select plant species with a high capacity for PMx accumulation to effectively enhance air quality. This study aimed to evaluate and compare the accuracy of two PMx quantification methods—light microscopy and filtration—which demonstrated a high correlation (R2 = 0.72), suggesting that both methods are reliable for assessing PMx accumulation on leaves. Light microscopy allowed for the visualization of PMx deposition, revealing the species warranting further analysis using the filtration method. Among the species analyzed, Euonymus japonicus, Ligustrum lucidum, Alnus glutinosa, Rubus ulmifolius, and Laurus nobilis demonstrated the highest total PMx accumulation, exceeding 50 µg cm−2, making them particularly valuable for air pollution mitigation. This study examined the correlation between leaf traits such as specific leaf area (SLA), leaf area (LA), leaf dissection index (LDI), and leaf roundness and PMx accumulation across the 30 different plant species. A multiple linear regression analysis indicated that these leaf traits significantly influenced PMx accumulation, with SLA and LA showing negative correlations and leaf roundness exhibiting a positive correlation with PMx deposition. In conclusion, this study highlights the importance of selecting plant species with specific leaf traits for effective air quality improvement in urban environments particularly in highly polluted areas, to enhance air quality and public health.

Background:. There remain arguments regarding whether fatty degeneration of the rotator cuff muscles improves following rotator cuff repair. The purpose of this study was to prospectively investigate changes in fatty degeneration of the rotator cuff muscles, quantitatively measured on magnetic resonance imaging (MRI) with use of transverse relaxation time (T2) mapping techniques, and to assess the relationship between these changes and clinical outcomes. Methods:. Patients were included if they were scheduled for arthroscopic rotator cuff repair using the suture-bridge technique between June 2014 and December 2015, underwent preoperative MRI including the T2 mapping sequence, and consented to participate in the study. Exclusion criteria consisted of trauma within 2 months before preoperative MRI, isolated subscapularis tears, patch augmentation, neuromuscular disease, and a follow-up duration of

An excess of ozone (O3) is currently stressing plant ecosystems and may negatively affect the nutrient use of plants. Plants may modify leaf turnover rates and nutrient allocation at the organ level to counteract O3 damage. We investigated leaf turnover rate and allocation of primary (C, N, P, K) and secondary macronutrients (Ca, S, Mg) under various O3 treatments (ambient concentration, AA, with a daily hourly average of 35 ppb; 1.5 × AA; 2.0 × AA) and fertilization levels (N: 0 and 80 kg N ha−1 y−1; P: 0 and 80 kg N ha−1 y−1) in an O3-sensitive poplar clone (Oxford: Populus maximowiczii Henry × P. berolinensis Dippel) in a Free-Air Controlled Exposure (FACE) experiment. The results indicated that both fertilization and O3 had a significant impact on the nutrient content. Specifically, fertilization and O3 increased foliar C and N contents (+5.8% and +34.2%, respectively) and root Ca and Mg contents (+46.3% and +70.2%, respectively). Plants are known to increase the content of certain elements to mitigate the damage caused by high levels of O3. The leaf turnover rate was accelerated as a result of increased O3 exposure, indicating that O3 plays a main role in influencing this physiological parameter. A PCA result showed that O3 fumigation affected the overall allocation of primary and secondary elements depending on the organ (leaves, stems, roots). As a conclusion, such different patterns of element allocation in plant leaves in response to elevated O3 levels can have significant ecological implications.