Structural basis for ion selectivity in potassium-selective channelrhodopsins.

KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.

Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine.

ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.

Electronic band structure change with structural transition of buckled Au2X monolayers induced by strain.

This study investigates the strain-induced structural transitions of η ↔ θ and the changes in electronic band structures of Au2X (X = S, Se, Te, Si, Ge) and Au4SSe. We focus on Au2S monolayers, which can form multiple meta-stable monolayers theoretically, including η-Au2S, a buckled penta-monolayer composed of a square Au lattice and S adatoms. The θ-Au2S is regarded as a distorted structure of η-Au2S. Based on density functional theory (DFT) calculations using a generalized gradient approximation, the conduction and the valence bands of θ-Au2S intersect at the Γ point, leading to linear dispersion, whereas η-Au2S has a band gap of 1.02 eV. The conduction band minimum depends on the specific Au-Au bond distance, while the valence band maximum depends on both Au-S and Au-Au interactions. The band gap undergoes significant changes during the η ↔ θ phase transition of Au2S induced by applying tensile or compressive in-plane biaxial strain to the lattice. Moreover, substituting S atoms with other elements alters the electronic band structures, resulting in a variety of physical properties without disrupting the fundamental Au lattice network. Therefore, the family of Au2X monolayers holds potential as materials for atomic scale network devices.

Hydrogen-induced Sulfur Vacancies on the MoS2 Basal Plane Studied by Ambient Pressure XPS and DFT Calculations.

Sulfur vacancy on an MoS2 basal plane plays a crucial role in device performance and catalytic activity; thus, an understanding of the electronic states of sulfur vacancies is still an important issue. We investigate the electronic states on an MoS2 basal plane by ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and density functional theory calculations while heating the system in hydrogen. The AP-XPS results show a decrease in the intensity ratio of S 2p to Mo 3d, indicating that sulfur vacancies are formed. Furthermore, low-energy components are observed in Mo 3d and S 2p spectra. To understand the changes in the electronic states induced by sulfur vacancy formation at the atomic scale, we calculate the core-level binding energies for the model vacancy surfaces. The calculated shifts for Mo 3d and S 2p with the formation of sulfur vacancy are consistent with the experimentally observed binding energy shifts. Mulliken charge analysis indicates that this is caused by an increase in the electronic density associated with the Mo and S atoms around the sulfur vacancy as compared to the pristine surface. The present investigation provides a guideline for sulfur vacancy engineering.

Engineering ferromagnetism in Ni(OH)2 nanosheets using tunable uniaxial pressure in graphene oxide/reduced graphene oxide.

The interlayer spaces in two dimensional (2D) layered materials such as graphene, metal oxides and metal chalcogenides can be used in a number of roles that include the trapping of gases, for ion transfer and for water purification applications. In such spaces, "inner" pressure occurs on guest species enclosed between the layers and its variation can, in principal, be used for precisely controlling particular guest properties. In this study, a mixture of two 2D materials including graphene oxide (GO) and nickel hydroxide (Ni(OH)2), was employed to yield an anisotropic GO-Ni(OH)2 hybrid 2D sheet. The inner pressure associated with this material was able to be tuned by reduction of the GO (to yield rGO) and this in turn was shown to affect the magnetic behaviour of Ni(OH)2. The ferromagnetic transition temperature (Tc) for Ni(OH)2 decreases as the interlayer distance became shorter, which is opposite to the behaviour observed for the application of hydrostatic pressure to the hybrid sheet. The uniaxial pressure affecting the interlayer of the 2D material, and generated by the reduction of GO to rGO, has the potential to not only influence the behaviour of a range of magnetic materials, but also individual properties of other types of functional materials.

Nanodiscs for Structural Biology in a Membranous Environment.

The structures of many membrane proteins have been analyzed in detergent micelles. However, the environment of detergent micelles differs somewhat from that of the lipid bilayer, where membrane proteins exhibit physiological functions. Therefore, a more membrane-like environment has been awaited for structural analysis of membrane proteins. Nanodiscs are "hockey-puck"-shaped lipid bilayer particles that distribute in a monodispersed manner in aqueous solution. We review how nanodiscs or protein-reconstituted nanodiscs are prepared and how they are utilized to analyze protein structure, dynamics, and interactions with lipid molecules using solution NMR and cryo-electron microscopy.

Visualizing Microglia with a Fluorescence Turn-On Ugt1a7c Substrate.

Microglia, the brain-resident macrophage, are involved in brain development and contribute to the progression of neural disorders. Despite the importance of microglia, imaging of live microglia at a cellular resolution has been limited to transgenic mice. Efforts have therefore been dedicated to developing new methods for microglia detection and imaging. Using a thorough structure-activity relationships study, we developed CDr20, a high-performance fluorogenic chemical probe that enables the visualization of microglia both in vitro and in vivo. Using a genome-scale CRISPR-Cas9 knockout screen, the UDP-glucuronosyltransferase Ugt1a7c was identified as the target of CDr20. The glucuronidation of CDr20 by Ugt1a7c in microglia produces fluorescence.

In vivo retinal and choroidal hypoxia imaging using a novel activatable hypoxia-selective near-infrared fluorescent probe.

PURPOSE: Retinal hypoxia plays a crucial role in ocular neovascular diseases, such as diabetic retinopathy, retinopathy of prematurity, and retinal vascular occlusion. Fluorescein angiography is useful for identifying the hypoxia extent by detecting non-perfusion areas or neovascularization, but its ability to detect early stages of hypoxia is limited. Recently, in vivo fluorescent probes for detecting hypoxia have been developed; however, these have not been extensively applied in ophthalmology. We evaluated whether a novel donor-excited photo-induced electron transfer (d-PeT) system based on an activatable hypoxia-selective near-infrared fluorescent (NIRF) probe (GPU-327) responds to both mild and severe hypoxia in various ocular ischemic diseases animal models. METHODS: The ocular fundus examination offers unique opportunities for direct observation of the retina through the transparent cornea and lens. After injection of GPU-327 in various ocular hypoxic diseases of mouse and rabbit models, NIRF imaging in the ocular fundus can be performed noninvasively and easily by using commercially available fundus cameras. To investigate the safety of GPU-327, electroretinograms were also recorded after GPU-327 and PBS injection. RESULT: Fluorescence of GPU-327 increased under mild hypoxic conditions in vitro. GPU-327 also yielded excellent signal-to-noise ratio without washing out in vivo experiments. By using near-infrared region, GPU-327 enables imaging of deeper ischemia, such as choroidal circulation. Additionally, from an electroretinogram, GPU-327 did not cause neurotoxicity. CONCLUSIONS: GPU-327 identified hypoxic area both in vivo and in vitro.

Effect of Luseogliflozin, a Sodium-Glucose Cotransporter 2 Inhibitor, and Dipeptidyl-Peptidase 4 Inhibitors on the Quality-of-Life and Treatment Satisfaction of Patients With Type 2 Diabetes Mellitus: A Subanalysis of a Multicenter, Open-Label, Randomized-Controlled Trial (J-SELECT Study).

INTRODUCTION: The effects of dipeptidyl peptidase-4 inhibitors (DPP-4is) and sodium-glucose cotransporter 2 inhibitors (SGLT2is) on quality of life (QOL) and treatment satisfaction have not been directly compared. This sub-analysis of a randomized-controlled trial with an SGLT2i, luseogliflozin, and DPP-4is compared their effects on QOL and treatment satisfaction of patients. METHODS: This study recruited 623 patients with type 2 diabetes mellitus who were drug-naïve or treated with antidiabetic agents other than SGLT2is and DPP-4is. The patients were randomized into luseogliflozin or DPP-4i group and followed for 52 weeks. This sub-analysis assessed QOL and treatment satisfaction using Oral Hypoglycemic Agent Questionnaire (OHA-Q) version 2 in the drug-naïve subgroup who were drug-naïve at baseline and with monotherapy with luseogliflozin or DPP-4i throughout the observation period (256 patients) at 24 and 52 weeks and in the add-on subgroup who were treated with OHAs other than SGLT2is and DPP-4is (204 patients) at baseline, 24 and 52 weeks. RESULTS: In the drug-naïve subgroup, total (50.8 ± 8.2 in luseogliflozin group and 53.1 ± 10.0 in DPP-4i group, p = 0.048) and somatic symptom scores (22.4 ± 5.0 in luseogliflozin group and 24.4 ± 5.8 in DPP-4i group, p = 0.005) at 52 weeks (but not at 24 weeks) were significantly higher in DPP-4i group than in luseogliflozin group. In add-on subgroup, changes in total (3.3 ± 7.8 in luseogliflozin group and 0.9 ± 7.6 in DPP-4i group, p = 0.030) and treatment convenience (1.2 ± 3.9 in luseogliflozin group and - 0.6 ± 4.2 in DPP-4i group, p = 0.002) from baseline to 24 weeks (but not at 52 weeks) were significantly greater in luseogliflozin group than in DPP-4i group. The QOL related to safety or glycemic control was comparable between the groups. CONCLUSIONS: Physicians should pay attention to side effects of SGLT2is to maintain the patients' QOL when SGLT2is are initiated or added-on. Add-on of luseogliflozin increased patients' QOL more than DPP-4is. Considering patients' QOL and treatment satisfaction is important for selecting SGLT2is or DPP-4is. TRIAL REGISTRATION: UMIN000030128 and jRCTs031180241.

Which is a better treatment for hypertensive patients with diabetes: a combination of losartan and hydrochlorothiazide or a maximum dose of losartan?

BACKGROUND: This 12-month study compared the effects of a combination of losartan 50 mg and hydrochlorothiazide 12.5 mg with a maximum dose of losartan (100 mg) in hypertensive patients with diabetes. METHODS: This was a multicenter randomized open-label study. RESULTS: A similar reduction in systolic/diastolic blood pressure from baseline to month 3 was observed in both groups. There was also a similar decrease in UACR in both groups. A significant decrease in uric acid was observed in the maximum-dose group only. eGFR decreased in the combination group after 1 year. CONCLUSIONS: The combination of losartan and a diuretic may be a useful option in such hypertensive patients with diabetes, provided that metabolic parameters are closely monitored. In patients with hyperuricemia and impaired renal function, a maximum dose of losartan may be more beneficial.

Thermally stable proton conductivity from nanodiamond oxide.

Herein, we report nanodiamond oxide (NDOx), obtained from modified Hummers' oxidation of nanodiamond (ND), showing excellent proton conductivity and thermal stability. NDOx possesses hydrophilicity resulting in higher water adsorption and the retention of functional groups at elevated temperatures can be attributed to the high proton conductivity and thermal stability, respectively.

Virally induced CRISPR/Cas9-based knock-in of fluorescent albumin allows long-term visualization of cerebral circulation in infant and adult mice.

Albumin, a protein produced by liver hepatocytes, represents the most abundant protein in blood plasma. We have previously engineered a liver-targeting adeno-associated viral vector (AAV) that expresses fluorescent protein-tagged albumin to visualize blood plasma in mice. While this approach is versatile for imaging in adult mice, transgene expression vanishes when AAV is administered in neonates due to dilution of the episomal AAV genome in the rapidly growing liver. Here, we use CRISPR/Cas9 genome editing to insert the fluorescent protein mNeonGreen (mNG) gene into the albumin (Alb) locus of hepatocytes to produce fluorescently labeled albumin (Alb-mNG). We constructed a CRISPR AAV that includes ∼1 kb homologous arms around Alb exon 14 to express Alb-mNG. Subcutaneous injection of this AAV with AAV-CMV-Cas9 in postnatal day 3 mice resulted in two-photon visualization of the cerebral cortex vasculature within ten days. The expression levels of Alb-mNG were persistent for at least three months and were so robust that vasomotion and capillary blood flow could be assessed transcranially in early postnatal mice. This knock-in approach provides powerful means for micro- and macroscopic imaging of cerebral vascular dynamics in postnatal and adult mice.

Osmotically Rupturing Phagosomes in Macrophages Using PNIPAM Microparticles.

The rupture of macrophage phagosomes has been implicated in various human diseases and plays a critical role in immunity. However, the mechanisms underlying this process are complex and not yet fully understood. This study describes the development of a robust engineering method for rupturing phagosomes based on a well-defined mechanism. The method utilizes microfabricated microparticles composed of uncrosslinked linear poly(N-isopropylacrylamide) (PNIPAM) as phagocytic objects. These microparticles are internalized into phagosomes at 37 °C. By exposing the cells to a cold shock at 0 °C, the vast majority of the microparticle-containing phagosomes rupture. The percentage of phagosomal rupture decreases with the increase of the cold-shock temperature. The osmotic pressure in the phagosomes and the tension in the phagosomal membrane are calculated using the Flory-Huggins theory and the Young-Laplace equation. The modeling results indicate that the osmotic pressure generated by dissolved microparticles is probably responsible for phagosomal rupture, are consistent with the experimentally observed dependence of phagosomal rupture on the cold-shock temperature, and suggest the existence of a cellular mechanism for resisting phagosomal rupture. Moreover, the effects of various factors including hypotonic shock, chloroquine, tetrandrine, colchicine, and l-leucyl-l-leucine O-methyl ester (LLOMe) on phagosomal rupture have been studied with this method. The results further support that the osmotic pressure generated by the dissolved microparticles causes phagosomal rupture and demonstrated usefulness of this method for studying phagosomal rupture. This method can be further developed, ultimately leading to a deeper understanding of phagosomal rupture.

Risk Factors Associated with Mortality among Mechanically Ventilated Patients with Coronavirus Disease 2019 Pneumonia: A Multicenter Cohort Study in Japan (J-RECOVER Study).

Objective Mortality analyses of patients with coronavirus disease 2019 (COVID-19) requiring invasive mechanical ventilation in Japan are limited. The present study therefore determined the risk factors for mortality in patients with COVID-19 requiring invasive mechanical ventilation. Methods This retrospective cohort study used the dataset from the Japanese multicenter research of COVID-19 by assembling real-word data (J-RECOVER) study that was conducted between January 1 and September 31, 2020. Independent risk factors associated with in-hospital mortality were evaluated using a multivariate logistic regression analysis. Kaplan-Meier estimates of the survival were calculated for different age groups. A subgroup analysis was performed to assess differences in survival rates according to additional risk factors, including an older age and chronic pulmonary disease. Patients A total of 561 patients were eligible. The median age was 67 (interquartile range: 56-75) years old, 442 (78.8%) were men, and 151 (26.9%) died in the hospital. Results Age, chronic pulmonary disease, and renal disease were significantly associated with in-hospital mortality. Compared with patients 18-54 years old, the adjusted odds ratios of patients 55-64, 65-74, and 75-94 years old were 3.34 (95% CI, 1.34-8.31), 7.07 (95% CI, 3.05-16.40), and 18.43 (95% CI, 7.94-42.78), respectively. Conclusion Age, chronic pulmonary disease, and renal disease were independently associated with mortality in patients with COVID-19 requiring invasive mechanical ventilation, and age was the most decisive indicator of a poor prognosis. Our results may aid in formulating treatment strategies and allocating healthcare resources.

Overall Efficacy and Safety of Sodium-Glucose Cotransporter 2 Inhibitor Luseogliflozin Versus Dipeptidyl-Peptidase 4 Inhibitors: Multicenter, Open-Label, Randomized-Controlled Trial (J-SELECT study).

INTRODUCTION: Evidence of a direct comparison between dipeptidyl-peptidase 4 inhibitors (DPP-4is) and sodium-glucose cotransporter 2 inhibitors (SGLT2is) remains lacking, and no clear treatment strategy or rationale has been established using these drugs. This study aimed to compare the overall efficacy and safety of DPP-4is and the SGLT2i luseogliflozin in patients with type 2 diabetes mellitus (T2DM). METHODS: Patients with T2DM who had not used antidiabetic agents or who had used antidiabetic agents other than SGLT2is and DPP-4is were enrolled in the study after written informed consent had been obtained. The enrolled patients were subsequently randomly assigned to either the luseogliflozin or DPP-4i group and followed up for 52 weeks. The primary (composite) endpoint was the proportion of patients who showed improvement in ≥ 3 endpoints among the following five endpoints from baseline to week 52: glycated hemoglobin (HbA1c), weight, estimated glomerular filtration rate (eGFR), systolic blood pressure, and pulse rate. RESULTS: A total of 623 patients were enrolled in the study and subsequently randomized to either the luseogliflozin or DPP-4i groups. The proportion of patients who showed improvement in ≥ 3 endpoints at week 52 was significantly higher in the luseogliflozin group (58.9%) than in the DPP-4i group (35.0%) (p < 0.001). When stratified by body mass index (BMI) (< 25 or ≥ 25 kg/m2) or age (< 65 or ≥ 65 years), regardless of BMI or age, the proportion of patients who achieved the composite endpoint was significantly higher in the luseogliflozin group than in the DPP-4i group. Hepatic function and high-density lipoprotein-cholesterol were also significantly improved in the luseogliflozin group compared with the DPP-4i group. The frequency of non-serious/serious adverse events did not differ between the groups. CONCLUSION: This study showed the overall efficacy of luseogliflozin compared with DPP-4is over the mid/long term, regardless of BMI or age. The results suggest the importance of assessing multiple aspects regarding the effects of diabetes management. TRIAL REGISTRATION NUMBER: jRCTs031180241.

Correction: SARS-CoV-2 suppression depending on the pH of graphene oxide nanosheets.

[This corrects the article DOI: 10.1039/D3NA00084B.].

SARS-CoV-2 suppression depending on the pH of graphene oxide nanosheets.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inactivation of pH-dependent graphene oxide (GO) nanosheets is presented. The observed virus inactivation using an authentic virus (Delta variant) and different GO dispersions at pH 3, 7, and 11 suggests that the higher pH of the GO dispersion yields a better performance compared to that of GO at neutral or lower pH. The current findings can be ascribed to the pH-driven functional group change and the overall charge of GO, favorable for the attachment between GO nanosheets and virus particles.

A novel tdTomato transgenic mouse model to visualize FAP-positive cancer-associated fibroblasts.

Fibroblast activation protein (FAP) generally shows low or undetectable expression in most normal tissues but is highly expressed in fibroblasts in almost all carcinomas. FAP is one of the potential molecules to detect activated fibroblasts and has multiple roles in tumour progression. We generated transgenic mice that specifically expressed tdTomato along with FAP promoter activity. Coculturing a mouse gastric cancer cell line and FAP-tdTomato transgenic mouse-derived fibroblasts showed that tdTomato expression was elevated in the cocultured fibroblasts. Moreover, stomach wall transplanted tumours in mice also showed FAP-tdTomato expression in fibroblasts of the stomach and each metastatic legion. These results indicated that FAP-tdTomato expression in fibroblasts was elevated by stimulation through the interaction with cancer cells. Functionally, collagen production was increased in FAP/tdTomato-positive fibroblasts cocultured with mouse cancer cells. These FAP-tdTomato transgenic mice have the potential to be used to investigate real-time FAP dynamics and the importance of FAP expression in tumour development.

Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.

Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.

Diabetic foot wounds in haemodialysis patients: 2-year outcome after percutaneous transluminal angioplasty and minor amputation.

Critical limb ischaemia (CLI) is known to be associated with high mortality. In some patients, surgery cannot be performed due to high risk of perioperative death and complications. In other cases, there is only pain at rest but no wound. Therefore, it is difficult to accurately predict the prognosis of individual patients. We examined the prognosis of CLI cases in which therapeutic footwear was made for ambulation after wounds healed. The subjects were 31 haemodialysis patients with diabetic foot wounds, which were treated with percutaneous transluminal angioplasty and minor amputation. The subjects were 22 men and 9 women. Female patients were significantly older than male patients (P = 0.046). Two-year postoperative outcomes were survival in 19 patients and death in 12 patients. Eight of twelve deceased patients had a history of coronary intervention. There were 8 deaths among 13 patients with such history, indicating a marginally significant increase in the mortality rate (P = 0.060). Re-amputation was performed in 6 of 19 patients who survived. Two years postoperatively, 41.9% of patients overall survived without re-amputation. It is important to increase the number of cases for further study to improve the well-being of CLI patients and to examine medical economics.