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The development of near‐infrared (NIR) fluorophores that have both excellent chemical stability and photostability, as well as efficient cell permeability, is highly demanded. In this study, we present phospha‐rhodamine (POR) dyes which display significantly improved performance for protein labeling. This is achieved by incorporating a 2‐carboxy‐3‐benzothiophenyl group at the 9‐position of the xanthene scaffold. The resulting cis and trans isomers were successfully isolated and structurally characterized using X‐ray diffraction. The HaloTag ligand conjugates of the two isomers exhibited different staining abilities in live cells. While the cis isomer showed non‐specific accumulation on the organelle membranes, the trans isomer selectively labeled the HaloTag‐fused proteins, enabling the long‐term imaging of cell division and the 5‐color imaging of cell organelles. Molecular dynamics simulations of the HaloTag ligand conjugates within the lipid membrane suggested that the cis isomer is more prone to forming oligomers in the membrane. In contrast, the oligomerization of the trans isomer is effectively suppressed by its interaction with the lipid molecules. By taking advantage of the superior labeling performance of the trans isomer and its NIR‐emissive properties, multi‐color time‐lapse super‐resolution 3D imaging, namely super‐resolution 5D‐imaging, of the interconnected network between the endoplasmic reticulum and microtubules was achieved in living cells. [ABSTRACT FROM AUTHOR]

An 81‐year‐old man initially underwent right hepatic lobectomy for liver cancer and was pathologically diagnosed with combined hepatocellular and cholangiocarcinoma (CHC). At 13 months after resection, multiple lymph node metastases were observed. We started atezolizumab plus bevacizumab (Atez/Bev), achieving a 7.5‐month progression‐free survival. Atez/Bev might exhibit efficacy for CHC patients. [ABSTRACT FROM AUTHOR]

The article titled "Inside Cover: Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging" presents a new photostable near-infrared labeling agent developed by Masayasu Taki, Yasushi Okada, Florence Tama, Shigehiro Yamaguchi, and their team. The compounds, which are stereoisomers based on phosphorus-bridged rhodamine, have different staining abilities in live cells. The trans-isomer can permeate organelle membranes and label target proteins, while the cis-isomer accumulates nonspecifically on lipid bilayers. The authors of the article are Qian Wu, Masayasu Taki, Yoshiki Tanaka, Manish Kesherwani, Quan Manh Phung, Sawako Enoki, Yasushi Okada, Florence Tama, and Shigehiro Yamaguchi. [Extracted from the article]

The article titled "Innentitelbild: Stereochemistry-Dependent Labeling of Organelles with a Near-Infrared-Emissive Phosphorus-Bridged Rhodamine Dye in Live-Cell Imaging" presents a new photostable near-infrared (NIR) labeling agent developed by Masayasu Taki, Yasushi Okada, Florence Tama, Shigehiro Yamaguchi, and their colleagues. The compounds, which are stereoisomers based on phosphorus-bridged rhodamine, have different staining abilities in live cells. The trans-isomer can permeate organelle membranes and label target proteins, while the cis-isomer accumulates nonspecifically on lipid bilayers. The authors of the article are Qian Wu, Masayasu Taki, Yoshiki Tanaka, Manish Kesherwani, Quan Manh Phung, Sawako Enoki, Yasushi Okada, Florence Tama, and Shigehiro Yamaguchi. [Extracted from the article]

Background and Aim: Gut microbiota composition is associated with the pathogenesis of non‐alcoholic fatty liver disease. However, the association between gut microbiota composition and non‐alcoholic fatty liver disease in non‐obese patients remains unclear. We compared clinical parameters and gut microbiota profiles of healthy controls and non‐obese and obese patients with non‐alcoholic fatty liver disease. Methods: We examined the clinical parameters and gut microbiota profiles by 16S rRNA sequences and short‐chain fatty acid levels in fecal samples from 51 non‐obese patients with non‐alcoholic fatty liver disease (body mass index <25 kg/m2) and 51 obese patients with non‐alcoholic fatty liver disease (body mass index ≥30 kg/m2) who underwent pathological examination and 87 controls at five hospitals in Japan. Results: Although no significant differences between the non‐obese and other groups were observed in alpha diversity, a significant difference was found in beta diversity. We observed a significant decrease in serum alanine aminotransferase levels, Eubacterium population, and butyric acid levels in non‐obese patients with non‐alcoholic fatty liver disease compared with those in obese patients with non‐alcoholic fatty liver disease. A significant negative correlation was found between the stage of hepatic fibrosis and Eubacterium abundance in non‐obese patients with non‐alcoholic fatty liver disease. Conclusions: The decrease in the abundance of Eubacterium that produces butyric acid may play an important role in the development of non‐alcoholic fatty liver disease in non‐obese individuals. This study was registered at the University Hospital Medical Information Network clinical trial registration system (UMIN000020917). [ABSTRACT FROM AUTHOR]

A transporter of the multidrug and toxic compound extrusion (MATE) family, Nicotiana tabacum MATE2 (NtMATE2), is located in the vacuole membrane of the tobacco plant root and is involved in the transportation of nicotine, a secondary or specialized metabolic compound in Solanaceae. Here, we report the crystal structures of NtMATE2 in its outward‐facing forms. The overall structure has a bilobate V‐shape with pseudo‐symmetrical assembly of the N‐ and C‐lobes. In one crystal structure, the C‐lobe cavity of NtMATE2 interacts with an unidentified molecule that may partially mimic a substrate. In addition, NtMATE2‐specific conformational transitions imply that an unprecedented movement of the transmembrane α‐helix 7 is related to the release of the substrate into the vacuolar lumen. [ABSTRACT FROM AUTHOR]

Diarrhea is largely caused by dysbiosis accompanying the hyperproliferation of Escherichia coli (E. coli). While current treatments can resolve the symptoms, they cannot suppress the proliferation of pathogenic bacteria in the intestine. Probiotics have numerous beneficial effects on host health, including restoring the balance of the intestinal microbiota. This study investigated the effect of the probiotic Bifidobacterium bifidum G9‐1 (BBG9‐1), which is active in intestinal dysbiosis, in the incidence of diarrhea, in the composition of the intestinal microbiota, and in the intestinal tissue of a rat model of phytohemagglutinin (PHA)‐induced diarrhea. The rats were treated with PHA, with and without BBG9‐1, and the microbiota composition throughout the intestine and stool was examined using high‐throughput 16S rRNA sequencing. In line with previous reports, PHA administration caused diarrhea as well as dysbiosis due to E. coli hyperproliferation. Histological findings indicated that the jejunal villus length was shortened. Rats that received BBG9‐1 showed clear improvements in dysbiosis, diarrhea symptoms, and jejunal villus length. Principal coordinates analysis demonstrated the microbiota profile to be more similar between the BBG9‐1 and normal groups than between the PHA and normal groups. These results indicated that BBG9‐1 suppresses the hyperproliferation of E. coli and restores the jejunal villus length, thereby improving dysbiosis, and in turn, alleviating the symptoms of diarrhea. [ABSTRACT FROM AUTHOR]

We developed a new 4.1"LCD for optimal 3D‐Heads Up Displays which enhance advanced safety driving support. This LCD requires high transmittance and contrast We achieved these optical properties by utilizing high aperture ratio pixels, optimized liquid crystal (LC) material and optical design We developed this new 3D‐HUD using a 4.1" display and we proved this LCD is optimal for AR‐HUD units. [ABSTRACT FROM AUTHOR]

Purpose: To compare the self‐sealing features and dimensional stability between the femtosecond laser (FL) and manual knife corneal incision. Methods: For the clinical study, 29 consecutive eyes from 29 patients and 28 eyes from 28 patients who underwent cataract surgery with FL corneal incision and manual knife incision, respectively, were enrolled. Immediately after cataract surgery, the self‐sealing features of the corneal incisions were evaluated. Scanning electron microscopy (SEM) images were obtained. For the experimental study, clear corneal incisions with a knife or FL with different energy settings (3, 6 and 9 μJ) were created in fresh porcine eyes, followed by a stress test. The incision width was measured before and after the stress test. Results: In the clinical study, the knife group had a higher self‐sealing score (0.60 ± 0.49 points) than the FL group (0.17 ± 0.38 points). In the experimental study, the deformation rate in the knife incision (5.04 ± 1.93) was significantly lower than that in the FL with any energy. The deformation rate in the 9 μJ (12.98 ± 2.76) was significantly higher than in the 3 μJ (8.54 ± 2.38) and 6 μJ (8.82 ± 2.85) FL energies. Scanning electron microscopy (SEM) images revealed that the corneal stromal surface of the knife incision was smoother than that of the FL. Higher energy FL showed more irregular surfaces. Conclusion: Higher FL energy tended to widen a clear corneal incision when mechanical stress was applied. The histological differences at the inner tunnel surface may cause differences in wound stability of the corneal incision. [ABSTRACT FROM AUTHOR]

We achieved high transmittance and high contrast with keeping high response speed by using high aperture ratio technology and high efficiency liquid crystal. Transmittance is improved by 149% from initial mass production by using this technology, We are available this new liquid crystal technology for 3D‐HUD with parallax barrier. [ABSTRACT FROM AUTHOR]

BepA (formerly YfgC) is an Escherichia coli periplasmic protein consisting of an N-terminal protease domain and a C-terminal tetratricopeptide repeat (TPR) domain. We have previously shown that BepA is a dual functional protein with chaperone-like and proteolytic activities involved in membrane assembly and proteolytic quality control of LptD, a major component of the outer membrane lipopolysaccharide translocon. Intriguingly, BepA can associate with the BAM complex: the β-barrel assembly machinery (BAM) driving integration of β-barrel proteins into the outer membrane. However, the molecular mechanism of BepA function and its association with the BAM complex remains unclear. Here, we determined the crystal structure of the BepA TPR domain, which revealed the presence of two subdomains formed by four TPR motifs. Systematic site-directed in vivo photo-cross-linking was used to map the protein-protein interactions mediated by the BepA TPR domain, showing that this domain interacts both with a substrate and with the BAM complex. Mutational analysis indicated that these interactions are important for the BepA functions. These results suggest that the TPR domain plays critical roles in BepA functions through interactions both with substrates and with the BAM complex. Our findings provide insights into the mechanism of biogenesis and quality control of the outer membrane. [ABSTRACT FROM AUTHOR]

Bifidobacterium, a major component of the intestinal microbiota, has been clinically used for the treatment of diarrhoea and constipation. 5-Fluorouracil (5-FU), widely used for cancer chemotherapy, is known to frequently induce intestinal mucositis accompanied by severe diarrhoea. The present study examined the effect of Bifidobacterium bifidum G9-1 (BBG9-1) on 5-FU-induced intestinal mucositis in mice. Intestinal mucositis was induced by repeated administration of 5-FU for 6 days. BBG9-1 was administered orally once daily for 9 days, beginning 3 days before the onset of 5-FU treatment. Repeated administration of 5-FU caused severe intestinal mucositis, characterised by shortening of villi and destruction of crypts, accompanied by increases in intestinal myeloperoxidase activity and inflammatory cytokine expression, body weight loss, and diarrhoea on day 6. Daily administration of BBG9-1 significantly reduced the severity of intestinal mucositis and inflammatory responses and tended to attenuate clinical symptoms. In contrast, BBG9-1 failed to prevent apoptosis induction on day 1 after the first 5-FU administration. The structure of the intestinal microbiota, as analysed by weighted UniFrac distance, was largely altered by 5-FU treatment, but this change was mitigated by daily administration of BBG9-1. Moreover, 5-FU treatment decreased the abundance of Firmicutes and increased the abundance of Bacteroidetes, but these responses were also significantly inhibited by daily administration of BBG9-1. These results suggest that BBG9-1 has an ameliorative effect against 5-FU-induced intestinal mucositis through the attenuation of inflammatory responses via improve dysbiosis. BBG9-1 could be useful for the prevention of intestinal mucositis during cancer chemotherapy. [ABSTRACT FROM AUTHOR]

An experimental system for serial femtosecond crystallography using an X-ray free-electron laser (XFEL) has been developed. It basically consists of a sample chamber, fluid injectors and a two-dimensional detector. The chamber and the injectors are operated under helium atmosphere at 1 atm. The ambient pressure operation facilitates applications to fluid samples. Three kinds of injectors are employed to feed randomly oriented crystals in aqueous solution or highly viscous fluid. Experiments on lysozyme crystals were performed by using the 10 keV XFEL of the SPring-8 Angstrom Compact free-electron LAser (SACLA). The structure of model protein lysozyme from 1 µm crystals at a resolution of 2.4 Å was obtained. [ABSTRACT FROM AUTHOR]

ABSTRACT Molecular studies have led to postulation of a relationship between gut microbiota and certain diseases. However, because studies of hitherto uncultured species in vivo are essential for characterizing the biology and pathogenic properties of gut bacteria, techniques for culturing and isolating such bacteria must be developed. Here, a technique is described that partially overcomes the obstacles that prevent detection of interbacterial communication in vitro and are thus responsible for the failure to culture certain bacterial species. For this purpose, a ring with a membrane filter at the bottom was designed and a relatively simple nutrient medium was used instead of conventional media. Gut bacteria were cocultivated in soft agar separated by the membrane filter to simulate interbacterial communication in vitro. Use of this soft agar coculture technique led to the successful isolation of hitherto uncultured bacteria and the demonstration of multistage interbacterial communication among gut bacteria in vitro. Cultivation and isolation of single colonies of bacteria that require other bacteria for growth will enhance efforts to better understand the physiological and pathogenic roles of gut microbiota. [ABSTRACT FROM AUTHOR]

YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4 Å resolution and belonged to space group P21, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9 Å, β = 100.3°. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal. [ABSTRACT FROM AUTHOR]

The MgtE family of Mg2+ transporters is ubiquitously distributed in all phylogenetic domains. Recent crystal structures of the full-length MgtE and of its cytosolic domain in the presence and absence of Mg2+ suggested a Mg2+-homeostasis mechanism, in which the MgtE cytosolic domain acts as a ‘Mg2+ sensor’ to regulate the gating of the ion-conducting pore in response to the intracellular Mg2+ concentration. However, complementary functional analyses to confirm the proposed model have been lacking. Moreover, the limited resolution of the full-length structure precluded an unambiguous characterization of these regulatory divalent-cation-binding sites. Here, we showed that MgtE is a highly Mg2+-selective channel gated by Mg2+ and elucidated the Mg2+-dependent gating mechanism of MgtE, using X-ray crystallographic, genetic, biochemical, and electrophysiological analyses. These structural and functional results have clarified the control of Mg2+ homeostasis through cooperative Mg2+ binding to the MgtE cytosolic domain. [ABSTRACT FROM AUTHOR]

The MgtE family of Mg2+ transporters is ubiquitously conserved in all domains of life. The cytosolic domains of the MgtE Mg2+ transporters include a cystathionine-β-synthase (CBS) domain which is known to play a regulatory function in transporter proteins. The cytosolic domain of MgtE from Thermus thermophilus was overexpressed, purified and crystallized in the presence and absence of Mg2+. The crystals formed in the presence of Mg2+ diffracted X-rays to 2.3 Å resolution using synchrotron radiation, belong to space group P6522 with unit-cell parameters a = b = 57.7, c = 317.6 Å and are expected to contain one molecule in the asymmetric unit. The crystals formed in the absence of Mg2+ diffracted X-rays to 3.5 Å resolution using synchrotron radiation, belong to space group P212121 with unit-cell parameters a = 77.0, b = 100.3, c = 100.3 Å and are expected to contain two molecules in the asymmetric unit. [ABSTRACT FROM AUTHOR]

A 73-year-old woman with idiopathic pulmonary fibrosis (IPF) had an elevated serum CA19-9 level, but not KL-6. Her condition worsened and she subsequently died and this was associated with a rise in the serum KL-6 level. At autopsy, the lung showed a honeycomb appearance macroscopically and, microscopically, hyaline membrane formation was seen. Immunohistochemical staining revealed partial colocalization of KL-6 and CA19-9 to dilated bronchiolar cells. These features suggest that the mechanisms that cause the synthesis and release of CA19-9 and KL-6 from damaged lung tissue in IPF are likely to differ from those in diffuse alveolar damage. In addition, serum KL-6 levels may reflect the severity of disease more sensitively than CA19-9 levels. [ABSTRACT FROM AUTHOR]

Sorbitol was effectively converted to isosorbide by treatment with [TMPA][NTf2] in the presence of catalytic amounts of TsOH under microwave heating at 180 °C. The reaction completed within 10 min and isosorbide was isolated to about 60 %. Ionic liquids were readily recovered by an extraction treatment and reused several times. [ABSTRACT FROM AUTHOR]

The cation diffusion facilitator (CDF) family proteins are ubiquitously distributed in the three domains of life and transport metals such as zinc and various heavy metals. Prokaryotic CDF proteins consists of an N-terminal putative six-transmembrane domain followed by a C-terminal cytosolic domain. The cytosolic domain of the CDF-family protein from Thermotoga maritima has been overexpressed, purified and crystallized. The selenomethionine-substituted crystals diffracted X-rays to 2.5 Å resolution using synchrotron radiation, belonged to space group R32, with unit-cell parameters a = b = 97.7, c = 83.4 Å, and are expected to contain one molecule in each asymmetric unit. [ABSTRACT FROM AUTHOR]

The MgtE family of Mg2+ transporters are ubiquitously conserved in all three domains. The genes encoding full-length MgtE from seven different species were cloned. Three of the seven MgtE transporters were overexpressed and purified for use in crystallization trials. Only Thermus thermophilus MgtE was successfully crystallized using the sitting-drop vapour-diffusion method. Selenomethionine-substituted (SeMet) crystals were obtained by cross-microseeding using the native microcrystals. The SeMet crystals diffracted X-rays to 3.5 Å resolution using synchrotron radiation and belong to space group C2221, with unit-cell parameters a = 118.3, b = 134.9, c = 366.2 Å. Structure determination is in progress. [ABSTRACT FROM AUTHOR]

The cytoplasm is the main place for protein translation from where nascent proteins are transported to their working areas, including the inside, outside, and membrane of the cell. The majority of newly synthesized membrane proteins is co‐translationally inserted into the membrane by the evolutionary conserved Sec translocon. In this issue of EMBO Reports, Kater et al [1] use single‐particle cryo‐electron microscopy to visualize a high‐resolution structure of the E. coli SecYEG translocon:ribosome‐nascent chain complex in a lipid environment constituted by nanodiscs. This snapshot represents an early intermediate state in membrane protein insertion and provides important information for understanding the molecular mechanism of membrane protein biogenesis. [ABSTRACT FROM AUTHOR]

The MgtE family of Mg(2+) transporters is ubiquitously conserved in all domains of life. The cytosolic domains of the MgtE Mg(2+) transporters include a cystathionine-beta-synthase (CBS) domain which is known to play a regulatory function in transporter proteins. The cytosolic domain of MgtE from Thermus thermophilus was overexpressed, purified and crystallized in the presence and absence of Mg(2+). The crystals formed in the presence of Mg(2+) diffracted X-rays to 2.3 A resolution using synchrotron radiation, belong to space group P6(5)22 with unit-cell parameters a = b = 57.7, c = 317.6 A and are expected to contain one molecule in the asymmetric unit. The crystals formed in the absence of Mg(2+) diffracted X-rays to 3.5 A resolution using synchrotron radiation, belong to space group P2(1)2(1)2(1) with unit-cell parameters a = 77.0, b = 100.3, c = 100.3 A and are expected to contain two molecules in the asymmetric unit.

The MgtE family of Mg(2+) transporters are ubiquitously conserved in all three domains. The genes encoding full-length MgtE from seven different species were cloned. Three of the seven MgtE transporters were overexpressed and purified for use in crystallization trials. Only Thermus thermophilus MgtE was successfully crystallized using the sitting-drop vapour-diffusion method. Selenomethionine-substituted (SeMet) crystals were obtained by cross-microseeding using the native microcrystals. The SeMet crystals diffracted X-rays to 3.5 A resolution using synchrotron radiation and belong to space group C222(1), with unit-cell parameters a = 118.3, b = 134.9, c = 366.2 A. Structure determination is in progress.