Complete pathologic response after laparoscopic hepatectomy following treatment with nivolumab and ipilimumab for anticancer drug-resistant MSI-high colon cancer liver metastasis consisting of poorly differentiated adenocarcinoma with squamous differentiation: A case report.

A 56-year-old man referred to our hospital for cecum cancer. Enhanced computed tomography (CT) found swollen reginal lymph nodes and liver metastasis. Magnetic Resonance Imaging (MRI) revealed a solitary lesion on liver (S2). We performed a laparoscopic ileocolic resection and liver partial resection. Tumor pathology showed that these tumors were moderate-differentiated adenocarcinoma (pT3N2bM1 Stage IVA). Genetic examination revealed MSI-high, KRAS wild type, and BRAF wild type. After surgery, two liver metastases were found in S4 and S7 as new lesion in EOB-MRI. We started chemotherapy with the FOLFOFIRI plus bevacizumab regimen, but two liver metastases were enlarged after six cycles of chemotherapy. As a second-line treatment, nivolumab and ipilimumab combination therapy was started. After three cycles of these therapy, both of these tumors shrinkage were observed. We performed laparoscopic liver resection. In specimens, there were no malignant cells. Pathological study revealed that in the initial surgery specimen, PD-L1 protein was detected in both primary and metastatic lesions, and HLA-DR, CK5/6 in liver. No recurrence was observed at 6 months after the surgery. In conclusion, we reported the case of anticancer drug-resistant MSI-high colon cancer liver metastasis was resected after treatment with immune-checkpoint inhibitors and a pathological complete response was found.

Mechanical, electronic, optical, piezoelectric and ferroic properties of strained graphene and other strained monolayers and multilayers: an update.

This is an update of a previous review (Naumiset al2017Rep. Prog. Phys.80096501). Experimental and theoretical advances for straining graphene and other metallic, insulating, ferroelectric, ferroelastic, ferromagnetic and multiferroic 2D materials were considered. We surveyed (i) methods to induce valley and sublattice polarisation (P) in graphene, (ii) time-dependent strain and its impact on graphene's electronic properties, (iii) the role of local and global strain on superconductivity and other highly correlated and/or topological phases of graphene, (iv) inducing polarisationPon hexagonal boron nitride monolayers via strain, (v) modifying the optoelectronic properties of transition metal dichalcogenide monolayers through strain, (vi) ferroic 2D materials with intrinsic elastic (σ), electric (P) and magnetic (M) polarisation under strain, as well as incipient 2D multiferroics and (vii) moiré bilayers exhibiting flat electronic bands and exotic quantum phase diagrams, and other bilayer or few-layer systems exhibiting ferroic orders tunable by rotations and shear strain. The update features the experimental realisations of a tunable two-dimensional Quantum Spin Hall effect in germanene, of elemental 2D ferroelectric bismuth, and 2D multiferroic NiI2. The document was structured for a discussion of effects taking place in monolayers first, followed by discussions concerning bilayers and few-layers, and it represents an up-to-date overview of exciting and newest developments on the fast-paced field of 2D materials.

Observation of ultrafast interfacial Meitner-Auger energy transfer in a Van der Waals heterostructure.

Atomically thin layered van der Waals heterostructures feature exotic and emergent optoelectronic properties. With growing interest in these novel quantum materials, the microscopic understanding of fundamental interfacial coupling mechanisms is of capital importance. Here, using multidimensional photoemission spectroscopy, we provide a layer- and momentum-resolved view on ultrafast interlayer electron and energy transfer in a monolayer-WSe2/graphene heterostructure. Depending on the nature of the optically prepared state, we find the different dominating transfer mechanisms: while electron injection from graphene to WSe2 is observed after photoexcitation of quasi-free hot carriers in the graphene layer, we establish an interfacial Meitner-Auger energy transfer process following the excitation of excitons in WSe2. By analysing the time-energy-momentum distributions of excited-state carriers with a rate-equation model, we distinguish these two types of interfacial dynamics and identify the ultrafast conversion of excitons in WSe2 to valence band transitions in graphene. Microscopic calculations find interfacial dipole-monopole coupling underlying the Meitner-Auger energy transfer to dominate over conventional Förster- and Dexter-type interactions, in agreement with the experimental observations. The energy transfer mechanism revealed here might enable new hot-carrier-based device concepts with van der Waals heterostructures.

A surgical resection of hepatic granuloma mimicking intrahepatic cholangiocarcinoma: a case report.

Hepatic granuloma is relatively rare, and benign tumor of the liver. Herein, we report an unusual case of hepatic granuloma mimicking intrahepatic cholangiocarcinoma (ICC). An 82-year-old woman with a history of viral hepatitis B was admitted for investigation of liver mass in the left lobe. Dynamic computed tomography revealed a mostly hypo-enhancing main tumor with a peripheral ring enhancement, and positron emission tomography demonstrated localized an abnormal accumulation of fludeoxyglucose. Considering the possibility of malignant disease, extended left hepatectomy was performed. The resected tumor was macroscopically a periductal infiltrating nodular type, 4.5 × 3.6 cm in diameter. The pathological findings showed that granuloma and coagulative necrosis were present, and diagnosis of hepatic granuloma was confirmed. Pathological studies demonstrated that periodic acid-Schiff stain, Grocott-Gomori stain and Ziehl-Neelsen stain were all negative in the lesion.

Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria.

Bacterial pathogens acquire heme from the host hemoglobin as an iron nutrient for their virulence and proliferation in blood. Concurrently, they encounter cytotoxic-free heme that escapes the heme-acquisition process. To overcome this toxicity, many gram-positive bacteria employ an ATP-binding cassette heme-dedicated efflux pump, HrtBA in the cytoplasmic membranes. Although genetic analyses have suggested that HrtBA expels heme from the bacterial membranes, the molecular mechanism of heme efflux remains elusive due to the lack of protein studies. Here, we show the biochemical properties and crystal structures of Corynebacterium diphtheriae HrtBA, alone and in complex with heme or an ATP analog, and we reveal how HrtBA extracts heme from the membrane and releases it. HrtBA consists of two cytoplasmic HrtA ATPase subunits and two transmembrane HrtB permease subunits. A heme-binding site is formed in the HrtB dimer and is laterally accessible to heme in the outer leaflet of the membrane. The heme-binding site captures heme from the membrane using a glutamate residue of either subunit as an axial ligand and sequesters the heme within the rearranged transmembrane helix bundle. By ATP-driven HrtA dimerization, the heme-binding site is squeezed to extrude the bound heme. The mechanism sheds light on the detoxification of membrane-bound heme in this bacterium.

Purely Cubic Spin Splittings with Persistent Spin Textures.

Purely cubic spin splittings in the band structure of bulk insulators have not been extensively investigated yet despite the fact that they may pave the way for novel spin-orbitronic applications and can also result in a variety of promising spin phenomena. By symmetry analysis and first-principles simulations, we report symmetry-enforced purely cubic spin splittings (SEPCSS) that can even lead to persistent spin textures. In particular, these SEPCSS can be thought to be complementary to the cubic Rashba and cubic Dresselhaus types of spin splittings. Strikingly, the presently discovered SEPCSS are expected to exist in the large family of materials crystallizing in the 6[over ¯]m2 and 6[over ¯] point groups, including the Ge_{3}Pb_{5}O_{11}, Pb_{7}Br_{2}F_{12}, and Pb_{7}Cl_{2}F_{12} compounds.

Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system.

The symbiotic nitrogen-fixing bacterium Bradyrhizobium japonicum is critical to the agro-industrial production of soybean because it enables the production of high yields of soybeans with little use of nitrogenous fertilizers. The FixL and FixJ two-component system (TCS) of this bacterium ensures that nitrogen fixation is only stimulated under conditions of low oxygen. When it is not bound to oxygen, the histidine kinase FixL undergoes autophosphorylation and transfers phosphate from adenosine triphosphate (ATP) to the response regulator FixJ, which, in turn, stimulates the expression of genes required for nitrogen fixation. We purified full-length B. japonicum FixL and FixJ proteins and defined their structures individually and in complex using small-angle x-ray scattering, crystallographic, and in silico modeling techniques. Comparison of active and inactive forms of FixL suggests that intramolecular signal transduction is driven by local changes in the sensor domain and in the coiled-coil region connecting the sensor and histidine kinase domains. We also found that FixJ exhibits conformational plasticity not only in the monomeric state but also in tetrameric complexes with FixL during phosphotransfer. This structural characterization of a complete TCS contributes both a mechanistic and evolutionary understanding to TCS signal relay, specifically in the context of the control of nitrogen fixation in root nodules.

Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses.

Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N2O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO2-) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies.

Crystal structure of bacterial haem importer complex in the inward-facing conformation.

Pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. Haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type II ATP-binding cassette (ABC) transporter. Here we present crystal structures of Burkholderia cenocepacia haem importer BhuUV complexed with the periplasmic haem-binding protein BhuT and in the absence of BhuT. The transmembrane helices of these structures show an inward-facing conformation, in which the cytoplasmic gate of the haem translocation pathway is completely open. Since this conformation is found in both the haem- and nucleotide-free form, the structure of BhuUV-T provides the post-translocation state and the missing piece in the transport cycle of the type II importer. Structural comparison with the outward-facing conformation reported for the haem importer ortholog HmuUV from Yersenia pestis gives mechanistic insights into conformational transitions and haem secretion during the haem transport cycle.

Regulatory Implications of Structural Changes in Tyr201 of the Oxygen Sensor Protein FixL.

FixL is a heme-based oxygen-sensing histidine kinase that induces the expression of nitrogen fixation genes under hypoxic conditions. Oxygen dissociation from heme iron in the sensor domain of FixL initiates protein conformational changes that are transmitted to the histidine kinase domain, activating autophosphorylation activity. Conversely, oxygen binding inhibits FixL kinase activity. It is essential to elucidate the changes that occur in the protein structure upon this oxygen dissociation for understanding of the allosteric transduction mechanism. We measured ultraviolet resonance Raman spectra of FixL and its mutants for deoxy, oxy, and carbonmonoxy forms to examine the changes in protein structure upon oxygen dissociation. The observed spectral changes indicated that Tyr201 and its neighboring residues undergo structural changes upon oxygen dissociation. Kinase assays showed that substitution of Tyr201 significantly decreased the inhibition of kinase activity upon oxygen binding. These data mean that weakening of the hydrogen bond of Tyr201 that is induced by oxygen dissociation is essential for inhibition of kinase activity. We also observed spectral changes in Tyr residues in the kinase domain upon oxygen dissociation from FixL, which is the first observation of oxygen-dependent structural changes in the kinase domain of FixL. The observed structural changes support the allosteric transduction pathway of FixL which we proposed previously [ Yano, S., Ishikawa, H., Mizuno, M., Nakamura, H., Shiro, Y., and Mizutani, Y. ( 2013 ) J. Phys. Chem. B 117 , 15786 - 15791 ].

Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae.

ChrA is a response regulator (RR) in the two-component system involved in regulating the degradation and transport of haem (Fe-porphyrin) in the pathogen Corynebacterium diphtheriae. Here, the crystal structure of full-length ChrA is described at a resolution of 1.8 Å. ChrA consists of an N-terminal regulatory domain, a long linker region and a C-terminal DNA-binding domain. A structural comparison of ChrA with other RRs revealed substantial differences in the relative orientation of the two domains and the conformation of the linker region. The structural flexibility of the linker could be an important feature in rearrangement of the domain orientation to create a dimerization interface to bind DNA during haem-sensing signal transduction.

Generation of a mouse line harboring a Bi-transgene expressing luciferase and tamoxifen-activatable creER(T2) recombinase in cartilage.

We have used an aggrecan gene enhancer to generate a transgenic murine line (Acan-CreER-Ires-Luc) expressing firefly luciferase and tamoxifen activatable Cre recombinase (Cre-ER(T2) ). The expression and efficiency of the inducible Cre recombinase activity were tested in double transgenic mice created by crossing the Acan-CreER-Ires-Luc line with a Rosa26-lacZ reporter mouse. The expression pattern of the transgene of our line was restricted to cartilage from embryonic to adult stages. ß-galactosidase staining was observed in growth plate, articular cartilage, as well as fibrocartilage of meniscus, trachea, and intervertebral discs. Similar staining was observed in a previously described Agc1 (tm(IRES-creERT2)) murine line. The presence of luciferase in our transgene allows the visualization of the transgene expression in live animals. Weekly measurements from 2 to 8 weeks of age showed a reduction in luminescence in knee joints between 2 and 4 weeks of age, but stabilization thereafter. Following the surgical induction of osteoarthritis at 12 weeks of age, the level of luminescence remained the same in the knee joints for 8 weeks. This Acan-CreER-Ires-Luc murine line allows indirect monitoring of the transcriptional activity of the Acan gene via expression of luciferase, while the inducible Cre recombinase activity facilitates studies involving gain or loss of gene expression in cartilage.

Ultraviolet resonance Raman observations of the structural dynamics of rhizobial oxygen sensor FixL on ligand recognition.

FixL is a heme-based oxygen-sensing histidine kinase that induces expression of nitrogen fixation genes under hypoxic conditions. Oxygen binding to heme iron in the sensor domain of FixL initiates protein conformational changes that are transmitted to the histidine kinase domain, inactivating autophosphorylation activity. Although FixL also can bind other diatomic ligands such as CO, the CO-bound FixL represents incomplete inhibition of kinase activity. Ultraviolet resonance Raman (UVRR) spectra revealed that oxygen binding to the truncated sensor domain of FixL markedly decreased the intensity of the Y8a band arising from Fα-10 Tyr. In contrast, no appreciable change in intensity of the Y8a band occurred after CO binding, and time-resolved UVRR spectra of the sensor domain of FixL upon O2 dissociation indicated that structural changes near Fα-10 Tyr occurred at ∼0.1 µs. These results suggest that O2 dissociation from FixL changes the protein conformation near the Fα-10 Tyr residue within a microsecond. The conformational changes of FixL upon O2 dissociation and the underlying sensing mechanism also are discussed.

Structure of PAS-linked histidine kinase and the response regulator complex.

We determined the structure of the complex of the sensory histidine kinase (HK) and its cognate response regulator (RR) in the two-component signal transduction system of Thermotoga maritima. This was accomplished by fitting the high-resolution structures of the isolated HK domains and the RR onto the electron density map (3.8 A resolution) of the HK/RR complex crystal. Based on the structural information, we evaluated the roles of both interdomain and intermolecular interactions in the signal transduction of the cytosolic PAS-linked HK and RR system, in particular the O(2)-sensor FixL/FixJ system. The PAS-sensor domain of HK interacts with the catalytic domain of the same polypeptide chain by creating an interdomain beta sheet. The interaction site between HK and RR, which was confirmed by NMR, is suitable for the intermolecular transfer reaction of the phosphoryl group, indicating that the observed interaction is important for the phosphatase activity of HK that dephosphorylates phospho-RR.

Heme-dependent autophosphorylation of a heme sensor kinase, ChrS, from Corynebacterium diphtheriae reconstituted in proteoliposomes.

Corynebacterium diphteriae employs the response regulator, ChrA, and the sensor kinase, ChrS, of a two-component signal transduction system to utilize host heme iron. Although ChrS is predicted to encode a heme sensor, the sensing mechanism remains to be characterized. In this report, ChrS expressed in Eshcherichia coli membranes was solubilized and purified using decylmaltoside. ChrS protein incorporated into proteoliposomes catalyzed heme-dependent autophosphorylation by ATP. Other metalloporphyrins and iron did not stimulate kinase activity. The UV-Vis spectrum of hemin in the ChrS-proteoliposomes indicated that heme directly interacts with ChrS. This is the first functional reconstitution of a bacterial heme-sensing protein.

Separation of phosphoprotein isotypes having the same number of phosphate groups using phosphate-affinity SDS-PAGE.

Herein, we demonstrate the separation of phosphoprotein isotypes having the same number of phosphate groups using phosphate-affinity SDS-PAGE. The phosphate-affinity site is a polyacrylamide-bound Phos-tag that enables the mobility shift detection of phosphoproteins from their nonphosphorylated counterparts. As the first practical example of the separation, we characterized the monophosphorylated Tau isotypes by each of three tyrosine kinases, c-Abl, MET, and Fyn. Each monophosphoisotype phosphorylated at the Tyr-394, Tyr-197, or Tyr-18 was detected as three distinct migration bands. As a further application, we extended this technique to the mobility shift analysis of His and Asp phosphoisotypes in the Sinorhizobium meliloti FixL/FixJ two-component system. FixL is autophosphorylated at the His-285 with ATP, and the phosphate group is transferred to the Asp-54 of FixJ and subsequently removed by the FixL phosphatase activity. Using this method, we first performed simultaneous detection of the phosphorylated and nonphosphorylated isotypes of FixL and FixJ generated in their phosphotransfer reaction in vitro. As a result, a monophosphoisotype of FixL containing the phosphorylated His residue was confirmed. As for FixJ, on the other hand, two monophosphoisotypes were detected as two distinct migration bands. One is a well-known isotype phosphorylated at the Asp-54. The other is a novel isotype phosphorylated at the His-84.

FTIR study on the hydrogen bond structure of a key tyrosine residue in the flavin-binding blue light sensor TePixD from Thermosynechococcus elongatus.

The BLUF (sensor of blue light using FAD) domain is a blue light receptor possessing a flavin molecule as an active cofactor. A conserved Tyr residue located adjacent to flavin has been proposed to be a key amino acid in the mechanism of the photoreaction of the BLUF domain. We have studied the structure of this key Tyr residue and the relevance to the photoreaction in the BLUF protein of the cyanobacterium Thermosynechococcus elongatus, TePixD, by means of Fourier transform infrared (FTIR) difference spectroscopy and density functional theory (DFT) calculations. Light-induced FTIR difference spectra of unlabeled and [4-13C]Tyr-labeled TePixD in H2O and D2O revealed that the nuCO/deltaCOH vibrations of a photosensitive Tyr side chain are located at 1265/1242 cm-1 in the dark-adapted state and at 1273/1235 cm-1 in the light-induced signaling state. These signals were assigned to the vibrations of Tyr8 near flavin from the absence of the effect of [4-13C]Tyr labeling in the Tyr8Phe mutant. DFT calculations of H-bonded complexes of p-cresol with amides as models of the Tyr8-Gln50 interactions showed that Tyr8 acts as a H-bond donor to the Gln50 in both of the dark and light states. Further DFT analysis suggested that this H-bond is strengthened upon photoconversion to the light state accompanied with a change in the H-bond angle. The change in the H-bond structure of Tyr8 is coupled to the flavin photoreaction probably through the Tyr8-Gln50-flavin H-bond network, suggesting a significant role of Tyr8 in the photoreaction mechanism of TePixD.

The signaling pathway in histidine kinase and the response regulator complex revealed by X-ray crystallography and solution scattering.

The structure of a histidine kinase (ThkA) complexed with a response regulator (TrrA) in the two-component regulatory system from hyperthermophile Thermotoga maritima was determined by a combination of X-ray crystallography at a resolution of 4.2 A and small-angle X-ray scattering (SAXS). The boundary of the three component domains (PAS-sensor, dimerization and catalytic domains) of ThkA and the bound TrrA molecule were unambiguously assigned in the electron density map at 4.2 A resolution. ThkA forms a dimer with crystallographic 2-fold symmetry and two monomeric TrrAs bind to the ThkA dimer. SAXS experiments also confirmed this association state in solution and specific binding between ThkA and TrrA (Kd=8.2x10(-11) M(-2)). The association interface between ThkA and TrrA contains the phosphotransfer His residue in the ThkA, indicative of an efficient receipt of the phosphoryl group. One Per-Arnt-Sim (PAS) domain does not interact with the other PAS domain, but with the catalytic domain of the same polypeptide chain and with one TrrA molecule. Observed inter-domain and inter-molecular interactions reveal a definite pathway of signal transduction in the kinase/regulator complex. In addition, we propose a responsible role of TrrA for the feedback regulation of sensing and/or kinase activities of ThkA.

Role of a putative third subunit YhcB on the assembly and function of cytochrome bd-type ubiquinol oxidase from Escherichia coli.

Recent proteome studies on the Escherichia coli membrane proteins suggested that YhcB is a putative third subunit of cytochrome bd-type ubiquinol oxidase (CydAB) (F. Stenberg, P. Chovanec, S.L. Maslen, C.V. Robinson, L.L. Ilag, G. von Heijne, D.O. Daley, Protein complexes of the Escherichia coli cell envelope. J. Biol. Chem. 280 (2005) 34409-34419). We isolated and characterized cytochrome bd from the DeltayhcB strain, and found that the formation of the CydAB heterodimer, the spectroscopic properties of bound hemes, and kinetic parameters for the ubiquinol-1 oxidation were identical to those of cytochrome bd from the wild-type strain. Anion-exchange chromatography and SDS-polyacrylamide gel electrophoresis showed that YhcB was not associated with the cytochrome bd complex. We concluded that YhcB is dispensable for the assembly and function of cytochrome bd. YhcB, which is distributed only in gamma-proteobacteria, may be a part of another membrane protein complex or may form a homo multimeric complex.