Protocol to identify the ligand binding site of Mincle using NMR spectroscopy

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor that can be targeted for inducing potent adjuvant effects. Mincle can recognize trehalose dimycolate and related glycolipids. Here, we present a protocol to identify the ligand binding mode of Mincle. We describe steps for preparing labeled Mincle ectodomain, data acquisition, and analysis of nuclear magnetic resonance experiments using non-detergent sulfobetaine-195. This protocol can be applied to other protein-ligand interactions that have aggregation problems for complex formation. For complete details on the use and execution of this protocol, please refer to Furukawa et al.1.

Biochemical and biophysical characterization of the RAS family small GTPase protein DiRAS3

DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.

Interactive effects of two rodent species on the seed dispersal of Japanese walnut

The effects of seed dispersers on plant fitness (seed dispersal effectiveness, SDE) have been evaluated based on the number (quantity) and recruitment probability (quality) of dispersed seeds. Although seeds of most zoochorous species are dispersed by two or more animal species, which may interact with each other, SDE has often been studied assuming a one-plant and one-animal species system. We compared the SDE of Japanese walnut (Juglans ailanthifolia) between squirrel-only and squirrel-mouse sites in natural forests of Hokkaido, Japan, and found that the SDE from the red squirrel (Sciurus vulgaris), considered a primary seed disperser, was altered by an alternative seed disperser species, the Japanese wood mouse (Apodemus speciosus). Seed removal rates at the squirrel-mouse site were significantly higher than those at the squirrel-only site, and both dispersed seeds and seedlings were less aggregated, with a strongly repulsive relationship with adult conspecific trees at the squirrel-mouse site. Seedlings established themselves at a location with fewer medium-sized trees (< 10 cm DBH) at the squirrel-mouse site. These results suggest that the interactive effect of the rodent species affects the SDE of Japanese walnut.

Structural basis for plastic glycolipid recognition of the C-type lectin Mincle

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor for cord factor, trehalose dimycolate (TDM), which serves as a potent component of adjuvants. The recognition of glycolipids by Mincle, especially their lipid parts, is poorly understood. Here, we performed nuclear magnetic resonance analysis, revealing that titration of trehalose harboring a linear short acyl chain showed a chemical shift perturbation of hydrophobic residues next to the Ca-binding site. Notably, there were split signals for Tyr201 upon complex formation, indicating two binding modes for the acyl chain. In addition, most Mincle residues close to the Ca-binding site showed no observable signals, suggesting their mobility on an ∼ ms scale even after complex formation. Mutagenesis study supported two putative lipid-binding modes for branched acyl-chain TDM binding. These results provide novel insights into the plastic-binding modes of Mincle toward a wide range of glycol- and glycerol-lipids, important for rational adjuvant development.

A Case Report of Radiotherapy for Skull Lesions of Langerhans Cell Histiocytosis With Dural Invasion

Background

Langerhans cell histiocytosis (LCH) is a rare disease, especially in adults. It is often associated with non-fatal bone and skin lesions and has relatively good radiosensitivity. In contrast, brain and lymph node metastases from LCH lesions are considered to be less sensitive to radiotherapy.

Case Report

At our institution, 30 Gy radiotherapy was used to treat bone lesions with dural invasion in a patient with adult-onset LCH. The patient was treated with chemotherapy and radiotherapy for 21 years since the initial diagnosis. After radiotherapy, the tumor shrank rapidly, and a complete response was achieved 1 year after treatment. The patient survived without local recurrence.

Conclusion

Here, we report the details of this case, along with a review of the literature. We suggest that even with invasion of the tissues around the bone lesions in LCH, local recurrence can be prevented by middle radiation doses.

Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice

Neuroligin 3 (NLGN3) and neurexins (NRXNs) constitute a canonical transsynaptic cell-adhesion pair, which has been implicated in autism. In autism spectrum disorder (ASD) development of sociality can be impaired. However, the molecular mechanism underlying NLGN3-mediated social development is unclear. Here, we identify non-canonical interactions between NLGN3 and protein tyrosine phosphatase δ (PTPδ) splice variants, competing with NRXN binding. NLGN3-PTPδ complex structure revealed a splicing-dependent interaction mode and competition mechanism between PTPδ and NRXNs. Mice carrying a NLGN3 mutation that selectively impairs NLGN3-NRXN interaction show increased sociability, whereas mice where the NLGN3-PTPδ interaction is impaired exhibit impaired social behavior and enhanced motor learning, with imbalance in excitatory/inhibitory synaptic protein expressions, as reported in the Nlgn3 R451C autism model. At neuronal level, the autism-related Nlgn3 R451C mutation causes selective impairment in the non-canonical pathway. Our findings suggest that canonical and non-canonical NLGN3 pathways compete and regulate the development of sociality.

Embryonic staging of bats with special reference to Vespertilio sinensis and its cochlear development

BACKGROUND

How bats deviate heterochronically from other mammals remains largely unresolved, reflecting the lack of a quantitative staging framework allowing comparison among species. The standard event system (SES) is an embryonic staging system allowing quantitative detection of interspecific developmental variations. Here, the first SES-based staging system for bats, using Asian parti-colored bat (Vespertilio sinensis) is introduced. General aspects of normal embryonic development and the three-dimensional development of the bat cochlea were described for the first time. Recoding the embryonic staging tables of 18 previously reported bat species and Mus musculus into the SES system, quantitative developmental comparisons were performed.

RESULTS

It was found that limb bud development of V. sinensis is relatively late among 19 bat species and late limb development is a shared trait of vespertilionid bats. The inner ear cochlear canal forms before the semicircular canal in V. sinensis while the cochlear canal forms after the semicircular canal in non-volant mammals.

CONCLUSIONS

The present approach using the SES system provides a powerful framework to detect the peculiarities of bat development. Incorporating the timing of gene expression patterns into the SES framework will further contribute to the understanding of the evolution of specialized features in bats.

C-terminal aromatic residue of Plasmodium ferredoxin important for the interaction with ferredoxin: NADP(H) oxidoreductase: possible involvement for artemisinin resistance of human malaria parasites

The malaria parasite (Plasmodium sp.) contains a plastid-derived organelle called the apicoplast, which is essential for the growth of the parasite. In this organelle, a redox system comprising plant-type ferredoxin (Fd) and Fd: NADP(H) oxidoreductase (FNR) supplies reducing power for the crucial metabolic pathways. Electron transfer between Plasmodium falciparum Fd (PfFd) and FNR (PfFNR) is performed with higher affinity and specificity than those of plant Fd and FNR. We investigated the structural basis for such superior protein–protein interaction by focussing on the Plasumodium-specific regions of PfFd. Significant contribution of the C-terminal region of PfFd for the electron transfer with PfFNR was revealed by exchanging the C-terminal three residues between plant Fd and PfFd. Further site-directed mutagenesis of the PfFd C-terminal residues indicated that the presence of aromatic residue at Positions 96 and 97 contributes to the lower Km for PfFNR. Physical binding analyses using fluorescence and calorimetric measurements supported the results. A mutation from Asp to Tyr at position 97 of PfFd was recently reported to be strongly associated with P. falciparum resistance to artemisinin, the front line anti-malarial drug. Thus, the enhanced interaction of PfFd D97Y protein with PfFNR could be involved in artemisinin resistance of human malaria parasites.

Estimation of multiple male mating frequency using paternity skew: An example from a grey-sided vole (Myodes rufocanus) population

Multiple male mating (MMM) causes sperm competition, which may play an important role in the evolution of reproductive traits. The frequency of multiple paternity (MP), where multiple males sire offspring within a single litter, has been used as an index of MMM frequency. However, MP frequency is necessarily lower than MMM frequency. The magnitude of the difference between MMM and MP frequency depends on litter size (LS) and fertilization probability skew (FPS), and this difference may be meaningfully large in animals with small LSs. In this study, we propose a method to estimate MMM frequency using an individual-based model with three variables (MP frequency, LS and FPS). We incorporated observed paternity skew data to infer a possible range of FPS that cannot be measured in free-living populations and tested the validity of our method using a data set from a grey-sided vole (Myodes rufocanus) population and from hypothetical populations. MP was found in 50 out of 215 litters (23.3%) in the grey-sided vole population, while MMM frequency was estimated in 67 of 215 litters (31.2%), with a certainty range of 59-88 (27.4%-40.9%). The point estimation of MMM frequency was realized, and the certainty range was limited within the practical range. The use of observed paternity skew was very effective at narrowing the certainty range of the estimate. Our method could contribute to a deeper understanding of the ecology of MMM in free-living populations.

NADP(H) allosterically regulates the interaction between ferredoxin and ferredoxin-NADP+ reductase

Ferredoxin‐NADP⁺ reductase (FNR) in plants receives electrons from ferredoxin (Fd) at the end of the photosynthetic electron transfer chain and converts NADP⁺ to NADPH. The interaction between Fd and FNR in plants was previously shown to be attenuated by NADP(H). Here, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three‐dimensional structure of this complex is available. NADPH, NADP⁺, and 2′5′‐ADP differentially affected the interaction, as revealed through kinetic and physical binding analyses. Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction to that for NADPH. We propose that the binding of NADP(H) causes a conformational change of FNR which is transferred to the Fd‐binding region through different domains of FNR, resulting in allosteric changes in the affinity for Fd.

The interaction between ferredoxin (Fd) and Fd‐NADP⁺ reductase (FNR) in plants is attenuated by NADP(H). Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction. We propose that the binding of NADP(H) leads to conformational changes of FNR, resulting in allosteric changes in the affinity for Fd.

Development of CVD Silica Membranes Having High Hydrogen Permeance and Steam Durability and a Membrane Reactor for a Water Gas Shift Reaction

Water gas shift reaction of carbon monoxide (CO) with membrane reactors should be a promising method for hydrogen mass-production because of its high CO conversion, high hydrogen purity and low carbon dioxide emission. For developing such membrane reactors, we need hydrogen permselective membranes with high hydrogen permeance with order of 10⁻⁶ mol m⁻² s⁻¹ Pa⁻¹ at 573 K and high steam durability. In this study, we have optimized the kind of substrates, precursors, vapor concentration, and chemical vapor deposition (CVD) time using the counter-diffusion CVD method for developing such membranes. The developed membrane prepared from hexamethyldisiloxane has a hydrogen permeance of 1.29 × 10⁻⁶ mol m⁻² s⁻¹ Pa⁻¹ at 573 K and high steam durability. We also conducted water gas shift reactions with membrane reactors installed the developed silica membranes. The results indicated that reactions proceed efficiently with the conversion around 95–97%, hydrogen purity around 94%, and hydrogen recovery around 60% at space velocity (SV) 7000.

P585Intra left ventricular hemodynamics assessed using 4D flow MRI in the patient with left ventricular thrombus

Background

Early detection of left ventricular mural thrombus (LVT) in patients with reduced ejection fraction (EF) is crucial in prevention of arterial embolism. 3D-cine phase-contrast magnetic resonance imaging (4D flow MRI) can visualize the intra-LV vortex flow in diastole and quantify the maximum flow velocity (Vmax) at the apex. it remains, however, unknown whether 4D flow MRI is useful for detecting LVT.

Purpose

The purpose of our study is to examine the intra-LV vortex formation and flow velocity in patients with severe LV dysfunction using 4D Flow MRI, and to compare differences in intra-LV flow dynamics between patients with and without LVT. We also examined the diagnostic accuracy to detect LVT by 4D flow MRI.

Methods

Twenty-nine patients with impaired LV function (LVEF 25.8±7.4%, 62.5±12.3 years old, 24 males, 11 with ischemic cardiomyopathy, 9 with LVT) underwent 4D flow MRI from January 2012 to August 2018 in our institution. Intra-LV vortex size was evaluated as vortex/LV area ratio by streamline imaging (Figure 1). The diagnostic accuracy to predict LVT by vortex size and Vmax at the apex was determined by ROC analysis.

Results

The vortex was smaller (vortex/LV area ratio; 30.6±7.0% vs. 45.1±9.0%, p<0.05) and Vmax at the apex was lower (0.20±0.04 m/s vs. 0.28±0.09 m/s, p=0.013) in patients with LVT compared to those without LVT. The AUC was 0.789 for Vmax (cut-off value=0.226 m/s, sensitivity=0.889, specificity=0.650) and was 0.900 for vortex/LV area ratio (cut-off value=34.7%, sensitivity=0.889, specificity=0.850).

Figure 1

Conclusion

The smaller size of intra-LV vortex and the lower flow velocity at the LV apex may have association with LVT formation in patients with reduced EF. 4D flow MRI might be useful to predict LVT formation. Large scale longitudinal study is warranted to evaluate the incidence of LVT in the patients with lower flow velocity.

Acknowledgement/Funding

None

Endoscopic and clinicopathological features of intramucosal, histologically mixed-type, low-grade, well-differentiated gastric tubular adenocarcinoma with the potential for late-onset lymph node metastasis

BACKGROUND

Intramucosal, histologically mixed-type, low-grade (LG), well-differentiated gastric tubular adenocarcinomas (tub1s; LG-tub1s) have larger mean diameters and exhibit a higher frequency of the gastric mucin phenotype (G-phenotype) than pure LG-tub1s. In proportion to their increases in diameter, G-phenotype differentiated-type early gastric cancer (EGC) tumours reportedly grow to eventually contain (an) undifferentiated-type component(s) and LG-tub1s, which are included in differentiated-type EGCs, reportedly exhibit changes in their glandular architectural and cytological atypia grades from LG to high-grade (HG) and can grow to contain a moderately differentiated tubular adenocarcinoma (tub2) component and undifferentiated components. Because they generally show a higher frequency of malignancy relative to tumours with a higher atypia grade and lower differentiation degree, it is suggested that, among mixed-type LG-tub1s, G-phenotype LG-tub1s containing an HG-tub2 component (LG-tub1s > HG-tub2) with undifferentiated components might lead to late-onset metastasis to lymph nodes even after a successful endoscopic submucosal dissection (ESD). We aimed to clarify the endoscopic and clinicopathological features of these G-phenotype LG-tub1s > HG-tub2.

METHODS

Of the 13,217 oesophagogastroduodenoscopies performed at our institutions between September 2008 and March 2016, 185 EGC lesions were evaluated in this retrospective observational study. Among these EGC lesions, 60 intramucosal LG-tub1s were divided into 53 tub1 (44 pure LG-tub1s and nine LG-tub1s containing HG-tub1) lesions and seven LG-tub1 > tub2 (LG-tub1 containing LG- and HG-tub2) lesions.

RESULTS

The frequencies of the superficial depressed type (P = 0.026), reddish colour (P = 0.006), HG of contained tub2s (P = 0.006), and G-phenotype (P = 0.028) were significantly higher in the LG-tub1 > tub2 group than those in the tub1 group. However, the largest lesion of the LG-tub1 > tub2 group had a superficial flat appearance, an isochromatic colour, an HG-tub2 and an undifferentiated component, and a large diameter greater than 30 mm, and it exhibited a G-phenotype.

CONCLUSIONS

Intramucosal G-phenotype LG-tub1s > HG-tub2 are potential premalignant stomach neoplasms that may have specific endoscopic and clinicopathological features. However, G-phenotype LG-tub1s > HG-tub2 with undifferentiated component, which potentially show higher malignancy than those without undifferentiated components might change from a reddish to isochromatic colour. Accurately diagnosing, treating, and following-up G-phenotype LG-tub1s > HG-tub2 might decrease the number of patients who experience late-onset metastasis after ESD.

Plasmodium-specific basic amino acid residues important for the interaction with ferredoxin on the surface of ferredoxin-NADP+ reductase

The malaria parasite (Plasmodium falciparum) possesses a plastid-derived, essential organelle called the apicoplast, which contains a redox system comprising plant-type ferredoxin (Fd) and Fd-NADP+ reductase (FNR). This system supplies reducing power for the crucial metabolic pathways in this organelle. Electron transfer between P. falciparum Fd (PfFd) and FNR (PfFNR) is performed with higher affinity and specificity than that of plant Fd and FNR. To investigate the mechanism for such superior protein-protein interaction, we searched for the Fd interaction sites on the surface of PfFNR. Basic amino acid residues on the FAD binding side of PfFNR were comprehensively substituted to acidic amino acids by site-directed mutagenesis. Kinetic analysis of electron transfer to PfFd and plant Fds, physical binding to immobilized PfFd and thermodynamics of the PfFd binding using these PfFNR mutants revealed that several basic amino acid residues including those in Plasmodium-specific insertion region are important for the interaction with PfFd. Majority of these basic residues are Plasmodium-specific and not conserved among plant and cyanobacteria FNRs. These results suggest that the interaction mode of Fd and FNR is diverged during evolution so that PfFd: PfFNR interaction meets the physiological requirement in the cells of Plasmodium species.

Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction

Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LRRTM1 and LRRTM2 bind to the Nrxn splice variant lacking an insert at the splice site 4 (S4). Here, we report the crystal structure of the Nrxn1β–LRRTM2 complex at 3.4 Å resolution. The Nrxn1β–LRRTM2 interface involves Ca²⁺-mediated interactions and overlaps with the Nrxn–neuroligin interface. Together with structure-based mutational analyses at the molecular and cellular levels, the present structural analysis unveils the mechanism of selective binding between Nrxn and LRRTM1/2 and its modulation by the S4 insertion of Nrxn.

Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Here authors solve the crystal structure of LRRTM2 in complex with its ligand Nrxn1β and shed light on how selective binding of ligands to LRRTM1/2 is achieved.

Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILRα immune cell receptor

Before entering host cells, herpes simplex virus-1 uses its envelope glycoprotein B to bind paired immunoglobulin-like type 2 receptor α (PILRα) on immune cells. PILRα belongs to the Siglec (sialic acid (SA)-binding immunoglobulin-like lectin)-like family, members of which bind SA. PILRα is the only Siglec member to recognize not only the sialylated O-linked sugar T antigen (sTn) but also its attached peptide region. We previously determined the crystal structure of PILRα complexed with the sTn-linked glycopeptide of glycoprotein B, revealing the simultaneous recognition of sTn and peptide by the receptor. However, the contribution of each glycopeptide component to PILRα binding was largely unclear. Here, we chemically synthesized glycopeptide derivatives and determined the thermodynamic parameters of their interaction with PILRα. We show that glycopeptides with different sugar units linking SA and peptides (i.e. "GlcNAc-type" and "deoxy-GlcNAc-type" glycopeptides) have lower affinity and more enthalpy-driven binding than the wild type (i.e. GalNAc-type glycopeptide). The crystal structures of PILRα complexed with these glycopeptides highlighted the importance of stereochemical positioning of the O4 atom of the sugar moiety. These results provide insights both for understanding the unique O-glycosylated peptide recognition by the PILRα and for the rational design of herpes simplex virus-1 entry inhibitors.

Production of Single-Chain Fv Antibodies Specific for GA-Pyridine, an Advanced Glycation End-Product (AGE), with Reduced Inter-Domain Motion

Due to their lower production cost compared with monoclonal antibodies, single-chain variable fragments (scFvs) have potential for use in several applications, such as for diagnosis and treatment of a range of diseases, and as sensor elements. However, the usefulness of scFvs is limited by inhomogeneity through the formation of dimers, trimers, and larger oligomers. The scFv protein is assumed to be in equilibrium between the closed and open states formed by assembly or disassembly of VH and VL domains. Therefore, the production of an scFv with equilibrium biased to the closed state would be critical to overcome the problem in inhomogeneity of scFv for industrial or therapeutic applications. In this study, we obtained scFv clones stable against GA-pyridine, an advanced glycation end-product (AGE), by using a combination of a phage display system and random mutagenesis. Executing the bio-panning at 37 °C markedly improved the stability of scFvs. We further evaluated the radius of gyration by small-angle X-ray scattering (SAXS), obtained compact clones, and also visualized open.

Population dynamics, synchrony, and environmental quality of Hokkaido voles lead to temporal and spatial Taylor's laws

Taylor's law (TL) asserts that the variance in a species' population density is a power-law function of its mean population density: log(variance) = a + b × log(mean). TL is widely verified. We show here that empirical time series of density of the Hokkaido gray-sided vole, Myodes rufocanus, sampled 1962-1992 at 85 locations, satisfied temporal and spatial forms of TL. The slopes (b ± standard error) of the temporal and spatial TL were estimated to be 1.613 ± 0.141 and 1.430 ± 0.132, respectively. A previously verified autoregressive Gompertz model of the dynamics of these populations generated time series of density which reproduced the form of temporal and spatial TLs, but with slopes that were significantly steeper than the slopes estimated from data. The density-dependent components of the Gompertz model were essential for the temporal TL. Adding to the Gompertz model assumptions that populations with higher mean density have reduced variance of density-independent perturbations and that density-independent perturbations are spatially correlated among populations yielded simulated time series that satisfactorily reproduced the slopes from data. The slopes (b ± standard error) of the enhanced simulations were 1.619 ± 0.199 for temporal TL and 1.575 ± 0.204 for spatial TL.

Validity of the Japanese Version of the Morningness-Eveningness Questionnaire

The Morningness-Eveningness (ME) scores and body temperature readings were collected from 25 students to assess the validity of Japanese version of Horne-Östberg's ME questionnaire. Significant differences between morning and evening types were found for acrophase (peak time) of body temperature, and ME score was significantly correlated with peak time of body temperature. These results suggest that the Japanese version of the questionnaire was valid.

Quasi-particles ultrafastly releasing kink bosons to form Fermi arcs in a cuprate superconductor

In a conventional framework, superconductivity is lost at a critical temperature (T_c) because, at higher temperatures, gluing bosons can no longer bind two electrons into a Cooper pair. In high-T_c cuprates, it is still unknown how superconductivity vanishes at T_c. We provide evidence that the so-called ≲70-meV kink bosons that dress the quasi-particle excitations are playing a key role in the loss of superconductivity in a cuprate. We irradiated a 170-fs laser pulse on Bi₂Sr₂CaCu₂O_8+δ and monitored the responses of the superconducting gap and dressed quasi-particles by time- and angle-resolved photoemission spectroscopy. We observe an ultrafast loss of superconducting gap near the d-wave node, or light-induced Fermi arcs, which is accompanied by spectral broadenings and weight redistributions occurring within the kink binding energy. We discuss that the underlying mechanism of the spectral broadening that induce the Fermi arc is the undressing of quasi-particles from the kink bosons. The loss mechanism is beyond the conventional framework, and can accept the unconventional phenomena such as the signatures of Cooper pairs remaining at temperatures above T_c.

Macrophages control innate inflammation

Macrophages play a critical role in the pathogenesis of metabolic diseases including gout and type 2 diabetes. The Nod-like receptor (NLR) family, pyrin domain containing 3 (NLRP3) forms the inflammasome with apoptosis-associated speck-like protein containing a CARD (ASC), the adaptor protein, and mediates inflammatory responses by macrophages. By compound screening, we found that tubulin polymerization inhibitors suppress NLRP3 inflammasome activation. NLRP3 inflammasome inducers reduce the NAD(+) level to inactivate the α-tubulin deacetylase Sirtuin 2, resulting in accumulation of acetylated α-tubulin. Acetylated α-tubulin mediates mitochondrial transport and subsequent proximity of ASC on mitochondria to NLRP3 on the endoplasmic reticulum. Thus, microtubule-driven transport of mitochondria is required for NLRP3 inflammasome activation. Macrophages are comprised of two subsets, M1 (inflammatory) and M2 (anti-inflammatory). Trib1 is an adaptor protein involved in protein degradation of immune-related transcription factors. We found that Trib1 is critical for the differentiation of F4/80(+) MR(+) tissue-resident M2-like macrophages. Mice lacking Trib1 in haematopoietic cells show severe lipodystrophy owing to increased lipolysis, even on a normal diet. In response to a high-fat diet, the mice show hypertriglyceridaemia and insulin resistance, together with increased proinflammatory cytokine production. Thus, Trib1 is critical for adipose tissue maintenance and suppression of metabolic disorders by controlling the differentiation of tissue-resident M2-like macrophages.

Refugia in glacial ages led to the current discontinuous distribution patterns of the dark red-backed vole Myodes rex on Hokkaido, Japan

The terrestrial mammalian fauna of the North Japanese island, Hokkaido, is more similar to that of Southern Siberia than to the main island of Japan, Honshu. Three species of the genus Myodes (Muridae, Rodentia) are found on Hokkaido, but not on Honshu. While Myodes rufocanus and M. rutilus are widely distributed across Hokkaido as well as the Eurasian continent, M. rex, which is endemic to Hokkaido and its adjacent islands, shows a discontinuous distribution pattern. We analyzed the phylogeographic history of M. rex using the mitochondrial DNA control region in order to interpret their discontinuous distribution pattern. Phylogenetic relationships among 54 distinct haplotypes showed that M. rex can be divided into four clades that occur on the northern, central, and southern regions of the Hokkaido mainland and on Rishiri Island, respectively. The phylogroups in the northern and central regions were largely separated in space, although several areas of sympatry were found. The phylogroup in the southern region, which was clearly separated from other phylogroups, showed markedly low genetic variability. All analyzed individuals from the population on Rishiri belonged to a separate lineage. Across a range of divergence rate estimates, we dated the basal divergence of all phylogroups to the mid to late Pleistocene, with subsequent signals of population expansion within lineages. We conclude that current phylogeographic structure in M. rex likely reflects Pleistocene survival in several separate refugia in situ. Past glacial ages have thus played an important role in shaping the current distribution patterns of mammalian species on Hokkaido.

Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance

Oligosaccharyltransferase (OST) is a membrane-bound enzyme that catalyzes the transfer of an oligosaccharide to an asparagine residue in glycoproteins. It possesses a binding pocket that recognizes Ser and Thr residues at the +2 position in the N-glycosylation consensus, Asn-X-Ser/Thr. We determined the crystal structures of the C-terminal globular domains of the catalytic subunits of two archaeal OSTs. A comparison with previously determined structures identified a segment with remarkable conformational plasticity, induced by crystal contact effects. We characterized its dynamic properties in solution by (15)N NMR relaxation analyses. Intriguingly, the mobile region contains the +2 Ser/Thr-binding pocket. In agreement, the flexibility restriction forced by an engineered disulfide crosslink abolished the enzymatic activity, and its cleavage fully restored activity. These results suggest the necessity of multiple conformational states in the reaction. The dynamic nature of the Ser/Thr pocket could facilitate the efficient scanning of N-glycosylation sequons along nascent polypeptide chains.

Molecular cloning, characterization of porcine IZUMO1, an IgSF family member

IZUMO1, belonging to the family of mammalian immunoglobulin proteins, has been well characterized in the mouse. Here, we describe the molecular cloning and expression analysis of porcine IZUMO1 (pIZUMO1). Partial sequence information published in the National Center for Biotechnology Information (NCBI) database was used to generate the full-length sequence for IZUMO1 using rapid amplification of cDNA ends (RACE). A search of the porcine genomic sequence in the NCBI database identified a bacterial artificial chromosome (BAC) encoding the pIZUMO1 gene. This BAC is derived from porcine chromosome 6 and is syntenic with the corresponding regions of mouse, bovine, and human genomes encoding the IZUMO gene family. This BAC was found to encode an IZUMO1 protein with a predicted amino acid sequence having high similarity with mouse and human IZUMO1. Western blot analysis of proteins from porcine tissues indicated that pIZUMO1 was specifically expressed in the sperm. Furthermore, to confirm whether pIZUMO1 forms complexes, we overexpressed pIZUMO1 in HEK293 cells. The recombinant pIZUMO1 from cell extracts was found to form complexes. Our finding suggests that pIZUMO1 forms homodimeric complex on the sperm membrane. Furthermore, an IVF inhibition assay with an antibody for the porcine IZUMO1 Ig-like domain showed that Ig-like domain effectively prevented pig sperm-egg interactions.