Identification of Tim4 as a phosphatidylserine receptor

In programmed cell death, a large number of cells undergo apoptosis, and are engulfed by macrophages to avoid the release of noxious materials from the dying cells. In definitive erythropoiesis, nuclei are expelled from erythroid precursor cells and are engulfed by macrophages. Phosphatidylserine is exposed on the surface of apoptotic cells and on the nuclei expelled from erythroid precursor cells; it works as an 'eat me' signal for phagocytes. Phosphatidylserine is also expressed on the surface of exosomes involved in intercellular signalling. Here we established a library of hamster monoclonal antibodies against mouse peritoneal macrophages, and found an antibody that strongly inhibited the phosphatidylserine-dependent engulfment of apoptotic cells. The antigen recognized by the antibody was identified by expression cloning as a type I transmembrane protein called Tim4 (T-cell immunoglobulin- and mucin-domain-containing molecule; also known as Timd4). Tim4 was expressed in Mac1+ cells in various mouse tissues, including spleen, lymph nodes and fetal liver. Tim4 bound apoptotic cells by recognizing phosphatidylserine via its immunoglobulin domain. The expression of Tim4 in fibroblasts enhanced their ability to engulf apoptotic cells. When the anti-Tim4 monoclonal antibody was administered into mice, the engulfment of apoptotic cells by thymic macrophages was significantly blocked, and the mice developed autoantibodies. Among the other Tim family members, Tim1, but neither Tim2 nor Tim3, specifically bound phosphatidylserine. Tim1- or Tim4-expressing Ba/F3 B cells were bound by exosomes via phosphatidylserine, and exosomes stimulated the interaction between Tim1 and Tim4. These results indicate that Tim4 and Tim1 are phosphatidylserine receptors for the engulfment of apoptotic cells, and may also be involved in intercellular signalling in which exosomes are involved.     

Identification of a factor that links apoptotic cells to phagocytes

Apoptotic cells are rapidly engulfed by phagocytes to prevent the release of potentially noxious or immunogenic intracellular materials from the dying cells, thereby preserving the integrity and function of the surrounding tissue. Phagocytes engulf apoptotic but not healthy cells, indicating that the apoptotic cells present a signal to the phagocytes, and the phagocytes recognize the signal using a specific receptor. Here, we report a factor that links apoptotic cells to phagocytes. We found that milk fat globule-EGF-factor 8 (MFG-E8), a secreted glycoprotein, was produced by thioglycollate-elicited macrophages. MFG-E8 specifically bound to apoptotic cells by recognizing aminophospholipids such as phosphatidylserine. MFG-E8, when engaged by phospholipids, bound to cells via its RGD (arginine-glycine-aspartate) motif--it bound particularly strongly to cells expressing alpha(v)beta(3) integrin. The NIH3T3 cell transformants that expressed a high level of alpha(v)beta(3) integrin were found to engulf apoptotic cells when MFG-E8 was added. MFG-E8 carrying a point mutation in the RGD motif behaved as a dominant-negative form, and inhibited the phagocytosis of apoptotic cells by peritoneal macrophages in vitro and in vivo. These results indicate that MFG-E8 secreted from activated macrophages binds to apoptotic cells, and brings them to phagocytes for engulfment.     

Discovery of X-rays from the protostellar outflow object HH2

Herbig-Haro (HH) objects have been known for 50 years to be luminous condensations of gas in star-forming regions, but their underlying physical nature is still being elucidated. Previously suggested models encompass newborn stars, stellar winds clashing with nebular material, dense pockets of interstellar gas excited by shocks from outflows, and interstellar 'bullets' (ref. 6). Recent progress has been made with the jet-induced shock model, in which material streams out of young stellar objects and collides with the surrounding interstellar medium. A clear prediction of this model is that the most energetic Herbig-Haro objects will emit X-rays, although they have not hitherto been detected. Here we report the discovery of X-ray emission from one of the brightest and closest Herbig-Haro objects, HH2, at a level consistent with the model predictions. We conclude that this Herbig-Haro object contains shock-heated material located at or near its leading edge with a temperature of about 106 K.     

Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo

Evolutionarily diverse eukaryotic cells share many conserved proteins of unknown function. Some are essential for cell viability, emphasising their importance for fundamental processes of cell biology but complicating their analysis. We have developed an approach to the large-scale characterization of such proteins, based on conditional and rapid degradation of the target protein in vivo, so that the immediate consequences of bulk protein depletion can be examined. Budding yeast strains have been constructed in which essential proteins of unknown function have been fused to a 'heat-inducible-degron' cassette that targets the protein for proteolysis at 37 degrees C (ref. 4). By screening the collection for defects in cell-cycle progression, here we identify three DNA replication factors that interact with each other and that have uncharacterized homologues in human cells. We have used the degron strains to show that these proteins are required for the establishment and normal progression of DNA replication forks. The degron collection could also be used to identify other, essential, proteins with roles in many other processes of eukaryotic cell biology.     

Haploinsufficiency of NSD1 causes Sotos syndrome

We isolated NSD1 from the 5q35 breakpoint in an individual with Sotos syndrome harboring a chromosomal translocation. We identified 1 nonsense, 3 frameshift and 20 submicroscopic deletion mutations of NSD1 among 42 individuals with sporadic cases of Sotos syndrome. The results indicate that haploinsufficiency of NSD1 is the major cause of Sotos syndrome.     

Calcium-dependent phospholipid scrambling by TMEM16F

In all animal cells, phospholipids are asymmetrically distributed between the outer and inner leaflets of the plasma membrane. This asymmetrical phospholipid distribution is disrupted in various biological systems. For example, when blood platelets are activated, they expose phosphatidylserine (PtdSer) to trigger the clotting system. The PtdSer exposure is believed to be mediated by Ca(2+)-dependent phospholipid scramblases that transport phospholipids bidirectionally, but its molecular mechanism is still unknown. Here we show that TMEM16F (transmembrane protein 16F) is an essential component for the Ca(2+)-dependent exposure of PtdSer on the cell surface. When a mouse B-cell line, Ba/F3, was treated with a Ca(2+) ionophore under low-Ca(2+) conditions, it reversibly exposed PtdSer. Using this property, we established a Ba/F3 subline that strongly exposed PtdSer by repetitive fluorescence-activated cell sorting. A complementary DNA library was constructed from the subline, and a cDNA that caused Ba/F3 to expose PtdSer spontaneously was identified by expression cloning. The cDNA encoded a constitutively active mutant of TMEM16F, a protein with eight transmembrane segments. Wild-type TMEM16F was localized on the plasma membrane and conferred Ca(2+)-dependent scrambling of phospholipids. A patient with Scott syndrome, which results from a defect in phospholipid scrambling activity, was found to carry a mutation at a splice-acceptor site of the gene encoding TMEM16F, causing the premature termination of the protein.     

Special variation of infiltration-growth processed bulk YBCO fabricated using new liquid source: Ba3Cu5O8 (1:1.3) and YbBa2Cu3Oy

Utilization of novel materials, particularly high-Tc (critical temperature) superconductors, is essential to pursue the United Nations' Sustainable Goals, as well as to meet the increasing worldwide demand for clean and carbon-free electric power technologies. Superconduct-ing magnets are beneficial in several real-life applications including transportation, energy production, magnetic resonance imaging (MRI), and drug delivery systems. To achieve high performance, one must develop uniform, large-grain, infiltration-growth (IG) processed bulk YBa2Cu3Oy (Y-123) super-magnets. In this study, we report the magnetic and microstructural properties of a large-grain, top-seeded, IG-pro-cessed Y-123 pellet, which is 20 mm in diameter and 6 mm in height; the pellet is produced utilizing liquid Yb-123+Ba3Cu5O8 as the liquid source. All the samples cut from the top of the bulk exhibit a sharp superconducting transition (approximately 1 K wide) with the onset Tc of approximately 90 K. However, in the samples cut from the bottom surface, the onset Tc values slightly decreased to between 88 and 90 K, al-though still exhibiting a sharp superconducting transition. The top and bottom samples exhibited the highest remnant value of Jc (critical cur-rent density) at 77 K H//c-axis of 50 and 55 kA/cm2, respectively. The remnant Jc and irreversibility field values significantly fluctuated, being fairly low in some bottom samples. Scanning electron microscopy identified nanometer size Y-211 (Y2BaCuO5) secondary-phase particles dis-persed in the Y-123 matrix. Energy-dispersive spectroscopy clarified that the decreased both Tc and Jc for the bottom samples were attributed to liquid phase dispersion within the Y-123 phase.     

Pigment chemistry: the red sweat of the hippopotamus

Within a few minutes of perspiration, the colourless, viscous sweat of the hippopotamus gradually turns red, and then brown as the pigment polymerizes. Here we isolate and characterize the pigments responsible for this colour reaction. The unstable red and orange pigments turn out to be non-benzenoid aromatic compounds that are unexpectedly acidic and have antibiotic as well as sunscreen activity.     

Experimental extraction of an entangled photon pair from two identically decohered pairs

Entanglement is considered to be one of the most important resources in quantum information processing schemes, including teleportation, dense coding and entanglement-based quantum key distribution. Because entanglement cannot be generated by classical communication between distant parties, distribution of entangled particles between them is necessary. During the distribution process, entanglement between the particles is degraded by the decoherence and dissipation processes that result from unavoidable coupling with the environment. Entanglement distillation and concentration schemes are therefore needed to extract pairs with a higher degree of entanglement from these less-entangled pairs; this is accomplished using local operations and classical communication. Here we report an experimental demonstration of extraction of a polarization-entangled photon pair from two decohered photon pairs. Two polarization-entangled photon pairs are generated by spontaneous parametric down-conversion and then distributed through a channel that induces identical phase fluctuations to both pairs; this ensures that no entanglement is available as long as each pair is manipulated individually. Then, through collective local operations and classical communication we extract from the two decohered pairs a photon pair that is observed to be polarization-entangled.     

Insect signalling: components of giant hornet alarm pheromone

Up to 74 people die each year in Japan after being stung by Hymenopteran insects, with hornets (Vespa spp.) being among the worst offenders. Here we identify a volatile, multi-component alarm pheromone in the venom of the world's largest hornet, V. mandarinia, and use field bioassays to show that 2-pentanol is its principal active component, and that 3-methyl-1-butanol and 1-methylbutyl 3-methylbutanoate act synergistically with it. The compound 1-methylbutyl 3-methylbutanoate, which may also be a foraging-site-marking pheromone, elicits a strong defensive reaction in the sympatric prey hornet V. simillima xanthoptera. As these chemicals are sometimes used in food flavourings and as fragrances in cosmetics, it is possible that they might provoke a seemingly unwarranted hornet attack on humans.