Essential role for TIRAP in activation of the signalling cascade shared by TLR2 and TLR4

Signal transduction through Toll-like receptors (TLRs) originates from their intracellular Toll/interleukin-1 receptor (TIR) domain, which binds to MyD88, a common adaptor protein containing a TIR domain. Although cytokine production is completely abolished in MyD88-deficient mice, some responses to lipopolysaccharide (LPS), including the induction of interferon-inducible genes and the maturation of dendritic cells, are still observed. Another adaptor, TIRAP (also known as Mal), has been cloned as a molecule that specifically associates with TLR4 and thus may be responsible for the MyD88-independent response. Here we report that LPS-induced splenocyte proliferation and cytokine production are abolished in mice lacking TIRAP. As in MyD88-deficient mice, LPS activation of the nuclear factor NF-kappaB and mitogen-activated protein kinases is induced with delayed kinetics in TIRAP-deficient mice. Expression of interferon-inducible genes and the maturation of dendritic cells is observed in these mice; they also show defective response to TLR2 ligands, but not to stimuli that activate TLR3, TLR7 or TLR9. In contrast to previous suggestions, our results show that TIRAP is not specific to TLR4 signalling and does not participate in the MyD88-independent pathway. Instead, TIRAP has a crucial role in the MyD88-dependent signalling pathway shared by TLR2 and TLR4.     

Common variants at 11q12, 10q26 and 3p11.2 are associated with prostate cancer susceptibility in Japanese

We have previously reported multiple loci associated with prostate cancer susceptibility in a Japanese population using a genome-wide association study (GWAS). To identify additional prostate cancer susceptibility loci, we genotyped nine SNPs that were nominally associated with prostate cancer (P < 1 × 10(-4)) in our previous GWAS in three independent studies of prostate cancer in Japanese men (2,557 individuals with prostate cancer (cases) and 3,003 controls). In a meta-analysis of our previous GWAS and the replication studies, which included a total of 7,141 prostate cancer cases and 11,804 controls from a single ancestry group, three new loci reached genome-wide significance on chromosomes 11q12 (rs1938781; P = 1.10 × 10(-10); FAM111A-FAM111B), 10q26 (rs2252004; P = 1.98 × 10(-8)) and 3p11.2 (rs2055109; P = 3.94 × 10(-8)). We also found suggestive evidence of association at a previously reported prostate cancer susceptibility locus at 2p11 (rs2028898; P = 1.08 × 10(-7)). The identification of three new susceptibility loci should provide additional insight into the pathogenesis of prostate cancer and emphasizes the importance of conducting GWAS in diverse populations.     

Variation in the bark call of the red squirrel ( Tamiasciurus hudsonicus )

Calls of the red squirrel ( Tamiasciurus hudsonicus; n = 122) were recorded in wild populations from 15 localities in Arizona, New Mexico, Colorado, Utah, Wyoming, Montana, Idaho, and Washington. Computer-generated audiospectrograms of 20- or 30-second samples from a calling bout of each individual were analyzed. Eighteen bark types (distinct forms of the bark call) were identified plus a 19th category that included rarely used, longer bark calls. The frequency of use of each bark type within the sample was recorded for each squirrel. Differences in frequency of use of the various bark types were found among subspecies, within subspecies, and within populations; additionally, the southern subspecies utilized a reduced number of bark types. The large number of different bark types and the variation in bark type usage within populations suggest the potential for communication of such information as individual identification, behavioral states, or gender identification.     

Conformational transition of Sec machinery inferred from bacterial SecYE structures

Over 30% of proteins are secreted across or integrated into membranes. Their newly synthesized forms contain either cleavable signal sequences or non-cleavable membrane anchor sequences, which direct them to the evolutionarily conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising alpha-, gamma- and beta-subunits, in eukaryotes). The translocon then functions as a protein-conducting channel. These processes of protein localization occur either at or after translation. In bacteria, the SecA ATPase drives post-translational translocation. The only high-resolution structure of a translocon available so far is that for SecYEbeta from the archaeon Methanococcus jannaschii, which lacks SecA. Here we present the 3.2-A-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state of SecYE, in which several transmembrane helices are shifted, as compared to the previous SecYEbeta structure, to create a hydrophobic crack open to the cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that the pre-open state might represent a SecYE conformational transition that is inducible by SecA binding. Moreover, we identified a SecA-SecYE interface that comprises SecA residues originally buried inside the protein, indicating that both the channel and the motor components of the Sec machinery undergo cooperative conformational changes on formation of the functional complex.     

Chenguodaite （Ag9FeTe2S4）： a new tellurosulfide mineral from the gold district of East Shandong Peninsula,China

Chenguodaite, approved by IMA-CNMMN （2004-042a）, was discovered in the Bunan quartz vein-type gold deposit in the gold district of East Shandong Peninsula. The mineral occurs in high grade Au-Ag-Cu ores, coexisting with galena, chalcopyrite, hessite, electrum, unnamed Ag6TeS2 and AglsFeBiTe3Se, enclosed and replaced by native silver and acanthite. In the reflected light microscope, the mineral has light gray color, indistinguishable anistropism and hardness around 2-3. The color indices of chenguodaite relative to ICE C illuminator are： x=0.3027, y=0.3076, Y=25.78%,λd=474 nm, Pe=3.68%, similar to those of canfieldite. The average chemical composition from 16 microprobe analyses is Ag8.97Fe1.00Te1.99S4.04, idealized to AggFeTe2S4. The polycrystalline X-ray diffraction of chenguodaite by Gandolfi camera and synchrotron oscillation photography results in 67 reflections with the 12 strongest being （relative intensity in bracket）： 6.742（69）, 6.416（39）, 5.951（33）, 3.265（100）, 2.981（24）, 2.649（22）, 2.25（24）, 2.188（71）, 2.142（22）, 2.123（31）, 2.044（23）, 1.949（33）, which are indexed to a primitive orthorhombic cell with a=12.769 （2） A, b= 14.814（2） A, c= 16.233 （1） A, V= 3070.6 A^3, Z= 9, Dcal.=6.85 g/cm^3. The name is for the late Prof. Chen Guoda, a famous Chinese geologist and the founder of Diwa-Geodepression theory of tectonics.     

Crystal structure of the MgtE Mg2+ transporter

The magnesium ion Mg2+ is a vital element involved in numerous physiological processes. Mg2+ has the largest hydrated radius among all cations, whereas its ionic radius is the smallest. It remains obscure how Mg2+ transporters selectively recognize and dehydrate the large, fully hydrated Mg2+ cation for transport. Recently the crystal structures of the CorA Mg2+ transporter were reported. The MgtE family of Mg2+ transporters is ubiquitously distributed in all phylogenetic domains, and human homologues have been functionally characterized and suggested to be involved in magnesium homeostasis. However, the MgtE transporters have not been thoroughly characterized. Here we determine the crystal structures of the full-length Thermus thermophilus MgtE at 3.5 A resolution, and of the cytosolic domain in the presence and absence of Mg2+ at 2.3 A and 3.9 A resolutions, respectively. The transporter adopts a homodimeric architecture, consisting of the carboxy-terminal five transmembrane domains and the amino-terminal cytosolic domains, which are composed of the superhelical N domain and tandemly repeated cystathionine-beta-synthase domains. A solvent-accessible pore nearly traverses the transmembrane domains, with one potential Mg2+ bound to the conserved Asp 432 within the pore. The transmembrane (TM)5 helices from both subunits close the pore through interactions with the 'connecting helices', which connect the cystathionine-beta-synthase and transmembrane domains. Four putative Mg2+ ions are bound at the interface between the connecting helices and the other domains, and this may lock the closed conformation of the pore. A structural comparison of the two states of the cytosolic domains showed the Mg2+-dependent movement of the connecting helices, which might reorganize the transmembrane helices to open the pore. These findings suggest a homeostasis mechanism, in which Mg2+ bound between cytosolic domains regulates Mg2+ flux by sensing the intracellular Mg2+ concentration. Whether this presumed regulation controls gating of an ion channel or opening of a secondary active transporter remains to be determined.     

Dodecagonal tiling in mesoporous silica

Recent advances in the fabrication of quasicrystals in soft matter systems have increased the length scales for quasicrystals into the mesoscale range (20 to 500 ?ngstr?ms). Thus far, dendritic liquid crystals, ABC-star polymers, colloids and inorganic nanoparticles have been reported to yield quasicrystals. These quasicrystals offer larger length scales than intermetallic quasicrystals (a few ?ngstr?ms), thus potentially leading to optical applications through the realization of a complete photonic bandgap induced via multiple scattering of light waves in virtually all directions. However, the materials remain far from structurally ideal, in contrast to their intermetallic counterparts, and fine control over the structure through a self-organization process has yet to be attained. Here we use the well-established self-assembly of surfactant micelles to produce a new class of mesoporous silicas, which exhibit 12-fold (dodecagonal) symmetry in both electron diffraction and morphology. Each particle reveals, in the 12-fold cross-section, an analogue of dodecagonal quasicrystals in the centre surrounded by 12 fans of crystalline domains in the peripheral part. The quasicrystallinity has been verified by selected-area electron diffraction and quantitative phason strain analyses on transmission electron microscope images obtained from the central region. We argue that the structure forms through a non-equilibrium growth process, wherein the competition between different micellar configurations has a central role in tuning the structure. A simple theoretical model successfully reproduces the observed features and thus establishes a link between the formation process and the resulting structure.     

Isolation and characterization of hemagglutinins from the spongeDysidea herbacea

Summary The spongeDysidea herbacea (Keller) was found to possess hemagglutinins. The major component, DHA-I, is a protein with a mol.wt of 26,000, which dissociates into subunits of equal size (14,000). It contains large amounts of glutamic acid and aspartic acid residues, but no half-cystine, methionine or histidine residues. DHA-I reacted with rabbit and human AB0 erythrocytes. D-galactose and lactose were effective inhibitors of DHA-I. The sponge also contained a minor component(s) which reacted preferentially with rabbit erythrocytes but not with human AB0 erythrocytes.Acknowledgment. We thank Dr. M. Yamazaki, Faculty of Pharmaceutical Sciences, Teikyo University, for testing mitogenic activity ofDysidea agglutinins. This study was partly supported by a grant-in-aid for Overseas Scientific Survey from the Ministry of Education, Science and Culture, Japan.     

Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains

Deubiquitinating enzymes (DUBs) remove ubiquitin from conjugated substrates to regulate various cellular processes. The Zn(2+)-dependent DUBs AMSH and AMSH-LP regulate receptor trafficking by specifically cleaving Lys 63-linked polyubiquitin chains from internalized receptors. Here we report the crystal structures of the human AMSH-LP DUB domain alone and in complex with a Lys 63-linked di-ubiquitin at 1.2 A and 1.6 A resolutions, respectively. The AMSH-LP DUB domain consists of a Zn(2+)-coordinating catalytic core and two characteristic insertions, Ins-1 and Ins-2. The distal ubiquitin interacts with Ins-1 and the core, whereas the proximal ubiquitin interacts with Ins-2 and the core. The core and Ins-1 form a catalytic groove that accommodates the Lys 63 side chain of the proximal ubiquitin and the isopeptide-linked carboxy-terminal tail of the distal ubiquitin. This is the first reported structure of a DUB in complex with an isopeptide-linked ubiquitin chain, which reveals the mechanism for Lys 63-linkage-specific deubiquitination by AMSH family members.