Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade

P. cynomolgi, a malaria-causing parasite of Asian Old World monkeys, is the sister taxon of P. vivax, the most prevalent malaria-causing species in humans outside of Africa. Because P. cynomolgi shares many phenotypic, biological and genetic characteristics with P. vivax, we generated draft genome sequences for three P. cynomolgi strains and performed genomic analysis comparing them with the P. vivax genome, as well as with the genome of a third previously sequenced simian parasite, Plasmodium knowlesi. Here, we show that genomes of the monkey malaria clade can be characterized by copy-number variants (CNVs) in multigene families involved in evasion of the human immune system and invasion of host erythrocytes. We identify genome-wide SNPs, microsatellites and CNVs in the P. cynomolgi genome, providing a map of genetic variation that can be used to map parasite traits and study parasite populations. The sequencing of the P. cynomolgi genome is a critical step in developing a model system for P. vivax research and in counteracting the neglect of P. vivax.     

Analysis of aerodynamic and thermodynamic parameters on the grassy marshland surface of Tibetan Plateau

The aerodynamic roughness z0m' the thermodynamic roughness zoh and the excess resistance to heat transfer kB are analyzed with the data obtained from Global Energy and Water Cycle Experiment ( GEWEX) Asian Monsoon Experiment on Tibetan Plateau (GAME/Tibet) in the Intensive Observation Period (IOP). 1998. Some new concepts on the aerodynamic and thermodynamic parameters over the grassy marshland surface of the Tibetan Plateau are proposed.     

Propagation of the polyamorphic transition of ice and the liquid-liquid critical point

Water has a rich metastable phase behaviour that includes transitions between high- and low-density amorphous ices, and between high- and low-density supercooled liquids. Because the transitions occur under conditions where crystalline ice is the stable phase, they are challenging to probe directly. In the case of the liquids, it remains unclear whether their mutual transformation at low temperatures is continuous, or discontinuous and terminating at a postulated second critical point of water that is metastable with respect to crystallization. The amorphous ices are more amenable to experiments, which have shown that their mutual transformation is sharp and reversible. But the non-equilibrium conditions of these studies make a firm thermodynamic interpretation of the results difficult. Here we use Raman spectroscopy and visual inspection to show that the transformation of high-density to low-density amorphous ices involves the propagation of a phase boundary-a region containing a mixture of both ices. We find that the boundary region becomes narrower as the transformation progresses, and at higher transformation temperatures. These findings strongly suggest that the polyamorphic ice transition is discontinuous; a continuous transformation should occur uniformly over the entire sample. Because the amorphous ices are structurally similar to their supercooled liquid counterparts, our results also imply that the liquids transform discontinuously at low temperatures and thus support the liquid-liquid critical-point theory.     

Synthesis and characterization of chiral mesoporous silica

Chirality is widely expressed in organic materials, perhaps most notably in biological molecules such as DNA, and in proteins, owing to the homochirality of their components (d-sugars and l-amino acids). But the occurrence of large-scale chiral pores in inorganic materials is rare. Although some progress has been made in strategies to synthesize helical and chiral zeolite-like materials, the synthesis of enantiomerically pure mesoporous materials is a challenge that remains unsolved. Here we report the surfactant-templated synthesis of ordered chiral mesoporous silica, together with a general approach for the structural analysis of chiral mesoporous crystals by electron microscopy. The material that we have synthesized has a twisted hexagonal rod-like morphology, with diameter 130-180 nm and length 1-6 micro m. Transmission electron microscopy combined with computer simulations confirm the presence of hexagonally ordered chiral channels of 2.2 nm diameter winding around the central axis of the rods. Our findings could lead to new uses for mesoporous silica and other chiral pore materials in, for example, catalysis and separation media, where both shape selectivity and enantioselectivity can be applied to the manufacturing of enantiomerically pure chemicals and pharmaceuticals.     

Structural basis for template-independent RNA polymerization

The 3'-terminal CCA nucleotide sequence (positions 74-76) of transfer RNA is essential for amino acid attachment and interaction with the ribosome during protein synthesis. The CCA sequence is synthesized de novo and/or repaired by a template-independent RNA polymerase, 'CCA-adding enzyme', using CTP and ATP as substrates. Despite structural and biochemical studies, the mechanism by which the CCA-adding enzyme synthesizes the defined sequence without a nucleic acid template remains elusive. Here we present the crystal structure of Aquifex aeolicus CCA-adding enzyme, bound to a primer tRNA lacking the terminal adenosine and an incoming ATP analogue, at 2.8 A resolution. The enzyme enfolds the acceptor T helix of the tRNA molecule. In the catalytic pocket, C75 is adjacent to ATP, and their base moieties are stacked. The complementary pocket for recognizing C74-C75 of tRNA forms a 'protein template' for the penultimate two nucleotides, mimicking the nucleotide template used by template-dependent polymerases. These results are supported by systematic analyses of mutants. Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization.     

Study on Growth of GdBaSrCu_3O_(7-δ) Single Crystal

1 Results It is generally known that CuO2 planes of layered cuprate superconductors play a major role on the variation of critical temperature,Tc.In order to investigate their microscopic and electronic properties,preparation of such materials in single crystal form with highly structure orientation is very important.Crystal growth techniques for copper oxide materials have greatly improved since the discovery of high Tc superconductor materials[1].However,a strong reaction between CuO flux and crucible material has been a serious problem in crystal growth by using crucible,especially in a self-flux slow cooling method that needs long time.It is important to avoid the contamination from crucible material and also the ‘creeping out' problem of CuO flux during long time and high sintering temperature.In this study,we attempted to grew the GdBaSrCu3O7-δ single crystals via self-flux slow cooling technique.They were grown from CuO-rich nonstoichiometric solutions as similar as the YBCO case with approximately cation and powder ratio used as reported before[2-3].     

TANK-binding kinase-1 delineates innate and adaptive immune responses to DNA vaccines

Successful vaccines contain not only protective antigen(s) but also an adjuvant component that triggers innate immune activation and is necessary for their optimal immunogenicity. In the case of DNA vaccines, this consists of plasmid DNA; however, the adjuvant element(s) as well as its intra- and inter-cellular innate immune signalling pathway(s) leading to the encoded antigen-specific T- and B-cell responses remain unclear. Here we demonstrate in vivo that TANK-binding kinase 1 (TBK1), a non-canonical IkappaB kinase, mediates the adjuvant effect of DNA vaccines and is essential for its immunogenicity in mice. Plasmid-DNA-activated, TBK1-dependent signalling and the resultant type-I interferon receptor-mediated signalling was required for induction of antigen-specific B and T cells, which occurred even in the absence of innate immune signalling through a well known CpG DNA sensor-Toll-like receptor 9 (TLR9) or Z-DNA binding protein 1 (ZBP1, also known as DAI, which was recently reported as a potential B-form DNA sensor). Moreover, bone-marrow-transfer experiments revealed that TBK1-mediated signalling in haematopoietic cells was critical for the induction of antigen-specific B and CD4(+) T cells, whereas in non-haematopoietic cells TBK1 was required for CD8(+) T-cell induction. These data suggest that TBK1 is a key signalling molecule for DNA-vaccine-induced immunogenicity, by differentially controlling DNA-activated innate immune signalling through haematopoietic and non-haematopoietic cells.