Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Fabrication of CuO nanoparticle interlinked microsphere cages by solution method

Here we report a very simple method to convert conventional CuO powders to nanoparticle interlinked microsphere cages by solution method. CuO is dissolved into aqueous ammonia, and the solution is diluted by alcohol and dip coating onto a glass substrate. Drying at 80 °C, the nanostructures with bunchy nanoparticles of Cu(OH)2can be formed. After the substrate immerges into the solution and we vaporize the solution, hollow microspheres can be formed onto the substrate. There are three phases in the as-prepared samples, monoclinic tenorite CuO, orthorhombic Cu(OH)2, and monoclinic carbonatodiamminecopper(II) (Cu(NH3)2CO3). After annealing at 150 °C, the products convert to CuO completely. At annealing temperature above 350 °C, the hollow microspheres became nanoparticle interlinked cages

Major vault protein suppresses obesity and atherosclerosis through inhibiting IKK-NF-kappa B signaling mediated inflammation

Macrophage-orchestrated, low-grade chronic inflammation plays a pivotal role in obesity and atherogenesis. However, the underlying regulatory mechanisms remain incompletely understood. Here, we identify major vault protein (MVP), the main component of unique cellular ribonucleoprotein particles, as a suppressor for NF-κB signaling in macrophages. Both global and myeloid-specific MVP gene knockout aggravates high-fat diet induced obesity, insulin resistance, hepatic steatosis and atherosclerosis in mice. The exacerbated metabolic disorders caused by MVP deficiency are accompanied with increased macrophage infiltration and heightened inflammatory responses in the microenvironments. In vitro studies reveal that MVP interacts with TRAF6 preventing its recruitment to IRAK1 and subsequent oligomerization and ubiquitination. Overexpression of MVP and its α-helical domain inhibits the activity of TRAF6 and suppresses macrophage inflammation. Our results demonstrate that macrophage MVP constitutes a key constraint of NF-κB signaling thereby suppressing metabolic diseases

Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station

A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.</p

Molecular cloning and expression analysis of hypoxia inducible factor 1α in tongue sole, Cynoglossus semilaevis (Actinopterygii: Pleuronectiformes: Cynoglossidae), subjected to acute hypoxia

Background. Hypoxia-inducible factor-1α (HIF-1α), a subunit of the HIF-1 protein, plays a key role in the regulation of genes involved in hypoxia physiological response. Tongue sole, Cynoglossus semilaevis Günther, 1873, a marine teleost, had been proved to be a hypoxia-tolerant species. In this study, the HIF-1α in tongue sole was cloned and its expression under acute hypoxia was examined to provide further basis for understanding the molecular response of tongue sole under hypoxia. Materials and methods. The full length of HIF-1α cDNA sequence was cloned from the liver of tongue sole by RT-PCR and RACE-PCR method. Then, the expression pattern of tongue sole HIF-1α under acute hypoxic conditions were detected using quantitative real-time PCR method. Results. The open reading frame of tongue sole HIF-1α is 2208 bp, encoding 735 amino acids. The amino acid sequence of tongue sole HIF-1α shared high identities (52.7%–81.8%) with HIF-1α from other vertebrates, and possessed six typical domains of the HIF-1 family (bHLH, PAS-A, PAS-B, PAC, N-TAD, and C-TAD). In adult fish, HIF-1α mRNAs were highly expressed in the liver, moderately in the heart, spleen, kidney, stomach, blood and gills, and low in intestine. Under acute hypoxia stress, expression of HIF-1α mRNAs were significantly up-regulated in many tissues, including the liver, spleen, stomach, blood, heart and gills. Conclusion. Tongue sole HIF-1α possessed the similar sequence length, shared higher identities and clustered well with other known HIF-1α, thus revealing a high degree conservation of HIF-1α during evolution. Tongue sole HIF-1α began to be up-regulated from 5 min to 120 min after hypoxia, indicating that it might play a significant role at the early stage of hypoxia

Invasion and control of water hyacinth (Eichhornia crassipes) in China

By the time of primary 21st century, water hyacinth had become a serious environmental problem in China. Water hyacinth contributes to the major part of ecological hazards from the invasion of foreign plant species, which is estimated about USD 7 billion a year in values. In the past 10 years, herbicides glyphosate, 2,4-D and paraquat have been used in controlling water hyacinth in China. Although the herbicides provided effective control on the weed in some areas, they could not provide the sustainable inhibition on the weed population, while would lead to pollution on water at various levels. At present, the herbicide application on water hyacinth is forbidden in many areas of China such as Shanghai. In this situation, the asexual reproduction inhibitor, KWH02, was invented for controlling water hyacinth and it provided about 70% of growth inhibition without any risk of dead plant pollution. It has been about 10 years for bio-control of water hyacinth in China. Works focused on mainly the efficacy and safety of the utilization of foreign insects. Researches on microorganism herbicides to control water hyacinth were started and obtained primary achievements in recent years. Although there are different opinions on how to face the water hyacinth problem in China, it is accepted widely that the control methods should be high efficient and safe with low cost. Some practical measures for integrated management of water hyacinth are suggested