Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Fouling in membrane bioreactors used in wastewater treatment

http://biofilms.bt.tudelft.nl/pdf/2007_WaterResearch_4_VanDerStar-et-al.pdf

Startup of reactors for anoxic ammonium oxidation: experiences from the first full-scale anammox reactor in Rotterdam.

In a world where environment protection and energy conservation are growing concerns, the development of electric vehicles (EV) and hybrid electric vehicles (HEV) has taken on an accelerated pace. The dream of having commercially viable EVs and HEVs is becoming a reality. EVs and HEVs are gradually available in the market. This paper will provide an overview of the present status of electric and hybrid vehicles worldwide and their state of the art, with emphasis on the engineering philosophy and key technologies. The importance of the integration of technologies of automobile, electric motor drive, electronics, energy storage, and controls and also the importance of the integration of society strength from government, industry, research institutions, electric power utilities, and transportation authorities are addressed. The challenge of EV commercialization is discussed.

/pdf/the-state-of-the-art-of-electric-and-hybrid-vehicles-54s99348gx.pdf

The state of the art of electric and hybrid vehicles

Treatment of organic pollution in industrial saline wastewater: a literature review

Nitrification of Source Separated Urine in a Sequencing Batch Reactor

Geologic marks related to extraterrestrial impact events, such as im pact split gravels, impact brecciate layers, impact dikes, microirghizites, micr otektites, especially meteoritic residues, were discovered on the boundary betwe en Sinian/Cambrian in Tianmenshan of Western Hunan, which may possibly demonstra te that an extraterrestrial impact event has ever occurred there on the SC bound ary.

Geological marks of a possible extraterrestrial impact event on the boundary b etween sinian/cambrian in tianmenshan

Pilot study of a membrane bio-reactor in treating fresh water sewage and saline sewage in Hong Kong.

生物膜法における有機性基質除去の解析手法と操作因子の影響;生物膜法における有機性基質除去の解析手法と操作因子の影響;Analysis method for organic substance removal by the biofilm method and effect of operating factors.

Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.

Guanghao Chen

Papers

Nitrification of Source Separated Urine in a Sequencing Batch Reactor

Geological marks of a possible extraterrestrial impact event on the boundary b etween sinian/cambrian in tianmenshan

Pilot study of a membrane bio-reactor in treating fresh water sewage and saline sewage in Hong Kong.

生物膜法における有機性基質除去の解析手法と操作因子の影響;生物膜法における有機性基質除去の解析手法と操作因子の影響;Analysis method for organic substance removal by the biofilm method and effect of operating factors.

Comparative Metabolic Modeling of Multiple Sulfate‐reducing Prokaryotes Reveals Versatile Energy Conservation Mechanisms