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

2.3. [4 + 4] Cycloadditions 1058 2.4. Photocycloadditions of Aromatic Compounds 1058 2.4.1. Benzene Derivatives 1058 2.4.2. Condensed Aromatic Compounds 1060 3. Photochemical Rearrangements 1061 4. Cyclizations 1064 4.1. Pericyclizations 1064 4.2. Norrish−Yang Reaction 1066 5. Photochemical Extrusion of Small Molecules 1067 6. Photochemical Electron Transfer 1068 6.1. Photochemical Electron-Transfer Reactions with a Catalytic Sensitizer 1068

Photochemical Reactions as Key Steps in Organic Synthesis

We introduce a measure of the local density of chirality of the electromagnetic field. This optical chirality determines the asymmetry in the rates of excitation between a small chiral molecule and its mirror image, and applies to molecules in electromagnetic fields with arbitrary spatial dependence. A continuity equation for optical chirality in the presence of material currents describes the flow of chirality, in a manner analogous to the Poynting theorem for electromagnetic energy. ``Superchiral'' solutions to Maxwell's equations show larger chiral asymmetry, in some regions of space, than is found in circularly polarized plane waves.

/pdf/optical-chirality-and-its-interaction-with-matter-4w9nb3y2se.pdf

Optical chirality and its interaction with matter.

Various present and future specialized applications of magnets require monodisperse, small magnetic particles, and the discovery of molecules that can function as nanoscale magnets was an important development in this regard. These molecules act as single-domain magnetic particles that, below their blocking temperature, exhibit magnetization hysteresis, a classical property of macroscopic magnets. Such 'single-molecule magnets' (SMMs) straddle the interface between classical and quantum mechanical behaviour because they also display quantum tunnelling of magnetization and quantum phase interference. Quantum tunnelling of magnetization can be advantageous for some potential applications of SMMs, for example, in providing the quantum superposition of states required for quantum computing. However, it is a disadvantage in other applications, such as information storage, where it would lead to information loss. Thus it is important to both understand and control the quantum properties of SMMs. Here we report a supramolecular SMM dimer in which antiferromagnetic coupling between the two components results in quantum behaviour different from that of the individual SMMs. Our experimental observations and theoretical analysis suggest a means of tuning the quantum tunnelling of magnetization in SMMs. This system may also prove useful for studying quantum tunnelling of relevance to mesoscopic antiferromagnets.

Exchange-biased quantum tunnelling in a supramolecular dimer of single-molecule magnets

We present 2.5-30 mum spectra from the Short-Wavelength Spectrometer of the Infrared Space Observatory for a total of 23 sources. The sources include embedded young stellar objects spanning a wide range of mass and luminosity, together with field stars sampling quiescent dark clouds and the diffuse interstellar medium. Expanding on results of previous studies, we use these spectra to investigate ice composition as a function of environment. The spectra reveal an extremely rich set of absorption features attributed to simple molecules in the ices. We discuss the observed properties of these absorption features and review their assignments. Among the species securely identified are H2O, CO, CO2, CH3OH, and CH4. Likely identified species include OCS, H2CO, and HCOOH. There is also evidence for NH3 and OCN- ice features, but these identifications are more controversial. Features that continue to defy identification include the 3.3-3.7 mum "ice band wing'' and the bulk of the 6.8 mum feature. In addition, we find evidence for excess absorption at 6.0 mum that cannot be attributed to H2O ice. We examine the degree of intercorrelation of the 6.8 mum, 4.62 mum ("XCN'') and 6.0 mum (excess) features. Our results are consistent with the interpretation of the 6.8 and 4.62 mum features as due to NH4+ and OCN- ions, respectively, though alternative explanations cannot currently be ruled out. We find that the optical depth correlations are dependent on the profile of the 6.8 mum feature but not on the mass of the YSO nor the ice temperature along the line of sight. We discuss the implications for our current understanding of ice processing. We briefly discuss the composition, origin, and evolution of interstellar ices.

/pdf/interstellar-ice-the-infrared-space-observatory-legacy-1fsfio7fnf.pdf

Interstellar Ice: The Infrared Space Observatory Legacy

The primordial appearance of chiral amino acids was an essential component of the asymmetric evolution of life on Earth. In this tutorial review we will explore the original life-generating, symmetry-breaking event and summarise recent thoughts on the origin of enantiomeric excess in the universe. We will then highlight the transfer of asymmetry from chiral photons to racemic amino acids and elucidate current experimental data on the photochemical synthesis of amino and diamino acid structures in simulated interstellar and circumstellar ice environments. The chirality inherent within actual interstellar (cometary) ice environments will be considered in this discussion: in 2014 the Rosetta Lander Philae onboard the Rosetta space probe is planned to detach from the orbiter and soft-land on the surface of the nucleus of comet 67P/Churyumov–Gerasimenko. It is equipped for the in situ enantioselective analysis of chiral prebiotic organic species in cometary ices. The scientific design of this mission will therefore be presented in the context of analysing the formation of amino acid structures within interstellar ice analogues as a means towards furthering understanding of the origin of asymmetric biological molecules.

Chirality, photochemistry and the detection of amino acids in interstellar ice analogues and comets

New crucial theoretical investigations on the origin of biomolecular chirality are reviewed briefly With the goal to investigate these theories our team is going to perform the 'chirality-experiment' in the near future with cometary matter In 2012 the robotical lander RoLand will detach from the orbiter of the ROSETTA spacecraft and set down on the surface of comet 46P/Wirtanen in order to separate and identify cometary organic compounds via GC-MS in situ Chiral organics will be separated into their enantiomers by application of 3 capillary columns coated with different kinds of stationary phases Non-volatile compounds like amino acids will be derivatized in especially developed gas phase alkylation steps avoiding reactions in the liquid phase The results of these preliminary gas phase reactions are presented in this article

ESA mission ROSETTA will probe for chirality of cometary amino acids.

Biological cofactors include functionalized derivatives of cyclic tetrapyrrole structures that incorporate different metal ions. They build up structural partnerships with proteins, which play a crucial role in biochemical reactions. Porphyrin, chlorin, bacteriochlorin, and corrin are the basic structures of cofactors (heme, chlorophyll, bacteriochlorophyll, siroheme, F 430, and vitamin B12). Laboratory and theoretical work suggest that the molecular building blocks of proteins (α-amino acids) and nucleic acids (carbohydrates, purines, and pyrimidines) were generated under prebiotic conditions. On the other hand, experimental data on the prebiotic chemistry of cofactors are rare. We propose to search directly for the pathways of the formation of cofactors in the laboratory. Herein we report on the detection of N-heterocycles and amines in the room-temperature residue obtained after photo- and thermal processing of an interstellar ice analogue under high vacuum at 12 K. Among them, hexahydro-1,3,5-triazine and its derivatives, together with monopyrrolic molecules, are precursors of porphinoid cofactors. Hexahydropyrimidine was also detected. This is the first detection of these compounds in experiments simulating circumstellar/interstellar conditions. Except for 2-aminopyrrole and 2,4-diaminofuran, which were only found in 13C-labeled experiments, all the reported species were detected in both 12C- and 13C-labeled experiments, excluding contamination. The molecules reported here might be present in circumstellar/interstellar grains and cometary dust and could be detected by the Stardust and Rosetta missions.

Precursors of biological cofactors from ultraviolet irradiation of circumstellar/interstellar ice analogues.

Life, as it is known to us, uses exclusively L-amino acid and D-sugar enantiomers for the molecular architecture of proteins and nucleic acids. This Minireview explores current models of the original symmetry-breaking influence that led to the exogenic delivery to Earth of prebiotic molecules with a slight enantiomeric excess. We provide a short overview of enantiomeric enhancements detected in bodies of extraterrestrial origin, such as meteorites, and interstellar ices simulated in the laboratory. Data are interpreted from different points of view, namely, photochirogenesis, parity violation in the weak nuclear interaction, and enantioenrichment through phase transitions. Photochemically induced enantiomeric imbalances are discussed more specifically in the topical context of the "chirality module" on board the cometary Rosetta spacecraft of the ESA. This device will perform the first enantioselective in situ analyses of samples taken from a cometary nucleus.

Molecular chirality in meteorites and interstellar ices, and the chirality experiment on board the ESA cometary Rosetta mission.

Tracing Life's Origin: From Amino Acids to Space Mission ROSETTA.- Stereochemistry for the Study of the Origin of Life.- Minority Report: Life's Chiral Molecules of Opposite Handedness.- When Crystals Deliver Chirality to Life.- When Parity Falls: The Weak Nuclear Interaction.- Chiral Fields: Light, Magnetism, and Chirality.- Key to the Prebiotic Origin of Amino Acids.- A New Record for Chiral Molecules in Meteorites.- The New Space Race: Chiral Molecules on Comets and on Mars.- Accelerating the Carousel: Amplification mechanisms.

Uwe J. Meierhenrich

Papers

Chirality, photochemistry and the detection of amino acids in interstellar ice analogues and comets

ESA mission ROSETTA will probe for chirality of cometary amino acids.

Precursors of biological cofactors from ultraviolet irradiation of circumstellar/interstellar ice analogues.

Molecular chirality in meteorites and interstellar ices, and the chirality experiment on board the ESA cometary Rosetta mission.

Amino Acids and the Asymmetry of Life: Caught in the Act of Formation