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.

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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.

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Interstellar Ice: The Infrared Space Observatory Legacy

The Molecular Basis of Olfactory Chemoreception

Pyrolytic methylation assisted enantioseparation of chiral hydroxycarboxylic acids

Enantiomer separation of hydrocarbons in preparation for ROSETTA's chirality experiment

Gas chromatographic separation of saturated aliphatic hydrocarbon enantiomers on permethylated β‐cyclodextrin

Biopolymers like DNA and proteins are strongly selective towards the chirality of their monomer units. The use of homochiral monomers is regarded as essential for the construction and function of biopolymers; the emergence of the molecular asymmetry is therefore considered as a fundamental step in Chemical Evolution. This work focuses on physicochemical mechanisms for the origin of biomolecular asymmetry. Very recently two groups, one from Allamandola at NASA Ames and the other from our Inter-European team, demonstrated simultaneously the spontaneous photoformation of a variety of chiral amino acid structures under simulated interstellar conditions. Since both groups used unpolarized light for the photoreaction the obtained amino acids turned out racemic as expected. The obtained experimental data support the assumption that tiny ice grains can furthermore play host to important asymmetric reactions when irradiated by interstellar circularly polarized ultraviolet light. It is possible that such ice grains could have become incorporated into the early cloud that formed our Solar System and ended up on Earth, assisting life to start. Several lines of evidence suggest that some of the building blocks of life were delivered to the primitive Earth via (micro-) meteoroids and/or comets. These results suggest that asymmetric interstellar photochemistry may have played a significant part in supplying Earth with some of the enantioenriched organic materials needed to trigger life. The search for the origin of biomolecular homochirality leads to a strong interest in the fields of asymmetric photochemistry with special emphasis on absolute asymmetric synthesis. We outline here the theoretical background on asymmetric interstellar ice photochemistry, summarize recent concepts and advances in the field, and discuss briefly its implications. The obtained data are crucial for the design of the enantioselective COSAC GC-MS experiment onboard the ROSETTA spacecraft to a comet to be launched in the very near future.

Uwe J. Meierhenrich

Papers

The Molecular Basis of Olfactory Chemoreception

Pyrolytic methylation assisted enantioseparation of chiral hydroxycarboxylic acids

Enantiomer separation of hydrocarbons in preparation for ROSETTA's chirality experiment

Gas chromatographic separation of saturated aliphatic hydrocarbon enantiomers on permethylated β‐cyclodextrin

Photochemical concepts on the origin of biomolecular asymmetry.