Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments

Bacterioplankton community structures under contrasting subtropical marine environments (Hong Kong waters) were analyzed using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of predominant bands for samples collected bimonthly from 2004 to 2006 at five stations. Generally, bacterial abundance was significantly higher in the summer than in the winter. The general seasonal variations of the bacterial community structure, as indicated by cluster analysis of the DGGE pattern, were best correlated with temperature at most stations, except for the station close to a sewage discharge outfall, which was best explained by pollution-indicating parameters (e.g. biochemical oxygen demand). Anthropogenic pollutions appear to have affected the presence and the intensity of DGGE bands at the stations receiving discharge of primarily treated sewage. The relative abundance of major bacterial species, calculated by the relative intensity of DGGE bands after PCR amplification, also indicated the effects of hydrological or seasonal variations and sewage discharges. For the first time, a systematic molecular fingerprinting analysis of the bacterioplankton community composition was carried out along the environmental and pollution gradient in a subtropical marine environment, and it suggests that hydrological conditions and anthropogenic pollutions altered the total bacterial community as well as the dominant bacterial groups. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.published_or_final_versio

Global organization of metabolic fluxes in the bacterium, Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions. We implement a flux balance analysis of the E. coli MG1655 metabolism, finding that the network utilization is highly uneven: while most metabolic reactions have small fluxes, the metabolism's activity is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high flux backbone. The identified behavior likely represents a universal feature of metabolic activity in all cells, with potential implications to metabolic engineering.Comment: 15 pages 4 figure

A direct image of the obscuring disk surrounding an active galactic nucleus

Active galactic nuclei (AGN) are generally accepted to be powered by the release of gravitational energy in a compact accretion disk surrounding a massive black hole. Such disks are also necessary to collimate powerful radio jets seen in some AGN. The unifying classification schemes for AGN further propose that differences in their appearance can be attributed to the opacity of the accreting material, which may obstruct our view of the central region of some systems. The popular model for the obscuring medium is a parsec-scale disk of dense molecular gas, although evidence for such disks has been mostly indirect, as their angular size is much smaller than the resolution of conventional telescopes. Here we report the first direct images of a pc-scale disk of ionised gas within the nucleus of NGC 1068, the archetype of obscured AGN. The disk is viewed nearly edge-on, and individual clouds within the ionised disk are opaque to high-energy radiation, consistent with the unifying classification scheme. In projection, the disk and AGN axes align, from which we infer that the ionised gas disk traces the outer regions of the long-sought inner accretion disk.Comment: 14 pages, LaTeX, PSfig, to appear in Nature. also available at http://hethp.mpe-garching.mpg.de/Preprint

Performance of Monolayer Graphene Nanomechanical Resonators with Electrical Readout

The enormous stiffness and low density of graphene make it an ideal material for nanoelectromechanical (NEMS) applications. We demonstrate fabrication and electrical readout of monolayer graphene resonators, and test their response to changes in mass and temperature. The devices show resonances in the MHz range. The strong dependence of the resonant frequency on applied gate voltage can be fit to a membrane model, which yields the mass density and built-in strain. Upon removal and addition of mass, we observe changes in both the density and the strain, indicating that adsorbates impart tension to the graphene. Upon cooling, the frequency increases; the shift rate can be used to measure the unusual negative thermal expansion coefficient of graphene. The quality factor increases with decreasing temperature, reaching ~10,000 at 5 K. By establishing many of the basic attributes of monolayer graphene resonators, these studies lay the groundwork for applications, including high-sensitivity mass detectors

Ripple Texturing of Suspended Graphene Atomic Membranes

Graphene is the nature's thinnest elastic membrane, with exceptional mechanical and electrical properties. We report the direct observation and creation of one-dimensional (1D) and 2D periodic ripples in suspended graphene sheets, using spontaneously and thermally induced longitudinal strains on patterned substrates, with control over their orientations and wavelengths. We also provide the first measurement of graphene's thermal expansion coefficient, which is anomalously large and negative, ~ -7x10^-6 K^-1 at 300K. Our work enables novel strain-based engineering of graphene devices.Comment: 15 pages, 4 figure

General Gauge Mediation with Gauge Messengers

We generalize the General Gauge Mediation formalism to allow for the possibility of gauge messengers. Gauge messengers occur when charged matter fields of the susy-breaking sector have non-zero F-terms, which leads to tree-level, susy-breaking mass splittings in the gauge fields. A classic example is that SU(5) / SU(3) x SU(2) x U(1) gauge fields could be gauge messengers. We give a completely general, model independent, current-algebra based analysis of gauge messenger mediation of susy-breaking to the visible sector. Characteristic aspects of gauge messengers include enhanced contributions to gaugino masses, (tachyonic) sfermion mass-squareds generated already at one loop, and also at two loops, and significant one-loop A-terms, already at the messenger scale.Comment: 79 pages, 5 figure

HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. Functional studies of the HCV IRES have focused on 80S ribosome formation but have not explored its role after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit's decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome's structure and function can be altered by bound RNAs, including those derived from cellular invaders

The cometary composition of a protoplanetary disk as revealed by complex cyanides

Observations of comets and asteroids show that the Solar Nebula that spawned our planetary system was rich in water and organic molecules. Bombardment brought these organics to the young Earth's surface, seeding its early chemistry. Unlike asteroids, comets preserve a nearly pristine record of the Solar Nebula composition. The presence of cyanides in comets, including 0.01% of methyl cyanide (CH3CN) with respect to water, is of special interest because of the importance of C-N bonds for abiotic amino acid synthesis. Comet-like compositions of simple and complex volatiles are found in protostars, and can be readily explained by a combination of gas-phase chemistry to form e.g. HCN and an active ice-phase chemistry on grain surfaces that advances complexity[3]. Simple volatiles, including water and HCN, have been detected previously in Solar Nebula analogues - protoplanetary disks around young stars - indicating that they survive disk formation or are reformed in situ. It has been hitherto unclear whether the same holds for more complex organic molecules outside of the Solar Nebula, since recent observations show a dramatic change in the chemistry at the boundary between nascent envelopes and young disks due to accretion shocks[8]. Here we report the detection of CH3CN (and HCN and HC3N) in the protoplanetary disk around the young star MWC 480. We find abundance ratios of these N-bearing organics in the gas-phase similar to comets, which suggests an even higher relative abundance of complex cyanides in the disk ice. This implies that complex organics accompany simpler volatiles in protoplanetary disks, and that the rich organic chemistry of the Solar Nebula was not unique.Comment: Definitive version of the manuscript is published in Nature, 520, 7546, 198, 2015. This is the author's versio

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis