Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly

The outer membrane usher protein Caf1A of the plague pathogen Yersinia pestis is responsible for the assembly of a major surface antigen, the F1 capsule. The F1 capsule is mainly formed by thin linear polymers of Caf1 (capsular antigen fraction 1) protein subunits. The Caf1A usher promotes polymerization of subunits and secretion of growing polymers to the cell surface. The usher monomer (811 aa, 90.5 kDa) consists of a large transmembrane β-barrel that forms a secretion channel and three soluble domains. The periplasmic N-terminal domain binds chaperone-subunit complexes supplying new subunits for the growing fiber. The middle domain, which is structurally similar to Caf1 and other fimbrial subunits, serves as a plug that regulates the permeability of the usher. Here we describe the identification, characterization, and crystal structure of the Caf1A usher C-terminal domain (Caf1A(C)). Caf1A(C) is shown to be a periplasmic domain with a seven-stranded β-barrel fold. Analysis of C-terminal truncation mutants of Caf1A demonstrated that the presence of Caf1A(C) is crucial for the function of the usher in vivo, but that it is not required for the initial binding of chaperone-subunit complexes to the usher. Two clusters of conserved hydrophobic residues on the surface of Caf1A(C) were found to be essential for the efficient assembly of surface polymers. These clusters are conserved between the FGL family and the FGS family of chaperone-usher systems.

Phase separation in thin films of end-grafted block copolymers

An atomic force microscopy investigation was carried out on various thick (30–120 nm) polymethyl methacrylate-bpolystyrene and poly(2-(dimethyl amino)ethyl methacrylate)-b-polystyrene films prepared via a grafting-from method. The structure of the films was examined with both topographic and phase imaging. Several different morphologies were observed including a perforated lamellar phase with irregular perforations. In addition, complementary small-angle X-ray scattering and reflectometry results measurements on a non-grafted polymer are presented.

Structure of the DNA octanucleotide d(ACGTACGT)2

d(ACGTACGT), C78H84N30O32P7.20H2O, Mr (DNA) = 2170, tetragonal, P43212 (No 96), a = 42.845 (1), b = 42.845(1), c = 24.804 (1) Å, V = 45532.5 (2) Å3, z = 8,(MoK) = 0.71069 Å,µ(MoK) = 0.10 mm-1, T = 295 K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 Å resolution. The self-complementary octanucleotide d(ACGTACGT)2 has been crystallized and its structure determined to a resolution of 1.9 Å. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A·T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified A-type conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15° and an average tilt angle of 0°. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.

Like the living end

Seven-part elegy for David Mather (1954-2010)

Mutation in TERMINAL FLOWER1 reverses the photoperiodic requirement for flowering in the wild strawberry, Fragaria vesca

Photoperiodic flowering has been extensively studied in the annual short-day and long-day plants rice and Arabidopsis while less is known about the control of flowering in perennials. In the perennial wild strawberry, Fragaria vesca L. (Rosaceae), short-day and perpetual flowering long-day accessions occur. Genetic analyses showed that differences in their flowering responses are caused by a single gene, the SEASONAL FLOWERING LOCUS which may encode the F. vesca homolog of TERMINAL FLOWER1 (FvTFL1). We show through high-resolution mapping and transgenic approaches that FvTFL1 is the basis of this change in flowering behavior and demonstrate that FvTFL1 acts as a photoperiodically regulated repressor. In short-day F. vesca, long photoperiods activate FvTFL1 mRNA expression and short days suppress it, promoting flower induction. These seasonal cycles in FvTFL1 mRNA level confer seasonal cycling of vegetative and reproductive development. Mutations in FvTFL1 prevent LD suppression of flowering, and the early flowering that then occurs under LD is dependent on the F. vesca homolog of FLOWERING LOCUS T. This photoperiodic response mechanism differs from those described in model annual plants. We suggest that this mechanism controls flowering within the perennial growth cycle in F. vesca, and demonstrate that a change in a single gene reverses the photoperiodic requirements for flowering.

Variation in the persistence of Escherichia coli O157:H7 in experimentally inoculated 6-week-old conventional lambs

Six-week-old lambs were inoculated orally with 10(9) cfu of an antibiotic-resistance marked four-strain mixture of enterohaemorrhagic Escherichia coli (EHEC) O157:H7 to investigate faecal excretion and intestinal colonisation. In the first experiment, three E. coli O157:H7 isolates were not detected in the faeces of any lambs beyond day 8 post inoculation (pi), or from any of the tissues derived from inoculated animals. One strain, 140065 Nal(r), was isolated from the caecum and colon of one lamb on day 9 pi, from the rectum of another on day 22 pi and persisted in the faeces for up to 28 days pi. All animals remained clinically normal throughout the study period and histological evidence of adhesion of E. coli O157:H7 to the intestinal mucosa was not found. In a separate experiment, four 6-week-old lambs were inoculated orally with 10(9) efu of E. coli O157:H7 strain 140065 Nal(r) alone. Faecal samples were positive for this strain until the end of the experiment (day 19 pi). This strain was also recovered from the gastrointestinal tract of lambs on days 6, 18 and 19 pi, but was not isolated at day 17 pi. When sampled separately, rectum and terminal colon contents contained higher numbers of the inoculated strain than the intestinal tissue at these sites. Animals inoculated with O157:117 strain 140065 Nal(r) alone produced soft faeces from day 5 pi onwards. Although attaching and effacing lesions were observed in the caecum, proximal colon and rectum in one animal on day 18 pi, the adherent bacteria did not stain with antiserum raised against the O157 antigen.

The expression of the end-Cenomanian oceanic anoxic event (OAE 2) in the Helvetic Alps

Upper Cenomanian pelagic sediments from the northern Alpine Helvetic fold-and-thrust belt (northern Tethyan margin) coeval with Oceanic Anoxic Event (OAE) 2 are characterized by the temporal persistence of micrite sedimentation and lack of organic carbon-rich layers. We studied an expanded section in the Chrummflueschlucht (east of Euthal, Switzerland), which encompasses the OAE 2 time interval. In order to identify the paleoceanographic and paleoenvironmental conditions during OAE 2 in this part of the northern Tethyan margin, and more specifically to trace eventual changes in nutrient levels and oxic conditions, we investigated the biostratigraphy (planktonic foraminifera), the bulk-rock mineralogy, and measured stable carbon- and oxygen-isotopes, total phosphorus (P) and redox-sensitive trace-element (RSTE) contents. We were able to determine – with some remaining uncertainties – the different planktonic foraminiferal biozones characteristic of the Cenomanian–Turonian boundary interval (Rotalipora cushmani, Whiteinella archaeocretacea and Helvetoglobotruncana helvetica zones). In the lower part of the section (R. cushmani total range zone), the bulk-rock δ13C record shows a long-term increase. Within sediments attributed to the W. archaeocretacea partial range zone, δ13C values reach a maximum of 3.3‰ (peak “a”). In the following the values decrease and increase again to arrive at a plateau with high δ13C values of around 3.1‰, which ends with a peak of 3.3‰ (peak “c”). At the top of the section, in sediments belonging to the H. helvetica total range zone, δ13C values decrease to post-OAE values of around 2.2‰. The last occurrence of R. cushmani is observed just above the positive δ13C shift characterizing OAE 2. P contents display small variations along the section with a long-term decreasing trend towards the top. Before the OAE 2 interval, P values show higher values and relatively good covariation with detrital input, indicating higher nutrient input before OAE 2. In sediments corresponding to the onset of the δ13C positive excursion, P content is marked by a sharp peak probably linked to a slowdown in sedimentation rates and/or the presence of a small hiatus, as is shown by the presence of glauconite and phosphatic grains. In the interval corresponding to OAE 2, P values remain low and increase slightly at the end of the positive shift in the δ13C record (in the H. helvetica total range zone). The average contents of RSTE (U, V, As, Co, Mo and Mn) remain low throughout the section and appreciable RSTE enrichments have not been observed for the sedimentary interval corresponding to OAE 2. No correlation is observed with stratigraphic trends in RSTE contents in organic-rich deeper-water sections. The presence of double-keeled planktonic foraminifera species during most of the Cenomanian/Turonian boundary event is another evidence of relatively well-oxygenated conditions in this part of the northern Tethyan outer shelf. Our results show that the Chrummflueschlucht section corresponds to one of the most complete section for the Cenomanian–Turonian boundary interval known from the Helvetic realm even if a small hiatus may be present at the onset of the δ13C record (peak “a”). The evolution of P contents suggests an increase in input of this nutritive element at the onset of OAE2. However, the trends in RSTE contents and the planktonic foraminifera assemblages show that the Helvetic realm has not been affected by strongly depleted oxygen conditions during OAE 2.

Mutual binding of polymer end-groups by complementary π–π-stacking: a molecular “Roman Handshake”

Self-complementary tweezer-molecules based on a naphthalenediimide core self-assemble into supramolecular dimers through mutual π–π-stacking and hydrogen bonding. The resulting motif is extremely stable in solution (Ka = 105 M−1), and its attachment to one terminal position of a poly(ethylene glycol) chain leads to a doubling of the polymer's apparent molecular weight.

Preferred orientation in an angled intercalation site of a chloro-substituted lambda- [Ru(TAP)2(dppz)]2+ complex bound to d(TCGGCGCCGA)2

The crystal structure of the ruthenium DNA ‘light-switch’ complex -[Ru(TAP)2(11-Cl-dppz)]2+ (TAP = tetraazaphenanthrene, dppz = dipyrido[3,2-a':2',3'-c]phenazine)) bound to the oligonucleotide duplex d(TCGGCGCCGA)2 is reported. The synthesis of the racemic ruthenium complex is described for the first time, and the racemate was used in this study. The crystal structure, at atomic resolution (1.0 Å), shows one ligand as a wedge in the minor groove, resulting in the 51 kinking of the double helix, as with the parent lambda-[Ru(TAP)2(dppz)]2+. Each complex binds to one duplex by intercalation of the dppz ligand and also by semi-intercalation of one of the orthogonal TAP ligands into a second symmetrically equivalent duplex. The 11-Cl substituent binds with the major component (66%) oriented with the 11-chloro substituent on the purine side of the terminal step of the duplex.

Projection of global wave climate change towards the end of the 21st century

Wind generated waves at the sea surface are of outstanding importance for both their practical relevance in many aspects, such as coastal erosion, protection, or safety of navigation, and for their scientific relevance in modifying fluxes at the air-sea interface. So far long-term changes in ocean wave climate have been studied mostly from a regional perspective with global dynamical studies emerging only recently. Here a global wave climate study is presented, in which a global wave model (WAM) is driven by atmospheric forcing from a global climate model (ECHAM5) for present day and potential future climate conditions represented by the IPCC (Intergovernmental Panel for Climate Change) A1B emission scenario. It is found that changes in mean and extreme wave climate towards the end of the twenty-first century are small to moderate, with the largest signals being a poleward shift in the annual mean and extreme significant wave heights in the mid-latitudes of both hemispheres, more pronounced in the Southern Hemisphere, and most likely associated with a corresponding shift in mid-latitude storm tracks. These changes are broadly consistent with results from the few studies available so far. The projected changes in the mean wave periods, associated with the changes in the wave climate in the mid to high latitudes, are also shown, revealing a moderate increase in the equatorial eastern side of the ocean basins. This study presents a step forward towards a larger ensemble of global wave climate projections required to better assess robustness and uncertainty of potential future wave climate change.

RNA interference suppression of genes in glycosyl transferase families 43 and 47 in wheat starchy endosperm causes large decreases in arabinoxylan content

The cell walls of wheat (Triticum aestivum) starchy endosperm are dominated by arabinoxylan (AX), accounting for 65% to 70% of the polysaccharide content. Genes within two glycosyl transferase (GT) families, GT43 (IRREGULAR XYLEM9 [IRX9] and IRX14) and GT47 (IRX10), have previously been shown to be involved in the synthesis of the xylan backbone in Arabidopsis, and close homologs of these have been implicated in the synthesis of xylan in other species. Here, homologs of IRX10 TaGT47_2 and IRX9 TaGT43_2, which are highly expressed in wheat starchy endosperm cells, were suppressed by RNA interference (RNAi) constructs driven by a starchy endosperm-specific promoter. The total amount of AX was decreased by 40% to 50% and the degree of arabinosylation was increased by 25% to 30% in transgenic lines carrying either of the transgenes. The cell walls of starchy endosperm in sections of grain from TaGT43_2 and TaGT47_2 RNAi transgenics showed decreased immunolabeling for xylan and arabinoxylan epitopes and approximately 50% decreased cell wall thickness compared with controls. The proportion of AX that was water soluble was not significantly affected, but average AX polymer chain length was decreased in both TaGT43_2 and TaGT47_2 RNAi transgenics. However, the long AX chains seen in controls were absent in TaGT43_2 RNAi transgenics but still present in TaGT47_2 RNAi transgenics. The results support an emerging picture of IRX9-like and IRX10-like proteins acting as key components in the xylan synthesis machinery in both dicots and grasses. Since AX is the main component of dietary fiber in wheat foods, the TaGT43_2 and TaGT47_2 genes are of major importance to human nutrition.

Comparison of D-region Doppler drift winds measured by the SuperDARN Finland HF radar over an annual cycle using the Kiruna VHF meteor radar

The SuperDARN chain of oblique HF radars has provided an opportunity to generate a unique climatology of horizontal winds near the mesopause at a number of high latitude locations, via the Doppler shifted echoes from sources of ionisation in the D-region. Ablating meteor trails form the bulk of these targets, but other phenomena also contribute to the observations. Due to the poor vertical resolution of the radars, care must be taken to reduce possible biases from sporadic-E layers and Polar Mesospheric Summer echoes that can affect the effective altitude of the geophysical parameters being observed. Second, there is strong theoretical and observational evidence to suggest that the radars are picking up echoes from the backward looking direction that will tend to reduce the measured wind strengths. The effect is strongly frequency dependent, resulting in a 20% reduction at 12 MHz and a 50% reduction at 10 MHz. A comparison of the climatologies observed by the Super-DARN Finland radar between September 1999 and September 2000 and that obtained from the adjacent VHF meteor radar located at Kiruna is also presented. The agreement between the two instruments was very good. Extending the analysis to the SuperDARN Iceland East radar indicated that the principles outlined above could be applied successfully to the rest of the SuperDARN network.

Sustainable urban metabolism as a link between bio-physical sciences and urban planning: the BRIDGE project

Urban metabolism considers a city as a system with flows of energy and material between it and the environment. Recent advances in bio-physical sciences provide methods and models to estimate local scale energy, water, carbon and pollutant fluxes. However, good communication is required to provide this new knowledge and its implications to endusers (such as urban planners, architects and engineers). The FP7 project BRIDGE (sustainaBle uRban plannIng Decision support accountinG for urban mEtabolism) aimed to address this gap by illustrating the advantages of considering these issues in urban planning. The BRIDGE Decision Support System (DSS) aids the evaluation of the sustainability of urban planning interventions. The Multi Criteria Analysis approach adopted provides a method to cope with the complexity of urban metabolism. In consultation with targeted end-users, objectives were defined in relation to the interactions between the environmental elements (fluxes of energy, water, carbon and pollutants) and socioeconomic components (investment costs, housing, employment, etc.) of urban sustainability. The tool was tested in five case study cities: Helsinki, Athens, London, Florence and Gliwice; and sub-models were evaluated using flux data selected. This overview of the BRIDGE project covers the methods and tools used to measure and model the physical flows, the selected set of sustainability indicators, the methodological framework for evaluating urban planning alternatives and the resulting DSS prototype.