Structural analysis of Salmonella enterica effector protein SopD

Salmonella outer protein D (SopD) is a type III secreted virulence effector protein from Salmonella enterica. Full-length SopD and SopD lacking 16 amino acids at the N-terminus (SopDDeltaN) have been expressed as fusions with GST in Escherichia coli, purified with a typical yield of 20-30 mg per litre of cell culture and crystallized. Biophysical characterization has been carried out mainly on SopDDeltaN. Analytical size exclusion chromatography shows that SopDDeltaN is monomeric and probably globular in aqueous solution. The secondary structure composition, calculated from the CD spectrum, is mixed (38% alpha-helix and 26% beta-strand). Sequence analysis indicates that SopD contains a coiled coil motif, as found in numerous other type III secretion system-associated proteins. This suggests that SopD has the potential for one or more heterotypic protein-protein interactions. Limited trypsin digestion of SopDDeltaN, monitored by both one-dimensional proton NMR spectroscopy and SDS-PAGE, shows that the protein has a large, protease-resistant core domain of 286 amino acid residues. This single-domain architecture suggests that SopD lacks a cognate chaperone. In crystallization trials, SopDDeltaN produced better crystals than either full-length SopD or trypsin-digested SopDDeltaN. Diffraction to 3.0 Angstrom resolution has so far been obtained from crystals of SopDDeltaN

Regional science policy and the growth of knowledge megacentres in bioscience clusters

Changes in epistemology in biosciences are generating important spatial effects. The most notable of these is the emergence of a few Bioscience Megacentres of basic and applied bioscience (molecular, post-genomic, proteomics, etc.) medical and clinical research, biotechnology research, training in these and related fields, academic entrepreneurship and commercial exploitation by clusters of drug discovery start-up and spin-off companies, along with specialist venture capital and other innovation system support services. Large pharmaceutical firms that used to lead such knowledge generation and exploitation processes are becoming increasingly dependent upon innovative drug solutions produced in such clusters, and Megacentres are now the predominant source of such commercial knowledge. Big pharma is seldom at the heart of Megacentres such as those the paper will argue are found in about four locations each in the USA and Europe, but remains important for some risk capital (milestone payments), marketing and distribution of drugs discovered. The reasons for this shift (which is also spatial to some extent) are as follows: first, bioscientific research requires the formation of collaboratory relationships among hitherto cognitively dissonant disciplines molecular biology, combinatorial chemistry, high throughput screening, genomics, proteomics and bioinformatics to name a few. Second, the canonical chance discovery model of bioscientific research is being replaced by rational drug design based on those technologies because of the need massively to reduce search costs and delivery timeframes. Third, the US and to some extent European 'Crusade against Cancer' and other pathologies has seen major increases in basic research budgets (e.g. to $27.3 billion in 2003 for the US National Institutes of Health) and foundation expenditure (e.g.$1billion in 2003 by the UK's Wellcome Trust; $1 billion approximately by the top ten US medical foundations, and a comparable sum from corporate foundations). Each of these tendencies weakens the knowledge generation role of 'big pharma'and strengthens that of Megacentres. But the process also creates major, new regional disparities, which some regional governances have recognised, causing them to develop responsibilities for regional science policy and funding to offset spatial biases intrinsic in traditional national (and in the EU, supranational) research funding regimes. Responses follow a variety of models ranging from market following to both regionalised (decentralising by the centre) and regionalist (ground-up), but in each case the role of Megacentres is justified in health terms. But their role in assisting fulfilment of regional economic growth visions is also clearly perceived and pronounced in policy terms.

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

On the Dynamics of Dengue Virus type 2 with Residence Times and Vertical Transmission

A two-patch mathematical model of Dengue virus type 2 (DENV-2) that accounts for vectors' vertical transmission and between patches human dispersal is introduced. Dispersal is modeled via a Lagrangian approach. A host-patch residence-times basic reproduction number is derived and conditions under which the disease dies out or persists are established. Analytical and numerical results highlight the role of hosts' dispersal in mitigating or exacerbating disease dynamics. The framework is used to explore dengue dynamics using, as a starting point, the 2002 outbreak in the state of Colima, Mexico

Sub-field normalization in the multiplicative case: average-based citation indicators

This paper investigates the citation impact of three large geographical areas –the U.S., the European Union (EU), and the rest of the world (RW)– at different aggregation levels. The difficulty is that 42% of the 3.6 million articles in our Thomson Scientific dataset are assigned to several sub-fields among a set of 219 Web of Science categories. We follow a multiplicative approach in which every article is wholly counted as many times as it appears at each aggregation level. We compute the crown indicator and the Mean Normalized Citation Score (MNCS) using for the first time sub-field normalization procedures for the multiplicative case. We also compute a third indicator that does not correct for differences in citation practices across sub-fields. It is found that: (1) No geographical area is systematically favored (or penalized) by any of the two normalized indicators. (2) According to the MNCS, only in six out of 80 disciplines –but in none of 20 fields– is the EU ahead of the U.S. In contrast, the normalized U.S./EU gap is greater than 20% in 44 disciplines, 13 fields, and for all sciences as a whole. The dominance of the EU over the RW is even greater. (3) The U.S. appears to devote relatively more –and the RW less– publication effort to subfields with a high mean citation rate, which explains why the U.S./EU and EU/RW gaps for all sciences as a whole increase by 4.5 and 5.6 percentage points in the un-normalized case.

Exosomes released from breast cancer carcinomas stimulate cell movement

For metastasis to occur cells must communicate with to their local environment to initiate growth and invasion. Exosomes have emerged as an important mediator of cell-to-cell signalling through the transfer of molecules such as mRNAs, microRNAs, and proteins between cells. Exosomes have been proposed to act as regulators of cancer progression. Here, we study the effect of exosomes on cell migration, an important step in metastasis. We performed cell migration assays, endocytosis assays, and exosome proteomic profiling on exosomes released from three breast cancer cell lines that model progressive stages of metastasis. Results from these experiments suggest: (1) exosomes promote cell migration and (2) the signal is stronger from exosomes isolated from cells with higher metastatic potentials; (3) exosomes are endocytosed at the same rate regardless of the cell type; (4) exosomes released from cells show differential enrichment of proteins with unique protein signatures of both identity and abundance. We conclude that breast cancer cells of increasing metastatic potential secrete exosomes with distinct protein signatures that proportionally increase cell movement and suggest that released exosomes could play an active role in metastasis

Sub-field normaliztion in the multiplicative case : high- and low- impact citation indicators

This paper uses high- and low-impact citation indicators for the evaluation of the citation performance of research units at different aggregate levels. To solve the problem of the assignment of individual articles to multiple sub-fields, it follows a multiplicative strategy according to which each paper is wholly counted as many times as necessary in the several categories to which it is assigned at each aggregation level. To control for wide differences in citation practices at the lowest level of aggregation, we apply a novel sub-field normalization procedure in the multiplicative case. The methodology is applied to a partition of the world into three geographical areas: the U.S., the European Union (EU), and the Rest of the World. The main findings are the following two. (i) Although normalization does not systematically bias the results against any area, it reduces the U.S./EU highimpact gap in the all-sciences case by a non-negligible 14.4%. (ii) The dominance of the U.S. over the EU in the basic and applied research published in the periodical literature is almost universal at all aggregation levels. From the high-impact perspective, for example, the U.S. is ahead of the EU in 77 out of 80 disciplines, and all of 20 fields. For all sciences as a whole, the U.S. high-impact indicator is 61% greater than that of the EU. The authors acknowledge financial support from the Santander Universities Global Division of Banco Santander. Ruiz-Castillo also acknowledges financial help from the Spanish MEC through grant SEJ2007- 67436. This paper is part of the SCIFI-GLOW Collaborative Project supported by the European Commission.s Seventh Research Framework Programme, Contract number SSH7-CT-2008-217436 European Community's Seventh Framework Program.

A saposin-lipoprotein nanoparticle system for membrane proteins.

A limiting factor in membrane protein research is the ability to solubilize and stabilize such proteins. Detergents are used most often for solubilizing membrane proteins, but they are associated with protein instability and poor compatibility with structural and biophysical studies. Here we present a saposin-lipoprotein nanoparticle system, Salipro, which allows for the reconstitution of membrane proteins in a lipid environment that is stabilized by a scaffold of saposin proteins. We demonstrate the applicability of the method on two purified membrane protein complexes as well as by the direct solubilization and nanoparticle incorporation of a viral membrane protein complex from the virus membrane. Our approach facilitated high-resolution structural studies of the bacterial peptide transporter PeptTSo2 by single-particle cryo-electron microscopy (cryo-EM) and allowed us to stabilize the HIV envelope glycoprotein in a functional state