Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases

Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques. We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus faecalis. We found agriculturally relevant toxins in Photorhabdus luminescens and Vibrio splendidus. These toxins belong to the ADP-ribosyltransferase family that has conserved structure despite low sequence identity. Therefore, our search for new toxins combined fold recognition with rules for filtering sequences – including a primary sequence pattern – to reduce reliance on sequence identity and identify toxins using structure. We used computers to build models and analyzed each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. We confirmed activity using a yeast growth test. In this era where an expanding protein structure library complements abundant protein sequence data – and we need high-throughput validation – our approach provides insight into the newest toxin ADP-ribosyltransferases

A New Integrated Approach to Taxonomy: The Fusion of Molecular and Morphological Systematics with Type Material in Benthic Foraminifera

This work was supported by NERC grant NE4/G018502/1 and NE/G020310/1 (Website: http://www.nerc.ac.uk). The authors also thank the following for their support the Carnegie Trust for the Universities of Scotland (Website: http://www.carnegie-trust.org) and the Estuarine Coastal and Shelf Science Association (Website: http://www.ecsanews.org). M.S. was also supported by the Swiss National Science Foundation (SNSF), fellowships for advanced researchers PA00P2_126226 and PA00P2_142065 (Website: http://www.snf.ch/en/Pages/default.aspx).A robust and consistent taxonomy underpins the use of fossil material in palaeoenvironmental research and long-term assessment of biodiversity. This study presents a new integrated taxonomic protocol for benthic foraminifera by unequivocally reconciling the traditional taxonomic name to a specific genetic type. To implement this protocol, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene is used in combination with 16 quantitative morphometric variables to fully characterise the benthic foraminiferal species concept of Elphidium williamsoni Haynes, 1973. A combination of live contemporary topotypic specimens, original type specimens and specimens of genetic outliers were utilised in this study. Through a series of multivariate statistical tests we illustrate that genetically characterised topotype specimens are morphologically congruent with both the holotype and paratype specimens of E. williamsoni Haynes, 1973. We present the first clear link between morphologically characterised type material and the unique SSU rRNA genetic type of E. williamsoni. This example provides a standard framework for the benthic foraminifera which bridges the current discontinuity between molecular and morphological lines of evidence, allowing integration with the traditional Linnaean roots of nomenclature to offer a new prospect for taxonomic stability.Publisher PDFPeer reviewe

Variability of the Tsushima Warm Current during the Pleistocene and its relationship with the evolution of the East Asian Monsoon. Preliminary results from IODP Expedition 346 (Sites U1427 and U1428/29) based on benthic ostracod assemblages

Abstract no. PP43D-1514The semi-enclosed marginal sea bordered by the Eurasian continent, the Korean peninsula and the Japanese Islands has an average depth of 1350 m and is connected with other marginal seas in the region by shallow and narrow straits. At present, the Tsushima Warm Current (TWC), a branch of the Kuroshio Current, is the only warm current flowing into the marginal sea west of Japan. The TWC carries both subtropical water originating from the North Pacific and fresher runoff water derived from East China Sea continental shelf. The northerly flow of the TWC through the shallow Tsushima Straits is ultimately controlled by relative sea level variations over time. IODP Expedition 346 Sites U1427 and U1428/29 are ideally located to record changes in (i) the intensity of the influx of the TWC, and (ii) the intermediate ventilation of the marginal sea over the last million years. The Japan Sea Intermediate Water (JSIW) corresponds to a vertical salinity minimum, found below the TWC, between 200 and 400-500 m water depth. The JSIW shows a relatively high oxygen concentration, related to the deep water convection in winter and linked to fresh water supply during winter monsoon intervals. Based on recent observations, it is thought during glacial and interglacial conditions, and millennial scale climate cycles the intensity of deep and intermediate water currents varied but the mechanisms of such variations are not fully known. Microfossil faunal proxies can be used for tracking bottom environmental conditions related to variability of the bottom water circulation intensity. Here, we present preliminary results obtained using ostracods (benthic microcrustaceans) that are abundant in the sedimentary sequences recovered at Sites U1427 and U1428/29, and are known to react sensitively to changes in water masses physico-chemical parameters. In particular, the variability of the genus Krithe through time is correlated with the sortable silt (carbonate-free, 10-63 µm sediment size distribution) to infer current speed and bottom water ventilation

Climate warming during Antarctic ice sheet expansion at the Middle Miocene transition

During the Middle Miocene climate transition about 14 million years ago, the Antarctic ice sheet expanded to near-modern volume. Surprisingly, this ice sheet growth was accompanied by a warming in the surface waters of the Southern Ocean, whereas a slight deep-water temperature increase was delayed by more than 200 thousand years. Here we use a coupled atmosphere–ocean model to assess the relative effects of changes in atmospheric CO2 concentration and ice sheet growth on regional and global temperatures. In the simulations, changes in the wind field associated with the growth of the ice sheet induce changes in ocean circulation, deep-water formation and sea-ice cover that result in sea surface warming and deep-water cooling in large swaths of the Atlantic and Indian ocean sectors of the Southern Ocean. We interpret these changes as the dominant ocean surface response to a 100-thousand-year phase of massive ice growth in Antarctica. A rise in global annual mean temperatures is also seen in response to increased Antarctic ice surface elevation. In contrast, the longer-term surface and deep-water temperature trends are dominated by changes in atmospheric CO2 concentration. We therefore conclude that the climatic and oceanographic impacts of the Miocene expansion of the Antarctic ice sheet are governed by a complex interplay between wind field, ocean circulation and the sea-ice system