Biological diversity of prokaryotic type IV secretion systems.

Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.

Inhibition of apoptosis by intracellular protozoan parasites

Protozoan parasites which reside inside a host cell avoid direct destruction by the immune system of the host. The infected cell, however, still has the capacity to counteract the invasive pathogen by initiating its own death, a process which is called programmed cell death or apoptosis. Apoptotic cells are recognised and phagocytosed by macrophages and the parasite is potentially eliminated together with the infected cell. This potent defence mechanism of the host cell puts strong selective pressure on the parasites which have, in turn, evolved strategies to modulate the apoptotic program of the host cell to their favour. Within the last decade, the existence of cellular signalling pathways which inhibit the apoptotic machinery has been demonstrated. It is not surprising that intracellular pathogens subvert these pathways to ensure their own survival in the infected cell. Molecular mechanisms which interfere with apoptotic pathways have been studied extensively for viruses and parasitic bacteria, but protozoan parasites have come into focus only recently. Intracellular protozoan parasites which have been reported to inhibit the apoptotic program of the host cell, are Toxoplasma gondii, Trypanosoma cruzi, Leishmania sp., Theileria sp., Cryptosporidium parvum, and the microsporidian Nosema algerae. Although these parasites differ in their mechanism of host cell entry and in their final intracellular localisation, they might activate similar pathways in their host cells to inhibit apoptosis. In this respect, two families of molecules, which are known for their capacity to interrupt the apoptotic program, are currently discussed in the literature. First, the expression of heat shock proteins is often induced upon parasite infection and can directly interfere with molecules of the cellular death machinery. Secondly, a more indirect effect is attributed to the parasite-dependent activation of NF-kappaB, a transcription factor that regulates the transcription of anti-apoptotic molecules.

Oceanography during TYDEMAN cruise DCM (DeepChlorMax) to the Equatorial Atlantic

The cruise with RV Tydeman was devoted to study permanently stratified plankton systems in the (sub)tropical ocean, which are characterised by a deep chlorophyll peak between 80 and 150 m. To minimise lateral effects by horizontal transport of nutrients and organic matter from river outflow and upwelling regions, stations were selected in the middle of the North Atlantic Ocean between the continents of America and Africa. (5 - 35° N and 50 - 15° W). Here the vertical distributions of light and nutrients control the abundance and growth of autotrophic algae in the thermically stratified water column. This phytoplankton is numerically dominated by the prokaryotic picoplankters Synechococcus spp. and Prochlorococcus spp., which are smaller than 2 ?m. The productivity of the 100 to 150 m deep euphotic zone can be high, because a high heterotrophic/autotrophic biomass ratio induces a rapid regeneration of nutrients and inorganic carbon. Primary grazers are mainly micro-organisms such as heterotrophic nannoflagellates and ciliates, which feed on the small algae and on bacteria. Heterotrophic bacteria can outnumber the autotrophic algae, because their number is related to the substrate pools of dissolved and particulate dead organic matter. These DOC and detritus pools reach equilibrium at a concentration, where the rate of their production (proportional to algal biomass) equals their mineralisation and sinking rate (proportional to the concentration and weight of POC and detritus). At a relatively low value of the weight-specific loss rates, the equilibrium concentration of these carbon pools and their load of bacteria can be high. The bacterial productivity is proportional to the mineralisation rate, which in a steady state can never be higher than the rate of primary production. Hence the ratio in turnover rate of bacteria and autotrophs tends to be reciprocally proportional to their biomass ratio.

Ground truthing the Cd/Ca-carbon isotope relationship in foraminifera of the Greenland-Iceland-Norwegian Seas

In order to examine whether the paleoceanographic nutrient proxies, d13C and cadmium/calcium in foraminiferal calcite, are well coupled to nutrients in the region of North Atlantic Deep Water formation, we present da ta from two transects of the Greenland-Iceland-Norwegian Seas. Along Transect A (74.3°N, 18.3°E to 75.0°N, 12.5°W, 15 stations), we measured phosphate and Cd concentrations of modern surface sea water. Along Transect B (64.5°N, 0.7°W to 70.4°N, 18.2°W, 14 stations) we measured Cd/Ca ratios and d13C of the planktonic foraminifera Neogloboquadrina pachyderma sinistral in core top sediments. Our results indicate that Cd and phosphate both vary with surface water mass and are well correlated along Transect A. Our planktonic foraminiferal d13C data indicate similar nutrient variation with water mass along Transect B. Our Cd/Ca data hint at the same type of nutrient variability, but interpretations are hampered by low values close to the detection limit of this technique and therefore relatively large error bars. We also measured Cd and phosphate concentrations in water depth profiles at three sites along Transect A and the d13C of the benthic foraminifera Cibicidoides wuellerstorfi along Transect B. Modern sea water depth profiles along Transect A have nutrient depletions at the surface and then constant values at depths greater than 100 meters. The d13C of planktonic and benthic foraminifera from Transect B plotted versus depth also reflect surface nutrient depletion and deep nutrient enrichment as seen at Transect A, with a small difference between intermediate and deep waters. Overall we see no evidence for decoupling of Cd/Ca ratio and d13C in foraminiferal calcite from water column nutrient concentrations along these transects in a region of North Atlantic Deep Water formation.

Chemobiostratigraphy of the Cretaceous/Paleocene boundary at ODP Hole 120-750A

An integrated biostratigraphic and stable isotope investigation was conducted on a high-latitude sequence across the Cretaceous/Paleogene (K/P) boundary recovered in Hole 750A in the southern Indian Ocean. The sequence consists of nannofossil chalk and is discontinuous across the boundary; missing is an estimated 0.3-m.y. late Maestrichtian and early Danian interval. Nonetheless, because calcareous nannofossil Zones NP1 and NP2 are well-developed, micropaleontological studies of the sequence have yielded a detailed record of Danian high-latitude microplankton evolution. In addition, stable carbon isotope analyses of planktonic and benthic foraminifer and bulk samples provide a record of late Maestrichtian and early Danian surface- and deep-water carbon isotope variations. Together, the carbon isotope and carbonate accumulation records serve as an index of regional marine net productivity across the boundary. Earliest Danian nannoplankton assemblages consisted mainly of persistent genera that were generally rare or absent in the Upper Cretaceous at Hole 750A. However, by 0.5-0.6 m.y. after the boundary, newly evolving Danian taxa became dominant. The turnover in nannofossil assemblages was accompanied by significant changes in rates of net productivity as gauged by carbon isotope distributions and carbonate accumulation rates. During the period dominated by persistent taxa, net productivity was extremely low, as reflected by the absence of vertical delta13C gradients and reduced carbonate accumulation rates. Later in the Danian, as new species evolved and flourished, vertical delta13C gradients reappeared and carbonate accumulation rates increased, signaling partial recovery of net productivity in this region. The absolute timing and magnitude of late Maestrichtian and early Danian biotic and geochemical changes in the southern Indian Ocean were similar to those recorded in other pelagic K/P boundary sequences from low- and mid-latitude Atlantic and Pacific sites, indicating that these events were ubiquitous.

Sedimentology on 19 cores from the South China Sea

Based on the study of 10 sediment cores and 40 core-top samples from the South China Sea (SCS) we obtained proxy records of past changes in East Asian monsoon climate on millennial to bidecadal time scales over the last 220,000 years. Climate proxies such as global sea level, estimates of paleotemperature, salinity, and nutrients in surface water, ventilation of deep water, paleowind strength, freshwater lids, fluvial and/or eolian sediment supply, and sediment winnowing on the sea floor were derived from planktonic and benthic stable-isotope records, the distribution of siliciclastic grain sizes, planktonic foraminifera species, and the UK37 biomarker index. Four cores were AMS-14C-dated. Two different regimes of monsoon circulation dominated the SCS over the last two glacial cycles, being linked to the minima and maxima of Northern Hemisphere solar insolation. (1) Glacial stages led to a stable estuarine circulation and a strong O2-minimum layer via a closure of the Borneo sea strait. Strong northeast monsoon and cool surface water occurred during winter, in part fed by an inflow from the north tip of Luzon. In contrast, summer temperatures were as high as during interglacials, hence the seasonality was strong. Low wetness in subtropical South China was opposed to large river input from the emerged Sunda shelf, serving as glacial refuge for tropical forest. (2) Interglacials were marked by a strong inflow of warm water via the Borneo sea strait, intense upwelling southeast of Vietnam and continental wetness in China during summer, weaker northeast monsoon and high sea-surface temperatures during winter, i.e. low seasonality. On top of the long-term variations we found millennial- to centennial-scale cold and dry, warm and humid spells during the Holocene, glacial Terminations I and II, and Stage 3. The spells were coeval with published variations in the Indian monsoon and probably, with the cold Heinrich and warm Dansgaard-Oeschger events recorded in Greenland ice cores, thus suggesting global climatic teleconnections. Holocene oscillations in the runoff from South China centered around periodicities of 775 years, ascribed to subharmonics of the 1500-year cycle in oceanic thermohaline circulation. 102/84-year cycles are tentatively assigned to the Gleissberg period of solar activity. Phase relationships among various monsoon proxies near the onset of Termination IA suggest that summer-monsoon rains and fluvial runoff from South China had already intensified right after the last glacial maximum (LGM) insolation minimum, coeval with the start of Antarctic ice melt, prior to the d18O signals of global sea-level rise. Vice versa, the strength of winter-monsoon winds decreased in short centennial steps only 3000-4000 years later, along with the melt of glacial ice sheets in the Northern Hemisphere.

Isotopic composition of foraminifera from sediments of DSDP Legs 3, 6-9, 17

Oxygen isotopic compositions of the tests of planktonic foraminifera from several Deep Sea Drilling Project sites provide a general picture of low-latitude marine temperatures from Maastrichtian time to the present. Bottom temperatures determined from the isotopic compositions of benthonic foraminifera are interpreted as being indicative of high-latitude surface temperatures. Prior to the beginning of middle Miocene time, high- and low-latitude temperatures changed in parallel fashion. Following an apparently small and short-lived drop in temperature near the Tertiary-Cretaceous boundary, temperatures remained warm and relatively constant through Paleocene and early and middle Eocene time; bottom temperatures then were on the order of 12°C. A sharp temperature drop in late Eocene time was followed by a more gradual lowering of temperature, culminating in a late Oligocene high-latitude temperature minimum of about 4°C. A temperature rise through early Miocene time was followed in middle Miocene time by a sudden divergence of high- and low-latitude temperatures: high-latitude temperatures dropped dramatically, perhaps corresponding to the onset of major glaciation in Antarctica, but low-latitude temperatures remained constant or perhaps increased. This uncoupling of high-and low-latitude temperatures is postulated to be related to the establishment of a circum-Antarctic circulation similar to that of today. A further drop in high-latitude temperatures in late Pliocene time probably signaled the onset of a major increase in polar glaciation, including extensive sea-ice formation. Early Miocene, small-amplitude (1 per mil) sympathetic fluctuations in isotopic compositions of planktonic and benthonic foraminifera have been identified. These have a period of several hundred thousand years. Superimposed upon these are much more rapid and smaller fluctuations (0.2 to 0.5 per mil) with a period of about 80000 to 90000 yr. This is similar to the period observed for Pleistocene isotopic temperature fluctuations. In low latitudes, much smaller vertical temperature gradients seem to have existed during Maastrichtian and Paleogene time than exist at present. The absence of a sharply defined thermocline during early Tertiary time is also suggested.

Pleistocene sedimentology of ODP Hole 133-820A from the northeastern Australian margin

A principal objective at Site 820, situated on the outer shelf, upper slope of the northeastern Australian continental margin, was to test the relationships between changes in Pleistocene sea level and sedimentary packages produced on a mixed carbonate-siliciclastic continental margin. To this end, we have examined the downcore distribution of grain size, magnetic susceptibility, and calcium-carbonate content throughout Hole 820A and, in particular, the top 35 meters below the seafloor (mbsf). These data are compared with variations in the oxygen-isotope signal defined for the same hole and are interpreted as indicating sea-level oscillations. The distribution of sand, mud, calcium carbonate of the mud fraction and total sample, and magnetic susceptibility during the last 20,000 yr defines the position of a sea-level regression (41,000-18,000 yr B.P.), a lowstand, early (18,000-9,400 yr B.P.) and late transgressions (9400-900 yr B.P.), and a highstand (4900 yr to the present). The regression is seen first in a high-carbonate content peak. Calcium carbonate constituents mainly comprise skeletal carbonate grains, with abundant planktonic and benthic foraminifers, and lime muds. The lowstand is characterized by a maximum abundance of the sand fraction, which contains dominantly skeletal carbonate grains and a minor abundance of lithoclasts. Sand-sized terrigenous sediments are proposed to have bypassed the continental shelf during a lowstand of sea level. Sedimentation rates throughout the regression and lowstand are low (3.0 cm/k.y.). The early transgression, marked by highest values in magnetic susceptibility, displays a rapid increase in sedimentation rate that coincided with an increase in terrigenous mud. Highest sedimentation rates of 82.3 cm/k.y. occurred during the late transgression, with increasing percentages of lime-mud. A decrease in noncarbonate constituents in the mud fraction during the late transgression and highstand of sea level is thought to be the result of restricted inner-shelf sedimentation of terrigenous sediments. The same relationship is also seen in the major sea-level oscillation, which is interpreted as isotope stage 6.

Stable isotope record of northeastern Australian Margin

Stable isotopic data obtained from planktonic and benthic foraminifers were used to study paleoceanographic changes along the northeastern Australian margin from late Miocene (10 Ma) to Holocene time, and to evaluate the influence of these changes on reef growth. The data indicate that variations in surface-water temperatures may have had an important effect on the reef complexes on the Queensland Plateau and possibly off the northeastern Australian margin. Three sites were studied: Leg 21, Site 209 on the eastern edge of the Queensland Plateau, and Leg 133, Site 811 on the western margin, and Site 817 on the lower southern slope of the plateau. Shallow-water bioclasts recovered from Holes 811A and 817A indicate extensive reef growth on the Queensland Plateau during the middle Miocene (before 12 Ma), signifying surface-water temperatures of 20°C or greater. The amount of reefal detritus produced during the late Miocene (10.0-5.2 Ma) decreased progressively, resulting in a reduction in area of the reef complexes. The isotopic data from planktonic foraminifers in these late Miocene age sediments indicate the presence of relatively cool surface waters (16°-19°C), which may have been a major factor contributing to the demise of the reefs on the Queensland Plateau. Surface waters remained cool until the middle Pleistocene (1.2-0.5 Ma), when the surface-water temperature apparently increased to approximately 25°C, recorded both in the isotopic data and by renewed reef growth. This increase occurred simultaneously (within the error of the age model) with the initiation of the Great Barrier Reef. We propose that cooling of surface waters during the early late Miocene contributed to reef decline on the Queensland Plateau, and that subsequent warming of surface waters during the middle Pleistocene promoted the initiation of reef growth on the northeastern Australian margin. Reef development on the Queensland Plateau never recovered to the middle Miocene extent because of a combination of tectonic (accelerated subsidence of the plateau) and paleoceanographic (the cooler surface waters present from the late Miocene throughout the Pliocene) factors. Variations in seafloor d18O appear to be controlled by regional factors, as indicated by the similarity of data from Sites 811 and 817 to those from Site 590 on Lord Howe Rise.