Abundances and d13C values of n-alkanes extracted from sediment samples of ODP Hole 116-717C

Siwalik paleosol and Bengal Fan sediment samples were analyzed for the abundance and isotopic composition of n-alkanes in order to test for molecular evidence of the expansion of C4 grasslands on the Indian subcontinent. The carbon isotopic compositions of high-molecular-weight alkanes in both the ancient soils and sediments record a shift from low d13C values (ca. -30 per mil) to higher values (ca. -22 per mil) prior to 6 Ma. This shift is similar in magnitude to that recorded by paleosol carbonate and fossil teeth, and is consistent with a relatively rapid transition from dominantly C3 vegetation to an ecosystem dominated by C4 plants typical of semi-arid grasslands. The n-alkane values from our paleosol samples indicate that the isotopic change began as early as 9 Ma, reflecting either a growing contribution of C4 plants to a dominantly C3 biomass or a decrease in water availability to C3 plants. Molecular and isotopic analyses of other compounds, including n-alcohols and low-molecular weight n-alkanes indicate paleosol organic matter contains contributions from a mixture of sources, including vascular plants, algae and/or cyanobacteria and microorganisms. A range of inputs is likewise reflected in the isotopic composition of the total organic carbon from these samples. In addition, the n-alkanes from two samples show little evidence for pedegenic inputs and we suggest the compounds were derived instead from the paleosol's parent materials. We suggest the record of vegetation in ancient terrestrial ecosystems is better reconstructed using isotopic signatures of molecular markers, rather than bulk organic carbon. This approach provides a means of expanding the spatial and temporal records of C4 plant biomass which will help to resolve possible tectonic, climatic or biological controls on the rise of this important component of the terrestrial biosphere.

Seawater carbonate chemistry, stable carbon isotope fractionation and growth rate during experiments with marine phytoplankton community, 1999

Stable carbon isotope fractionation (%) of 7 marine phytoplankton species grown in different irradiance cycles was measured under nutrient-replete conditions at a high light intensity in batch cultures. Compared to experiments under continuous light, all species exhibited a significantly higher instantaneous growth rate (pi), defined as the rate of carbon fixation during the photo period, when cultivated at 12:12 h. 16:8 h, or 186 h light:dark (L/D) cycles. Isotopic fractionation by the diatoms Skeletonema costatum, Asterionella glacialis, Thalassiosira punctigera, and Coscinodiscus wailesii (Group I) was 4 to 6% lower in a 16:8 h L/D cycle than under continuous light, which we attribute to differences in pi. In contrast, E, in Phaeodactylum tn'cornutum, Thalassiosira weissflogii, and in the dinoflagellate Scrippsiella trochoidea (Group 11) was largely insensitive to day length-related differences in instantaneous growth rate. Since other studies have reported growth-rate dependent fractionation under N-limited conditions in P. tricornutum, pi-related effects on fractionation apparently depend on the factor controlling growth rate. We suggest that a general relationship between E, and pi/[C02,,,] may not exist. For 1 species of each group we tested the effect of variable CO2 concentration, [COz,,,], on isotopic fractionation. A decrease in [CO2,,,] from ca 26 to 3 pm01 kg-' caused a decrease in E, by less than 3%0 This indicates that variation in h in response to changes in day length has a similar or even greater effect on isotopic fractionation than [COz,,,] m some of the species tested. In both groups E, tended to be higher in smaller species at comparable growth rates. In 24 and 48 h time series the algal cells became progressively enriched in 13C during the day and the first hours of the dark period, followed by l3C depletion in the 2 h before beginning of the following Light period. The daily amplitude of the algal isotopic composition (613C), however, was <1.5%0, which demonstrates that diurnal variation in Fl3C is relatively small.

Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi (PML B93/11A)

The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments. This is important in regulating marine carbon cycling and ocean-atmosphere CO2 exchange. The present rise in atmospheric CO2 levels causes significant changes in surface ocean pH and carbonate chemistry. Such changes have been shown to slow down calcification in corals and coralline macroalgae, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica . This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.

Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi (PML B92/11), 2000

We have measured the stable carbon isotopic composition of bulk organic matter (POC), alkenones, sterols, fatty acids, and phytol in the coccolithophorid Emiliania huxleyi grown in dilute batch cultures over a wide range of CO2 concentrations (1.1-53.5 micromol L-1). The carbon isotope fractionation of POC (POC) varied by ca. 7 per mil and was positively correlated with aqueous CO2 concentration [CO2aq]. While this result confirms general trends observed for the same alga grown in nitrogen-limited chemostat cultures, considerable differences were obtained in absolute values of POC and in the slope of the relationship of POC with growth rate and [CO2aq]. Also, a significantly greater offset was obtained between the delta13C of alkenones and bulk organic matter in this study compared with previous work (5.4, cf. 3.8 per mil). This suggests that the magnitude of the isotope offset may depend on growth conditions. Relative to POC, individual fatty acids were depleted in 13C by 2.3 per mil to 4.1 per mil, phytol was depleted in 13C by 1.9 per mil, and the major sterol 24-methylcholesta-5,22E-dien-3beta-ol was depleted in 13C by 8.5 per mil. This large spread of delta13C values for different lipid classes in the same alga indicates the need for caution in organic geochemical studies when assigning different sources to lipids that might have delta13C values differing by just a few per mil. Increases in [CO2aq] led to dramatic increases in the alkenone contents per cell and as a proportion of organic carbon, but there was no systematic effect on values of U37k- used for reconstructions of paleo sea surface temperature.

Mapping the Antarctic Polar Front: Weekly realizations from 2002 to 2014, links to NetCDF file and MPEG4 movie

We map the weekly position of the Antarctic Polar Front (PF) in the Southern Ocean over a 12-year period (2002-2014) using satellite sea surface temperature (SST) estimated from cloud-penetrating microwave radiometers. Our study advances previous efforts to map the PF using hydrographic and satellite data and provides a unique realization of the PF at weekly resolution across all longitudes. The mean path of the PF is asymmetric; its latitudinal position spans from 44 to 64° S along its circumpolar path. SST at the PF ranges from 0.6 to 6.9 °C, reflecting the large spread in latitudinal position. The average intensity of the front is 1.7 °C per 100 km, with intensity ranging from 1.4 to 2.3 °C per 100 km. Front intensity is significantly correlated with the depth of bottom topography, suggesting that the front intensifies over shallow bathymetry. Realizations of the PF are consistent with the corresponding surface expressions of the PF estimated using expendable bathythermograph data in the Drake Passage and Australian and African sectors. The climatological mean position of the PF is similar, though not identical, to previously published estimates. As the PF is a key indicator of physical circulation, surface nutrient concentration, and biogeography in the Southern Ocean, future studies of physical and biogeochemical oceanography in this region will benefit from the provided data set.

Functional domains for assembly of histones H3 and H4 into the chromatin of Xenopus embryos

Histones H3 and H4 have a well defined structural role in the nucleosome and an established role in the regulation of transcription. We have made use of a microinjection strategy using Xenopus embryos to define the minimal structural components of H3 and H4 necessary for nucleosome assembly into metazoan chromosomes in vivo. We find that both the N-terminal tail of H4, including all sites of acetylation, and the C-terminal α-helix of the H4 histone fold domain are dispensable for chromatin assembly. The N-terminal tail and an N-terminal α-helix of H3 are also dispensable for chromatin assembly. However, the remainder of the H3 and H4 histone folds are essential for incorporation of these proteins into chromatin. We suggest that elements of the histone fold domain maintain both nucleosomal integrity and have distinct functions essential for cell viability.

Neural mechanisms underlying binocular fusion and stereopsis: Position vs. phase

The visual system utilizes binocular disparity to discriminate the relative depth of objects in space. Since the striate cortex is the first site along the central visual pathways at which signals from the left and right eyes converge onto a single neuron, encoding of binocular disparity is thought to begin in this region. There are two possible mechanisms for encoding binocular disparity through simple cells in the striate cortex: a difference in receptive field (RF) position between the two eyes (RF position disparity) and a difference in RF profile between the two eyes (RF phase disparity). Although there have been studies supporting each of the two encoding mechanisms, both mechanisms have not been examined in a single study. Therefore, the relative roles of the two mechanisms have not been determined. To address this issue, we have mapped left and right eye RFs of simple cells in the cat’s striate cortex using binary m-sequence noise, and then we have estimated RF position and phase disparities. We find that RF position disparities are generally limited to small values that are not sufficient to encode large binocular disparities. In contrast, RF phase disparities cover a wide range of binocular disparities and exhibit dependencies on orientation and spatial frequency in a manner expected for a mechanism that encodes binocular disparity. These results indicate that binocular disparity is mainly encoded through RF phase disparity. However, RF position disparity may play a significant role for cells with high spatial frequency selectivity, which are constrained to small RF phase disparities.

ATP- and Cytosol-dependent Release of Adaptor Proteins from Clathrin-coated Vesicles: A Dual Role for Hsc70

Clathrin-coated vesicles (CCV) mediate protein sorting and vesicular trafficking from the plasma membrane and the trans-Golgi network. Before delivery of the vesicle contents to the target organelles, the coat components, clathrin and adaptor protein complexes (APs), must be released. Previous work has established that hsc70/the uncoating ATPase mediates clathrin release in vitro without the release of APs. AP release has not been reconstituted in vitro, and nothing is known about the requirements for this reaction. We report a novel quantitative assay for the ATP- and cytosol- dependent release of APs from CCV. As expected, hsc70 is not sufficient for AP release; however, immunodepletion and reconstitution experiments establish that it is necessary. Interestingly, complete clathrin release is not a prerequisite for AP release, suggesting that hsc70 plays a dual role in recycling the constituents of the clathrin coat. This assay provides a functional basis for identification of the additional cytosolic factor(s) required for AP release.

The Schizosaccharomyces pombe hst4+ Gene Is a SIR2 Homologue with Silencing and Centromeric Functions

Although silencing is a significant form of transcriptional regulation, the functional and mechanistic limits of its conservation have not yet been established. We have identified the Schizosaccharomyces pombe hst4+ gene as a member of the SIR2/HST silencing gene family that is defined in organisms ranging from bacteria to humans. hst4Δ mutants grow more slowly than wild-type cells and have abnormal morphology and fragmented DNA. Mutant strains show decreased silencing of reporter genes at both telomeres and centromeres. hst4+ appears to be important for centromere function as well because mutants have elevated chromosome-loss rates and are sensitive to a microtubule-destabilizing drug. Consistent with a role in chromatin structure, Hst4p localizes to the nucleus and appears concentrated in the nucleolus. hst4Δ mutant phenotypes, including growth and silencing phenotypes, are similar to those of the Saccharomyces cerevisiae HSTs, and at a molecular level, hst4+ is most similar to HST4. Furthermore, hst4+ is a functional homologue of S. cerevisiae HST3 and HST4 in that overexpression of hst4+ rescues the temperature-sensitivity and telomeric silencing defects of an hst3Δ hst4Δ double mutant. These results together demonstrate that a SIR-like silencing mechanism is conserved in the distantly related yeasts and is likely to be found in other organisms from prokaryotes to mammals.

Virulence of a Mycobacterium tuberculosis clinical isolate in mice is determined by failure to induce Th1 type immunity and is associated with induction of IFN-α/β

To understand how virulent mycobacteria subvert host immunity and establish disease, we examined the differential response of mice to infection with various human outbreak Mycobacterium tuberculosis clinical isolates. One clinical isolate, HN878, was found to be hypervirulent, as demonstrated by unusually early death of infected immune-competent mice, compared with infection with other clinical isolates. The differential effect on survival required lymphocyte function because severe combined immunodeficiency (SCID) mice infected with HN878 or other clinical isolates all died at the same rate. The hypervirulence of HN878 was associated with failure to induce M. tuberculosis-specific proliferation and IFN-γ production by spleen and lymph node cells from infected mice. In addition, 2- to 4-fold lower levels of tumor necrosis factor-α (TNF-α), IL-6, IL-12, and IFN-γ mRNAs were observed in lungs of HN878-infected mice. IL-10, IL-4, and IL-5 mRNA levels were not significantly elevated in lungs of HN878 infected mice. In contrast, IFN-α mRNA levels were significantly higher in lungs of these mice. To further investigate the role of Type 1 IFNs, mice infected with HN878 were treated intranasally with purified IFN-α/β. The treatment resulted in increased lung bacillary loads and even further reduced survival. These results suggest that the hypervirulence of HN878 may be due to failure of this strain to stimulate Th1 type immunity. In addition, the lack of development of Th1 immunity in response to HN878 appears to be associated with increased induction of Type 1 IFNs.

Indium-cadmium-oxide films having exceptional electrical conductivity and optical transparency: Clues for optimizing transparent conductors

Materials with high electrical conductivity and optical transparency are needed for future flat panel display, solar energy, and other opto-electronic technologies. InxCd1-xO films having a simple cubic microstructure have been grown on amorphous glass substrates by a straightforward chemical vapor deposition process. The x = 0.05 film conductivity of 17,000 S/cm, carrier mobility of 70 cm2/Vs, and visible region optical transparency window considerably exceed the corresponding parameters for commercial indium-tin oxide. Ab initio electronic structure calculations reveal small conduction electron effective masses, a dramatic shift of the CdO band gap with doping, and a conduction band hybridization gap caused by extensive Cd 5s + In 5s mixing.

Human CD100, a novel leukocyte semaphorin that promotes B-cell aggregation and differentiation.

Herein we describe the molecular characterization of the human leukocyte activation antigen CD100 and identify it as the first semaphorin, to our knowledge, in the immune system. Semaphorins have recently been described as neuronal chemorepellants that direct pioneering neurons during nervous system development. In this study we demonstrate that CD100 induces B cells to aggregate and improves their viability in vitro. We show that CD100 modifies CD40-CD40L B-cell signaling by augmenting B-cell aggregation and survival and down-regulating CD23 expression. Thus, these results suggest that semaphorins as exemplified by CD100 also play a functional role in the immune system.

T lymphocytes that infiltrate tumors and atherosclerotic plaques produce heparin-binding epidermal growth factor-like growth factor and basic fibroblast growth factor: a potential pathologic role.

Despite significant infiltration into tumors and atherosclerotic plaques, the role of T lymphocytes in these pathological conditions is still unclear. We have demonstrated that tumor-infiltrating lymphocytes (TILs) and plaque-infiltrating lymphocytes (PILs) produce heparin-binding epidermal growth factor-like growth factor (HB-EGF) and basic fibroblast growth factor (bFGF) in vitro under nonspecific conditions and in vivo in tumors by immunohistochemical staining. HB-EGF and bFGF derived from TILs and PILs directly stimulated tumor cells and vascular smooth muscle cells (SMCs) in vitro, respectively, while bFGF displayed angiogenic properties. Therefore, T cells may play a critical role in the SMC hyperplasia of atherosclerosis and support tumor progression by direct stimulation and angiogenesis.