Stable carbon and oxygen isotope record of Cibicidoides from DSDP/ODP holes

High-resolution delta18O records from the equatorial Pacific (site 503B), equatorial Atlantic (site 665A), and North Atlantic (site 606A) based on the benthic foraminifera Cibicidoides wuellerstorfi show the 2.4 Ma onset of major northern hemispheric glaciation to be a package of three events occurring at 2.39, 2.35, and 2.31 Ma in which a periodicity of about 40 kyr is evident. The amplitude of the signals at the three sites indicates that these events were 1/2 to 2/3 the size of the latest Quaternary glaciation and also indicates cooling of northern source bottom water by 2.7°-4.1°C relative to southern source water during glaciations. Carbon isotopes indicate that southern source waters were less oxygenated than in the Quaternary and that there was reduced production of northern source water during glacial intervals. The dominant presence of southern source water in the eastern basin of the equatorial Atlantic, regardless of climatic cycles, throughout the late Pliocene indicates a greater influence of these waters relative to northern source waters in the late Pliocene ocean.

Stable isotope ratios and foraminiferal abundance of sediment cores from the Western Iberian Margin

Rapid climate changes at the onset of the last deglaciation and during Heinrich Event H4 were studied in detail at IMAGES cores MD95-2039 and MD95-2040 from the Western Iberian margin. A major reorganisation of surface water hydrography, benthic foraminiferal community structure, and deepwater isotopic composition commenced already 540 years before the Last Isotopic Maximum (LIM) at 17.43 cal. ka and within 670 years affected all environments. Changes were initiated by meltwater spill in the Nordic Seas and northern North Atlantic that commenced 100 years before concomitant changes were felt off western Iberia. Benthic foraminiferal associations record the drawdown of deepwater oxygenation during meltwater and subsequent Heinrich Events H1 and H4 with a bloom of dysoxic species. At a water depth of 3380 m, benthic oxygen isotopes depict the influence of brines from sea ice formation during ice-rafting pulses and meltwater spill. The brines conceivably were a source of ventilation and provided oxygen to the deeper water masses. Some if not most of the lower deep water came from the South Atlantic. Benthic foraminiferal assemblages display a multi-centennial, approximately 300-year periodicity of oxygen supply at 2470-m water depth. This pattern suggests a probable influence of atmospheric oscillations on the thermohaline convection with frequencies similar to Holocene climate variations. For Heinrich Events H1 and H4, response times of surface water properties off western Iberia to meltwater injection to the Nordic Seas were extremely short, in the range of a few decades only. The ensuing reduction of deepwater ventilation commenced within 500-600 years after the first onset of meltwater spill. These fast temporal responses lend credence to numerical simulations that indicate ocean-climate responses on similar and even faster time scales.

Pleistocene and late Miocene Calcareous nannofossil biostratigraphy of ODP Hole 150-905A

Continental rise Site 905 yielded upper Miocene and Pliocene uniform hemipelagic mud (a contourite) from approximately 215 to 540 meters below seafloor. The nannofossil biostratigraphy of this interval was reexamined using closely spaced samples from core interiors. Additionally, total nannofossil abundances and dominant species and species group abundances were determined to evaluate the potential of this section for extracting sequence stratigraphic information. The data indicate that the putative hiatuses at the end of the late Pliocene (Zones NN17 and NN18) and in the early Pliocene (Zones NN13 and NN14) probably are condensed intervals, but the base of the late Miocene is almost certainly marked by an unconformity. Judging from carbonate content and sedimentation rate both, nannofossil abundance may be governed by carbonate dissolution or by siliciclastic dilution. Consequently, condensed sections cannot be identified by the abundance of pelagic component in the sediment alone, as is possible in equivalent age Gulf of Mexico sediments. Where nannofossil preservation is adequate in consecutive samples, as in the early Pliocene and latest late Miocene, total nannofossil abundance fluctuates regularly and with a periodicity of less than 105 yr, which suggests that dilution of the pelagic component occurred with a frequency probably related to astronomical forcing.

Temperatures, salinity, and stable oxygen isotope values of bottom water and of the mollusc shell Arctica islandica from Nantucket Shoals

The carbonate shell of the bivalve Arctica islandica has been recognized, for more than a decade, as a potentially important marine geochemical biorecorder owing to this species' great longevity (200+ years) and wide geographic distribution throughout the northern North Atlantic Ocean, a region vital to global climate and ocean circulation. However, until now this potential has not been realized owing to the difficulty of precisely sampling the shell of this slow growing species. Using newly available automated microsampling techniques combined with micromass stable isotope mass spectrometry, a stable oxygen isotope record (1956-1957 and 1961-1970) has been obtained from a live-captured, 38-year-old A. islandica specimen collected near the former position of the Nantucket Shoals Lightship (41°N. 69°W). The shell's delta18O signal is compared with an expected signal derived from ambient bottom temperature and salinity data recorded at the lightship for the same period. The results show that A islandica's delta18O record (1) is in phase with its growth banding, confirming the annual periodicity of this species' growth bands, (2) is in oxygen isotopic equilibrium with the ambient seawater, (3) shows a consistent shell growth shutdown temperature of ~6°C. which translates into an ~8-month (May-December) shell growth period at this location, and (4) records the ambient bottom temperature with a precision of ~ +/-1.2°C. These results add important information on the life history of this commercially important shellfish species and demonstrate that A. islandica shells can be used to reconstruct inter- and intra-annual records of the continental shelf bottom temperature.

CaCO3 content, terrigenous components, foraminifera abundance and age of sediment core MD95-2006, Barra Fan, UK

Lithology, lithic petrology, planktonic foraminiferal abundances, and clastic grain sizes have been determined in a 30 m-long core recovered from the Barra Fan off northwest Scotland. The record extends back to around 45 kyr B.P., with sedimentation rates ranging between 50 and 200 cm/kyr. The abundance of ice-rafted debris indicates 16 glacimarine events, including temporal equivalents to Heinrich events 1-4. Enhanced concentrations of basaltic material derived from the British Tertiary Province suggest that the glacimarine sediments record variations in a glacial source on the Hebrides shelf margin. Glacimarine zones are separated by silty intervals with high planktonic foraminifera concentrations that reflect an interstadial circulation regime in the Rockall Trough. The results suggest that the last British Ice Sheet fluctuated with a periodicity of 2000-3000 years, in common with the Dansgaard-Oeschger climate cycle.

(Supplementary Table 1) Iceberg-rafted debris (IBRD) mass accumulation rates (MAR) of IODP site 318-U1361

The Pliocene and Early Pleistocene, between 5.3 and 0.8 million years ago, span a transition from a global climate state that was 2-3 °C warmer than present with limited ice sheets in the Northern Hemisphere to one that was characterized by continental-scale glaciations at both poles. Growth and decay of these ice sheets was paced by variations in the Earth's orbit around the Sun. However, the nature of the influence of orbital forcing on the ice sheets is unclear, particularly in light of the absence of a strong 20,000-year precession signal in geologic records of global ice volume and sea level. Here we present a record of the rate of accumulation of iceberg-rafted debris offshore from the East Antarctic ice sheet, adjacent to the Wilkes Subglacial Basin, between 4.3 and 2.2 million years ago. We infer that maximum iceberg debris accumulation is associated with the enhanced calving of icebergs during ice-sheet margin retreat. In the warmer part of the record, between 4.3 and 3.5 million years ago, spectral analyses show a dominant periodicity of about 40,000 years. Subsequently, the powers of the 100,000-year and 20,000-year signals strengthen. We suggest that, as the Southern Ocean cooled between 3.5 and 2.5 million years ago, the development of a perennial sea-ice field limited the oceanic forcing of the ice sheet. After this threshold was crossed, substantial retreat of the East Antarctic ice sheet occurred only during austral summer insolation maxima, as controlled by the precession cycle.

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

Polymers of N-substituted glycines (“peptoids”) containing chiral centers at the α position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of ≈6 Å. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.

Description of microcolumnar ensembles in association cortex and their disruption in Alzheimer and Lewy body dementias

The cortex of the brain is organized into clear horizontal layers, laminae, which subserve much of the connectional anatomy of the brain. We hypothesize that there is also a vertical anatomical organization that might subserve local interactions of neuronal functional units, in accord with longstanding electrophysiological observations. We develop and apply a general quantitative method, inspired by analogous methods in condensed matter physics, to examine the anatomical organization of the cortex in human brain. We find, in addition to obvious laminae, anatomical evidence for tightly packed microcolumnar ensembles containing approximately 11 neurons, with a periodicity of about 80 μm. We examine the structural integrity of this new architectural feature in two common dementing illnesses, Alzheimer disease and dementia with Lewy bodies. In Alzheimer disease, there is a dramatic, nearly complete loss of microcolumnar ensemble organization. The relative degree of loss of microcolumnar ensembles is directly proportional to the number of neurofibrillary tangles, but not related to the amount of amyloid-β deposition. In dementia with Lewy bodies, a similar disruption of microcolumnar ensemble architecture occurs despite minimal neuronal loss. These observations show that quantitative analysis of complex cortical architecture can be applied to analyze the anatomical basis of brain disorders.

NMR structure of the calreticulin P-domain

The NMR structure of the rat calreticulin P-domain, comprising residues 189–288, CRT(189–288), shows a hairpin fold that involves the entire polypeptide chain, has the two chain ends in close spatial proximity, and does not fold back on itself. This globally extended structure is stabilized by three antiparallel β-sheets, with the β-strands comprising the residues 189–192 and 276–279, 206–209 and 262–265, and 223–226 and 248–251, respectively. The hairpin loop of residues 227–247 and the two connecting regions between the β-sheets contain a hydrophobic cluster, where each of the three clusters includes two highly conserved tryptophyl residues, one from each strand of the hairpin. The three β-sheets and the three hydrophobic clusters form a repeating pattern of interactions across the hairpin that reflects the periodicity of the amino acid sequence, which consists of three 17-residue repeats followed by three 14-residue repeats. Within the global hairpin fold there are two well-ordered subdomains comprising the residues 219–258, and 189–209 and 262–284, respectively. These are separated by a poorly ordered linker region, so that the relative orientation of the two subdomains cannot be precisely described. The structure type observed for CRT(189–288) provides an additional basis for functional studies of the abundant endoplasmic reticulum chaperone calreticulin.

Proteomic analysis of the bacterial cell cycle

A global approach was used to analyze protein synthesis and stability during the cell cycle of the bacterium Caulobacter crescentus. Approximately one-fourth (979) of the estimated C. crescentus gene products were detected by two-dimensional gel electrophoresis, 144 of which showed differential cell cycle expression patterns. Eighty-one of these proteins were identified by mass spectrometry and were assigned to a wide variety of functional groups. Pattern analysis revealed that coexpression groups were functionally clustered. A total of 48 proteins were rapidly degraded in the course of one cell cycle. More than half of these unstable proteins were also found to be synthesized in a cell cycle-dependent manner, establishing a strong correlation between rapid protein turnover and the periodicity of the bacterial cell cycle. This is, to our knowledge, the first evidence for a global role of proteolysis in bacterial cell cycle control.

Possible forcing of global temperature by the oceanic tides

An approximately decadal periodicity in surface air temperature is discernable in global observations from A.D. 1855 to 1900 and since A.D. 1945, but with a periodicity of only about 6 years during the intervening period. Changes in solar irradiance related to the sunspot cycle have been proposed to account for the former, but cannot account for the latter. To explain both by a single mechanism, we propose that extreme oceanic tides may produce changes in sea surface temperature at repeat periods, which alternate between approximately one-third and one-half of the lunar nodal cycle of 18.6 years. These alternations, recurring at nearly 90-year intervals, reflect varying slight degrees of misalignment and departures from the closest approach of the Earth with the Moon and Sun at times of extreme tide raising forces. Strong forcing, consistent with observed temperature periodicities, occurred at 9-year intervals close to perihelion (solar perigee) for several decades centered on A.D. 1881 and 1974, but at 6-year intervals for several decades centered on A.D. 1923. As a physical explanation for tidal forcing of temperature we propose that the dissipation of extreme tides increases vertical mixing of sea water, thereby causing episodic cooling near the sea surface. If this mechanism correctly explains near-decadal temperature periodicities, it may also apply to variability in temperature and climate on other times-scales, even millennial and longer.

Actin-Bundling Protein Isolated from Pollen Tubes of Lily : Biochemical and Immunocytochemical Characterization

A 135-kD actin-bundling protein was purified from pollen tubes of lily (Lilium longiflorum) using its affinity to F-actin. From a crude extract of the pollen tubes, this protein was coprecipitated with exogenously added F-actin and then dissociated from F-actin by treating it with high-ionic-strength solution. The protein was further purified sequentially by chromatography on a hydroxylapatite column, a gel-filtration column, and a diethylaminoethyl-cellulose ion-exchange column. In the present study, this protein is tentatively referred to as P-135-ABP (Plant 135-kD Actin-Bundling Protein). By the elution position from a gel-filtration column, we estimated the native molecular mass of purified P-135-ABP to be 260 kD, indicating that it existed in a dimeric form under physiological conditions. This protein bound to and bundled F-actin prepared from chicken breast muscle in a Ca2+-independent manner. The binding of 135-P-ABP to actin was saturated at an approximate stoichiometry of 26 actin monomers to 1 dimer of P-135-ABP. By transmission electron microscopy of thin sections, we observed cross-bridges between F-actins with a longitudinal periodicity of 31 nm. Immunofluorescence microscopy using rhodamine-phalloidin and antibodies against the 135-kD polypeptide showed that P-135-ABP was colocalized with bundles of actin filaments in lily pollen tubes, leading us to conclude that it is the factor responsible for bundling the filaments.

Nramp defines a family of membrane proteins.

Nramp (natural resistance-associated macrophage protein) is a newly identified family of integral membrane proteins whose biochemical function is unknown. We report on the identification of Nramp homologs from the fly Drosophila melanogaster, the plant Oryza sativa, and the yeast Saccharomyces cerevisiae. Optimal alignment of protein sequences required insertion of very few gaps and revealed remarkable sequence identity of 28% (yeast), 40% (plant), and 55% (fly) with the mammalian proteins (46%, 58%, and 73% similarity), as well as a common predicted transmembrane topology. This family is defined by a highly conserved hydrophobic core encoding 10 transmembrane segments. Other features of this hydrophobic core include several invariant charged residues, helical periodicity of sequence conservation suggesting conserved and nonconserved faces for several transmembrane helices, a consensus transport signature on the intracytoplasmic face of the membrane, and structural determinants previously described in ion channels. These characteristics suggest that the Nramp polypeptides form part of a group of transporters or channels that act on as yet unidentified substrates.

Geochemistry of Globigerinoides ruber from ODP Hole 130-806B

A sea surface temperature (SST) record based on planktonic foraminiferal magnesium/calcium ratios from a site in the western equatorial Pacific warm pool reveals that glacial-interglacial oscillations in SST shifted from a period of 41,000 to 100,000 years at the mid-Pleistocene transition, 950,000 years before the present. SST changes at both periodicities were synchronous with eastern Pacific cold-tongue SSTs but preceded changes in continental ice volume. The timing and nature of tropical Pacific SST changes over the mid-Pleistocene transition implicate a shift in the periodicity of radiative forcing by atmospheric carbon dioxide as the cause of the switch in climate periodicities at this time.

Pliocene-Pleistocene biostratigraphic datums of ODP Site 184-1148

Based on the stable isotopic analysis of planktonic and benthic foraminifers from Ocean Drilling Program Core 1148 of the northern South China Sea (SCS), Pliocene-Pleistocene isotope stratigraphy and events have been reconstructed. The benthic foraminiferal delta18O record shows that the Pacific intermediate water had a greater influence upon the SCS or the Pacific deep water above ~2600 m was warmer before ~3.2Ma than at present. After that, the benthic delta18O conspicuously increased during the ~3.2-2.5 Ma period, in correspondence to the formation of the Northern Hemisphere ice sheet, whereas the planktonic delta18O signal suggests a stepwise overall decrease of sea surface temperature during the ~2.2-0.9 Ma period. Compared to the equatorial Pacific records, the decrease in planktonic (Globigerinoides ruber) delta13C during the ~3.2-2.2 Ma period is particularly striking, suggesting that fertility of surface water increased noticeably. According to the modern delta13C distribution of G. ruber in the northern SCS, it is inferred that the East Asian winter monsoon strengthened during this interval. Afterwards, there were several conspicuous decreases of G. ruber delta13C at ~1.7, 1.3, 0.9, 0.45 and 0.15 Ma BP, that is, about every 0.4 Ma, suggesting that the East Asian winter monsoon became episodically stronger. This is confirmed by changes in relative abundance of planktonic foraminifer species Neogloboquadrina dutertrei, a typical East Asian winter monsoon proxy. The deepwater delta13C of the SCS is close to that of the Pacific, but lighter than that of the Atlantic, implying that the pattern of deep water originating mainly from the Atlantic and through the Pacific entering the SCS existed at least since the early Pliocene. After 1.4 Ma, the benthic delta13C signal decreased conspicuously but with a periodicity of ~100 ka, suggesting that the deep-water ventilation of the SCS was reduced, probably corresponding to a decrease of the North Atlantic Deep Water and/or further isolation of the SCS deep basin from the Pacific during glaciations.