Benthonic foraminifera of ODP Site 116-717

We report on benthic foraminifer results from Site 717 in the Distal Bengal Fan. Only 80 out of 380 samples contained useful benthic foraminifer information. However, we were able to identify four assemblages: 1. A present-day one dominated by Nuttallides umbonifera with some North Atlantic species; 2. An agglutinated fauna consisting of one species; 3. A reworked assemblage consisting of shallow-water forms; and 4. A reworked fauna consisting of an abundance of all kinds of forms including Cretaceous species. The reworked assemblage 4, we believe, represents a period when fan sediments were blocked from this area by east-west trending intraplate deformation. In the remainder of the core section, sedimentation appears to be dominated by Fan deposition with abundant terrestrial debris. In the infrequent pelagic intervals, it appears that abyssal water masses changed little since the late Miocene.

Mg/Ca ratios of Cenozoic benthic foraminifera from the Indian and South Atlantic Ocean

We investigate the evolution of Cenozoic climate and ice volume as evidenced by the oxygen isotopic composition of seawater (delta18Osw) derived from benthic foraminiferal Mg/Ca ratios to constrain the temperature effect contained in foraminiferal delta18O values. We have constructed two benthic foraminiferal Mg/Ca records from intermediate water depth sites (Ocean Drilling Program sites 757 and 689 from the subtropical Indian Ocean and the Weddell Sea, respectively). Together with the previously published composite record of Lear et al. (2002, doi:10.1126/science.287.5451.269) and the Neogene record from the Southern Ocean of Billups and Schrag (2002, doi:10.1029/2000PA000567), we obtain three, almost complete representations of the delta18Osw for the past 52 Myr. We discuss the sensitivity of early Cenozoic Mg/Ca-derived paleotemperatures (and hence the delta18Osw) to assumptions about seawater Mg/Ca ratios. We find that during the middle Eocene (~ 49-40 Ma), modern seawater ratios yield Mg/Ca-derived temperatures that are in good agreement with the oxygen isotope paleothermometer assuming ice-free conditions. Intermediate waters cooled during the middle Eocene reaching minimum temperatures by 40 Ma. The corresponding delta18Osw reconstructions support ice growth on Antarctica beginning by at least 40 Ma. At the Eocene/Oligocene boundary, Mg/Ca ratios (and hence temperatures) from Weddell Sea site 689 display a well-defined maximum. We caution against a paleoclimatic significance of this result and put forth that the partitioning coefficient of Mg in benthic foraminifera may be sensitive to factors other than temperature. Throughout the remainder of the Cenozoic, the temporal variability among delta18Osw records is similar and similar to longer-term trends in the benthic foraminiferal delta18O record. An exception occurs during the Pliocene when delta18Osw minima in two of the three records suggest reductions in global ice volume that are not apparent in foraminiferal delta18O records, which provides a new perspective to the ongoing debate about the stability of the Antarctic ice sheet. Maximum delta18Osw values recorded during the Pleistocene at Southern Ocean site 747 agree well with values derived from the geochemistry of pore waters (Schrag et al., 1996, doi:10.1126/science.272.5270.1930) further highlighting the value of the new Mg/Ca calibrations of Martin et al. (2002, doi:10.1016/S0012-821X(02)00472-7) and Lear et al. (2002, doi:10.1016/S0016-7037(02)00941-9) applied in this study. We conclude that the application of foraminiferal Mg/Ca ratios allows a refined view of Cenozoic ice volume history despite uncertainties related to the geochemical cycling of Mg and Ca on long time scales.

Middle Miocene to Quaternary diatom biostratigraphy of DSDP Site 90-594

A diatom biostratigraphy is presented for middle Miocene through Quaternary sediments recovered from the Chatham Rise east of New Zealand's South Island. The upper 590 m of the 639.5-m composite-section Site 594 represents approximately 16 m.y. and is characterized by moderately to very poorly preserved diatoms of antarctic to temperate affinity. Pliocene through Quaternary assemblages are poorly preserved and dominated by antarctic-subantarctic species which provide detailed biostratigraphic control. Recognized are 11 of 14 zones of the middle upper Miocene to Quaternary Neogene Southern Ocean diatom zonation (NSD 7-NSD 20) of Ciesielski (1983; this chapter). Four Neogene Southern Ocean diatom zones (NSD 3-NSD 6) are recognized in the lower middle Miocene to middle upper Miocene of Site 594. Assemblages of this interval have a mixed high-latitude and temperate affinity; however, poor preservation limits correlation to high- and temperate-latitude zonal schemes. Neogene North Pacific diatom zones and subzones of NNPD 3 through NNPD 5 (Barron, in press, b) are correlated to Neogene Southern Ocean diatom zones NSD 3 through NSD 7: the upper portions of the Actinocyclus ingens Zone (NNPD 3) is correlative to the upper Nitzschia maleinterpretaria Zone (NSD 3); the Denticulopsis lauta Zone (NNPD 4) and Subzones a and b are correlative to the lower Coscinodiscus lewisianus Zone (NSD 4); and the D. hustedtü-D. lauta Zone (NNPD 5) and its Subzones a through d encompass the upper C. lewisianus Zone (NSD 4), N. grossepunctata Zone (NSD 5), N. denticuloides Zone (NSD 6), and the lower D. hustedtii-D. lauta Zone (NSD 7). A major disconformity spans the late Gilbert to early Gauss Chron (3.9-2.8 Ma). A second disconformity brackets the Miocene/Pliocene boundary; the section missing covers late Chron 5 and the early Gilbert chron (5.5-4.6 Ma). The remainder of the siliceous-fossil-bearing Miocene sediments at Site 594 appear to be correlative to lower paleomagnetic Chronozone 5 through upper Chronozone 16. Uppermost lower Miocene or lowermost middle Miocene sediments in the basal 50 m of Hole 594A are barren of diatoms.

Cretaceous planktonic foraminifera of the Kerguelen Plateau

An almost complete Upper Cretaceous sedimentary sequence recently recovered on the Kerguelen Plateau (southern Indian Ocean) during ODP Leg 183 was analysed for planktonic foraminifera in order to refine and integrate the zonal schemes previously proposed for the Southern Ocean area. Detailed biostratigraphic analysis carried out on holes 1135A, 1136A and 1138A (poleward of 50°S palaeolatitude during Late Cretaceous time) has allowed recognition of low and mid-high latitude bioevents, useful for correlation across latitudes, in addition to known Austral bioevents. The low latitude biozonation can be applied to Turonian sediments, because of the occurrence of Helvetoglobotruncana helvetica, which marks the boundary between Whiteinella archaeocretacea and Helvetoglobotruncana helvetica zones. The base of the Whiteinella archeocretacea Zone falls within the uppermost Cenomanian-Turonian black shale level in Hole 1138A. The stratigraphic interval from upper Turonian to uppermost Santonian can be resolved using bioevents recognized in the mid-high latitude sections. They are, in stratigraphic order: the last occurrence of Falsotruncana maslakovae in the Coniacian, the first occurrence of Heterohelix papula at the Coniacian/Santonian boundary, the extinction of the marginotruncanids in the late Santonian, and the first occurrence of Globigerinelloides impensus in the latest (?) Santonian. The remainder of the Late Cretaceous fits rather well in the Austral zonal scheme, except that Globigerinelloides impensus exhibits a stratigraphic range in agreement with its record at the mid-high latitude sections and extends further downwards than previously recorded at southern sites. Therefore, despite the poor recovery in certain intervals and the presence of several hiatuses of local and regional importance as revealed by correlation among holes, a more detailed zonal scheme has been obtained (mainly for the less resolved Turonian-Santonian interval). Remarks on some species often overlooked in literature are also provided.

Neogene magneto- and biostratigraphy of ODP Leg 104 holes

Silicoflagellate assemblages of ODP Leg 104 Neogene sequences are the basis of an interpretation of changes in the Neogene paleoenvironment of the Norwegian Sea. Fluctuations in the percentages of temperature and nutrient-sensitive taxonomic groups document major changes in sea-surface conditions. A brief, but distinct, cooling event occurred at 18.0-17.5 Ma which resulted in the disappearance of Naviculopsis. Following this early Miocene cooling a long period of increasing surface-water temperature occurred, leading up to a thermal high in the early middle Miocene (14.0 Ma). The early late Miocene (10.0-9.0 Ma) was distinctly cooler than the middle Miocene, but warmer than the remainder of the Neogene. Conditions between 13.0 and 10.0 Ma are unrecorded because of a regional hiatus, which is the earliest evidence for an end to the more temperate and stable conditions of the early to middle middle Miocene. A major plunge in temperatures occurred between 8.5 and 7.4 Ma and during the remainder of the late Miocene and Pliocene; from 7.4 to 2.65 Ma subpolar conditions prevailed. Silicoflagellates disappeared, except for sporadic occurrences, at 2.64 Ma with the beginning of dominant glacial sedimentation. Biogenic opal is absent in sediments younger than 0.76 Ma, indicating the dominance of glacial conditions with extensive sea ice.

Silicoflagellate abundances in sediments of ODP Leg 207 sites

The Ocean Drilling Program (ODP) drilled at five sites in the western Atlantic Ocean during Leg 207. The objective of the drilling was to recover samples from the shallow buried Cretaceous and Paleocene sediments on the Demerara Rise off Suriname, South America. These sediments are being studied for a number of paleoceanographic studies of the low-latitude Atlantic off the coast of Suriname (this volume). For this report two sites, Sites 1257 and 1258, were selected for silicoflagellate study because shipboard results suggested these two sites as the only ones with siliceous microfossils of Paleocene-Eocene age. The Demarara Rise is a predominant submarine plateau located off the coast of Suriname and French Guyana. This plateau stretches 380 km along the coast and is 220 km wide. The depth to seafloor along the depth transect drilled during ODP Leg 207 ranges from 1000 to 4500 m, but most of the remainder of the plateau lies in shallow water of 700 m. Much of this area is covered with 2-3 km of sediments. The Demerara Rise is built on rifted Precambrian continental crust. The plateau was one of the last places to be in contact with West Africa during the opening of the Atlantic Ocean (see Shipboard Scientific Party, 2004). Site 1257 (9°27'N, 54°20'W; water depth = 2951 m) is located on a terrace on the northwestern Demerara Rise ~400 km from Suriname. This is the second deepest water depth location drilled during Leg 207. Sediments from this area range in age from Miocene to Albian. This area is part of the transform fault that separated from Central America and western Africa. Three holes were drilled at Site 1257. Site 1258 (9°26'N, 54°43'W; water depth = 3192 m) is located on the western slope of the Demerara Rise ~380 km north of Suriname. This site is the distal and deepest site of the paleoceanographic depth transect drilled across Demerara Rise during Leg 207. The area is located on a ridge of Paleocene sediments cropping out on the seafloor. Three holes were drilled at Site 1258, but only one is studied.

Stable carbon and oxygen isotope ratios of benthic foraminifera from Paleocene to Oligocene sediments

Benthic oxygen and carbon isotopic results from a depth transect on Maud Rise, Antarctica, provide the first evidence for Warm Saline Deep Water (WSDW) in the Paleogene oceans. Distinct reversals occur in the oxygen isotopic gradient between the shallower Hole 689B (Eocene depth ~1400 m; present-day depth 2080 m) and the deeper Hole 690B (Eocene depth ~2250 m; present-day depth 2914 m). The isotopic reversals, well developed by at least 46 Ma (middle middle Eocene), existed for much of the remaining Paleogene. We do not consider these reversals to be artifacts of differential diagenesis between the two sites or to have resulted from other potentially complicating factors. This being so, the results show that deep waters at Hole 690B were significantly warmer than deep waters at the shallower Hole 689B. A progressive decrease and eventual reversal in benthic to planktonic delta18O gradients in Hole 690B, demonstrate that the deeper waters became warmer relative to Antarctic surface waters during the Eocene. The warmer deep waters of the Paleogene are inferred to have been produced at middle to low latitudes, probably in the Tethyan region which contained extensive shallow-water platforms, ideal sites for the formation of high salinity water through evaporative processes. The ocean during the Eocene, and perhaps the Paleocene, is inferred to have been two-layered, consisting of warm, saline deep waters formed at low latitudes and overlain by cooler waters formed at high latitudes. This thermospheric ocean, dominated by halothermal circulation we name Proteus. The Neogene and modern psychrospheric ocean Oceanus is dominated by thermohaline circulation of deep waters largely formed at high latitudes. An intermediate condition existed during the Oligocene, with a three-layered ocean that consisted of cold, dense deep waters formed in the Antarctic (Proto-AABW), overlain by warm, saline deep waters from low latitudes, and in turn overlain by cool waters formed in the polar regions. This we name Proto-oceanus which combined both halothermal and thermohaline processes. The sequence of high latitude, major, climatic change inferred from the oxygen isotopic records is as follows: generally cooler earlier Paleocene; warming during the late Paleocene; climax of Cenozoic warmth during the early Eocene and continuing into the early middle Eocene; cooling mainly in a series of steps during the remainder of the Paleogene. Superimposed upon this Paleogene pattern, the Paleocene/Eocene boundary is marked by a brief but distinct warming that involved deep to surface waters and a reduction in surface to deep carbon and oxygen isotopic gradients. This event coincided with major extinctions among the deep-sea benthic foraminifers as shown by Thomas (1990 doi:10.2973/odp.proc.sr.113.123.1990). Salinity has played a major role in deep ocean circulation, and thus paleotemperatures cannot be inferred directly from the oxygen isotopic composition of Paleogene benthic foraminifers without first accounting for the salinity effect.

Strontium-isotope stratigraphy and oxygen- and carbon-isotope record of Middle Jurassic to Early Cretaceous belemnites in the South Atlantic

87Sr/86Sr data of belemnites are presented from a Middle Jurassic-Early Cretaceous succession from the Falkland Plateau (Deep Sea Drilling Project Sites 511 and 330) that was deposited in a periodically anoxic, semi-enclosed shallow water basin. Diagenetically screened strontium-isotope values of 0.706789 rise to 0.707044 before increasing sharply to 0.707428 in the uppermost part of the sampled succession. Comparison with published strontium calibration curves suggests that the oldest samples were Callovian to Oxfordian in age, whilst the remainder of the Jurassic part of the succession consisted of Kimmeridgian and Early Tithonian age sediments. The nannofossil, dinoflagellate and molluscan assemblages provide comparable age determinations. The strontium-isotope analysis of the youngest belemnites points to a Hauterivian-Barremian age, whilst age interpretations based upon the fauna provide a wide age range from the Barremian to early Albian. Strontium-isotope stratigraphy of this succession hence offers increased age resolution providing data regarding the timing of episodes of bottom water anoxia which have been recorded throughout the South Atlantic Basin. Well-preserved belemnite specimens display an oxygen-isotope range between +0.08 and -2.22? (PDB, Peedee belemnite international standard) and a carbon-isotope range from +2.35 to -1.33? (PDB). Delta13C values become increasingly negative through the Late Jurassic-Early Cretaceous and in concert with the 87Sr/86Sr data reveal a trend that could be accounted for by increasing levels of weathering and erosion. The oxygen-isotope data if interpreted in terms of palaeotemperature are consistent with warm palaeotemperatures in the Kimmeridgian and slightly cooler temperatures for the Tithonian and Early Cretaceous parts of the succession. The proposed relative Kimmeridgian warmth (based upon strontium-isotope age assignments) is thus in good agreement with other published palaeotemperature records.

Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform

The scrapie prion protein (PrPSc) is the major, and possibly the only, component of the infectious prion; it is generated from the cellular isoform (PrPC) by a conformational change. N-terminal truncation of PrPSc by limited proteolysis produces a protein of ≈142 residues designated PrP 27–30, which retains infectivity. A recombinant protein (rPrP) corresponding to Syrian hamster PrP 27–30 was expressed in Escherichia coli and purified. After refolding rPrP into an α-helical form resembling PrPC, the structure was solved by multidimensional heteronuclear NMR, revealing many structural features of rPrP that were not found in two shorter PrP fragments studied previously. Extensive side-chain interactions for residues 113–125 characterize a hydrophobic cluster, which packs against an irregular β-sheet, whereas residues 90–112 exhibit little defined structure. Although identifiable secondary structure is largely lacking in the N terminus of rPrP, paradoxically this N terminus increases the amount of secondary structure in the remainder of rPrP. The surface of a long helix (residues 200–227) and a structured loop (residues 165–171) form a discontinuous epitope for binding of a protein that facilitates PrPSc formation. Polymorphic residues within this epitope seem to modulate susceptibility of sheep and humans to prion disease. Conformational heterogeneity of rPrP at the N terminus may be key to the transformation of PrPC into PrPSc, whereas the discontinuous epitope near the C terminus controls this transition.

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.

Cloning and expression of a cDNA encoding a bovine brain brefeldin A-sensitive guanine nucleotide-exchange protein for ADP-ribosylation factor

A 200-kDa guanine nucleotide-exchange protein (p200 or GEP) for ADP-ribosylation factors 1 and 3 (ARF1 and ARF3) that was inhibited by brefeldin A (BFA) was purified earlier from cytosol of bovine brain cortex. Amino acid sequences of four tryptic peptides were 47% identical to that of Sec7 from Saccharomyces cerevisiae, which is involved in vesicular trafficking in the Golgi. By using a PCR-based procedure with two degenerate primers representing sequences of these peptides, a product similar in size to Sec7 that contained the peptide sequences was generated. Two oligonucleotides based on this product were used to screen a bovine brain library, which yielded one clone that was a partial cDNA for p200. The remainder of the cDNA was obtained by 5′ and 3′ rapid amplification of cDNA ends (RACE). The ORF of the cDNA encodes a protein of 1,849 amino acids (≈208 kDa) that is 33% identical to yeast Sec7 and 50% identical in the Sec7 domain region. On Northern blot analysis of bovine tissues, a ≈7.4-kb mRNA was identified that hybridized with a p200 probe; it was abundant in kidney, somewhat less abundant in lung, spleen, and brain, and still less abundant in heart. A six-His-tagged fusion protein synthesized in baculovirus-infected Sf9 cells demonstrated BFA-inhibited GEP activity, confirming that BFA sensitivity is an intrinsic property of this ARF GEP and not conferred by another protein component of the complex from which p200 was originally purified.

In vivo functions of the Saccharomyces cerevisiae Hsp90 chaperone

In the highly concentrated environment of the cell, polypeptide chains are prone to aggregation during synthesis (as nascent chains await the emergence of the remainder of their folding domain), translocation, assembly, and exposure to stresses that cause previously folded proteins to unfold. A large and diverse group of proteins, known as chaperones, transiently associate with such folding intermediates to prevent aggregation, but in many cases the specific functions of individual chaperones are still not clear. In vivo, Hsp90 (heat shock protein 90) plays a role in the maturation of components of signal transduction pathways but also exhibits chaperone activity with diverse proteins in vitro, suggesting a more general function. We used a unique temperature-sensitive mutant of Hsp90 in Saccharomyces cerevisiae, which rapidly and completely loses activity on shift to high temperatures, to examine the breadth of Hsp90 functions in vivo. The data suggest that Hsp90 is not required for the de novo folding of most proteins, but it is required for a specific subset of proteins that have greater difficulty reaching their native conformations. Under conditions of stress, Hsp90 does not generally protect proteins from thermal inactivation but does enhance the rate at which a heat-damaged protein is reactivated. Thus, although Hsp90 is one of the most abundant chaperones in the cell, its in vivo functions are highly restricted.

Asparagine-proline sequence within membrane-spanning segment of SREBP triggers intramembrane cleavage by Site-2 protease

The NH2-terminal domains of membrane-bound sterol regulatory element-binding proteins (SREBPs) are released into the cytosol by regulated intramembrane proteolysis, after which they enter the nucleus to activate genes encoding lipid biosynthetic enzymes. Intramembrane proteolysis is catalyzed by Site-2 protease (S2P), a hydrophobic zinc metalloprotease that cleaves SREBPs at a membrane-embedded leucine-cysteine bond. In the current study, we use domain-swapping methods to localize the residues within the SREBP-2 membrane-spanning segment that are required for cleavage by S2P. The studies reveal a requirement for an asparagine-proline sequence in the middle third of the transmembrane segment. We propose a model in which the asparagine-proline sequence serves as an NH2-terminal cap for a portion of the transmembrane α-helix of SREBP, allowing the remainder of the α-helix to unwind partially to expose the peptide bond for cleavage by S2P.

Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate

On exposure to mildly acidic conditions, apomyoglobin forms a partially folded intermediate, I. The A, B, G, and H helices are significantly structured in this equilibrium intermediate, whereas the remainder of the protein is largely unfolded. We report here the effects of mutations at helix pairing sites on the stability of I in three classes of mutants that: (i) truncate hydrophobic side chains in native helix packing sites, (ii) truncate hydrophobic side chains not involved in interhelical contacts, and (iii) extend hydrophobic side chains at residues not involved in interhelical contacts. Class I mutants significantly decrease the stability and cooperativity of folding of the intermediate. Class II and III mutants show smaller effects on stability and have little effect on cooperativity. Qualitatively similar results to those found in I were obtained for all three classes of mutants in native myoglobin (N), demonstrating that hydrophobic burial is fairly specific to native helix packing sites in I as well as in N. These results suggest that hydrophobic burial along native-like interhelical contacts is important for the formation of the cooperatively folded intermediate.

Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding

To test a different approach to understanding the relationship between the sequence of part of a protein and its conformation in the overall folded structure, the amino acid sequence corresponding to an α-helix of T4 lysozyme was duplicated in tandem. The presence of such a sequence repeat provides the protein with “choices” during folding. The mutant protein folds with almost wild-type stability, is active, and crystallizes in two different space groups, one isomorphous with wild type and the other with two molecules in the asymmetric unit. The fold of the mutant is essentially the same in all cases, showing that the inserted segment has a well-defined structure. More than half of the inserted residues are themselves helical and extend the helix present in the wild-type protein. Participation of additional duplicated residues in this helix would have required major disruption of the parent structure. The results clearly show that the residues within the duplicated sequence tend to maintain a helical conformation even though the packing interactions with the remainder of the protein are different from those of the original helix. It supports the hypothesis that the structures of individual α-helices are determined predominantly by the nature of the amino acids within the helix, rather than the structural environment provided by the rest of the protein.