Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus

Most of the cultivated species of citrus have narrow genetic basis. Relationships among species and cultivars are obscured by sexual compatibility, polyembryony, apomixis and a high incidence of somatic mutations. DNA analysis is crucial in genetic studies not only for citrus breeding programs but also for characterization of hybrids and species. In this paper, single nucleotide polymorphisms ( SNPs) were investigated in 58 accessions of Citrus, hybrids and related genera. Genomic sequences of 'Pera IAC' sweet orange ( Citrus sinensis L. Osbeck) were used for primer design and selection of sequence tagged sites (STSs) for identification of SNPs. Analysis of 36 STSs showed identical sequences among 40 of the 41 sweet orange accessions studied. However, these accessions were heterozygous for many SNPs. Ten selected STSs were analyzed in 17 additional accessions from 13 species and hybrids. Comparing to the 'Pera IAC' sweet orange accession, a total of 150 polymorphic nucleotides were identified and most of the alterations were transitions ( 52.7%). The greatest number of SNPs was observed in Poncirus trifoliata ( L.) Raf. and the smallest in 'Ponkan' mandarin ( Citrus reticulata Blanco). At the intra-specific level, 'Bafa Gigante' ( Citrus sinensis L. Osbeck) was the only sweet orange accession with a divergent SNPs genotype, which corroborates the hypothesis of a hybrid origin for this accession. Although the STSs analyzed represent randomly sampled genomic sequences, they provided consistent information about the level of polymorphism and showed the potential of SNPs markers for characterization and phylogenetic studies.

Mapping eIF5A binding sites for Dys1 and Lia1: In vivo evidence for regulation of eIF5A hypusination

The evolutionarily conserved factor eIF5A is the only protein known to undergo hypusination, a unique posttranslational modification triggered by deoxyhypusine synthase (Dys1). Although eIF5A is essential for cell viability, the function of this putative translation initiation factor is still obscure. To identify eIF5A-binding proteins that could clarify its function, we screened a two-hybrid library and identified two eIF-5A partners in S. cerevisiae: Dys1 and the protein encoded by the gene YJR070C, named Lia1 (Ligand of eIF5A). The interactions were confirmed by GST pulldown. Mapping binding sites for these proteins revealed that both eIF5A domains can bind to Dys1, whereas the C-terminal domain is sufficient to bind Lia1. We demonstrate for the first time in vivo that the N-terminal α-helix of Dys1 can modulate enzyme activity by inhibiting eIF5A interaction. We suggest that this inhibition be abrogated in the cell when hypusinated and functional eIF5A is required. © 2003 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

Structure of myotoxin II, a catalytically inactive Lys49 phospholipase A2 homologue from Atropoides nummifer venom

Lys49 snake-venom phospholipase A2 (PLA2) homologues are highly myotoxic proteins which, although lacking catalytic activity, possess the ability to disrupt biological membranes, inducing significant muscle-tissue loss and permanent disability in severely envenomed patients. Since the structural basis for their toxic activity is still only partially understood, the structure of myotoxin II, a monomeric Lys49 PLA2 homologue from Atropoides nummifer, has been determined at 2.08 Å resolution and the anion-binding site has been characterized. © 2006 International Union of Crystallography. All rights reserved.

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

Purification, characterization, and specificity determination of a new serine protease secreted by penicillium waksmanii

The purpose of this work was to purify a protease from Penicillium waksmanii and to determine its biochemical characteristics and specificity. The extracellular protease isolated that was produced by P. waksmanii is a serine protease that is essential for the reproduction and growth of the fungus. The protease isolated showed 32 kDa, and has optimal activity at pH 8.0 and 35 C towards the substrate Abz-KLRSSKQ-EDDnp. The protease is active in the presence of CaCl2, KCl, and BaCl, and partially inhibited by CuCl2, CoCl2 and totally inhibited by AlCl3 and LiCl. In the presence of 1 M urea, the protease remains 50 % active. The activity of the protease increases 60 % when it is exposed to 0.4 % nonionic surfactant-Triton X-100 and loses 10 % activity in the presence of 0.4 % Tween-80. Using fluorescence resonance energy transfer analysis, the protease showed the most specificity for the peptide Abz-KIRSSKQ-EDDnp with k cat/K m of 10,666 mM-1 s-1, followed by the peptide Abz-GLRSSKQ-EDDnp with a k cat/K m of 7,500 mM -1 s-1. Basic and acidic side chain-containing amino acids performed best at subsite S1. Subsites S2, S3, S′ 2, and S′ 1, S ′ 3 showed a preference for binding for amino acids with hydrophobic and basic amino acid side chain, respectively. High values of k cat/K m were observed for the subsites S2, S3, and S′ 2. The sequence of the N-terminus (ANVVQSNVPSWGLARLSSKKTGTTDYTYD) showed high similarity to the fungi Penicillium citrinum and Penicillium chrysogenum, with 89 % of identity at the amino acid level. © 2012 Springer Science+Business Media New York.

Biophysical characterization of the recombinant importin-α from neurospora crassa

Neurospora crassa has been widely used as a model organism and contributed to the development of biochemistry and molecular biology by allowing the identification of many metabolic pathways and mechanisms responsible for gene regulation. Nuclear proteins are synthesized in the cytoplasm and need to be translocated to the nucleus to exert their functions which the importin-α receptor has a key role for the classical nuclear import pathway. In an attempt to get structural information of the nuclear transport process in N. crassa, we present herein the cloning, expression, purification and structural studies with N-terminally truncated IMPα from N. crassa (IMPα-Nc). Circular dichroism analysis revealed that the IMPα-Nc obtained is correctly folded and presents a high structural conservation compared to other importins-α. Dynamic light scattering, analytical size-exclusion chromatography experiments and molecular dynamics simulations indicated that the IMPα-Nc unbound to any ligand may present low stability in solution. The IMPα-Nc theoretical model displayed high similarity of its inner concave surface, which binds the cargo proteins containing the nuclear localization sequences, among IMPα from different species. However, the presence of non-conserved amino acids relatively close to the NLS binding region may influence the binding specificity of IMPα-Nc to cargo proteins. Copyright © 2012 Bentham Science Publishers. All Rights Reserved.

A Preliminary Linkage Map of the Hard Tick, Ixodes Scapularis

Blackwell Publishing Ltd. A linkage map of the Ixodes scapularis genome was constructed, based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F1 intercross progeny from a single, field-collected P1 female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of ~ 10 9 bp, the relationship of physical to genetic distance was found to be ~ 300 kb/cM in the I. scapularis genome.

A preliminary linkage map of the tick, Ixodes scapularis

A linkage map of the Ixodes scapularis genome was constructed based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F1 intercross progeny from a single, field-collected P1 female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of ∼109 bp, the relationship of physical to genetic distance is ∼300 kb/cM in the I. scapularis genome.

drp, A novel cell density regulated protein

Growing cells are continuously processing signals of all varieties and responding to these signals by changes in cellular gene expression. One signal that cells in close proximity relay to each other is cell-cell contact. Non-transformed cells respond to cell-cell contact by arrest of growth and entry into G$\sb0,$ a process known as contact inhibition. Transformed cells do not respond to contact inhibition and continue to grow to high cell density, forming foci when in cell culture and tumors in the living organism. The events surrounding the generation, transduction, and response to cellular contact are poorly understood. In the present study, a novel gene product, drp, is shown to be expressed at high levels in cultured cells at high cell density. This density regulated protein, drp, has an apparent molecular weight of 70 kDa. Northern analysis shows drp to be highly expressed in cardiac and skeletal muscle and least abundant in lung and kidney tissues. By homology to two independently derived sequence tagged sites (STSs) used in the human genome project, drp or a closely related sequence maps to human chromosome 12. Density-dependent increases in drp expression have been demonstrated in six different cell lines including NIH 3T3, Hela and a human teratocarcinoma cell line, PA-1. Cells exhibit increased drp expression both when they are plated at increasing concentrations per unit area, or plated at low density and allowed to grow naturally to higher cell density. Cells at high density can exhibit several phenotypes including growth arrest, accumulation of soluble factors in the media, and increased numbers of cell contacts. Growth arrest by serum starvation or TGF-$\beta$ treatment fails to produce an increase in drp expression. Similarly, treatment of low density cells with conditioned media from high density cells fails to elicit drp expression. These results argue that neither soluble factors accumulated or expressed at high density nor simple exit from the cell cycle is sufficient to produce an increase in drp expression. The expression of drp appears to be uniquely regulated by cell density alone. ^

Sediment geochemistry of ODP Leg 127 sites

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the final preserved chemistry of Japan Sea sediments are evaluated by investigating the rare earth element (REE), major element, and trace element concentrations in 59 squeeze-cake whole-round and 27 physical-property sample residues from Sites 794, 795, and 797, cored during ODP Leg 127. The most important variation in sedimentary chemical composition is the increase in SiO2 concentration through the Pliocene diatomaceous sequences, which dilutes most other major and trace element components by various degrees. This biogenic input is largest at Site 794 (Yamato Basin), moderately developed at Site 797 (Yamato Basin), and of only minor importance at Site 795 (Japan Basin), potentially reflecting basinal contrasts in productivity with the Yamato Basin recording greater biogenic input than the Japan Basin and with the easternmost sequence of Site 794 lying beneath the most productive waters. There are few systematic changes in solid-phase chemistry resulting from the opal-A/opal-CT or opal-CT/quartz silica phase transformations. Most major and trace element concentrations are controlled by the aluminosilicate fraction of the sediment, although the effects of diagenetic silica phases and manganese carbonates are of localized importance. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the upper Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. SumREE at Site 795 also is affiliated strongly with aluminosilicate phases and yet is diluted only slightly by siliceous input. At Site 797, SumREE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. Ce/Ce* profiles at all three sites increase essentially monotonically with depth and record progressive diagenetic LREE fractionation. The observed Ce/Ce* increases are not responding to changes in the paleoceanographic oxygenation state of the overlying water, as there is no independent evidence to suggest the proper oceanographic conditions. Ce/Ce* correlates slightly better with depth than with age at the two Yamato Basin sites. The downhole increase in Ce/Ce* at Sites 794 and 797 is a passive response to the diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and Lan/Ybn suggests that other processes mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column and that an additional ~38% is recycled at or near the seafloor. Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply buried interstitial waters.

Geochemistry, clay mineralogy and grain size distribution in various sediment cores drilled during ODP Leg 119 on the Antarctic continental shelf off Prydz Bay

Drilling was undertaken at five sites (739-743) on ODP Leg 119 on a transect across the continental shelf of Prydz Bay, East Antarctica, to elucidate the long-term glacial history of the area and to examine the importance of the area with respect to the development of the East Antarctic ice sheet as a whole. In addition to providing a record of glaciation spanning 36 m.y. or more, Leg 119 has provided information concerning the development of a continental margin under the prolonged influence of a major ice sheet. This has allowed the development of a sedimentary model that may be applicable not only to other parts of the Antarctic continental margin, but also to northern high-latitude continental shelves. The cored glacial sedimentary record in Prydz Bay consists of three major sequences, dominated by diamictite: 1. An upper flat-lying sequence that ranges in thickness from a few meters in inner and western Prydz Bay to nearly 250 m in the outer or eastern parts of the bay. The uppermost few meters consist of Holocene diatom ooze and diatomaceous mud with a minor ice-rafted component overlying diamicton and diamictite of late Miocene to Quaternary age. The diamictite is mainly massive, but stratified varieties and minor mudstone and diatomite also occur. 2. An upper prograding sequence cored at Sites 739 and 743, unconformly below the flat-lying sequence. This consists of a relatively steep (4° inclination) prograding wedge with a number of discrete sedimentary packages. At Sites 739 and 743 the sequence is dominated by massive and stratified diamictite, some of which shows evidence of slumping and minor debris flowage. 3. A lower, more gently inclined, prograding sequence lies unconformably below the flat-lying sequence at Site 742 and the upper prograding sequence at Site 739. This extends to the base of both sites, to 316 and 487 mbsf, respectively. It is dominated by massive, relatively clast-poor diamictite which is kaolinite-rich, light in color, and contains sporadic carbonate-cemented layers. The lower part of Site 742 includes well-stratified diamictites and very poorly sorted mudstones. The base of this site has indications of large-scale soft-sediment deformation and probably represents proximity to the base of the glacial sequence. Facies analysis of the Prydz Bay glacial sequence indicates a range of depositional environments. Massive diamictite is interpreted largely as waterlain till, deposited close to the grounding line of a floating glacier margin, although basal till and debris flow facies are also present. Weakly stratified diamictite is interpreted as having formed close to or under the floating ice margin and influenced by the input of marine diatomaceous sediment (proximal glaciomarine setting). Well-stratified diamictite has a stronger marine input, being more diatom-rich, and probably represents a proximal-distal glaciomarine sediment with the glaciogenic component being supplied by icebergs. Other facies include a variety of mudstones and diatom-rich sediments of marine origin, in which an ice-rafted component is still significant. None of the recovered sediments are devoid of a glacial influence. The overall depositional setting of the prograding sequence is one in which the grounded ice margin is situated close to the shelf edge. Progradation was achieved primarily by deposition of waterlain till. The flat-lying sequence illustrates a complex sequence of advances and retreats across the outer part of the shelf, with intermittent phases of ice loading and erosion. The glacial chronology is based largely on diatom stratigraphy, which has limited resolution. It appears that ice reached the paleoshelf break by earliest Oligocene, suggesting full-scale development of the East Antarctic ice sheet by that time. The ice sheet probably dominated the continental margin for much of Oligocene to middle Miocene time. Retreat, but not total withdrawal of the ice sheet, took place in late Miocene to mid-Pliocene time. The late Pliocene to Pleistocene was characterized by further advances across, and progradation of, the continental shelf. Holocene time has been characterized by reduced glacial conditions and a limited influence of glacial processes on sedimentation.

Geochemistry of felsic rocks and minerals of ODP Hole 135-841B

A felsic volcanic series (605-825 mbsf) overlain by upper Eocene shallow-water sediments (500-605 mbsf) and basalticandesitic sills that intruded into sediments of Holocene to Miocene age (0-500 mbsf) was drilled in the forearc region of the Lau Basin at a water depth of 4810 m. The volcanic sequence at Site 841 includes altered and mineralized calc-alkaline rhyolites and dacites, dacitic tuffs, lapilli tuffs, flow breccias, and welded tuffs. These rocks formed subaerially or in a very shallow-water environment suffering a subsidence of >5000 m since Eocene times. Calculations of gains and losses of the major components during alteration show most pronounced changes in the uppermost 70 m of the volcanic sequence. Here, Al, Fe, Mg, and K are enriched, whereas Si and Na are strongly depleted. Illite, vermiculite, chlorite, and hematite predominate in this part of the hole. Throughout the section, quartz, plagioclase, kaolinite, and calcite are present. Sulfide mineralization (up to 10 vol%) consisting mainly of disseminated pyrite (with minor pyrrhotite inclusions) and marcasite together with minor amounts of chalcopyrite is pervasive throughout. Locally, a few sulfide-bearing quartz-carbonate veins as well as Ti-amphibole replacement by rutile and then by pyrite were observed. Strong variations in the As content of sulfides (from 0 to 0.69 wt%) from the same depth interval and local enrichments of Co, Ni, and Cu in pyrite are interpreted to result from fluctuations in fluid composition. Calculations of oxygen and sulfur fugacities indicate that fO2 and fS2 were high at the top and lower at the bottom of the sequence. Sulfur isotope determinations on separated pyrite grains from two samples give d34S values of +6.4ë and +8.4ë, which are close to those reported from Kuroko and Okinawa Trough massive sulfide deposits and calc-alkaline volcanic rocks of the Japanese Ryukyu Island Arc. Calculated chlorite formation temperatures of 265°-290°C at the top of the sequence are consistent with minimum formation temperatures of fluid inclusions in secondary quartz, revealing a narrow range of 270°-297°C. Chlorite formation temperatures are constant downhole and do not exceed 300°C. The presence of marcasite and 4C-type pyrrhotite indicates a formation temperature of <= 250°C. At a later stage, illite was formed at the top of the volcanic series at temperatures well below 200°C.

Paleocene to middle Eocene calcareous nannofossils of Maude Rise, Weddell Sea

Cores from Sites 689 and 690 of Ocean Drilling Program Leg 113 provide the most continuous Paleocene and Eocene sequence yet recovered by deep sea drilling in the high latitudes of the Southern Ocean. The nannofossil-foraminifer oozes and chalks recovered from Maud Rise at 65°S in the Weddell Sea provide a unique opportunity for biostratigraphic study of extremely high southern latitude carbonate sediments. The presence of warm water index fossils such as the discoasters and species of the Tribrachiatus plexus facilitate the application of commonly used low latitude calcareous nannofossil biostratigraphic zonation schemes for the upper Paleocene and lower Eocene intervals. In the more complete section at Site 690, Okada and Bukry Zones CP1 through CP10 can be identified for the most part with the possible exception of Zone CP3. Several hiatuses are present in the sequence at Site 689 with the most notable being at the Cretaceous/Tertiary and Paleocene/Eocene boundaries. Though not extremely diverse, the assemblage of discoasters in the upper Paleocene and lower Eocene calcareous oozes is indicative of warm, relatively equable climates during that interval. A peak in discoaster diversity in uppermost Paleocene sediments (Zone CP8) corresponds to a negative shift in 5180 values. Associated coccolith assemblages are quite characteristic of high latitudes with abundant Chiasmolithus, Prinsius, and Toweius. Climatic cooling is indicated for middle Eocene sediments by assemblages that contain very abundant Reticulofenestra, lack common discoasters and sphenoliths and are much less diverse overall. Two new taxa are described, Biscutum? neocoronum n. sp. and Amithalithina sigmundii n. gen., n. sp.

Rare earth element data for sediments from ODP Leg 127

The relative effects of paleoceanographic and paleogeographic variations, sediment lithology, and diagenetic processes on the recorded rare earth element (REE) chemistry of Japan Sea sediments are evaluated by investigating REE total abundances and relative fractionations in 59 samples from Ocean Drilling Program Leg 127. REE total abundances (Sum REE) in the Japan Sea are strongly dependent upon the paleoceanographic position of a given site with respect to terrigenous and biogenic sources. REE concentrations at Site 794 (Yamato Basin) overall correspond well to aluminosilicate chemical indices and are strongly diluted by SiO2 within the late Miocene-Pliocene diatomaceous sequence. Eu/Eu* values at Site 794 reach a maximum through the diatomaceous interval as well, most likely suggesting an association of Eu/Eu* with the siliceous component, or reflecting slight incorporation of a detrital feldspar phase. Sum REE at Site 795 (Japan Basin) also is affiliated strongly with aluminosilicate phases, yet is diluted only slightly by siliceous input. At Site 797 (Yamato Basin), REE is not as clearly associated with the aluminosilicate fraction, is correlated moderately to siliceous input, and may be sporadically influenced by detrital heavy minerals originating from the nearby rifted continental fragment composing the Yamato Rise. The biogenic influence is largest at Site 794, moderately developed at Site 797, and of only minor importance at Site 795, reflecting basinal contrasts in productivity such that the Yamato Basin records greater biogenic input than the Japan Basin, while the most productive waters overlie the easternmost sequence of Site 794. Ce/Ce* profiles at all three sites increase monotonically with depth, and record progressive diagenetic LREE fractionation. The observed Ce/Ce* record does not respond to changes in oxygenation state of the overlying water, and Ce/Ce* correlates slightly better with depth than with age. The downhole increase in Ce/Ce* at Site 794 and Site 797 is a passive response to diagenetic transfer of LREE (except Ce) from sediment to interstitial water. At Site 795, the overall lack of correlation between Ce/Ce* and La_n/Yb_n suggests that other processes are occurring which mask the diagenetic behavior of all LREEs. First-order calculations of the Ce budget in Japan Sea waters and sediment indicate that ~20% of the excess Ce adsorbed by settling particles is recycled within the water column, and that an additional ~38% is recycled at or near the seafloor (data from Masuzawa and Koyama, 1989). Thus, because the remaining excess Ce is only ~10% of the total Ce, there is not a large source of Ce to the deeply buried sediment, further suggesting that the downhole increase in Ce/Ce* is a passive response to diagenetic behavior of the other LREEs. The REE chemistry of Japan Sea sediment therefore predicts successive downhole addition of LREEs to deeply-buried interstitial waters.

Oxygen and carbon isotope composition of Globoquadrina venezuelana and Oridorsalis umbonatus at DSDP Leg 85 Holes

Oxygen and carbon isotope stratigraphies are given for the planktonic foraminifer Globoquadrina venezuelana (a deep-dwelling species) at three DSDP sites located along a north-south transect at approximately 133°W across the Pacific equatorial high-productivity zone. The records obtained at Sites 573 and 574 encompass the lower Miocene. At Site 575 the record includes the middle Miocene and extends into the lowermost lower Miocene. The time resolution of the planktonic foraminifer isotope record varies from 50,000 to 500,000 yr. The benthic foraminifer Oridorsalis umbonatus was analyzed for isotope composition at a few levels of Site 575. Isotope stratigraphies for all three sites are compared with carbonate, foraminifer preservation, and grain size records. We identified a number of chemostratigraphic signals that appear to be synchronous with previously recognized signals in the western equatorial Pacific and the tropical Indian Ocean, and thus provide useful tools for chronostratigraphic correlations. The sedimentary sequence at Site 573 is incomplete and condensed, whereas the sequences from Sites 574 and 575 together provide a complete lower Miocene record. The expanded nature of this record, which was recovered with minimum disturbance and provides excellent calcareous and siliceous biostratigraphic control, offers a unique opportunity to determine the precise timing of early Miocene events. Paleomagnetic data from the hydraulic piston cores at Site 575 for the first time allow late early Miocene paleoceanographic events to be tied directly to the paleomagnetic time scale. The multiple-signal stratigraphies provide clues for paleoceanographic reconstruction during the period of preconditioning before the major middle Miocene cooling. In the lowermost lower Miocene there is a pronounced shift toward greater d13C values (by -1%) within magnetic Chron 16 (between approximately 17.5 and 16.5 Ma). The "Chron 16 Carbon Shift" coincides with the cessation of an early Miocene warming trend visible in the d18O signals. Values of d13C remain high until approximately 15 Ma, then decrease toward initial (early Miocene) values near 13.5 Ma. The broad lower to middle Miocene d13C maximum appears to correlate with the deposition of organic-carbon-rich sediments around the margin of the northern Pacific in the Monterey Formation of California and its lateral equivalents. The sediments rimming the Pacific were probably deposited under coastal upwelling conditions that may have resulted from the development of a strong permanent thermocline. Deposition in the upwelling areas occurred partly under anaerobic conditions, which led to the excess extraction of organic carbon from the ocean. The timing of the middle Miocene cooling, which began after the Chron 16 Carbon Shift, suggests that the extraction of organic carbon preconditioned the ocean-atmosphere system for subsequent cooling. A major carbonate dissolution event in the late early Miocene, starting at approximately 18.7 Ma, is associated with the enrichment in 13C. The maximum dissolution is coeval with the Chron 16 Carbon Shift. It corresponds to a prominent acoustic horizon that can be traced throughout the equatorial Pacific.