Planktonic foraminifera at DSDP Holes 72-516 and 72-518

Quantitative analysis was performed on the Quaternary planktonic foraminiferal fauna from Site 516, near the crest of the Rio Grande Rise, and Site 518, on the lower western flank of the Rise. From Hole 516, 46 samples were taken, and from Hole 518, 80 samples were taken. The mean interval between samples is 20 to 25 cm. About 50 species of Quaternary and Pliocene planktonic foraminifers were identified. Quaternary sediments, dated by the initial evolutionary appearance of Globorotalia truncatulinoides and other criteria, have thickness, of 9.8 m in Hole 516 and 16 m in Hole 518. The Globorotalia truncatulinoides Zone is subdivided into four subzones or biostratigraphic horizons (from lower to upper): (1) Globorotalia crassaformis viola, (2) Globorotalia crassaformis hessi, (3) Globigerina calida calida, and (4) Globigerinoides ruber (pink). Thickness of these horizons in Hole 516 establishes the age of the boundaries between them as 1.47, 0.81, and 0.28 Ma, respectively. All the Quaternary planktonic foraminiferal complexes sampled are subtropical. The region of the Rio Grande Rise, therefore, has been within the southern subtropical gyre continuously for the last 2 Ma. The average annual surface water temperatures were reconstructed for the Quaternary at both sites. A micropaleontologic method for the paleotemperature analysis of the thanatocoenosis registers an average Quaternary temperature of 21.2°C at Site 516 and 21.7°C at Site 518. The temperature fluctuations increase up to 3.5°C during the accumulation of the two last horizons (since 0.81 Ma). Temperature peaks are tentatively compared with oxygen isotopic stages and with continental glaciations. Levels at which planktonic foraminiferal species disappear correspond to coldwater intervals. In the Quaternary of Site 518, some layers show signs of dissolution. Corrosive to CaCO3, the northward flow of Antarctic Bottom Water through the Vema Channel increases during the cold periods. Site 518 has two layers of redeposited foraminiferal sand with Pliocene foraminifers. The average rate of the Quaternary sedimentation in Hole 516 is 0.52 cm per thousand years, and in Hole 518 it is 0.84 cm per thousand years.

Crustal uplift rates of 4 GPS stations near Jakobshavn Isbrae (2006-2009)

We analyze 2006-2009 data from four continuous Global Positioning System (GPS) receivers located between 5 and 150 km from the glacier Jakobshavn Isbrae, West Greenland. The GPS stations were established on bedrock to determine the vertical crustal motion due to the unloading of ice from Jakobshavn Isbrae. All stations experienced uplift, but the uplift rate at Kangia North, only 5 km from the glacier front, was about 10 mm/yr larger than the rate at Ilulissat, located only ~45 km further away. This suggests that most of the uplift is due to the unloading of the Earth's surface as Jakobshavn thins and loses mass. Our estimate of Jakobshavn's contribution to uplift rates at Kangia North and Ilulissat are 14.6 ± 1.7 mm/yr and 4.9 ± 1.1 mm/yr, respectively. The observed rates are consistent with a glacier thinning model based on repeat altimeter surveys from NASA's Airborne Topographic Mapper (ATM), which shows that Jakobshavn lost mass at an average rate of 22 ± 2 km**3/yr between 2006 and 2009. At Kangia North and Ilulissat, the predicted uplift rates computed using thinning estimates from the ATM laser altimetry are 12.1 ± 0.9 mm/yr and 3.2 ± 0.3 mm/yr, respectively. The observed rates are slightly larger than the predicted rates. The fact that the GPS uplift rates are much larger closer to Jakobshavn than further away, and are consistent with rates inferred using the ATM-based glacier thinning model, shows that GPS measurements of crustal motion are a potentially useful method for assessing ice-mass change models.

Classification of coral reef types in Torres Strait (GIS files in zip-archive 319 kB)

Coral reefs represent major accumulations of calcium carbonate (CaCO3). The particularly labyrinthine network of reefs in Torres Strait, north of the Great Barrier Reef (GBR), has been examined in order to estimate their gross CaCO3 productivity. The approach involved a two-step procedure, first characterising and classifying the morphology of reefs based on a classification scheme widely employed on the GBR and then estimating gross CaCO3 productivity rates across the region using a regional census-based approach. This was undertaken by independently verifying published rates of coral reef community gross production for use in Torres Strait, based on site-specific ecological and morphological data. A total of 606 reef platforms were mapped and classified using classification trees. Despite the complexity of the maze of reefs in Torres Strait, there are broad morphological similarities with reefs in the GBR. The spatial distribution and dimensions of reef types across both regions are underpinned by similar geological processes, sea-level history in the Holocene and exposure to the same wind/wave energetic regime, resulting in comparable geomorphic zonation. However, the presence of strong tidal currents flowing through Torres Strait and the relatively shallow and narrow dimensions of the shelf exert a control on local morphology and spatial distribution of the reef platforms. A total amount of 8.7 million tonnes of CaCO3 per year, at an average rate of 3.7 kg CaCO3 m-2 yr-1 (G), were estimated for the studied area. Extrapolated production rates based on detailed and regional census-based approaches for geomorphic zones across Torres Strait were comparable to those reported elsewhere, particularly values for the GBR based on alkalinity-reduction methods. However, differences in mapping methodologies and the impact of reduced calcification due to global trends in coral reef ecological decline and changing oceanic physical conditions warrant further research. The novel method proposed in this study to characterise the geomorphology of reef types based on classification trees provides an objective and repeatable data-driven approach that combined with regional census-based approaches has the potential to be adapted and transferred to different coral reef regions, depicting a more accurate picture of interactions between reef ecology and geomorphology.

Isotopic composition of strontium in planktonic foraminiferas from sediments of the DSDP Holes 90-588 and 94-607

Measurements of 87Sr/86Sr on samples of planktonic foraminifers were used to reconstruct changes in the Sr isotopic composition of seawater for the past 8 Ma. The late Neogene was marked by a general, but not regular, increase in 87S/86Sr with two breaks in slope at 5.5 and 2.5 Ma. These times mark the beginning of two periods of steep increase in 87Sr/86Sr values, relative to preceding periods characterized by essentially constant values. During the last 2.5 Ma, 87Sr/86Sr values increased at an average rate of 0.000054/Ma. This steep increase suggests that the modem ocean is not in Sr isotopic equilibrium relative to its major input fluxes. A non-equilibrium model for the modern Sr budget suggests that the residence time of Sr is ~2.5 Ma, which is significantly less than previously accepted estimates of 4-5 Ma. Modelling results suggest that the increase in 87Sr/86Sr over the past 8 Ma could have resulted from a 25% increase in the riverine flux of Sr or an increase in the average 87Sr/86Sr of this flux by 0.0006. The dominant cause of increasing 87Sr/86Sr values of seawater during the late Neogene is believed to be increased rates of uplift and chemical weathering of mountainous regions. Calculations suggest that uplift and weathering of the Himalayan-Tibetan region alone can account for the majority of the observed 87Sr/86Sr increase since the early Late Miocene. Exhumation of Precambrian shield areas by continental ice-sheets may have contributed secondarily to accelerated mechanical and chemical weathering of old crustal silicates with high 87Sr/86Sr values. In fact, the upturn in 87Sr/86Sr at 2.5 Ma coincides with increased glacial activity in the Northern Hemisphere. A variety of geochemical (87Sr/86Sr, Ge/Si, d13C, CCD, etc.) and sedimentologic data (accumulation rates) from the marine sedimentary record are compatible with a progressive increase in the chemical weathering rate of continents and dissolved riverine fluxes during the late Cenozoic. We hypothesize that chemical weathering of the continents and dissolved riverine fluxes to the oceans reached a maximum during the late Pleistocene because of repeated glaciations, increased continental exposure by lowered sea level, and increased continental relief resulting from high rates of tectonism.

Rates of sulfide formation and oxidation in the Black Sea waters in February-April 1991

Rate of hydrogen sulfide oxidation in the redox zone of the Black Sea and rate of hydrogen sulfide formation due to bacterial sulfate reduction in the upper layer of anaerobic waters were measured in February-April 1991. These measurements were made using sulfur radioisotope under conditions close to those in situ. It was established that hydrogen sulfide is oxidized in the layer of oxygen and hydrogen sulfide coexistence under the upper boundary of the hydrogen sulfide layer. Maximum rate of hydrogen sulfide oxidation was recorded within the limits of density values dT of 16.20-16.30, while varying in the layer from 2 to 4.5 µmol/day. The average rate of hydrogen sulfide oxidation was 1.5-3 times higher than that during the warm season. Sulfide formation was not observed at most of the stations in the examined lower portion of the pycnocline layer (140 to 400 m). Noticeable sulfate reduction was detected only at one station on the northwestern shelf. Intensified hydrodynamics in the upper layers of the water mass during the cold season can be a probable reason for such noticeable changes in sulfur dynamics in the water mass of the Black Sea. Data suggesting that hydrogen sulfide oxidation proceeds under the hydrogen sulfide boundary indicate absence of the so-called "suboxic zone" in this basin.

Model of interactive visualization of diffusion processes from different strains, and source routes and spatial diffusion of capuchin monkeys over the past 6 million years

Source routes and Spatial Diffusion of capuchin monkeys over the past 6 million years, rebuilt in the SPREAD 1.0.6 from the MCC tree. The map shows the 10 different regions to which distinctive samples were associated. The different transmission routes have been calculated from the average rate over time. Only rates with Bayes factor> 3 were considered as significantly different from zero. Significant diffusion pathways are highlighted with color varying from dark brown to red, being the dark brown less significant rates and deep red the most significant rates.

Pliocene to Pleistocene calcium carbonate and organic carbon record of ODP Hole 117-722B

Site 722 provides high resolution records of percent CaCO3, magnetic susceptibility, d18O, organic carbon, and coarse fraction for the past 3.4 m.y. from the crest of the Owen Ridge, northwestern Arabian Sea. Within this time interval, most of the carbonate percent variations can be attributed to terrigenous dilution and do not reflect changes in the carbonate system. From the late Pliocene to Present, the average rate of calcium carbonate accumulation increases from 1 to 3 g/cm**2/k.y. and the average accumulation of organic carbon decreases from 75 to 30 mg/cm**2/k.y. The carbonate component is more dissolved in the older interval. The long-term variations in carbonate accumulation may reflect a greater input of organic matter in the late Pliocene, which decomposes to produce CO2 and dissolve carbonate. Magnetic susceptibility and % noncarbonate (100 - CaCO3%) reflect changes in the amount of the lithogenic component in the sediments. The period of variation of lithogenic material is the same period as the original forcing of the regional summer monsoon, however, the timing matches global aridity patterns and global ice volume (sea level) changes. This preliminary analysis suggests that the high frequency variation of lithogenic material persists for at least the last 3.4 m.y. Within the last million years, calcium carbonate accumulation has a large amplitude signal that covaries with major changes in ice volume. Both calcium carbonate and noncarbonate (mostly terrigenous) accumulation are greatest during glacial stages. Interglacial intervals are characterized by low mass accumulation rates, increased foraminifer fragmentation, and increased opal concentration. The accumulation of organic carbon matches the high frequency changes in sedimentation rates. We attribute this high correlation to enhanced preservation of organic carbon by increased sedimentation rate. Of the three major biological components studied, only opal exhibits the variations expected for a biological productivity system forced by monsoonal upwelling driven by changes in northern hemisphere summer radiation.

Long-term foliar persistence and efficacy of spinosad against beet armyworm under greenhouse conditions.

BACKGROUND: The immediate lethality caused by spinosad has been widely studied on Spodoptera exigua (H ¿ ubner). However, long-term effects can also provide valuable information on insecticide toxic action. Here, the persistence of spinosad on Capsicum annuum L. foliage and the lethal and sublethal effects of greenhouse-aged foliar residues of this insecticide on third instars of S. exigua are reported. RESULTS: Foliage was collected at 0, 3, 5, 10, 20, 30, 40 and 50 days after application, and spinosad residues were measured. Residues decreased over time according to first-order kinetics. The average rate constant and half-life of disappearance were 4.44×10?3 and156 daysand5.80×10?3 and120 days for60and120 mg L?1 respectively. Larval mortalitygradually decreased, corresponding to the residues, but was still appreciable (35 and 65% for 60 and 120 mg L?1 respectively) when the larvae were fed with foliage collected 50 days after treatment. Subsequently, pupal development was reduced and varied between 20 and 60% and between 21 and 41% for 60 and 120 mg L?1, respectively, in all ages of leaf residues that were bioassayed. At all time points, the consumption rate by the larvae was reduced between 62 and 84% for both concentrations that were bioassayed. CONCLUSION: It is concluded that, under the present greenhouse conditions, the degradation of spinosad was slower than that reported by other authors in the field, and, because of that, its residues could cause lethal and sublethal effects to S. exigua larvae.

The Use of Patents to Assess National Innovation Systems: Evidences from Spanish Biotechnology

Spain’s economy recorded a high rate of growth from the mid-1990s onwards. At the same time, the resources allocated to Research and Development (R&D) grew at a much faster pace than in other European Union (EU) countries. Spain’s growth recorded an average rate of 2.93% from the early 1990s to 2004. Over the same period, the average growth in the EU was 0.46%. This circumstance, together with several sound policy decisions implemented between 2004 and 2009, ushered in a “golden age of Spanish biotechnology”. In terms of the national patent licenses issued by the Spanish Patent and Trademark Office (SPTO) between 2004 and 2009, the number in biotechnology grew from 84 to 151. However, the current economic situation in Spain, along with a series of political decisions taken over the past two or three years to cut spending on R&D, predicts a sharp downturn in the performance of Spanish biotechnology. This scenario makes Spain one of the best places to study the successes and failures of the management of science and allows transfer this experience to the other international regions. We need to analyze the influence of political decisions as a major factor with a bearing on the quality of science. Using patents as an indicator of scientific development, this paper analyzes the evolution of the biotechnology sector in Spain and its relationship with scientific policy and the management of R&D.

Suppression of protein synthesis in brain during hibernation involves inhibition of protein initiation and elongation

Protein synthesis (PS) has been considered essential to sustain mammalian life, yet was found to be virtually arrested for weeks in brain and other organs of the hibernating ground squirrel, Spermophilus tridecemlineatus. PS, in vivo, was below the limit of autoradiographic detection in brain sections and, in brain extracts, was determined to be 0.04% of the average rate from active squirrels. Further, it was reduced 3-fold in cell-free extracts from hibernating brain at 37°C, eliminating hypothermia as the only cause for protein synthesis inhibition (active, 0.47 ± 0.08 pmol/mg protein per min; hibernator, 0.16 ± 0.05 pmol/mg protein per min, P < 0.001). PS suppression involved blocks of initiation and elongation, and its onset coincided with the early transition phase into hibernation. An increased monosome peak with moderate ribosomal disaggregation in polysome profiles and the greatly increased phosphorylation of eIF2α are both consistent with an initiation block in hibernators. The elongation block was demonstrated by a 3-fold increase in ribosomal mean transit times in cell-free extracts from hibernators (active, 2.4 ± 0.7 min; hibernator, 7.1 ± 1.4 min, P < 0.001). No abnormalities of ribosomal function or mRNA levels were detected. These findings implicate suppression of PS as a component of the regulated shutdown of cellular function that permits hibernating ground squirrels to tolerate “trickle” blood flow and reduced substrate and oxygen availability. Further study of the factors that control these phenomena may lead to identification of the molecular mechanisms that regulate this state.

Cytotoxic T lymphocytes and viral turnover in HIV type 1 infection

To understand the role of the immune system in limiting HIV type 1 replication, it is critical to know to what extent the rapid turnover of productively infected cells is caused by viral cytopathicity or by immune-mediated lysis. We show that uncultured peripheral blood mononuclear cells of many patients contain cytotoxic T lymphocytes (CTL) that lyse target cells—at plausible peripheral blood mononuclear cell-to-target ratios—with half-lives of less than 1 day. In 23 patients with CD4 counts ranging from 10 to 900 per μl, the average rate of CTL-mediated lysis corresponds to a target cell half-life of 0.7 day. We develop mathematical models to calculate the turnover rate of infected cells subjected to immune-mediated lysis and viral cytopathicity and to estimate the fraction of cells that are killed by CTL as opposed to virus. The models provide new interpretations of drug treatment dynamics and explain why the observed rate of virus decline is roughly constant for different patients. We conclude that in HIV type 1 infection, CTL-mediated lysis can reduce virus load by limiting virus production, with small effects on the half-life of infected cells.

Long term trends in the evolution of H(3) HA1 human influenza type A

We have studied the HA1 domain of 254 human influenza A(H3N2) virus genes for clues that might help identify characteristics of hemagglutinins (HAs) of circulating strains that are predictive of that strain’s epidemic potential. Our preliminary findings include the following. (i) The most parsimonious tree found requires 1,260 substitutions of which 712 are silent and 548 are replacement substitutions. (ii) The HA1 portion of the HA gene is evolving at a rate of 5.7 nucleotide substitutions/year or 5.7 × 10−3 substitutions/site per year. (iii) The replacement substitutions are distributed randomly across the three positions of the codon when allowance is made for the number of ways each codon can change the encoded amino acid. (iv) The replacement substitutions are not distributed randomly over the branches of the tree, there being 2.2 times more changes per tip branch than for non-tip branches. This result is independent of how the virus was amplified (egg grown or kidney cell grown) prior to sequencing or if sequencing was carried out directly on the original clinical specimen by PCR. (v) These excess changes on the tip branches are probably the result of a bias in the choice of strains to sequence and the detection of deleterious mutations that had not yet been removed by negative selection. (vi) There are six hypervariable codons accumulating replacement substitutions at an average rate that is 7.2 times that of the other varied codons. (vii) The number of variable codons in the trunk branches (the winners of the competitive race against the immune system) is 47 ± 5, significantly fewer than in the twigs (90 ± 7), which in turn is significantly fewer variable codons than in tip branches (175 ± 8). (viii) A minimum of one of every 12 branches has nodes at opposite ends representing viruses that reside on different continents. This is, however, no more than would be expected if one were to randomly reassign the continent of origin of the isolates. (ix) Of 99 codons with at least four mutations, 31 have ratios of non-silent to silent changes with probabilities less than 0.05 of occurring by chance, and 14 of those have probabilities <0.005. These observations strongly support positive Darwinian selection. We suggest that the small number of variable positions along the successful trunk lineage, together with knowledge of the codons that have shown positive selection, may provide clues that permit an improved prediction of which strains will cause epidemics and therefore should be used for vaccine production.

Real time observation of anaphase in vitro.

We used digital fluorescence microscopy to make real-time observations of anaphase chromosome movement and changes in microtubule organization in spindles assembled in Xenopus egg extracts. Anaphase chromosome movement in these extracts resembled that seen in living vertebrate cells. During anaphase chromosomes moved toward the spindle poles (anaphase A) and the majority reached positions very close to the spindle poles. The average rate of chromosome to pole movement (2.4 microns/min) was similar to earlier measurements of poleward microtubule flux during metaphase. An increase in pole-to-pole distance (anaphase B) occurred in some spindles. The polyploidy of the spindles we examined allowed us to observe two novel features of mitosis. First, during anaphase, multiple microtubule organizing centers migrated 40 microns or more away from the spindle poles. Second, in telophase, decondensing chromosomes often moved rapidly (7-23 microns/min) away from the spindle poles toward the centers of these asters. This telophase chromosome movement suggests that the surface of decondensing chromosomes, and by extension those of intact nuclei, bear minus-end-directed microtubule motors. Preventing the inactivation of Cdc2/cyclin B complexes by adding nondegradable cyclin B allowed anaphase A to occur at normal velocities, but reduced the ejection of asters from the spindles, blocked chromosome decondensation, and inhibited telophase chromosome movement. In the presence of nondegradable cyclin B, chromosome movement to the poles converted bipolar spindles into pairs of independent monopolar spindles, demonstrating the role of sister chromatid linkage in maintaining spindle bipolarity.

The organization of seismicity on fault networks.

Although models of homogeneous faults develop seismicity that has a Gutenberg-Richter distribution, this is only a transient state that is followed by events that are strongly influenced by the nature of the boundaries. Models with geometrical inhomogeneities of fracture thresholds can limit the sizes of earthquakes but now favor the characteristic earthquake model for large earthquakes. The character of the seismicity is extremely sensitive to distributions of inhomogeneities, suggesting that statistical rules for large earthquakes in one region may not be applicable to large earthquakes in another region. Model simulations on simple networks of faults with inhomogeneities of threshold develop episodes of lacunarity on all members of the network. There is no validity to the popular assumption that the average rate of slip on individual faults is a constant. Intermediate term precursory activity such as local quiescence and increases in intermediate-magnitude activity at long range are simulated well by the assumption that strong weakening of faults by injection of fluids and weakening of asperities on inhomogeneous models of fault networks is the dominant process; the heat flow paradox, the orientation of the stress field, and the low average stress drop in some earthquakes are understood in terms of the asperity model of inhomogeneous faulting.

Immunoglobulin variable region hypermutation in hybrids derived from a pre-B- and a myeloma cell line.

Somatic mutation of the variable (V) regions of immunoglobulin genes occurs in vivo at rates that have been estimated to be between 10(-3) and 10(-4) per bp per generation. To study this process in vitro, the 18.81 pre-B-cell line and hybrids derived by fusing 18.81 to the NSO myeloma fusion partner were transfected with a mu heavy-chain construct containing a nonsense mutation in the V region (Vn) or the constant region (Cn). Mutation was quantitated by reversion analysis using the ELISA spot assay to detect single cells secreting IgM. Fluctuation analysis revealed that V-region mutations spontaneously occurred in 18.81 cells at an average rate of 5.8 x 10(-6) per bp per cell generation and in selected 18.81-NSO hybrids at greatly increased rates of 1.6 x 10(-3) to 5.8 x 10(-4) per bp per generation. The Vn construct also reverted frequently in transgenic mice, indicating that it contained sufficient information to mutate at high rates both in vivo and in vitro. Sequence analysis of reverted genes revealed that reversion was due to point mutations. Since the rates and nature of the mutations that are occurring in these transfected genes are similar to those reported in vivo, it should be possible to use this system to identify the cis-acting sequences and trans-acting factors that are responsible for V-region somatic hypermutation.