A family of fibrinogen-related proteins that precipitates parasite-derived molecules is produced by an invertebrate after infection

After infection with the digenetic trematode Echinostoma paraensei, hemolymph of the snail Biomphalaria glabrata contains lectins comprised of 65-kDa subunits that precipitate polypeptides secreted by E. paraensei intramolluscan larvae. Comparable activity is lacking in hemolymph of uninfected snails. Three different cDNAs with sequence similarities to peptides derived from the 65-kDa lectins were obtained and unexpectedly found to encode fibrinogen-related proteins (FREPs). These FREPs also contained regions with sequence similarity to Ig superfamily members. B. glabrata has at least five FREP genes, three of which are expressed at increased levels after infection. Elucidation of components of the defense system of B. glabrata is relevant because this snail is an intermediate host for Schistosoma mansoni, the most widely distributed causative agent of human schistosomiasis. These results are novel in suggesting a role for invertebrate FREPs in recognition of parasite-derived molecules and also provide a model for investigating the diversity of molecules functioning in nonself-recognition in an invertebrate.

Interaction of Coatomer with Aminoglycoside Antibiotics: Evidence That Coatomer Has at Least Two Dilysine Binding Sites

Coatomer is the soluble precursor of the COPI coat (coat protein I) involved in traffic among membranes of the endoplasmic reticulum and the Golgi apparatus. We report herein that neomycin precipitates coatomer from cell extracts and from purified coatomer preparations. Precipitation first increased and then decreased as the neomycin concentration increased, analogous to the precipitation of a polyvalent antigen by divalent antibodies. This suggested that neomycin cross-linked coatomer into large aggregates and implies that coatomer has two or more binding sites for neomycin. A variety of other aminoglycoside antibiotics precipitated coatomer, or if they did not precipitate, they interfered with the ability of neomycin to precipitate. Coatomer is known to interact with a motif (KKXX) containing adjacent lysine residues at the carboxyl terminus of the cytoplasmic domains of some membrane proteins resident in the endoplasmic reticulum. All of the antibiotics that interacted with coatomer contain at least two close amino groups, suggesting that the antibiotics might be interacting with the di-lysine binding site of coatomer. Consistent with this idea, di-lysine itself blocked the interaction of antibiotics with coatomer. Moreover, di-lysine and antibiotics each blocked the coating of Golgi membranes by coatomer. These data suggest that certain aminoglycoside antibiotics interact with di-lysine binding sites on coatomer and that coatomer contains at least two of these di-lysine binding sites.

Paleoproterozoic snowball Earth: Extreme climatic and geochemical global change and its biological consequences

Geological, geophysical, and geochemical data support a theory that Earth experienced several intervals of intense, global glaciation (“snowball Earth” conditions) during Precambrian time. This snowball model predicts that postglacial, greenhouse-induced warming would lead to the deposition of banded iron formations and cap carbonates. Although global glaciation would have drastically curtailed biological productivity, melting of the oceanic ice would also have induced a cyanobacterial bloom, leading to an oxygen spike in the euphotic zone and to the oxidative precipitation of iron and manganese. A Paleoproterozoic snowball Earth at 2.4 Giga-annum before present (Ga) immediately precedes the Kalahari Manganese Field in southern Africa, suggesting that this rapid and massive change in global climate was responsible for its deposition. As large quantities of O2 are needed to precipitate this Mn, photosystem II and oxygen radical protection mechanisms must have evolved before 2.4 Ga. This geochemical event may have triggered a compensatory evolutionary branching in the Fe/Mn superoxide dismutase enzyme, providing a Paleoproterozoic calibration point for studies of molecular evolution.

The biotic crisis and the future of evolution

The biotic crisis overtaking our planet is likely to precipitate a major extinction of species. That much is well known. Not so well known but probably more significant in the long term is that the crisis will surely disrupt and deplete certain basic processes of evolution, with consequences likely to persist for millions of years. Distinctive features of future evolution could include a homogenization of biotas, a proliferation of opportunistic species, a pest-and-weed ecology, an outburst of speciation among taxa that prosper in human-dominated ecosystems, a decline of biodisparity, an end to the speciation of large vertebrates, the depletion of “evolutionary powerhouses” in the tropics, and unpredictable emergent novelties. Despite this likelihood, we have only a rudimentary understanding of how we are altering the evolutionary future. As a result of our ignorance, conservation policies fail to reflect long-term evolutionary aspects of biodiversity loss.

Illite and hydrocarbon exploration

Illite is a general term for the dioctahedral mica-like clay mineral common in sedimentary rocks, especially shales. Illite is of interest to the petroleum industry because it can provide a K-Ar isotope date that constrains the timing of basin heating events. It is critical to establish that hydrocarbon formation and migration occurred after the formation of the trap (anticline, etc.) that is to hold the oil. Illite also may precipitate in the pores of sandstone reservoirs, impeding fluid flow. Illite in shales is a mixture of detrital mica and its weathering products with diagenetic illite formed by reaction with pore fluids during burial. K-Ar ages are apparent ages of mixtures of detrital and diagenetic end members, and what we need are the ages of the end members themselves. This paper describes a methodology, based on mineralogy and crystallography, for interpreting the K-Ar ages from illites in sedimentary rocks and for estimating the ages of the end members.

A Saccharomyces cerevisiae homolog of the human adrenoleukodystrophy transporter is a heterodimer of two half ATP-binding cassette transporters.

The adrenoleukodystrophy protein (ALDP) and the 70-kDa peroxisomal membrane protein (PMP70) are half ATP-binding cassette (ABC) transporters in the human peroxisome membrane. ALDP and PMP70 share sequence homology and both are implicated in genetic diseases. PXA1 and YKL741 are Saccharomyces cerevisiae genes that encode homologs of ALDP and PMP70. Pxa1p, a putative ortholog of ALDP, is involved in peroxisomal beta-oxidation of fatty acids while YKL741 is an open reading frame found by the yeast genome sequencing project. Here we designate YKL741 as PXA2 and show that its protein product, Pxa2p, like Pxa1p, is associated with peroxisomes but not required for their assembly. Yeast strains carrying gene disruption of PXA1, PXA2, or both have similar and, in the case of the latter, nonadditive phenotypes. We also find that the stability of Pxa1p, but not Pxa2p, is markedly reduced in the absence of the other. Finally, we find that Pxa1p and Pxa2p coimmuno-precipitate. These genetic and physical data suggest that Pxa1p and Pxa2p heterodimerize to form a complete peroxisomal ABC transporter involved in fatty acid beta-oxidation. This result predicts the presence of similar heterodimeric ABC transporters in the mammalian peroxisome membrane.

The 37/40-kilodalton autoantigen in insulin-dependent diabetes mellitus is the putative tyrosine phosphatase IA-2.

Major targets for autoantibodies associated with the development of insulin-dependent diabetes mellitus (IDDM) include tryptic fragments with a molecular mass of 37 kDa and/or 40 kDa of a pancreatic islet cell antigen of unknown identity. The assay identifying autoantibodies against the 37/40-kDa antigen in human sera is based on the immunoprecipitation of 35S-labeled rat insulinoma cell proteins with sera from IDDM patients, followed by limited trypsin digestion of the immunoprecipitated material. To identify cDNA clones coding for the 37/40-kDa antigen, we have screened a cDNA expression library from rat insulinoma cells with a serum from an IDDM patient that precipitated the 37/40-kDa antigen in our assay. Among the cDNA products that reacted with the IDDM serum, we identified one cDNA clone whose open reading frame encodes a protein with a predicted mass of 105 kDa that we termed "ICA105" for 105-kDa islet cell antibody. The deduced amino acid sequence has high homology to a recently cloned putative tyrosine phosphatase IA-2 from human and mouse cDNA libraries. Translation of the cDNA in vitro results in a polypeptide with the expected molecular mass of 105 kDa. The evidence that ICA105 is indeed the precursor of the 37/40-kDa tryptic fragments is based on the following three results: (i) Sera from IDDM patients containing autoantibodies to the 37/40-kDa antigen precipitate the in vitro translated polypeptide, whereas sera from healthy subjects as well as sera from IDDM patients not reactive with the 37/40-kDa antigen do not precipitate the cDNA product. (ii) Immunoprecipitation of the in vitro translated protein with sera containing autoantibodies to the 37/40-kDa antigen followed by limited trypsin digestion of the precipitated proteins results in a 40-kDa polypeptide. (iii) The protein derived from our cDNA but not from an unrelated control cDNA clone can block immunoprecipitation of the 37/40-kDa antigen from a labeled rat insulinoma cell extract. The availability of the cloned 37/40-kDa antigen should facilitate the identification of individuals at risk of IDDM with increased accuracy. Furthermore, the identification of the 37/40-kDa antigen as the putative tyrosine phosphatase IA-2 is of relevance in elucidating the role of this antigen in the development of IDDM.

Ukrainian economy on the verge of recession. OSW Commentary No. 96, 2012-11-21

In the third quarter of 2012, Ukraine’s economy recorded negative growth (-1.3%) for the first time since its 2009 economic crisis. Q4 GDP is projected to suffer a further decline, bringing Ukraine into formal recession. In addition to the worsening macroeconomic indicators, Ukraine is also facing a series of concomitant economic problems: a growing trade deficit, industrial decline, shrinking foreign exchange reserves, and the weakening of the hryvnia. Poor economic growth is expected to result in lower than projected budget revenues, which in turn could lead to the sequestration of the budget in December. The decline evident across the key economic indicators in the second half of 2012 brings to a close a period of relative economic stability and two years of economic growth, which had been seen as a significant personal achievement of President Viktor Yanukovych and the ruling Party of Regions. The health of the Ukrainian economy largely depends on the state of the country’s export- -oriented industries. The current economic forecasts for foreign markets are not very optimistic. It is impossible to determine whether the current economic downturn is likely to be merely temporary or whether it heralds the onset of a prolonged economic crisis. The limited capacity to deal with the growing economic problems may mean that Kiev will need to seek financial support from abroad. This is particularly significant with regard to external debt servicing, since in 2013 Ukraine will need to pay back around 9 billion USD, including over 5.5 billion USD to the International Monetary Fund. In order to overcome the recession and stabilise public finances, the government may be forced to take a series of unpopular measures, including raising the price of natural gas and utilities. These measures have been stipulated by the IMF as a condition of further financial assistance and the disbursement of the 12 billion USD stabilisation loan granted to Ukraine in July 2010. The only alternative for Western loans and economic reforms appears to be financial support from Russia. The price for Moscow’s help might however turn out to be very high, and precipitate a turn in Kiev’s foreign policy towards a gradual re-integration of former Soviet republics under Moscow-led geopolitical projects.

Balkan Pitfalls. ACES Working Papers, 2011

The Western Balkans are becoming increasingly mired in political conflicts, social disquiet, ethnic disputes, and state fragilities that can precipitate a new phase of regional instability. At the same time, the major international players may be unprepared and ill equipped to manage or resolve the emerging conflicts. While the U.S. and NATO have scaled down their presence in the region, the EU’s capabilities and effectiveness are coming under closer scrutiny.

Data compilation of ESOP

The work in this sub-project of ESOP focuses on the advective and convective transforma-tion of water masses in the Greenland Sea and its neighbouring areas. It includes observational work on the sub-mesoscale and analysis of hydrographic data up to the gyre-scale. Observations of active convective plumes were made with a towed chain equipped with up to 80 CTD sensors, giving a horizontal and vertical resolution of the hydrographic fields of a few metres. The observed scales of the penetrative convective plumes compare well with those given by theory. On the mesoscale the structure of homogeneous eddies formed as a result of deep convection was observed and the associated mixing and renewal of the intermediate layers quantified. The relative importance and efficiency of thermal and haline penetrative convection in relation to the surface boundary conditions (heat and salt fluxes and ice cover) and the ambient stratification are studied using the multi year time series of hydro-graphic data in the central Greenland Sea. The modification of the water column of the Greenland Sea gyre through advection from and mixing with water at its rim is assessed on longer time scales. The relative contributions are quantified using modern water mass analysis methods based on inverse techniques. Likewise the convective renewal and the spreading of the Arctic Intermediate Water from its formation area is quantified. The aim is to budget the heat and salt content of the water column, in particular of the low salinity surface layer, and to relate its seasonal and interannual variability to the lateral fluxes and the fluxes at the air-sea-ice interface. This will allow to estimate residence times for the different layers of the Greenland Sea gyre, a quantity important for the description of the Polar Ocean carbon cycle.

Chemical composition and solubility of ocean phosphatized rocks in seawater

In order to elucidate possibility of limestone phosphatization during contact with seawater two sets of experiments were carried out: that of solubility of natural phosphates in seawater and that of deposition of phosphorus onto calcareous phase. Concentration of phosphorus in seawater used for solubility experiments varied from 39 to 338 µ/l, temperature was 5.5-17.5°C and pH 7.8-7.9. The lowest solubility was characteristic of ancient crystallized samples. The deposition experiments showed that in case when concentration of dissolved phosphate in seawater reaches 3 mg/l it might be sorbed on solid CaCO3 phase without forming its own mineral. The latter is able to form rapidly but only if magnesium is not present in solution. In magnesium-free water calcium phosphates precipitate when concentration of dissolved phosphorus is higher than 0.9-1.2 mg/l. These results show that phosphatization of limestones in marine environment takes place during their contact with pore water but not with marine bottom water.

Description of the fossil manganese nodules found in the Oligocene clay deposits of Moravia, Brno area, Czech Republic

In the green Oligocene clay of Krizanovice (former Krzyzanowicz) the author found numerous black nodules. In the 3-4 centimeter thick black crust of a particular specimen the concentration in MnO2 is evaluated at 46.6% MnO2. The determination was done using the Volhard's method (precipitation of Fe by ZnO and titration with KMnO4). Only the dissoleved part in HCL was analysed. The non soluble residue was essentially a silica precipitate in the form of many gray flakes. The specific gravity of the crust was evaluated at 3.8. In the internal yellow core the amount of manganese is about 2.39% MnO2. Due to the light color it is judged to probably be in the form of Mn2O3.

Feldspar size measurements of tephra layers from ODP Leg 165 sites

Crystal size measurements have been carried out on tephra fall layers of Miocene to recent age from Sites 998, 999, and 1000 in the western Caribbean Sea. Maximum crystal size is used as a proxy for the grain size characteristics of the layers and an index of atmospheric dispersal from source eruptions. Crystal sizes range from 50 to 650 µm with the majority falling between 200 and 300 µm. All three sites exhibit a coarsening in the grain size of tephra layers with increasing age to the early Miocene that broadly correlates with an increase in the frequency of layers. Analysis of the present lower and upper level atmospheric circulation in the western Caribbean suggests that the layers were derived from source eruptions to the west of the sites somewhere in the Central American region. Minimum distances to these sources are of the order of 700 km. Crystal sizes in tephra layers at these distances are consistent with their derivation from energetic pyroclastic flow-forming eruptions that injected tephra to stratospheric levels by large-scale co-ignimbrite and plinian-style plumes. Coarsening of the layers during the Miocene peak of explosive volcanism cannot be attributed to any major change in paleowind intensity and is taken to represent the occurrence of more energetic eruptions that were able to disperse tephra over larger areas.

Geochemistry of nodules from a young seamount

Manganese nodules made of radiating rods of well crystallized birnessite were sampled at 8 degree 481.2'N, 103 degree 53.8W, 1875 m below sea level by a dredge that also collected hyaloclastite and basaltic talus. The nodule field is on the floor of a caldera within a young tholeiitic seamount and was discovered and photographed during a deep-two survey. It is interpreted as a brecciated hydrothermal deposit, crystallized from an amorphous manganese oxide precipitate that formed when seawater-based hydrothermal fluids mixed with oxidized seawater. The nodules and surrounding igneous rocks have subsequently been encrusted with hydrogenous ferromanganese oxides.

(Table 1) Mean sizes of Hydrobia ulvae juveniles in the littoral zone of the Chernaya Inlet (Kandalaksha Bay, White Sea) in July-September 1995

Based on observations and experiments carried out within the White Sea silty-sandy littoral zone in 1994-1997 data on biology of development and behavior of Hydrobia ulvae juveniles over water column and in sediments were obtained. Hydrobiid juveniles 0.125-0.150 mm in size appear in plankton during the second half of June and in two to three weeks they precipitate on sediments reaching 0.300-0.350 mm in size. Specific biological features of the White Sea hydrobiids are a short reproductive period and a short period of juvenile growth related to long under-ice time and decelerated warming of shallow waters. Distribution of juvenile individuals of H. ulvae is primarily determined by hydrodynamics and microtopography of the littoral zone. Redistribution of the juveniles permanently takes place, since all size groups of the juveniles are equally subjected to migration. During the first few weeks after settling mortality of juvenile mudsnails is 85%.