Particulate matter and organic compounds in snow, ice, and water of the Lazarev and Cooperation Seas

Integrated studies of particulate matter and organic compounds in surface waters and the snow-ice cover by means of geochemical (concentrations of the particulate matter, Corg, hydrocarbons, lipids, and chlorophyll a) and optical techniques were performed in the Southern Ocean and in the East Atlantic Ocean along the vessel's route: Africa - Antarctica - Africa - St. Petersburg. Correlations between studied compounds were found. It was shown that supply of pollutants affects not only concentrations but also proportions of the considered compounds. New data were obtained on the processes of accumulation of particulate matter and organic compounds under ice formation.

Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification

The impact of ocean acidification (OA) on coral calcification, a subject of intense current interest, is poorly understood in part because of the presence of symbionts in adult corals. Early life history stages of Acropora spp. provide an opportunity to study the effects of elevated CO(2) on coral calcification without the complication of symbiont metabolism. Therefore, we used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO(2) on gene expression in primary polyps of Acropora millepora, using as reference a novel comprehensive transcriptome assembly developed for this study. Gene ontology analysis of this whole transcriptome data set indicated that CO(2) -driven acidification strongly suppressed metabolism but enhanced extracellular organic matrix synthesis, whereas targeted analyses revealed complex effects on genes implicated in calcification. Unexpectedly, expression of most ion transport proteins was unaffected, while many membrane-associated or secreted carbonic anhydrases were expressed at lower levels. The most dramatic effect of CO(2) -driven acidification, however, was on genes encoding candidate and known components of the skeletal organic matrix that controls CaCO(3) deposition. The skeletal organic matrix effects included elevated expression of adult-type galaxins and some secreted acidic proteins, but down-regulation of other galaxins, secreted acidic proteins, SCRiPs and other coral-specific genes, suggesting specialized roles for the members of these protein families and complex impacts of OA on mineral deposition. This study is the first exhaustive exploration of the transcriptomic response of a scleractinian coral to acidification and provides an unbiased perspective on its effects during the early stages of calcification.

OSIRIS observations of meter-sized exposures of H2O ice at the surface of 67P/Churyumov-Gerasimenko and interpretation using laboratory experiments

Since OSIRIS started acquiring high-resolution observations of the surface of the nucleus of comet 67P/Churyumov-Gerasimenko, over one hundred meter-sized bright spots have been identified in numerous types of geomorphologic regions, but mostly located in areas receiving low insolation. The bright spots are either clustered, in debris fields close to decameter-high cliffs, or isolated without structural relation to the surrounding terrain. They can be up to ten times brighter than the average surface of the comet at visible wavelengths and display a significantly bluer spectrum. They do not exhibit significant changes over a period of a few weeks. All these observations are consistent with exposure of water ice at the surface of boulders produced by dislocation of the weakly consolidated layers that cover large areas of the nucleus. Laboratory experiments show that under simulated comet surface conditions, analog samples acquire a vertical stratification with an uppermost porous mantle of refractory dust overlaying a layer of hard ice formed by recondensation or sintering under the insulating dust mantle. The evolution of the visible spectrophotometric properties of samples during sublimation is consistent with the contrasts of brightness and color seen at the surface of the nucleus. Clustered bright spots are formed by the collapse of overhangs that is triggered by mass wasting of deeper layers. Isolated spots might be the result of the emission of boulders at low velocity that are redepositioned in other regions.

Study of the Influence of Reference System in Surface Finishing Parameters Evaluation.

In the present paper the influence of the reference system with regard to the characterization of the surface finishing is analyzed. The effect of the reference system’s choice on the most representative surface finishing parameters (e.g. roughness average Ra and root mean square values Rq) is studied. The study can also be applied to their equivalent parameters in waviness and primary profiles. Based on ISO and ASME standards, three different types of regression lines (central, mean and orthogonal) are theoretically and experimentally analyzed, identifying the validity and applicability fields of each one depending on profile’s geometry. El presente trabajo realiza un estudio de la influencia que supone la elección del sistema de referencia en la determinación los valores de los parámetros más relevantes empleados en la caracterización del acabado superficial tales como la rugosidad media aritmética Ra o la rugosidad media cuadrática Rq y sus equivalentes en los perfiles de ondulación y completo. Partiendo de la definición establecida por las normas ISO y ASME, se analizan tres tipos de líneas de regresión cuadrática (línea central, línea media y línea ortogonal), delimitando los campos de validez y de aplicación de cada una de ellas en función de la geometría del perfil. Para ello se plantean diversos tipos de perfiles y se desarrolla un estudio teórico y experimental de los mismos.

Hydrogeochemistry of surface and spring waters in the surroundings of the CO2 injection site at Hontomín–Huermeces (Burgos, Spain)

In this paper the very first geochemical and isotopic data related to surface and spring waters and dissolved gases in the area of Hontomín–Huermeces (Burgos, Spain) are presented and discussed. Hontomín–Huermeces has been selected as a pilot site for the injection of pure (>99%) CO2. Injection and monitoring wells are planned to be drilled close to 6 oil wells completed in the 1980s for which detailed stratigraphical logs are available, indicating the presence of a confined saline aquifer at the depth of about 1500 m into which less than 100,000 tons of iquid CO2 will be injected, possibly starting in 2013. The chemical and features of the spring waters suggest that they are related to a shallow hydrogeological system as the concentration of the Total Dissolved Solids approaches 800 mg/L with a Ca2+(Mg2+)-HCO3− composition, similar to that of the surface waters. This is also supported by the oxygen and hydrogen isotopic ratios that have values lying between those of the Global and the Mediterranean Meteoric Water Lines. Some spring waters close to the oil wells are haracterized by relatively high concentrations of NO3− (up to 123 mg/L), unequivocally suggesting an anthropogenic source that adds to the main water–rock interaction processes. The latter can be referred to Ca-Mg-carbonate and, at a minor extent, Al-silicate dissolution, being the outcropping sedimentary rocks characterized by Palaeozoic to Quaternary rocks. Anomalous concentrations of Cl−, SO42−, As, B and Ba were measured in two springs discharging a few hundred meters from the oil wells and in the Rio Ubierna. These contents are significantly higher than those of the whole set of the studied waters and are possibly indicative of mixing processes, although at very low extent, between deep and shallow aquifers. No evidence of deep-seated gases interacting with the Hontomín–Huermeces waters was recognized in the chemistry of the disolved gases. This is likely due to the fact that they are mainly characterized by an atmospheric source as highlighted by the high contents of N2, O2 and Ar and by N2/Ar ratios that approach that of ASW (Air Saturated Water) and possibly masking any contribution related to a deep source. Nevertheless, significant concentrations (up to 63% by vol.) of isotopically negative CO2 (<−17.7‰ V-PDB) were found in some water samples, likely related to a biogenic source. The geochemical and isotopic data of this work are of particular importance when a monitoring program will be established to verify whether CO2 leakages, induced by the injection of this greenhouse gas, may be affecting the quality of the waters in the shallow hydrological circuits at Hontomín–Huermeces. In this respect, carbonate chemistry, the isotopic carbon of dissolved CO2 and TDIC (Total Dissolved Inorganic Carbon) and selected trace elements can be considered as useful parameters to trace the migration of the injected CO2 into near-surface environments.

Crystal structure of the BTB domain from PLZF

The BTB domain (also known as the POZ domain) is an evolutionarily conserved protein–protein interaction motif found at the N terminus of 5–10% of C2H2-type zinc-finger transcription factors, as well as in some actin-associated proteins bearing the kelch motif. Many BTB proteins are transcriptional regulators that mediate gene expression through the control of chromatin conformation. In the human promyelocytic leukemia zinc finger (PLZF) protein, the BTB domain has transcriptional repression activity, directs the protein to a nuclear punctate pattern, and interacts with components of the histone deacetylase complex. The association of the PLZF BTB domain with the histone deacetylase complex provides a mechanism of linking the transcription factor with enzymatic activities that regulate chromatin conformation. The crystal structure of the BTB domain of PLZF was determined at 1.9 Å resolution and reveals a tightly intertwined dimer with an extensive hydrophobic interface. Approximately one-quarter of the monomer surface area is involved in the dimer intermolecular contact. These features are typical of obligate homodimers, and we expect the full-length PLZF protein to exist as a branched transcription factor with two C-terminal DNA-binding regions. A surface-exposed groove lined with conserved amino acids is formed at the dimer interface, suggestive of a peptide-binding site. This groove may represent the site of interaction of the PLZF BTB domain with nuclear corepressors or other nuclear proteins.

Analysis of receptor signaling pathways by mass spectrometry: Identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors

Oligomerization of receptor protein tyrosine kinases such as the epidermal growth factor receptor (EGFR) by their cognate ligands leads to activation of the receptor. Transphosphorylation of the receptor subunits is followed by the recruitment of signaling molecules containing src homology 2 (SH2) or phosphotyrosine interaction domains (PID). Additionally, several cytoplasmic proteins that may or may not associate with the receptor undergo tyrosine phosphorylation. To identify several components of the EGFR signaling pathway in a single step, we have immunoprecipitated molecules that are tyrosine phosphorylated in response to EGF and analyzed them by one-dimensional gel electrophoresis followed by mass spectrometry. Combining matrix-assisted laser desorption/ionization (MALDI) and nanoelectrospray tandem mass spectrometry (MS/MS) led to the identification of nine signaling molecules, seven of which had previously been implicated in EGFR signaling. Several of these molecules were identified from low femtomole levels of protein loaded onto the gel. We identified Vav-2, a recently discovered guanosine nucleotide exchange factor that is expressed ubiquitously, as a substrate of the EGFR. We demonstrate that Vav-2 is phosphorylated on tyrosine residues in response to EGF and associates with the EGFR in vivo. Binding of Vav-2 to the EGFR is mediated by the SH2 domain of Vav-2. In keeping with its ubiquitous expression, Vav-2 seems to be a general signaling molecule, since it also associates with the platelet-derived growth factor (PDGF) receptor and undergoes tyrosine phosphorylation in fibroblasts upon PDGF stimulation. The strategy suggested here can be used for routine identification of downstream components of cell surface receptors in mammalian cells.

An in vitro study of the dynamic features of the major histocompatibility complex class I complex relevant to its role as a versatile peptide-receptive molecule

The major histocompatibility complex class I complex consists of a heavy chain and a light chain (β2-microglobulin, β2m), which assemble with a short endogenously derived peptide in the endoplasmic reticulum. The class I peptide can be directly exchanged, either at the cell surface or, as recently described, in vesicles of the endocytic compartments, thus allowing exogenous peptides to enter the class I presentation pathway. To probe the interactions between the components of the class I molecule, we analyzed the exchange of peptide and β2m by using purified, recombinant H2-Kb/peptide complexes in a cell-free in vitro system. The exchange of competitor peptide was primarily dependent on the off-rate of the original peptide in the class I binding groove. Peptide exchange was not enhanced by the presence of exogenous β2m, as exchange occurred to the same extent in its absence. Thus, the exchange of peptide and β2m are independent events. The exchange rate of β2m also was not affected by the dissociation rates of the original peptides. Furthermore, peptides could substantially exchange into class I molecules over a pH range of 5.5 to 7.5, conditions prevalent in certain endocytic compartments. We conclude that the dynamic properties of the components of class I molecules explain its function as a highly peptide-receptive molecule. The major histocompatibility complex class I can readily receive peptides independent of the presence of exogenous β2m, even at a low pH. Such properties are relevant to class I peptide acquisition, which can occur at the cell surface, as well as in specialized endosomes.

Negative Factor from SIV Binds to the Catalytic Subunit of the V-ATPase to Internalize CD4 and to Increase Viral Infectivity

The accessory protein negative factor (Nef) from human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is required for optimal viral infectivity and the progression to acquired immunodeficiency syndrome (AIDS). Nef interacts with the endocytic machinery, resulting in the down-regulation of cluster of differentiation antigen 4 (CD4) and major histocompatibility complex class I (MHCI) molecules on the surface of infected cells. Mutations in the C-terminal flexible loop of Nef result in a lower rate of internalization by this viral protein. However, no loop-dependent binding of Nef to adaptor protein-2 (AP-2), which is the adaptor protein complex that is required for the internalization of proteins from the plasma membrane, could be demonstrated. In this study we investigated the relevance of different motifs in Nef from SIVmac239 for its internalization, CD4 down-regulation, binding to components of the trafficking machinery, and viral infectivity. Our data suggest that the binding of Nef to the catalytic subunit H of the vacuolar membrane ATPase (V-ATPase) facilitates its internalization. This binding depends on the integrity of the whole flexible loop. Subsequent studies on Nef mutant viruses revealed that the flexible loop is essential for optimal viral infectivity. Therefore, our data demonstrate how Nef contacts the endocytic machinery in the absence of its direct binding to AP-2 and suggest an important role for subunit H of the V-ATPase in viral infectivity.

Hepatitis B virus transactivator protein, HBx, associates with the components of TFIIH and stimulates the DNA helicase activity of TFIIH.

Human hepatitis B virus genome encodes a protein, termed HBx, that is widely recognized as a transcriptional transactivator. While HBx does not directly bind cis-acting transcriptional control elements, it has been shown to associate with cellular proteins that bind DNA. Because HBx transactivated a large number of viral/cellular transcriptional control elements, we looked for its targets within the components of the basal transcriptional machinery. This search led to the identification of its interactions with TFIIH. Here, we show that HBx interacts with yeast and mammalian TFIIH complexes both in vitro and in vivo. These interactions between HBx and the components of TFIIH are supported by several lines of evidence including results from immunoprocedures and direct methods of measuring interactions. We have identified ERCC3 and ERCC2 DNA helicase subunits of holoenzyme TFIIH as targets of HBx interactions. Furthermore, the DNA helicase activity of purified TFIIH from rat liver and, individually, the ERCC2 component of TFIIH is stimulated in the presence of HBx. These observations suggest a role for HBx in transcription and DNA repair.

Local stress, not systemic factors, regulate gene expression of the cardiac renin-angiotensin system in vivo: a comprehensive study of all its components in the dog.

Cardiac hypertrophy is associated with altered expression of the components of the cardiac renin-angiotensin system (RAS). While in vitro data suggest that local mechanical stimuli serve as important regulatory modulators of cardiac RAS activity, no in vivo studies have so far corroborated these observations. The aims of this study were to (i) examine the respective influence of local, mechanical versus systemic, soluble factors on the modulation of cardiac RAS gene expression in vivo; (ii) measure gene expression of all known components of the RAS simultaneously; and (iii) establish sequence information and an assay system for the RAS of the dog, one of the most important model organisms in cardiovascular research. We therefore examined a canine model of right ventricular hypertrophy and failure (RVHF) in which the right ventricle (RV) is hemodynamically loaded, the left ventricle (LV) is hemodynamically unloaded, while both are exposed to the same circulating milieu of soluble factors. Using specific competitive PCR assays, we found that RVHF was associated with significant increases in RV mRNA levels of angiotensin converting enzyme and angiotensin II type 2 receptor, and with significant decreases of RV expression of chymase and the angiotensin II type 1 receptor, while RV angiotensinogen and renin remained unchanged. All components remained unchanged in the LV. We conclude that (i) dissociated regional regulation of RAS components in RV and LV indicates modulation by local, mechanical, not soluble, systemic stimuli; (ii) components of the cardiac RAS are independently and differentially regulated; and (iii) opposite changes in the expression of angiotensin converting enzyme and chymase, and of angiotensin II type I and angiotensin II type 2 receptors, may indicate different physiological roles of these RAS components in RVHF.

An abundantly expressed mucin-like protein from Toxocara canis infective larvae: the precursor of the larval surface coat glycoproteins.

Evasion of host immunity by Toxocara canis infective larvae is mediated by the nematode surface coat, which is shed in response to binding by host antibody molecules or effector cells. The major constituent of the coat is the TES-120 glycoprotein series. We have isolated a 730-bp cDNA from the gene encoding the apoprotein precursor of TES-120. The mRNA is absent from T. canis adults but hyperabundant in larvae, making up approximately 10% of total mRNA, and is trans-spliced with the nematode 5' leader sequence SL1. It encodes a 15.8-kDa protein (after signal peptide removal) containing a typical mucin domain: 86 amino acid residues, 72.1% of which are Ser or Thr, organized into an array of heptameric repeats, interspersed with proline residues. At the C-terminal end of the putative protein are two 36-amino acid repeats containing six Cys residues, in a motif that can also be identified in several genes in Caenorhabditis elegans. Although TES-120 displays size and charge heterogeneity, there is a single copy gene and a homogeneous size of mRNA. The association of overexpression of some membrane-associated mucins with immunosuppression and tumor metastasis suggests a possible model for the role of the surface coat in immune evasion by parasitic nematodes.

Macrophage-colony-stimulating factor regulates expression of the integrins alpha 4 beta 1 and alpha 5 beta 1 by murine bone marrow macrophages.

We observed that when monocyte/macrophage precursors derived from murine bone marrow were treated with macrophage-colony-stimulating factor (M-CSF), there was a dose-dependent increase in both the number of adherent cells and the degree to which the cells were highly spread. Attachment was supported by fibronectin, but not by vitronectin or laminin, suggesting that the integrins alpha 4 beta 1 and/or alpha 5 beta 1 might mediate this event. Binding to fibronectin was blocked partially by antibodies to either integrin, and inhibition was almost complete when the antibodies were used in combination. By a combination of surface labeling with 125I and metabolic labeling with [35S]methionine and [35S]cysteine, we demonstrated that M-CSF treatment led to increased synthesis and surface expression of the two beta 1 integrins. Since attachment to fibronectin and/or stromal cells plays an important role in the maturation of other hematopoietic lineages, we propose that the action of M-CSF in the differentiation of immature monocytes/macrophages includes stimulated expression of the integrins alpha 4 beta 1 and alpha 5 beta 1, leading to interactions with components of the marrow microenvironment necessary for cell maturation.

Correlation of the Corneal Toricity Between Anterior and Posterior Corneal Surfaces in the Normal Human Eye

Purpose: To evaluate the correlation of the magnitude of corneal toricity and power vector components of both corneal surfaces measured with a Scheimpflug photography-based system. Methods: A total of 117 healthy normal eyes of 117 subjects selected randomly with ages ranging from 7 to 80 years were included. All eyes received an anterior segment and corneal analysis with the Sirius system (CSO) evaluating the anterior and posterior mean toricity for 3 and 7 mm (aAST and pAST). The vector components J0 and J45 as well as the overall strength blur (B) were calculated for each keratometric measurement using the procedure defined by Thibos and Horner. Results: The coefficient of correlation between aAST and pAST was 0.52 and 0.62 and the mean anteroposterior ratio for toricity was 0.46 ± 0.39 and 0.57 ± 0.75 for 3 and 7 mm, respectively. These ratios correlated significantly with aAST, anterior corneal J0, and manifest refraction J0 (r ≥ 0.39, P < 0.01). The coefficient of correlation was 0.69 and 0.81 between anterior and posterior J0 for 3 and 7 mm, respectively. For J45, the coefficients were 0.62 and 0.71, respectively. The linear regression analysis revealed that the pAST and power vectors could be predicted from the anterior corneal data (R2 ≥ 0.40, P < 0.01). Conclusions: The toricity and astigmatic power vector components of the posterior corneal surface in the human healthy eye are related to those of the anterior and therefore can be predicted consistently from the anterior toricity and astigmatic power vectors.