Direct and indirect effects of grazing on the phytoplankton seasonal succession in an oligotrophic lake

We examined the simultaneous dynamics of phytoplankton and zooplanktonin an oligotrophic lake, as well as the algal response to experimentalmanipulations of herbivore population structure and density.The seasonal succession of phytoplankton is characterized bya shift in dominance from eukaryotic species to prokaryoticcyanobacteria, as in a eutrophic lake. This unusual patternfor an oligotrophic lake is related to the release of zooplanktonphosphorus, rather than to the amount of total phosphorus. Thehighest estimated values of this released phosphorus occur duringthe co-dominance of small-sized species and of one calanoidpopulation, both under natural and experimental conditions.Our experimental results clearly reveal that a blue-green speciesreplaces non-blue-green ones when environmental conditions renderlow or intermediate values for released phosphorus, irrespectiveof the grazing pressure. The absence of predators or high levelsof released phosphorus stimulate non-blue-green growth. Theseresults agree with the successional pattern observed for thealgal assemblage under natural conditions. Nutrient recyclingplays an essential role in the maintenance of the metabolismof the pelagic system, and therefore the prevalence of a topdownregulation mechanism as proposed for such low-nutrient environmentsshould be reconsidered.     

CD8 T cell epitope distribution in viruses reveals patterns of protein biosynthesis

Distinguishing T cell epitope distribution patterns is relevant for epitope-vaccine design. To that end, we invest0069gated the distribution of known CD8 T cell epitopes from Hepatitis C Virus, Human Immunodeficiency Virus-1 and Influenza A Virus using χ(2) statistics. We found that epitopes are not distributed in the viral proteomes proportionally to the size of the source proteins. Specifically, capsid and matrix proteins pack significantly more epitopes than those expected by their size. Such non-homogeneous distribution cannot be accounted by underlying MHC I-peptide binding preferences nor it is related to sequence variability. Instead, we propose that it might be related to preferential protein translation/biosynthesis. Overall, these results support the prioritization of structural antigens for epitope identification and vaccine design.     

Distribution and density of bacteria in subtropical flooded rice growing areas in Brazil.

Since microorganisms are important components in the structure and function of water systems, the present paper reports work done to identify groups making up bacterial communities present in rice irrigation water. To this end, water samples were collected in five rice-growing areas of Rio Grande do Sul State, Brazil. The identification of the main bacterial groups found in flooded areas was carried out based on colony morphology, taking into account shape, elevation, and edges. Internal and external cell structure was characterized as cocci or rod, gram-positive or gram-negative, and spore forming or not. The results obtained regarding density and bacterial distribution in the water samples from rice growing areas of RS showed a higher abundance of morphotypes of bacterial colonies in the irrigation channels (F(1,12) = 8.74; p < 0.05) when compared to the culture plots in the five production regions, and in the final culture phase (F(1,12) = 8.86; p < 0.05). In the five rice production areas the occurrence of gram-positive and spore-forming rods was prevalent. Rods showed more abundance (F(1,26) = 15.12; p < 0.05) in the early culture phase, with a significant prevalence of gram-positive rods (F(1,26) = 25.99; p < 0.05) in all rice growing regions under investigation. The group of spore-forming bacteria was significantly more abundant (F(1,30) = 14.06; p < 0.05) when compared with the non-spore-forming ones in all investigated regions. Data showed that the irrigated rice crop affects the density and morphotype colonies in the bacteria found in the water used to flood rice-growing plots.     

Binding and activation of pea chloroplast fructose-1,6-bisphosphatase by homologous thioredoxins m and f

Fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11) binds its putative physiological activator thioredoxin f (Trx f ) at pH 7.9, the pH in the stroma of the illuminated chloroplast. Since Trx m , described as specific in NADP⁺-malate dehydrogenase (NADPMDH) activation, appears in pea (Pisum sativum L.) also to be functional in FBPase modulation, we have here analyzed the effect of pH and the redox status of the chloroplast stroma in the pea FBPase binding of homologous Trx f and m . Both pea Trx were strongly bound by purified FBPase when they were preincubated at pH 7.9 with 2.5 m M dithiothreitol (DTT), but not when the reductant was omitted. As occurs with Trx f the Trx m /FBPase ratio of the complex was 4, but this was only observed with a Trx m /FBPase concentration ratio > 10 in the preincubation mixture. The FBPase-Trx m binding disappeared in the presence of 100 m M NaCl, even with 2.5 m M DTT at pH 7.9, with a concomitant appearance of different aggregation states of the FBPase subunit. A similar FBPase-Trx m complex was detected in the stromal solution when pea chloroplasts were lysed at pH 7.9 in the presence of DTT. No interaction was observed between NADP-MDH and Trx f or m , either in the presence or in the absence of DTT. Pea FBPase showed sigmoidal activation kinetics with pea Trx m , and an S_0.5 of 133 n M versus 6.6 n M with pea Trx f . About 10-fold higher concentration of the former than that of the latter was required for obtaining maximum activity; however, the V_max with Trx f was only 2-fold higher than that with Trx m . We conclude that pea FBPase binds and is activated by the homologous Trx m , even though to a lesser extent than with Trx f . We also deduce that in the light the conditions in the chloroplast stroma are optimal for forming an FBPase-Trx complex.     

Developmentally regulated glycosylation of the CD8alphabeta coreceptor stalk modulates ligand binding.

The functional consequences of glycan structural changes associated with cellular differentiation are ill defined. Herein, we investigate the role of glycan adducts to the O-glycosylated polypeptide stalk tethering the CD8alphabeta coreceptor to the thymocyte surface. We show that immature CD4(+)CD8(+) double-positive thymocytes bind MHCI tetramers more avidly than mature CD8 single-positive thymocytes, and that this differential binding is governed by developmentally programmed O-glycan modification controlled by the ST3Gal-I sialyltransferase. ST3Gal-I induction and attendant core 1 sialic acid addition to CD8beta on mature thymocytes decreases CD8alphabeta-MHCI avidity by altering CD8alphabeta domain-domain association and/or orientation. Hence, glycans on the CD8beta stalk appear to modulate the ability of the distal binding surface of the dimeric CD8 globular head domains to clamp MHCI.     

Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms

Major histocompatibility complex class I (MHCI) and class II (MHCII) molecules display peptides on antigen-presenting cell surfaces for subsequent T-cell recognition. Within the human population, allelic variation among the classical MHCI and II gene products is the basis for differential peptide binding, thymic repertoire bias and allograft rejection. While available 3D structural analysis suggests that polymorphisms are found primarily within the peptide-binding site, a broader informatic approach pinpointing functional polymorphisms relevant for immune recognition is currently lacking. To this end, we have now analyzed known human class I (774) and class II (485) alleles at each amino acid position using a variability metric (V). Polymorphisms (V>1) have been identified in residues that contact the peptide and/or T-cell receptor (TCR). Using sequence logos to investigate TCR contact sites on HLA molecules, we have identified conserved MHCI residues distinct from those of conserved MHCII residues. In addition, specific class II (HLA-DP, -DQ, -DR) and class I (HLA-A, -B, -C) contacts for TCR binding are revealed. We discuss these findings in the context of TCR restriction and alloreactivity.     

Biochemical and functional analysis of smallpox growth factor (SPGF) and anti-SPGF monoclonal antibodies

Variola, the causative agent of smallpox, is a highly infectious double-stranded DNA virus of the orthopox genus that replicates within the cytoplasm of infected cells. For unknown reasons prominent skin manifestations, including "pox," mark the course of this systemic human disease. Here we characterized smallpox growth factor (SPGF), a protein containing an epidermal growth factor (EGF)-like domain that is conserved among orthopox viral genomes, and investigated its possible mechanistic link. We show that after recombinant expression, refolding, and purification, the EGF domain of SPGF binds exclusively to the broadly expressed cellular receptor, erb-B1 (EGF receptor), with subnanomolar affinity, stimulating the growth of primary human keratinocytes and fibroblasts. High affinity monoclonal antibodies specific for SPGF reveal in vivo immunoprotection in a murine vaccinia pneumonia model by a mechanism distinct from viral neutralization. These findings suggest that blockade of pathogenic factor actions, in general, may be advantageous to the infected host.     

Peptide variants of viral CTL epitopes mediate positive selection and emigration of Ag-specific thymocytes in vivo

During development, thymocytes carrying TCRs mediating low-affinity interactions with MHC-bound self-peptides are positively selected for export into the mature peripheral T lymphocyte pool. Thus, exogenous administration of certain altered peptide ligands (APL) with reduced TCR affinity relative to cognate Ags may provide a tool to elicit maturation of desired TCR specificities. To test this "thymic vaccination" concept, we designed APL of the viral CTL epitopes gp33-41 and vesicular stomatitis virus nucleoprotein octapeptide N52-59 relevant for the lymphocytic choriomeningitis virus-specific P14- and vesicular stomatitis virus-specific N15-TCRs, respectively, and examined their effects on thymocytes in vivo using irradiation chimeras. Injection of APL into irradiated congenic (Ly-5.1) mice, reconstituted with T cell progenitors from the bone marrow of P14 RAG2(-/-) (Ly-5.2) or N15 RAG2(-/-) (Ly-5.2) transgenic mice, resulted in positive selection of T cells expressing the relevant specificity. Moreover, the variants led to export of virus-specific T cells to lymph nodes, but without inducing T cell proliferation. These findings show that the mature T cell repertoire can be altered by in vivo peptide administration through manipulation of thymic selection.     

Lipoylating and biotinylating enzymes contain a homologous catalytic module

Biotin and lipoic acid moieties are the covalently attached coenzyme cofactors of several multicomponent enzyme complexes that catalyze key metabolic reactions. Attachment of these moieties to the biotinyl- and lipoyl-dependent enzymes is post-translationally catalyzed by specific biotinylating and lipoylating protein enzymes. In Escherichia coli, two different enzymes, LplA and LipB, catalyze independent pathways for the lipoylation of the relevant enzymes, whereas only one enzyme, the BirA protein, is responsible for all the biotinylation. Counterparts of the E. coli BirA, LplA, and LipB enzymes have been previously identified in many organisms, but homology among the three families has never been reported. Computational analysis based on PSI-BLAST profiles and secondary structure predictions indicates, however, that lipoylating and biotinylating enzymes are evolutionarily related protein families containing a homologous catalytic module. Sequence conservation among the three families is very poor, but a single lysine residue is strictly conserved in all of them, which, according to the available X-ray crystal structure of the E. coli BirA protein, is expected to contribute to the binding of lipoic acid in the LplA and LipB enzymes.     

Cannabinoids as potential new analgesics.

Among other pharmacological properties analgesia is one of the important features of cannabinoids with therapeutical prospects. Cannabinoids have been shown to produce antinociception in experimental animals and humans. Recently a new system of neuromodulation based upon the existence of cannabinoid receptors and their endogenous agonists has emerged. This has been proposed as another of the endogenous pain control systems. Current evidence indicate an interaction between cannabinoid and opioid systems, the latter being of known relevance in nociception. The fact that either exogenous or endogenous opioids enhanced cannabinoid-induced antinociception suggests simultaneous activation of both opioid and cannabinoid receptors by drugs as a new analgesic strategy.