Co-option of an oral-aboral patterning mechanism to control left-right differentiation: the direct-developing sea urchin Heliocidaris erythrogramma is sinistralized, not ventralized, by NiCl2

Larval dorsoventral (DV) and left-right (LR) axial patterning unfold progressively in sea urchin development, leading to commitment of the major embryonic regions by the gastrula stage. The direct-developing sea urchin Heliocidaris erythrogramma has lost oral-aboral differentiation along the DV axis but has accelerated vestibular ectoderm development on the left side. NiCl(2) radializes indirect-developing sea urchins by shifting cells toward a ventral fate (oral ectoderm). We treated embryos of H. erythrogramma and the indirect-developing H. tuberculata with NiCl(2). H. tuberculata was ventralized exactly like other indirect developers, establishing that basic patterning mechanisms are conserved in this genus. H. erythrogramma was also radialized; timing, dosage response, and some morphological features were similar to those in other sea urchins. Ectodermal explant and recombination experiments demonstrate that the effect of nickel is autonomous to the ectoderm, another feature in common with indirect developers. However, H. erythrogramma is distinctly sinistralized rather than ventralized, its cells shifting toward a left-side fate (vestibular ectoderm). This geometric contrast in the midst of pervasive functional similarity suggests that nickel-sensitive processes in H. erythrogramma axial patterning, homologous to those in indirect developers, have been redeployed, and hence co-opted, from their ancestral role in DV axis determination to a new role in LR axis determination. We discuss DV and LR axial patterning and their evolutionary transformation.     

Carbonic anhydrase activity in acetate grown Methanosarcina barkeri

Cell extracts (27000xg supernatant) of acetate grown Methanosarcina barkeri were found to have carbonic anhydrase activity (0.41 U/mg protein), which was lost upon heating or incubation with proteinase K. The activity was inhibited by Diamox (apparent K _i=0.5 mM), by azide (apparent K _i=1 mM), and by cyanide (apparent K _i=0.02 mM). These and other properties indicate that the archaebacterium contains the enzyme carbonic anhydrase (EC 4.2.1.1). Evidence is presented that the protein is probably located in the cytoplasm. Methanol or H₂/CO₂ grown cells of M. barkeri showed no or only very little carbonic anhydrase activity. After transfer of these cells to acetate medium the activity was induced suggesting a function of this enzyme in acetate fermentation to CO₂ and CH₄. Interestingly, Desulfobacter postgatei and Desulfotomaculum acetoxidans, which oxidize acetate to 2 CO₂ with sulfate as electron acceptor, were also found to exhibit carbonic anhydrase activity (0.2 U/mg protein).     

Modulation of cell surface heparan sulfate structure by growth of cells in the presence of chlorate

Swiss mouse 3T3 cells, when grown in the presence of 5 mM chlorate, an inhibitor of PAPS synthesis, produce heparan sulfate glycosaminoglycan chains containing only about 8% of the sulfate normally present and which have lost the ability to bind to fibronectin. These undersulfated chains are sensitive to nitrous acid at pH 4.5, indicating that many glucosaminyl residues have unsubstituted amino groups. The iduronic acid content of the heparan sulfate produced in the presence of chlorate is reduced to less than 7% as compared to the 36% in that from untreated cells. The chlorate-treated cells do not demonstrate any alterations in their growth control. However, the spreading behavior of these cells is altered to a flat rounded morphology compared to the more typical fibroblastic appearance of the untreated cell. The sulfation of chondroitin chains is also inhibited, but at a lower chlorate concentration which does not alter growth control or the spreading ability of the cells. These data indicate that (a) 3T3 cell surface heparan sulfate proteoglycan is not involved in growth control but may be involved in cell spreading, (b) the use of chlorate should be a valuable method for the study of the biosynthesis and structure/function relationships of sulfated glycosaminoglycans, and (c) the temporal sequence of the heparan sulfate chain modification reactions predicted from results of studies with cell-free extracts also operates in the cell.     

Exploring Nitrilase Sequence Space for Enantioselective Catalysis

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 10⁶ to 10¹⁰ members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses.     

Pathogen-induced elicitin production in transgenic tobacco generates a hypersensitive response and nonspecific disease resistance.

The rapid and effective activation of disease resistance responses is essential for plant defense against pathogen attack. These responses are initiated when pathogen-derived molecules (elicitors) are recognized by the host. We have developed a strategy for creating novel disease resistance traits whereby transgenic plants respond to infection by a virulent pathogen with the production of an elicitor. To this end, we generated transgenic tobacco plants harboring a fusion between the pathogen-inducible tobacco hsr 203J gene promoter and a Phytophthora cryptogea gene encoding the highly active elicitor cryptogein. Under noninduced conditions, the transgene was silent, and no cryptogein could be detected in the transgenic plants. In contrast, infection by the virulent fungus P. parasitica var nicotianae stimulated cryptogein production that coincided with the fast induction of several defense genes at and around the infection sites. Induced elicitor production resulted in a localized necrosis that resembled a P. cryptogea-induced hypersensitive response and that restricted further growth of the pathogen. The transgenic plants displayed enhanced resistance to fungal pathogens that were unrelated to Phytophthora species, such as Thielaviopsis basicola, Erysiphe cichoracearum, and Botrytis cinerea. Thus, broad-spectrum disease resistance of a plant can be generated without the constitutive synthesis of a transgene product.     

Differentiation and structural decline in the leaves and bark of birch (Betula pendula) under low ozone concentrations

Summary Leaf and bark structure of a birch clone (Betula pendula Roth) continuously exposed to charcoal-filtered air or charcoal-filtered air plus ozone (0.05, 0.075, 0.1 l 1^-1) was investigated throughout one growing season. Increasing ozone dose influenced leaf differentiation by reducing leaf area and increasing inner leaf air space, density of cells developing into stomata, scales and hairs. When approximately the same ozone dose had been reached, macroscopical and microscopical symptoms appeared irrespective of the ozone concentration used during treatment. Structural decline began in mesophyll cells around stomatal cavities (droplet-like exudates on the cell walls), continued with disintegration of the cytoplasma and ended in cell collapse. Epidermal cells showed shrinkage of the mucilaginous layer (related to water loss). Their collapse marked the final stage of leaf decline. When subsidiary cells collapsed, guard cells passively opened for a transitory period before collapsing and closing. With increasing ozone dose starch remained accumulated along the small leaf veins and in guard cells. IIK-positive grains were formed in the epidermal cells. This contrasted with the senescent leaves, where starch was entirely retranslocated. Injury symptoms in stem and petiole proceeded from the epidermis to the cambium. Reduced tissue area indicated reduced cambial activity. In plants grown in filtered air and transferred into ozone on 20 August, injury symptoms developed faster than in leaves formed in the presence of ozone. Results are discussed with regard to O₃-caused acclimation and injury mechanisms.     

A method for establishing stable concentration gradients in agar suitable for studying chemotaxis on a solid surface.

A simple technique has been developed for establishing stable gradients of a substance in agar. The technique involves the creation of a spherically symmetric concentration profile in which concentration varies inversely with the distance from the source and is independent of the diffusion coefficient of the substance. It has been shown that the gradients established with this technique are stable for at least 190 h. and, on a theoretical basis, they can be kept stable for more than 1000 h. Time-variant gradients can also be established, if desired, using the same system and limiting either the source or the agar sink. It must be emphasized that a stable gradient cannot be obtained by using a shallow agar layer as a sink. The use of such conditions (e.g. the agar in a standard petri dish) can result only in time-variant gradients. The solution to the diffusion equation in a spherically symmetric system establishes the expected concentration profile, the basis for adjusting it, and the parameters that control the behavior of the system. Some useful applications for examining chemotaxis on a solid surface as well as possible further developments are discussed.     

Structural Insights into the Inhibition of Zika Virus NS2B-NS3 Protease by a Small-Molecule Inhibitor

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Environmental dynamics of dissolved black carbon in wetlands

Wetlands are ecosystems commonly characterized by elevated levels of dissolved organic carbon (DOC), and although they cover a surface area less than 2 % worldwide, they are an important carbon source representing an estimated 15 % of global annual DOC flux to the oceans. Because of their unique hydrological characteristics, fire can be an important ecological driver in pulsed wetland systems. Consequently, wetlands may be important sources not only of DOC but also of products derived from biomass burning, such as dissolved black carbon (DBC). However, the biogeochemistry of DBC in wetlands has not been studied in detail. The objective of this study is to determine the environmental dynamics of DBC in different fire-impacted wetlands. An intensive, 2-year spatial and temporal dynamics study of DBC in a coastal wetland, the Everglades (Florida) system, as well as one-time sampling surveys for the other two inland wetlands, Okavango Delta (Botswana) and the Pantanal (Brazil), were reported. Our data reveal that DBC dynamics are strongly coupled with the DOC dynamics regardless of location, season or recent fire history. The statistically significant linear regression between DOC and DBC was applied to estimate DBC fluxes to the coastal zone through two main riverine DOC export routes in the Everglades ecosystem. The presence of significant amounts of DBC in these three fire-impacted ecosystems suggests that sub-tropical wetlands could represent an important continental-ocean carrier of combustion products from biomass burning. The discrimination of DBC molecular structure (i.e. aromaticity) between coastal and terrestrial samples, and between samples collected in wet and dry season, suggests that spatially-significant variation in DBC source strength and/or degree of degradation may also influence DBC dynamics.