Geochemistry of tetrapyrrole, tetraterpenoid, and perylene pigments in sediments from the Gulf of California

Results and discussion cover pigment analyses of 36 sediment samples recovered by Deep Sea Drilling Project Leg 64, and six samples from the Leg 64 site-survey cruise in the Guaymas Basin (Scripps Institution of Oceanography, Leg 3). Pigments investigated were tetrapyrroles, tetraterpenoids, and the PAH compound perylene. Traces of mixed nickel and copper ETIO-porphyrins were ubiquitous in all sediment samples, except for the very surface (i.e., <2 m sub-bottom), and their presence is taken as an indication of minor influxes of previously oxidized allochthonous (terrestrial) organic matter. Phorbides and chlorins isolated from Site 479 sediment samples (i.e., the oxygen-minimum locale, northeast of the Guaymas Basin) well represent the reductive diagenesis ("Treibs Scheme"; see Baker and Palmer, 1978; Treibs, 1936) of chlorophyll derivatives. Three forms of pheophytin-a, plus a variety of phorbides, were found to give rise to freebase porphyrins, nickel phylloerythrin, and nickel porphyrins, with increasing depth of burial (increasing temperature). Sediments from Sites 481, 10G, and 18G yielded chlorophyll derivatives characteristic of early oxidative alterations. Included among these pigments are allomerized pheophytin-a, purpurin-18, and chlorin-p6. The high thermal gradient imposed upon the late Quaternary sediments of Site 477 greatly accelerated chlorophyll diagenesis in the adjacent overlying sediments, that is, the production of large quantities of free-base desoxophylloerythroetioporphyrin (DPEP) occurred in a section (477-7-5) presently only 49.8 meters sub-bottom. Present depth and age of these sediments are such that only chlorins and phorbides would be expected. Carotenoid (i.e., tetraterpenoids) concentrations were found to decrease rapidly with increasing sub-bottom depth. Less deeply buried sediments (e.g., 0-30 m) yielded mixtures of carotenes and oxygen-substituted carotenoids. Oxygencontaining (oxy-, oxo-, epoxy-) carotenoids were found to be lost preferentially with increased depth of burial. Early carotenoid diagenesis is suggested as involving interacting reductions and dehydrations whereby dehydro-, didehydro-, and retro-carotenes are generated. Destruction of carotenoids as pigments may involve oxidative cleavage of the isoprenoid chain through epoxy intermediates, akin to changes in the senescent cells of plants. Perylene was found to be a common component of the extractable organic matter from all sediments investigated. The generation of alkyl perylenes was found to parallel increases in the existing thermal regime at all sites. Igneous sills and sill complexes within the sediment profile of Site 481 altered (i.e., scrambled) the otherwise straightforward thermally induced alkylation of perylene. The degree of perylene alkylation is proposed as an indicator of geothermal stress for non-contemporaneous marine sediments.

Decline in Coccolithophore Diversity and Impact on Coccolith Morphogenesis Along a Natural CO2 Gradient

A natural pH gradient caused by marine CO2 seeps off Vulcano Island (Italy) was used to assess the effects of ocean acidification on coccolithophores, which are abundant planktonic unicellular calcifiers. Such seeps are used as natural laboratories to study the effects of ocean acidification on marine ecosystems, since they cause long-term changes in seawater carbonate chemistry and pH, exposing the organisms to elevated CO2 concentrations and therefore mimicking future scenarios. Previous work at CO2 seeps has focused exclusively on benthic organisms. Here we show progressive depletion of 27 coccolithophore species, in terms of cell concentrations and diversity, along a calcite saturation gradient from Omega calcite 6.4 to <1. Water collected close to the main CO2 seeps had the highest concentrations of malformed Emiliania huxleyi. These observations add to a growing body of evidence that ocean acidification may benefit some algae but will likely cause marine biodiversity loss, especially by impacting calcifying species, which are affected as carbonate saturation falls.

Individual codes, GenBank accession numbers and GenBank accession links for Mediterranean sponges

Metabolomic analysis has shown the chemical richness of the sponge-associated actinomycetes Streptomyces sp. SBT349, Nonomureae sp. SBT364, and Nocardiopsis sp. SBT366. The genomes of these actinomycetes were sequenced and the genomic potential for secondary metabolism was evaluated. Their draft genomes have sizes of 8.0, 10, and 5.8Mb having 687, 367, and 179 contigs with a GC content of 71.6, 70.7, and 72.7%, respectively. Moreover, antiSMASH 3.0 predicted 108, 149, and 75 secondary metabolite gene clusters, respectively which highlight the metabolic capacity of the three actinomycete species to produce diverse classes of natural products.

Mathematical analysis of a model of chemotaxis arising from morphogenesis

We consider non-negative solution of a chemotaxis system with non constant chemotaxis sensitivity function X. This system appears as a limit case of a model formorphogenesis proposed by Bollenbach et al. (Phys. Rev. E. 75, 2007).Under suitable boundary conditions, modeling the presence of a morphogen source at x=0, we prove the existence of a global and bounded weak solution using an approximation by problems where diffusion is introduced in the ordinary differential equation. Moreover,we prove the convergence of the solution to the unique steady state provided that ? is small and ? is large enough. Numerical simulations both illustrate these results and give rise to further conjectures on the solution behavior that go beyond the rigorously proved statements.

Dyrk1A Influences Neuronal Morphogenesis Through Regulation of Cytoskeletal Dynamics in Mammalian Cortical Neurons

Down syndrome (DS) is the most frequent genetic cause of mental retardation. Cognitive dysfunction in these patients is correlated with reduced dendritic branching and complexity, along with fewer spines of abnormal shape that characterize the cortical neuronal profile of DS. DS phenotypes are caused by the disruptive effect of specific trisomic genes. Here, we report that overexpression of dual-specificity tyrosine phosphorylation-regulated kinase 1A, DYRK1A, is sufficient to produce the dendritic alterations observed in DS patients. Engineered changes in Dyrk1A gene dosage in vivo strongly alter the postnatal dendritic arborization processes with a similar progression than in humans. In cultured mammalian cortical neurons, we determined a reduction of neurite outgrowth and synaptogenesis. The mechanism underlying neurite dysgenesia involves changes in the dynamic reorganization of the cytoskeleton.

Fission yeast orb6, a ser/thr protein kinase related to mammalian rho kinase and myotonic dystrophy kinase, is required for maintenance of cell polarity and coordinates cell morphogenesis with the cell cycle

The molecular mechanisms that coordinate cell morphogenesis with the cell cycle remain largely unknown. We have investigated this process in fission yeast where changes in polarized cell growth are coupled with cell cycle progression. The orb6 gene is required during interphase to maintain cell polarity and encodes a serine/threonine protein kinase, belonging to the myotonic dystrophy kinase/cot1/warts family. A decrease in Orb6 protein levels leads to loss of polarized cell shape and to mitotic advance, whereas an increase in Orb6 levels maintains polarized growth and delays mitosis by affecting the p34cdc2 mitotic kinase. Thus the Orb6 protein kinase coordinates maintenance of cell polarity during interphase with the onset of mitosis. orb6 interacts genetically with orb2, which encodes the Pak1/Shk1 protein kinase, a component of the Ras1 and Cdc42-dependent signaling pathway. Our results suggest that Orb6 may act downstream of Pak1/Shk1, forming part of a pathway coordinating cell morphogenesis with progression through the cell cycle.

Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a

Chlorophyll b is an ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. Its biosynthesis plays a key role in the adaptation to various light environments. We isolated six chlorophyll b-less mutants by insertional mutagenesis by using the nitrate reductase or argininosuccinate lyase genes as tags and examined the rearrangement of mutant genomes. We found that an overlapping region of a nuclear genome was deleted in all mutants and that this encodes a protein whose sequence is similar to those of methyl monooxygenases. This coding sequence also contains putative binding domains for a [2Fe-2S] Rieske center and for a mononuclear iron. The results demonstrate that a chlorophyll a oxygenase is involved in chlorophyll b formation. The reaction mechanism of chlorophyll b formation is discussed.

Postgastrulation Smad2-deficient embryos show defects in embryo turning and anterior morphogenesis

SMAD2 is a member of the transforming growth factor β and activin-signaling pathway. To examine the role of Smad2 in postgastrulation development, we independently generated mice with a null mutation in this gene. Smad2-deficient embryos die around day 7.5 of gestation because of failure of gastrulation and failure to establish an anterior–posterior (A-P) axis. Expression of the homeobox gene Hex (the earliest known marker of the A-P polarity and the prospective head organizer) was found to be missing in Smad2-deficient embryos. Homozygous mutant embryos and embryonic stem cells formed mesoderm derivatives revealing that mesoderm induction is SMAD2 independent. In the presence of wild-type extraembryonic tissues, Smad2-deficient embryos developed beyond 7.5 and up to 10.5 days postcoitum, demonstrating a requirement for SMAD2 in extraembryonic tissues for the generation of an A-P axis and gastrulation. The rescued postgastrulation embryos showed malformation of head structures, abnormal embryo turning, and cyclopia. Our results show that Smad2 expression is required at several stages during embryogenesis.

Analysis of the role of the Spitzenkörper in fungal morphogenesis by computer simulation of apical branching in Aspergillus niger

High-resolution video microscopy, image analysis, and computer simulation were used to study the role of the Spitzenkörper (Spk) in apical branching of ramosa-1, a temperature-sensitive mutant of Aspergillus niger. A shift to the restrictive temperature led to a cytoplasmic contraction that destabilized the Spk, causing its disappearance. After a short transition period, new Spk appeared where the two incipient apical branches emerged. Changes in cell shape, growth rate, and Spk position were recorded and transferred to the fungus simulator program to test the hypothesis that the Spk functions as a vesicle supply center (VSC). The simulation faithfully duplicated the elongation of the main hypha and the two apical branches. Elongating hyphae exhibited the growth pattern described by the hyphoid equation. During the transition phase, when no Spk was visible, the growth pattern was nonhyphoid, with consecutive periods of isometric and asymmetric expansion; the apex became enlarged and blunt before the apical branches emerged. Video microscopy images suggested that the branch Spk were formed anew by gradual condensation of vesicle clouds. Simulation exercises where the VSC was split into two new VSCs failed to produce realistic shapes, thus supporting the notion that the branch Spk did not originate by division of the original Spk. The best computer simulation of apical branching morphogenesis included simulations of the ontogeny of branch Spk via condensation of vesicle clouds. This study supports the hypothesis that the Spk plays a major role in hyphal morphogenesis by operating as a VSC—i.e., by regulating the traffic of wall-building vesicles in the manner predicted by the hyphoid model.

Localization of the C terminus of the assembly domain of hepatitis B virus capsid protein: Implications for morphogenesis and organization of encapsidated RNA

The capsid protein of hepatitis B virus, consisting of an “assembly” domain (residues 1–149) and an RNA-binding “protamine” domain (residues 150–183), assembles from dimers into icosahedral capsids of two different sizes. The C terminus of the assembly domain (residues 140–149) functions as a morphogenetic switch, longer C termini favoring a higher proportion of the larger capsids, it also connects the protamine domain to the capsid shell. We now have defined the location of this peptide in capsids assembled in vitro by engineering a mutant assembly domain with a single cysteine at its C terminus (residue 150), labeling it with a gold cluster and visualizing the cluster by cryo-electron microscopy. The labeled protein is unimpaired in its ability to form capsids. Our density map reveals a single undecagold cluster under each fivefold and quasi-sixfold vertex, connected to sites at either end of the undersides of the dimers. Considering the geometry of the vertices, the C termini must be more crowded at the fivefolds. Thus, a bulky C terminus would be expected to favor formation of the larger (T = 4) capsids, which have a greater proportion of quasi-sixfolds. Capsids assembled by expressing the full-length protein in Escherichia coli package bacterial RNAs in amounts equivalent to the viral pregenome. Our density map of these capsids reveals a distinct inner shell of density—the RNA. The RNA is connected to the protein shell via the C-terminal linkers and also makes contact around the dimer axes.

Heme oxygenase 1 is required for mammalian iron reutilization

The majority of iron for essential mammalian biological activities such as erythropoiesis is thought to be reutilized from cellular hemoproteins. Here, we generated mice lacking functional heme oxygenase 1 (Hmox1; EC 1.14.99.3), which catabolizes heme to biliverdin, carbon monoxide, and free iron, to assess its participation in iron homeostasis. Hmox1-deficient adult mice developed an anemia associated with abnormally low serum iron levels, yet accumulated hepatic and renal iron that contributed to macromolecular oxidative damage, tissue injury, and chronic inflammation. Our results indicate that Hmox1 has an important recycling role by facilitating the release of iron from hepatic and renal cells, and describe a mouse model of human iron metabolic disorders.