Sulfated polysaccharides from marine sponges: conspicuous distribution among different cell types and involvement on formation of in vitro cell aggregates

Marine sponges (Porifera) display an ancestral type of cell-cell adhesion, based on carbohydrate-carbohydrate interaction. The aim of the present work was to investigate further details of this adhesion by using, as a model, the in vitro aggregation of dissociated sponge cells. Our results showed the participation of sulfated polysaccharides in this cell-cell interaction, as based on the following observations: (1) a variety of sponge cells contained similar sulfated polysaccharides as surface-associated molecules and as intracellular inclusions; (2) ³⁵S-sulfate metabolic labeling of dissociated sponge cells revealed that the majority (two thirds) of the total sulfated polysaccharide occurred as a cell-surface-associated molecule; (3) the aggregation process of dissociated sponge cells demanded the active de novo synthesis of sulfated polysaccharides, which ceased as cell aggregation reached a plateau; (4) the typical well-organized aggregates of sponge cells, known as primmorphs, contained three cell types showing sulfated polysaccharides on their cell surface; (5) collagen fibrils were also produced by the primmorphs in order to fill the extracellular spaces of their inner portion and the external layer surrounding their entire surface. Our data have thus clarified the relevance of sulfated polysaccharides in this system of in vitro sponge cell aggregation. The molecular basis of this system has practical relevance, since the culture of sponge cells is necessary for the production of molecules with biotechnological applications.     

The Characterization of Twenty Sequenced Human Genomes

We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.     

Bacterial Community Diversity in the Brazilian Atlantic Forest Soils

The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29–54%), Proteobacteria (16–38%), and Verrucomicrobia (0.6–14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41–152) and species (263–446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.     

Antioxidative enzymatic protection in leaves of two contrasting cowpea cultivars under salinity

The aim of this work was to investigate the role of the antioxidant enzymes in salt tolerance comparing the salt-sensitive (Pérola) and a salt-tolerant (Pitiúba) cultivar of cowpea [Vigna unguiculata (L.) Walp.]. Salt stress (100 mM NaCl for 8 d) reduced the leaf growth rate more in the sensitive cultivar. The salt-induced decrease in the relative water content, Na⁺ accumulation and increase in leaf electrolyte leakage was similar in both cultivars. Salt stress induced a higher increase in the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX) and phenol peroxidase (POX) in the tolerant cultivar than in sensitive one.     

Toxicity of unsaturated fatty acids to the biohydrogenating ruminal bacterium, <Emphasis Type="Italic">Butyrivibrio fibrisolvens</Emphasis>

Background  

Health-promoting polyunsaturated fatty acids (PUFA) are abundant in forages grazed by ruminants and in vegetable and fish oils used as dietary supplements, but only a small proportion of PUFA finds its way into meat and milk, because of biohydrogenation in the rumen. Butyrivibrio fibrisolvens plays a major role in this activity. The aim of this study was to investigate the mechanisms by which PUFA affect the growth of B. fibrisolvens, how PUFA are metabolized and the metabolic response to growth in the presence of PUFA.     

The Impact of the Allee Effect in Dispersal and Patch-Occupancy Age on the Dynamics of Metapopulations

In this paper, we introduce a Levins-type metapopulation model with empty and occupied patches, and dispersing population. We structure the proportion of occupied patches according to the patch-occupancy age. We observe that patch-occupancy age may destabilize the metapopulation, leading to persistent oscillations. We also allow for the dispersal rate to vary with the proportion of empty patches in a monotone or unimodal way. The unimodal dependence leads to multiple non-trivial equilibria and bistability when the reproduction number of the metapopulation < 1 but greater than a lower critical value ^*. We show that the metapopulation will persist independently of its initial status if > 1.     

Merging theory and mechanism in studies of gynodioecy

In gynodioecious species, females and hermaphrodites coexist and the genetics of sex determination is usually nuclear cytoplasmic. Maintaining nuclear-cytoplasmic gynodioecy requires polymorphism for the feminizing genes (contained in the mitochondria) and the genes that restore male fertility (contained in the nucleus). This complex polymorphism depends, in part, on there being negative pleiotropic effects (i.e. costs) of the nuclear restorer alleles. Here, we combine information from theoretical studies and studies on the molecular action of restorer alleles in crops to interpret the probable costs of such alleles, and suggest how various aspects of the theoretical models could be tested. In doing so, we highlight how crops can be used to address evolutionary questions about the maintenance of nuclear-cytoplasmic gynodioecy.     

Crystal structure of scytalidoglutamic peptidase with its first potent inhibitor provides insights into substrate specificity and catalysis

Scytalidoglutamic peptidase (SGP) from Scytalidium lignicolum is the founding member of the newly discovered\ family of peptidases, G1, so far found exclusively in fungi. The crystal structure of SGP revealed a previously undescribed fold for peptidases and a unique catalytic dyad of residues Gln53 and Glu136. Surprisingly, the beta-sandwich structure of SGP is strikingly similar to members of the carbohydrate-binding concanavalin A-like lectins/glucanases superfamily. By analogy with the active sites of aspartic peptidases, a mechanism employing nucleophillic attack by a water molecule activated by the general base functionality of Glu136 has been proposed. Here, we report the first crystal structures of SGP in complex with two transition state peptide analogs designed to mimic the tetrahedral intermediate of the proteolytic reaction. Of these two analogs, the one containing a central S-hydroxyl group is a potent sub-nanomolar inhibitor of SGP. The inhibitor binds non-covalently to the concave surface of the upper beta-sheet and enables delineation of the S4 to S3' substrate specificity pockets of the enzyme. Structural differences in these pockets account for the unique substrate preferences of SGP among peptidases having an acidic pH optimum. Inhibitor binding is accompanied by a structuring of the region comprising residues Tyr71-Gly80 from being mostly disordered in the apoenzyme and leading to positioning of crucial active site residues for establishing enzyme-inhibitor contacts. In addition, conformational rearrangements are seen in a disulfide bridged surface loop (Cys141-Cys148), which moves inwards, partially closing the open substrate binding cleft of the native enzyme. The non-hydrolysable scissile bond analog of the inhibitor is located in the active site forming close contacts with Gln53 and Glu136. The nucleophilic water molecule is displaced and a unique mode of binding is observed with the S-OH of the inhibitor occupying the oxyanion binding site of the proposed tetrahedral intermediate. Details of the enzyme-inhibitor interactions and mechanistic interpretations are discussed.     

Inheritance of chloroplast DNA is not strictly maternal in Silene vulgaris (Caryophyllaceae): evidence from experimental crosses and natural populations

Chloroplast DNA (cpDNA) is maternally inherited in the majority, but not all, of angiosperm species. The mode of inheritance of cpDNA is a critical determinant of its molecular evolution and of its population genetic structure. Here, we present the results of investigations of the inheritance of cpDNA in Silene vulgaris, a plant used in a variety of studies in which cpDNA is an important component. PCR/RFLP markers were used to compare mother and offspring cpDNA genotypes sampled from two natural populations, and mother, father, and offspring genotypes obtained from controlled greenhouse crosses. Ten of 215 offspring cpDNA genotypes studied in the controlled crosses and three of 156 offspring from natural populations did not match that of the mother, demonstrating rare nonmaternal inheritance. That the chloroplast genome is occasionally transmitted through pollen is discussed in the context of using S. vulgaris cpDNA as a marker in studies of seed dispersal and when considering the joint evolution of the chloroplast and mitochondrial genomes.