Panbiogeographical analysis of the shark genus Rhizoprionodon (Chondrichthyes,Carcharhiniformes, Carcharhinidae)

The distributional patterns of the seven species of Rhizoprionodon were analysed using the panbiogeographical method of track analysis. The individual tracks of Rhizoprionodon suggest that the genus is mainly an Indian–Atlantic Ocean group. Five generalized tracks were found: (1) Caribbean, defined by R. porosus and R. terraenovae; (2) eastern coast of South America, defined by R. porosus and R. lalandei; (3) Indian Ocean, defined by R. acutus and R. oligolinx; (4) north‐western Australia, defined by R. acutus, R. oligolinx and R. taylori; (5) north‐north‐eastern Australia, defined by R. acutus and R. taylori. Only R. longurio was not included in any generalized track, and its distribution is restricted to the eastern Pacific Ocean. Two biogeographical nodes were found at the intersection of the generalized tracks 1 and 2 (Caribbean Sea) and generalized tracks 4 and 5 (north Australia). The generalized tracks overlap with those found in several unrelated marine taxa. Overall, the generalized tracks are associated with warm currents. The biogeographical nodes found (Caribbean and Australian) are coincident with the global distribution of mangroves.     

Chemical constituents of Papulaspora immersa, an endophyte from Smallanthus sonchifolius (Asteraceae), and their cytotoxic activity

Papulaspora immersa H. H. Hotson was isolated from roots and leaves of Smallanthus sonchifolius (Poepp. and Endl. ) H. Rob. (Asteraceae), traditionally known as Yacon. The fungus was cultured in rice, and, from the AcOEt fraction, 14 compounds were isolated. Among them, (22E,24R)‐8,14‐epoxyergosta‐4,22‐diene‐3,6‐dione ( 4 ), 2,3‐epoxy‐1,2,3,4‐tetrahydronaphthalene‐c‐1,c‐4,8‐triol ( 10 ), and the chromone papulasporin ( 13 ) were new secondary metabolites. The spectral data of the known natural products were compared with the literature data, and their structures were established as the (24R)‐stigmast‐4‐en‐3‐one ( 1 ), 24‐methylenecycloartan‐3β‐ol ( 2 ), (22E,24R)‐ergosta‐4,6,8(14),22‐tetraen‐3‐one ( 3 ), (?)‐(3R,4R)‐4‐hydroxymellein ( 5 ), (?)‐(3R)‐5‐hydroxymellein ( 6 ), 6,8‐dihydroxy‐3‐methylisocoumarin ( 7 ), (?)‐(4S)‐4,8‐dihydroxy‐α‐tetralone ( 8 ), naphthalene‐1,8‐diol ( 9 ), 6,7,8‐trihydroxy‐3‐methylisocoumarin ( 11 ), 7‐hydroxy‐2,5‐dimethylchromone ( 12 ), and tyrosol ( 14 ). Compound 4 showed the highest cytotoxic activity against the human tumor cell lines MDA‐MB435 (melanoma), HCT‐8 (colon), SF295 (glioblastoma), and HL‐60 (promyelocytic leukemia), with IC₅₀ values of 3.3, 14.7, 5.0 and 1.6 μM , respectively. Strong synergistic effects were also observed with compound 5 and some of the isolated steroidal compounds.     

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

Background

Predicting drug-protein interactions from heterogeneous biological data sources is a key step for in silico drug discovery. The difficulty of this prediction task lies in the rarity of known drug-protein interactions and myriad unknown interactions to be predicted. To meet this challenge, a manifold regularization semi-supervised learning method is presented to tackle this issue by using labeled and unlabeled information which often generates better results than using the labeled data alone. Furthermore, our semi-supervised learning method integrates known drug-protein interaction network information as well as chemical structure and genomic sequence data.

Results

Using the proposed method, we predicted certain drug-protein interactions on the enzyme, ion channel, GPCRs, and nuclear receptor data sets. Some of them are confirmed by the latest publicly available drug targets databases such as KEGG.

Conclusions

We report encouraging results of using our method for drug-protein interaction network reconstruction which may shed light on the molecular interaction inference and new uses of marketed drugs.

     

Patterns of Gene Duplication in <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> and <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

In this paper we present a new method for detecting block duplications in a genome. It is more stringent than previous ones in that it requires a more rigorous definition of paralogous genes and that it requires the paralogous proteins on the two blocks to be contiguous. In addition, it provides three criterion choices: (1) the same composition (i.e., having the same paralogues in the two windows), (2) the same composition and gene order, and (3) the same composition, gene order, and gene orientation. The method is completely automated, requiring no visual inspection as in previous methods. We applied it to analyze the complete genomes of S. cerevisiae and C. elegans. In yeast we detected fewer duplicated blocks than previously reported. In C. elegans, however, we detected more block duplications than previously reported, indicating that although our method has a more stringent definition of block duplication than previous ones, it may be more sensitive in detection because it considers every possible window rather than only fixed nonoverlapping windows. Our results show that block duplication is a common phenomenon in both organisms. The patterns of block duplication in the two species are, however, markedly different. The yeast shows much more extensive block duplication than the nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in the yeast the majority of block duplications occurred between chromosomes, while in the nematode most block duplications occurred within chromosomes.     

Detection of gene duplications and block duplications in eukaryotic genomes

Several eukaryotic genomes have been completely sequenced and this provides an opportunity to investigate the extent and characteristics (e.g., single gene duplication, block duplication, etc.) of gene duplication in a genome. Detecting duplicate genes in a genome, however, is not a simple problem because of several complications such as domain shuffling, the existence of isoforms derived from alternative splicing, and annotational errors in the databases. We describe a method for overcoming these difficulties and the extents of gene duplication in the genomes of Drosophila melanogaster, Caenorhabditis elegans, and yeast inferred from this method. We also describe a method for detecting block duplications in a genome. Application of this method showed that block duplication is a common phenomenon in both yeast and nematode. The patterns of block duplication in the two species are, however, markedly different. Yeast shows much more extensive block duplication than nematode, with some chromosomes having more than 40% of the duplications derived from block duplications. Moreover, in yeast the majority of block duplications occurred between chromosomes, while in nematode most block duplications occurred within chromosomes.     

The yellow-flowered species of Cuphea (Lythraceae), including three new taxa

Among the predominantly purple- and red-flowered species of the genusCuphea, only seven yellow floral tube and/or yellow-petaled members in three sections were known. We add here two new species and one new variety.Cuphea congesta from Venezuela andC. splendida var.viridiflava from Bolivia are new to sect.Melvilla.Cuphea xanthopetala from Brazil is described in sect.Euandra and expands the presence of this feature to a fourth section of the genus. A key is provided to allCuphea with yellow floral tubes and/or yellow petals to expedite determinations when these exceptional character states are present.     

Partial purification of new milk-clotting enzyme produced by Nocardiopsis sp

Numerous attempts have been made to replace calf rennet with other milk clotting proteases because of limited supply and increasingly high prices. The aim of this work was to investigate the characteristic of the milk-clotting enzyme from Nocardiopsis sp. The partial purification extract was obtained by fractional precipitation with ammonium sulphate. Of the fractions obtained by precipitation, 40-60% possessed the milk-clotting activity (156.25 U/mg). The chromatography of 40-100% ammonium sulphate fraction in DEAE-cellulose yielded four fractions (F4, F5, F6, F7) with milk-clotting activity. The F5 yielded the best milk-clotting activity (20 U/ml). Both crude and partially purified extract were active at the range pH 4.5-11.0, however, optimum activity was displayed at pH 11.0 and pH 7.5, respectively. The milk-clotting activity was highest at 55 degrees C for both crude and partially purified extract. The crude and partial purification extract were inactivated at 65 and 75 degrees C after 30 min.     

On the classes of aminoacyl-tRNA synthetases and the error minimization in the genetic code

As a consequence of the existence of two classes of aminoacyl-tRNA synthetases (aaRSs), we defined two types of mutations: g (mutations that do not change the class of the involved amino acids) and u (those which change the class). We have found that the mean chemical distance resulting from g mutations is smaller than that corresponding to u mutations, indicating that g mutations are responsible for most of the known minimization of the genetic code. This supports models for the origin and evolution of the code, in which new amino acids were added after duplications or modification of existing aaRSs.     

Chemotaxis and chemical defenses in seaweed susceptibility to herbivory

Recent studies have show that small marine herbivores with limited mobility (mesograzers) often feed on macroalgae chemically defended against fishes or sea-urchins. In order to verify the involved mechanisms of chemotaxis or chemical defense into this process in Brazilian littoral, two species of brown alga Dictyota menstrualis and Dictyota mertensii were studied against the limited mobility herbivores, the amphipod Parhyale hawaiensis and the crab Pachygrapsus transversus. These two species were studied in order to verify the action of their crude extracts in the defense and chemotaxis processes related to limited mobility of these herbivores. Feeding preference assays revealed that P. hawaiensis do not eaten these Dictyota species. P. transversus do not eaten D. menstrualis either, but consumed large amounts of D. mertensii. Chemical deterrent assays showed that extracts of these species act as feeding deterrent to both species of herbivores. In addition, chemotaxis assays demonstrated that both herbivores are significantly negative chemotactic probably due to the presence of complementary metabolites into artificial foods. Considering that both Dictyota species exhibit active extracts against these small herbivores, we suppose that the non-occurrence of these herbivore species in close relationship with the seaweeds D. menstrualis and D. mertensii may explain the defense action of both extracts related to these mesograzers.