Evolution of GnRH ligands and receptors in gnathostomata

Gonadotropin-releasing hormone (GnRH) is the final common signaling molecule used by the brain to regulate reproduction in all vertebrates. Until now, a total of 24 GnRH structural variants have been characterized from vertebrate, protochordate and invertebrate nervous tissue. Almost all vertebrates already investigated have at least two GnRH forms coexisting in the central nervous system. Furthermore, it is now well accepted that three GnRH forms are present both in early and late evolved teleostean fishes. The number and taxonomic distribution of the different GnRH variants also raise questions about the phylogenetic relationships between them. Most of the GnRH phylogenetic analyses are in agreement with the widely accepted idea that the GnRH family can be divided into three main groups. However, the examination of the gnathostome GnRH phylogenetic relationships clearly shows the existence of two main paralogous GnRH lineages: the 'midbrain GnRH" group and the "forebrain GnRH" group. The first one, represented by chicken GnRH-II forms, and the second one composed of two paralogous lineages, the salmon GnRH cluster (only represented in teleostean fish species) and the hypophysotropic GnRH cluster, also present in tetrapods. This analysis suggests that the two forebrain clades share a common precursor and reinforces the idea that the salmon GnRH branch has originated from a duplication of the hypophysotropic lineage. GnRH ligands exert their activity through G protein-coupled receptors of the rhodopsin-like family. As with the ligands, multiple GnRHRs are expressed in individual vertebrate species and phylogenetic analyses have revealed that all vertebrate GnRHRs cluster into three main receptor types. However, new data and a new phylogenetic analysis propose a two GnRHR type model, in which different rounds of gene duplications may have occurred in different groups within each lineage.     

Molecular characterization of the proteinase-encoding gene, prb1, related to mycoparasitism by Trichoderma harzianum

The soil fungus Trichoderma harzianum is a mycoparasitic fungus known for its use as a biocontrol agent of phytopathogenic fungi. Among other factors, Trichoderma produces a series of antibiotics and fungal cell wall-degrading enzymes. These enzymes are believed to play an important role in mycoparasitism. Among the hydrolytic enzymes, we have identified a basic proteinase (Prb1) which is induced by either autoclaved mycelia, fungal cell wall preparation or chitin; however, the induction does not occur in the presence of glucose. The proteinase was purified and biochemically characterized as a serine proteinase of 31 kDa and pl 9.2. Based on the sequence of three internal peptides, synthetic oligonudeotide probes were designed. These probes allowed subsequent isolation of a cDNA and its corresponding genomic clone. The deduced amino acid sequence indicates that the proteinase is synthesized as a pre-proenzyme and allows its classification as a serine proteinase. Northen analysis shows that the induction of this enzyme is due to an increase in the corresponding mRNA level.     

Influence of the geometry around the manganese ion on the peroxidase and catalase activities of Mn(III)-Schiff base complexes

The peroxidase and catalase activities of eighteen manganese-Schiff base complexes have been studied. A correlation between the structure of the complexes and their catalytic activity is discussed on the basis of the variety of systems studied. Complexes 1-18 have the general formulae [MnLⁿ(D)₂](X)(H₂O/CH₃OH)_m, where Lⁿ = L¹-L¹³; D = H₂O, CH₃OH or Cl; m = 0-2.5 and X = NO₃⁻, Cl⁻, ClO₄⁻, CH₃COO⁻, C₂H₅COO⁻ or C₅H₁₁COO⁻. The dianionic tetradentate Schiff base ligands H₂Lⁿ are the result of the condensation of different substituted (OMe-, OEt-, Br-, Cl-) hydroxybenzaldehyde with diverse diamines (1,2-diaminoethane for H₂L¹-H₂L²; 1,2-diamino-2-methylethane for H₂L³-H₂L⁴; 1,2-diamino-2,2-dimethylethane for H₂L⁵; 1,2-diphenylenediamine for H₂L⁶-H₂L⁷; 1,3-diaminopropane for H₂L⁸-H₂L¹¹; 1,3-diamino-2,2-dimethylpropane for H₂L¹²-H₂L¹³). The new Mn(III) complexes [MnL¹(H₂O)Cl](H₂O)_2.5 (2), [MnL²(H₂O)₂](NO₃)(H₂O) (4), [MnL⁶(H₂O)₂][MnL⁶(CH₃OH)(H₂O)](NO₃)₂(CH₃OH) (8), [MnL⁶(H₂O)(OAc)](H₂O) (9) and [MnL⁷(H₂O)₂](NO₃)(CH₃OH)₂ (12) were isolated and characterised by elemental analysis, magnetic susceptibility and conductivity measurements, redox studies, ESI spectrometry and UV, IR, paramagnetic ¹H NMR, and EPR spectroscopies. X-ray crystallographic studies of these complexes and of the ligand H₂L⁶ are also reported. The crystal structures of the rest of the complexes have been previously published and herein we have only revised their study by those techniques still not reported (EPR and ¹H NMR for some of these compounds) and which help to establish their structures in solution. Complexes 1-12 behave as more efficient mimics of peroxidase or catalase in contrast with 13-18. The analysis between the catalytic activity and the structure of the compounds emphasises the significance of the existence of a vacant or a labile position in the coordination sphere of the catalyst.     

A fluctuation-driven mechanism for slow decision processes in reverberant networks

The spike activity of cells in some cortical areas has been found to be correlated with reaction times and behavioral responses during two-choice decision tasks. These experimental findings have motivated the study of biologically plausible winner-take-all network models, in which strong recurrent excitation and feedback inhibition allow the network to form a categorical choice upon stimulation. Choice formation corresponds in these models to the transition from the spontaneous state of the network to a state where neurons selective for one of the choices fire at a high rate and inhibit the activity of the other neurons. This transition has been traditionally induced by an increase in the external input that destabilizes the spontaneous state of the network and forces its relaxation to a decision state. Here we explore a different mechanism by which the system can undergo such transitions while keeping the spontaneous state stable, based on an escape induced by finite-size noise from the spontaneous state. This decision mechanism naturally arises for low stimulus strengths and leads to exponentially distributed decision times when the amount of noise in the system is small. Furthermore, we show using numerical simulations that mean decision times follow in this regime an exponential dependence on the amplitude of noise. The escape mechanism provides thus a dynamical basis for the wide range and variability of decision times observed experimentally.     

The Brazilian Portuguese Lexicon: An Instrument for Psycholinguistic Research

In this article, we present the Brazilian Portuguese Lexicon, a new word-based corpus for psycholinguistic and computational linguistic research in Brazilian Portuguese. We describe the corpus development, the specific characteristics on the internet site and database for user access. We also perform distributional analyses of the corpus and comparisons to other current databases. Our main objective was to provide a large, reliable, and useful word-based corpus with a dynamic, easy-to-use, and intuitive interface with free internet access for word and word-criteria searches. We used the Núcleo Interinstitucional de Linguística Computacional’s corpus as the basic data source and developed the Brazilian Portuguese Lexicon by deriving and adding metalinguistic and psycholinguistic information about Brazilian Portuguese words. We obtained a final corpus with more than 30 million word tokens, 215 thousand word types and 25 categories of information about each word. This corpus was made available on the internet via a free-access site with two search engines: a simple search and a complex search. The simple engine basically searches for a list of words, while the complex engine accepts all types of criteria in the corpus categories. The output result presents all entries found in the corpus with the criteria specified in the input search and can be downloaded as a.csv file. We created a module in the results that delivers basic statistics about each search. The Brazilian Portuguese Lexicon also provides a pseudoword engine and specific tools for linguistic and statistical analysis. Therefore, the Brazilian Portuguese Lexicon is a convenient instrument for stimulus search, selection, control, and manipulation in psycholinguistic experiments, as also it is a powerful database for computational linguistics research and language modeling related to lexicon distribution, functioning, and behavior.     

Latitudinal patterns of range size and species richness of New World woody plants

Aim  Relationships between range size and species richness are contentious, yet they are key to testing the various hypotheses that attempt to explain latitudinal diversity gradients. Our goal is to utilize the largest data set yet compiled for New World woody plant biogeography to describe and assess these relationships between species richness and range size.
Location  North and South America.
Methods  We estimated the latitudinal extent of 12,980 species of woody plants (trees, shrubs, lianas). From these estimates we quantified latitudinal patterns of species richness and range size. We compared our observations with expectations derived from two null models.
Results   Peak richness and the smallest- and largest-ranged species are generally found close to the equator. In contrast to prominent diversity hypotheses: (1) mean latitudinal extent of tropical species is greater than expected; (2) latitudinal extent appears to be decoupled from species richness across New World latitudes, with abrupt transitions across subtropical latitudes; and (3) mean latitudinal extents show equatorial and north temperate peaks and subtropical minima. Our results suggest that patterns of range size and richness appear to be influenced by three broadly overlapping biotic domains (biotic provinces) for New World woody plants.
Main conclusions  Hypotheses that assume a direct relationship between range size and species richness may explain richness patterns within these domains, but cannot explain gradients in richness across the New World.     

Actin acting at the Golgi

The organization, assembly and remodeling of the actin cytoskeleton provide force and tracks for a variety of (endo)membrane-associated events such as membrane trafficking. This review illustrates in different cellular models how actin and many of its numerous binding and regulatory proteins (actin and co-workers) participate in the structural organization of the Golgi apparatus and in trafficking-associated processes such as sorting, biogenesis and motion of Golgi-derived transport carriers.     

Monomer composition and sequence of sodium alginate extracted at pilot plant scale from three commercially important seaweeds from Mexico

The marine waters of the Baja California peninsula (Mexico) are a rich source of brown seaweeds with a great potential for exploitation. For that reason, Sargassum sinicola, Eisenia arborea, and Macrocystis pyrifera collected from different locations were subjected to extraction of sodium alginate using a pilot-plant scale process developed in our facilities. The composition and sequence parameters of the recovered alginate were studied by infrared and nuclear magnetic resonance spectroscopy. The spectral analysis of the products revealed that sodium alginate from S. sinicola contains a greater proportion of guluronate monomers (64%) than that from E. arborea (48%), and M. pyrifera (38%). Computation of the frequencies of diads and triads indicated that the alginate from S. sinicola was constructed by intercalated guluronate-blocks of 14 residues in length. In contrast, the length of the G-block in the alginates from E. arborea and M. pyrifera were 7 and 4 residues, respectively. The results show that S. sinicola, E. arborea, and M. pyrifera are sources of sodium alginate with different mannuronate/guluronate ratios, as well as a varied building-block length. In consequence, aqueous dispersions of sodium alginate from the three studied species are expected to exhibit different physical properties.     

Exploring the interplay of stability and function in protein evolution

A new split β‐lactamase assay promises experimental testing of the interplay of protein stability and function. Proteins are sufficiently stable to act effectively within cells. However, mutations generally destabilize structure, with effects on free energy that are comparable to the free energy of folding. Assays of protein functionality and stability in vivo enable a quick study of factors that influence these properties in response to targeted mutations. These assays can help molecular engineering but can also be used to target important questions, including why most proteins are marginally stable, how mutations alter structural makeup, and how thermodynamics, function, and environment shape molecular change. Processes of self‐organization and natural selection are determinants of stability and function. Non‐equilibrium thermodynamics provides crucial concepts, e.g., cells as emergent energy‐dissipating entities that do work and build their own parts, and a framework to study the sculpting role of evolution at different scales.