GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data

SUMMARY: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate. AVAILABILITY: http://garban.tecnun.es.     

Immunization against luteinizing hormone-releasing hormone fusion proteins does not decrease prostate cancer in the transgenic adenocarcinoma mouse prostate model

This study was undertaken to test the effect of immunization against luteinizing hormone-releasing hormone (LHRH) fusion proteins on the development and progression of prostate cancer in the transgenic adenocarcinoma mouse prostate (TRAMP) model. Two LHRH fusion proteins, ovalbumin with seven LHRH peptides (OV-LHRH-7), and thioredoxin with seven LHRH peptides (TH-LHRH-7) were used in a cocktail vaccine. Two groups of male TRAMP mice were immunized with the cocktail. Primary immunizations were at either 4 or 8 weeks of age. LHRH immunized mice (n=19) were compared with castrated (n=19) and intact mice (n=18) for testosterone concentration, tumor weight, and lifespan. Immunization against LHRH in the TRAMP mice resulted in significant production of antibodies to LHRH compared with surgically castrated and intact control mice. Testicular weight was significantly reduced in the LHRH immunized groups compared with intact control mice. Serum testosterone was reduced (P<0.05) in the immunized mice compared with intact control mice and was not different from that of castrated mice (P>0.05). Tumor weight was variable and inconsistent throughout all treatment groups. Lifespan was not increased by immunization against LHRH or castration. Intact control mice (lived the longest (227+/-11 days), whereas immunized mice lived 206+/-11 days and castrated mice lived 213+/-13 days. Tumors from immunized TRAMP mice appeared more aggressive than tumors of castrated and intact mice, as demonstrated by 35% expression of gross lung tumors in the immunized mice whereas none were observed in the castrated or intact TRAMP mice. Prostate cancer is initially dependent upon androgens for growth and development, but cells have the ability to escape androgen dependence and progress to an androgen independent state, which was evident in this study. The TRAMP mouse model immunized against LHRH may have utility in future studies and treatments of the androgen independent prostate cancer.     

Molecular genetic approaches to microtubule-associated protein function

Protein function in vivo can be studied by deleting (knock-out) the gene that encodes it, and search for the consequences. This procedure involves different technologies, including recombinant DNA procedures, cell biology methods and histological and immunocytochemical analysis. In this work we have reviewed these procedures when they have been applied to ascertain the function of several microtubule-associated proteins. These proteins have been previously involved, through in vitro experiments, in having a role in the microtubule stabilization. Here, we will summarize the generation and characterization of different microtubule-associated protein knock-out mice. Special attention will be paid to MAP1B knock-out mice. Amongst the different MAPs knock-out mice these show the strongest phenotype, the most likely for being MAP1B, the MAP that is expressed earliest in neurogenesis. Molecular genetics could be considered as a valid and useful procedure to truly establish the in vivo functions of a protein, although it is necessary to be aware of possible artifacts such as the generation of some kinds of RNA alternative splicing. To avoid this the best strategy to be used must consider the deletion of the exon that contains the functional domains of the protein.     

Tau aggregation into fibrillar polymers: taupathies

Different neurological disorders, known as taupathies have been recently described. In these disorders it has been suggested that modifications in the microtubule-associated protein tau could cause neural degeneration in specific regions. Although these regions are different in the different taupathies, some common features appear to occur in all of them: abnormal hyperphosphorylation of tau and aberrant tau aggregation. These two features are commented upon in this review.     

Two active-site tyrosyl residues of protein TrwC act sequentially at the origin of transfer during plasmid R388 conjugation

Protein TrwC is the relaxase-helicase responsible for the initiation and termination reactions of DNA processing during plasmid R388 conjugation. Site-directed mutagenesis was used to change to phenylalanine each of a set of four conserved tyrosyl residues in the sequence of the N-terminal relaxation domain of the protein. Simultaneous mutation of both Y18 and Y26 was required to abolish in vitro cleavage and strand-transfer reactions catalyzed by protein TrwC on oligonucleotides containing the nic site. Thus, both Y18 and Y26 could be involved independently in the formation of oligonucleotide-protein covalent complexes that constitute presumed intermediates of these reactions. This hypothesis was confirmed by the observation of Y18 and Y26-specific peptide-oligonucleotide adducts after protease digestion of TrwC and mutant derivatives. Finally mutation Y18F, but not mutation Y26F, abolished nic-cleavage of a supercoiled DNA containing the R388 origin of transfer (oriT). These data allowed the construction of a model for conjugative DNA processing in which Y18 specifically catalyzes the initial cleavage reaction, while Y26 is used for the second strand-transfer reaction, which terminates conjugation. The model suggests a control mechanism that can be effective at each conjugative replication cycle.     

Genetic and biochemical manipulations of the small ribosomal subunit from Thermus thermophilus HB8

Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains regions interpretable either as RNA chains or as protein motifs. To assist phasing at higher resolution we introduced recombinant methods aimed at extensive selenation for MAD phasing. We are focusing on several ribosomal proteins that can be quantitatively detached by chemical means. These proteins can be modified and subsequently reconstituted into depleted ribosomal cores. They also can be used for binding heavy atoms, by incorporating chemically reactive binding sites, such as -SH groups, into them. In parallel we are co-crystallizing the ribosomal particles with tailor made ligands, such as antibiotics or cDNA to which heavy-atoms have been attached or diffuse the latter compounds into already formed crystals.     

Effects of phosphinotricin treatment on glutamine synthetase isoforms in Scots pine seedlings

The occurrence of GS isoenzymes has been investigated in Scots pine (Pinus sylvestris) seedlings. A transient increase of glutamine synthetase (GS, EC 6.3.1.2) activity was observed in the cotyledon whorl of plants treated with the herbicide phosphinotricin (PPT). The increase in GS activity was accompanied by a parallel accumulation of GS1 protein, which remained at high levels throughout the PPT treatment. Two-dimensional SDS-PAGE western analysis showed that pine extracts contained two GS1 polypeptides which differ in their corresponding isoelectric points. Analysis of crude extracts by ion-exchange chromatography led to the separation of two GS isoforms. The first peak (GS1-a) eluted from the columns at a low ionic strength (0.15-0.18 M KCl), whereas the second one (GS1-b) was detected at 0.5 M KCl. A detailed molecular study of both GS holoenzymes confirmed that their subunits were similar in size (about 41 kDa) but different in charge. All these data clearly demonstrate the presence of two GS1 forms in Scots pine cotyledons. Moreover, a comparison of isolated GS isoproteins with the recombinantly expressed Scots pine cytosolic subunit suggests that GS1-a corresponds to the previously characterized cDNA (pGSP114) whereas GS1-b is a minor GS isoenzyme with increased relative abundance in phosphinotricin treated plants.     

Some Like It Fat: Comparative Ultrastructure of the Embryo in Two Demosponges of the Genus Mycale (Order Poecilosclerida) from Antarctica and the Caribbean

During embryogenesis, organisms with lecithotrophic indirect development usually accumulate large quantities of energetic reserves in the form of yolk that are necessary for larval survival. Since all sponges have lecithotrophic development, yolk formation is an ineludible step of their embryogenesis. Sponge yolk platelets have a wide range of morphological forms, from entirely lipid or protein platelets to a combined platelet showing both lipids and proteins and even glycogen. So far, there are no comparative studies on the nature and content of yolk in congeneric species of sponges inhabiting contrasting environments, which could have putative effects on the larval adaptation to environmental conditions. Here, we have taken advantage of the worldwide distribution of the sponge genus Mycale, in order to compare the embryogenesis and yolk formation in two species inhabiting contrasting latitudinal areas: M. acerata from Antarctic waters and M. laevis from the Caribbean. We have compared their brooded embryos and larvae using scanning and transmission electron microscopy, and calculated their energetic signatures based on the nature of their yolk. While the general morphological feature of embryos and larvae of both species were very similar, the main difference resided in the yolk nature. The Antarctic species, M. acerata, showed exclusively lipid yolk, whereas the Caribbean species, M. laevis, showed combined platelets of lipids and proteins and less frequently protein yolk platelets. The larvae of M. acerata were estimated to possess a two-fold energetic signature compared to that of M. laevis, which may have important ecological implications for their survival and for maintaining large population densities in the cold waters of the Southern Ocean.     

Wood Specific Gravity Variations and Biomass of Central African Tree Species: The Simple Choice of the Outer Wood

Context

Wood specific gravity is a key element in tropical forest ecology. It integrates many aspects of tree mechanical properties and functioning and is an important predictor of tree biomass. Wood specific gravity varies widely among and within species and also within individual trees. Notably, contrasted patterns of radial variation of wood specific gravity have been demonstrated and related to regeneration guilds (light demanding vs. shade-bearing). However, although being repeatedly invoked as a potential source of error when estimating the biomass of trees, both intraspecific and radial variations remain little studied. In this study we characterized detailed pith-to-bark wood specific gravity profiles among contrasted species prominently contributing to the biomass of the forest, i.e., the dominant species, and we quantified the consequences of such variations on the biomass.

Methods

Radial profiles of wood density at 8% moisture content were compiled for 14 dominant species in the Democratic Republic of Congo, adapting a unique 3D X-ray scanning technique at very high spatial resolution on core samples. Mean wood density estimates were validated by water displacement measurements. Wood density profiles were converted to wood specific gravity and linear mixed models were used to decompose the radial variance. Potential errors in biomass estimation were assessed by comparing the biomass estimated from the wood specific gravity measured from pith-to-bark profiles, from global repositories, and from partial information (outer wood or inner wood).

Results

Wood specific gravity profiles from pith-to-bark presented positive, neutral and negative trends. Positive trends mainly characterized light-demanding species, increasing up to 1.8 g.cm^-3 per meter for Piptadeniastrum africanum, and negative trends characterized shade-bearing species, decreasing up to 1 g.cm^-3 per meter for Strombosia pustulata. The linear mixed model showed the greater part of wood specific gravity variance was explained by species only (45%) followed by a redundant part between species and regeneration guilds (36%). Despite substantial variation in wood specific gravity profiles among species and regeneration guilds, we found that values from the outer wood were strongly correlated to values from the whole profile, without any significant bias. In addition, we found that wood specific gravity from the DRYAD global repository may strongly differ depending on the species (up to 40% for Dialium pachyphyllum).

Main Conclusion

Therefore, when estimating forest biomass in specific sites, we recommend the systematic collection of outer wood samples on dominant species. This should prevent the main errors in biomass estimations resulting from wood specific gravity and allow for the collection of new information to explore the intraspecific variation of mechanical properties of trees.     

Regulation of GSK3 isoforms by phosphatases PP1 and PP2A

Dephosphorylation of phospho GSK3 isoforms, from COS-7 cells, was determined in vitro and in cultured cells in the absence or the presence of okadaic acid and lithium. Our results indicate a preferential dephosphorylation of phospho GSK3α by PP2A phosphatase, whereas dephosphorylation of phospho GSK3β mainly takes place by PP1 phosphatase.