Effects of depth and bottom communities on the distribution of highly territorial reef fish in the northwestern region of Cuba

The main goal of the study was to investigate changes in reef fish species abundance and its correlation with selected environmental variables. Three main questions guided the analyses: (i) Do the analytical methods have a significant influence on the results; (ii) What are the main assemblage variation axes; and (iii) What are the factors correlating best with assemblage composition. Highly territorial fish assemblages of several coral reefs along the northwestern region of Cuba were assessed using a stationary point visual census technique. A total of 39 701 individuals of 26 species from the families Chaetodontidae, Labridae and Pomacentridae were counted in 841 censuses; almost 80% of the fish belonged to just four species: bluehead (Thalassoma bifasciatum), bicolor damselfish (Stegastes partitus), slippery dick (Halichoeres bivittatus) and blue chromis (Chromis cyanea). Several multivariate techniques (cluster analysis, non‐metric multidimensional scaling and canonical correspondence analysis) were used to explore main patterns in assemblage composition variation. It was found that the results did not differ significantly when analyzing the same data set. Furthermore, it was shown that the combined use of different multivariate techniques enhanced the interpretation of fish assemblage composition changes. Depth was the main variable explaining variation in the composition of fish assemblages in the studied reefs. The densities of corals and gorgonians were also strongly associated with depth. Sponge density made an additional significant contribution to the explanatory model. Results of this research could be used as a baseline reference for future analyses of the impact of human actions in the study area. (e.g. oil spills, change in fishing intensity, other pollution events, tourism development).     

Temporal evolution of the ABO allele frequencies in the Canary Islands: the impact of the European colonization

The indigenous Canary Islands population suffered a strong cultural and genetic impact when they were colonized by Europeans in the fifteenth century. The molecular analysis of the ABO blood group gene on aboriginal and seventeenth to eighteenth century remains confirms the demographic history of the islands depicted by previous archaeological, anthropological, and genetic studies. ABO allele frequencies clearly related Canarian aborigines with North African Berber populations, its most probable source of origin, and is far related to Iberian and to the current population of the archipelago. The historical sample shows a congruent intermediate position testifying already a strong European influence that would go in augment since then to present times, affecting all the islands with the important exception of La Gomera.     

Cytotoxic palladium complexes of bioreductive quinoxaline N1,N4-dioxide prodrugs

Four new palladium(II) complexes with the formula Pd(L)₂, where L are quinoxaline-2-carbonitrile N¹,N⁴-dioxide derivatives, were synthesized as a contribution to the chemistry and pharmacology of metal compounds with this class of pharmacologically interesting bioreductive prodrugs. Compounds were characterized by elemental, conductometric and thermogravimetric analyses, fast atom bombardment mass spectrometry (FAB-MS) and electronic, Fourier transform infrared (FTIR) and ¹H-nuclear magnetic resonance spectroscopies. The complexes were subjected to cytotoxic evaluation on V79 cells in hypoxic and aerobic conditions. In addition, a preliminary study on interaction with plasmid DNA in normoxia was performed. Complexes showed different in vitro biological behavior depending on the nature of the substituent on the quinoxaline ring. Pd(L1)₂ and Pd(L2)₂, where L1 is 3-aminoquinoxaline-2-carbonitrile N¹,N⁴-dioxide and L2 is 3-amino-6(7)-methylquinoxaline-2-carbonitrile N¹,N⁴-dioxide, showed non selective cytotoxicity, being cytotoxic either in hypoxic or in aerobic conditions. On the other hand, Pd(L3)₂, where L3 is 3-amino-6(7)-chloroquinoxaline-2-carbonitrile N¹,N⁴-dioxide, resulted in vitro more potent cytotoxin in hypoxia (P = 5.0 μM) than the corresponding free ligand (P = 9.0 μM) and tirapazamine (P = 30.0 μM), the first bioreductive cytotoxic drug introduced into clinical trials. In addition, it showed a very good selective cytotoxicity in hypoxic conditions, being non-cytotoxic in normoxia. Its hypoxic cytotoxicity relationship value, HCR, was of the same order than those of other hypoxia selective cytotoxins (i.e., Mitomycine C, Misonidazole and the N-oxide RB90740). Interaction of the complexes with plasmid DNA in normoxia showed dose dependent ability to relax the negative supercoiled forms via different mechanisms. Pd(L2)₂ introduced a scission event in supercoiled DNA yielding the circular relaxed form. Meanwhile, both Pd(L1)₂ and Pd(L3)₂ produced the loss of negative supercoils rendering a family of topoisomers with reduced electrophoretic mobility. Pd(L3)₂ showed a more marked effect than Pd(L1)₂. Indeed, for the highest doses assayed, Pd(L3)₂ was even able to introduce positive supercoils on the plasmid DNA.     

Enhancement of Novozym-435 catalytic properties by physical or chemical modification

Physical (ionic exchange of ionic polymers) or chemical (aminoethylamidation, succinylation, hydroxyethylamidation) modifications of Novozym 435 have been performed and the resulting biocatalysts have been assayed in diverse reactions. The coating of the immobilized enzyme with dextran-sulphate via ionic exchange permitted to increase the asymmetric factor of the biocatalyst from A = 13 (ee = 83%) to 24 (ee > 90%) in the hydrolysis of 3-phenylglutaric acid dimethyl diester, producing the (R)-monomethyl ester. The chemical succinylation of Novozym 435 permitted to enhance the biocatalyst enantiospecificity from E = 1 to 13 in the hydrolysis of (±)-mandelic acid methyl ester. In the hydrolysis of (±)-2-O-butyryl-2-phenylacetic acid, the enantiospecificity of Novozym 435 was very high towards the S-enantiomer (E > 100) but it was inverted after the chemical hydroxyethylamidation of the immobilized enzyme (E = 6.6 towards R-enantiomer).Thus, these simple protocols seem to be a very powerful tool to generate a library of biocatalysts from Novozym 435 with very different catalytic properties.     

Surface energetics to assess biomass attachment onto hydrophobic interaction adsorbents in expanded beds

Cell-to-support interaction and cell-to-cell aggregation phenomena have been studied in a model system composed of intact yeast cells and Phenyl-Streamline adsorbents. Biomass components and beaded adsorbents were characterized by contact angle determinations with three diagnostic liquids and zeta potential measurements. Subsequently, free energy of interaction vs. distance profiles between interacting surfaces was calculated in the aqueous media provided by operating mobile phases. The effect of pH and ammonium sulphate concentration within the normal operating ranges was evaluated. Calculation indicated that moderate interaction between cell particles and adsorbent beads can develop in the presence of salt. Cell-to-cell aggregation was suspected to occur at high salt concentration and neutral pH. Predictions based on the application of the XDLVO approach were confirmed by independent experimental methods like biomass deposition experiments and laser diffraction spectroscopy. Understanding biomass attachment onto hydrophobic supports can help in alleviating process limitations normally encountered during expanded bed adsorption of bioproducts.     

Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

Background

Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies.

Results

We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae.

Conclusion

Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.

     

Helicobacter Pylori's Plasticity Zones Are Novel Transposable Elements

Background

Genes present in only certain strains of a bacterial species can strongly affect cellular phenotypes and evolutionary potentials. One segment that seemed particularly rich in strain-specific genes was found by comparing the first two sequenced Helicobacter pylori genomes (strains 26695 and J99) and was named a “plasticity zone”.

Principal Findings

We studied the nature and evolution of plasticity zones by sequencing them in five more Helicobacter strains, determining their locations in additional strains, and identifying them in recently released genome sequences. They occurred as discrete units, inserted at numerous chromosomal sites, and were usually flanked by direct repeats of 5′AAGAATG, a sequence generally also present in one copy at unoccupied sites in other strains. This showed that plasticity zones are transposable elements, to be called TnPZs. Each full length TnPZ contained a cluster of type IV protein secretion genes (tfs3), a tyrosine recombinase family gene (“xerT”), and a large (≥2800 codon) orf encoding a protein with helicase and DNA methylase domains, plus additional orfs with no homology to genes of known function. Several TnPZ types were found that differed in gene arrangement or DNA sequence. Our analysis also indicated that the first-identified plasticity zones (in strains 26695 and J99) are complex mosaics of TnPZ remnants, formed by multiple TnPZ insertions, and spontaneous and transposable element mediated deletions. Tests using laboratory-generated deletions showed that TnPZs are not essential for viability, but identified one TnPZ that contributed quantitatively to bacterial growth during mouse infection and another that affected synthesis of proinflammatory cytokines in cell culture.

Conclusions

We propose that plasticity zone genes are contained in conjugative transposons (TnPZs) or remnants of them, that TnPZ insertion is mediated by XerT recombinase, and that some TnPZ genes affect bacterial phenotypes and fitness.     

A Nanoconjugate Apaf-1 Inhibitor Protects Mesothelial Cells from Cytokine-Induced Injury

Background

Inflammation may lead to tissue injury. We have studied the modulation of inflammatory milieu-induced tissue injury, as exemplified by the mesothelium. Peritoneal dialysis is complicated by peritonitis episodes that cause loss of mesothelium. Proinflammatory cytokines are increased in the peritoneal cavity during peritonitis episodes. However there is scarce information on the modulation of cell death by combinations of cytokines and on the therapeutic targets to prevent desmesothelization.

Methodology

Human mesothelial cells were cultured from effluents of stable peritoneal dialysis patients and from omentum of non-dialysis patients. Mesothelial cell death was studied in mice with S. aureus peritonitis and in mice injected with tumor necrosis factor alpha and interferon gamma.Tumor necrosis factor alpha and interferon gamma alone do not induce apoptosis in cultured mesothelial cells. By contrast, the cytokine combination increased the rate of apoptosis 2 to 3-fold over control. Cell death was associated with the activation of caspases and a pancaspase inhibitor prevented apoptosis. Specific caspase-8 and caspase-3 inhibitors were similarly effective. Co-incubation with both cytokines also impaired mesothelial wound healing in an in vitro model. However, inhibition of caspases did not improve wound healing and even impaired the long-term recovery from injury. By contrast, a polymeric nanoconjugate Apaf-1 inhibitor protected from apoptosis and allowed wound healing and long-term recovery. The Apaf-1 inhibitor also protected mesothelial cells from inflammation-induced injury in vivo in mice.

Conclusion

Cooperation between tumor necrosis factor alpha and interferon gamma contributes to mesothelial injury and impairs the regenerative capacity of the monolayer. Caspase inhibition attenuates mesothelial cell apoptosis but does not facilitate regeneration. A drug targeting Apaf-1 allows protection from apoptosis as well as regeneration in the course of inflammation-induced tissue injury.     

Structural and mechanical properties of TTR105-115 amyloid fibrils from compression experiments

Amyloid fibrils, originally associated with neurodegenerative diseases, are now recognized to have interesting mechanical properties. By using synchrotron x-ray diffraction at high pressure in a diamond anvil cell we determined the bulk modulus of TTR105-115 amyloid fibrils in water and in silicone oil to be 2.6 and 8.1 GPa, respectively. The compression characteristics of the fibrils are quite different in the two media, revealing the presence of cavities along the axis of the fibrils, but not between the β-sheets, which are separated by a dry interface as in a steric zipper motif. Our results emphasize the importance of peptide packing in determining the structural and mechanical properties of amyloid fibrils.