Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction

Citrus canker is a plant disease caused by Gram‐negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm‐enriched fraction was performed for XAC cells grown in pathogenicity‐inducing (XAM‐M) and pathogenicity‐non‐inducing (nutrient broth) media using two‐dimensional electrophoresis combined with liquid chromatography‐tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up‐regulated proteins related to cellular envelope metabolism included glucose‐1‐phosphate thymidylyltransferase, dTDP‐4‐dehydrorhamnose‐3,5‐epimerase and peptidyl‐prolyl cis–trans‐isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real‐time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up‐regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60‐kDa chaperonin and glyceraldehyde‐3‐phosphate dehydrogenase were identified, suggesting the presence of post‐translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence‐related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies.     

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid–Vibrio mutualism

Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors “outside the squid” influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.     

Biosemiotics,the Extended Synthesis,and Ecological Information: Making Sense of the Organism-Environment Relation at the Cognitive Level

This paper argues that the Extended Synthesis, ecological information, and biosemiotics are complementary approaches whose engagement will help us explain the organism-environment interaction at the cognitive level. The Extended Synthesis, through niche construction theory, can explain the organism-environment interaction at an evolutionary level because niche construction is a process guided by information. We believe that the best account that defines information at this level is the one offered by biosemiotics and, within all kinds of biosemiotic information available, we believe that ecological information (information for affordances) is the best candidate for making sense of the organism-environment relation at the cognitive level. This entanglement of biosemiotics, ecological information and the Extended Synthesis is promising for understanding the multidimensional character of the organism-environment reciprocity as well as the relation between evolution, cognition, and meaning.     

Mathematical modeling of adhesion of bacteria to host cell lines

A mathematical model which describes adhesion of bacteria to host cell lines is presented. The model is flexible enough to account for the following situations: extracellular bacteria are either in exponential or in stationary phase. Adhesion is described as a reversible binding process in which the bacteria attach to or detach from specific receptors uniformly distributed on the cell surface. In turn, attached bacteria can either replicate or, conversely, they are restrained to remain in stationary phase. In the first case, however, we must consider the problem of whether the decrease of unoccupied receptors as adhesion progresses imposes a limit to the replicating capacity of the attached bacteria. The effect exerted by the multiplicity of infection (MOI), i.e. the ratio of the number of bacteria to the number of host cells, on the process of adhesion is also contemplated by the model. This has revealed that experiments performed at the same values of MOI can show completely different levels of adhered bacteria, depending on the number of host cells in the assays. This finding demonstrates that the report of the MOI values is insufficient to characterize comparative studies of bacterial adhesion since it could lead to a misunderstanding of the corresponding data. Simplified models based on the steady-state approximation and in equilibrium analysis by means of a Lagmuir adsorption isotherm for the attached bacteria are also discussed. This allows us to define the adhesion coefficient (β) in a given bacterium-cell system so that, with the exception of those systems where these coefficients cannot be defined, larger values of β are related to a greater adhesion capacity. An overview of the procedures to perform quantitative adhesion data analysis is outlined. Finally, theoretical predictions are compared with experimental results from the literature.     

Study of the conformational profile of the norbornane analogues of phenylalanine.

The conformational profile of the eight stereoisomeric 2-amino-3-phenylnorbornane-2-carboxylic acids (2-amino-3-phenylbicyclo[2.2.1]heptane-2-carboxylic acids) has been assessed by computational methods. These molecules constitute a series of four enantiomeric pairs that can be considered as rigid analogues of either L- or D-phenylalanine. The conformational space of their N-acetyl methylamide derivatives has been explored within the molecular mechanics framework, using the parm94 set of parameters of the AMBER force field. Local minimum energy conformations have been further investigated at the ab initio level by means of the Hartree-Fock and second order Moller-Plesset perturbation energy calculations using a 6-31G(d) basis set. The results of the present work suggest that the bulky norbornane structure induces two kinds of conformational constraints on the residues. On one hand, those of a steric nature directly imposed by the bicycle on the peptide backbone and, on the other hand, those that limit the orientations attainable by the phenyl ring which, in turn, reduces further the flexibility of the peptide backbone. A comparative analysis of the conformational profile of the phenylnorbornane amino acids with that of the norbornane amino acids devoid of the beta-phenyl substituent suggests that the norbornane system hampers the residue to adopt extended conformations in favour of C7-like structures. However, the bicycle itself does not impart a clear preference for any of the two possible C7 minima. It is the aromatic side chain, which is forced to adopt an almost eclipsed orientation, that breaks this symmetry introducing a marked preference for a single region of the (phi, psi) conformational space in each of the phenylalanine norbornane analogues investigated.     

Weight-length relationships for intertidal fish fauna in a mangrove estuary in Northern Brazil

Weight‐length relationships (WLR) are presented for 40 fish species inhabiting the mangrove creeks in the Curuçá Estuary in Northern Brazil. Samples were taken bimonthly between July 2003 and 2004 with a fyke net. This study represents the first reference available on WLR for 28 fish species.     

A comparative study of the function of heterospecific vocal mimicry in European passerines

Although heterospecific vocal imitation is well documented inpasserines, the evolutionary correlates of this phenomenon arepoorly known. Here, we studied interspecific variation in vocalmimicry in a comparative study of 241 European songbirds. Wetested whether vocal mimicry is a mode of repertoire acquisitionor whether it resulted from imperfect song learning. We alsoinvestigated the effect of the degree of contact with the vocalenvironment (with species having larger ranges, abundance, orbeing long lived having a higher degree of mimicry) and a possiblelink with cognitive capacity (an overall larger brain in specieswith mimicry). Finally, we determined the potential evolutionaryrole of vocal mimicry in different interspecific contexts, predictingthat mimicry may affect the intensity of brood parasitism, predation,or degree of hybridization. While controlling for research effortand phylogenetic relationships among taxa, we found that effectsizes for intersong interval, brain size, breeding dispersal,abundance, age-dependent expression of repertoires, and predationrisk reached a level that may indicate evolutionary importance.Vocal mimicry seems to be a consequence of song continuity ratherthan song complexity, may partially have some cognitive componentbut may also be dependent on the vocal environment, and mayattract the attention of predators. However, estimates of sexualselection and interspecific contacts due to brood parasitismand hybridization varied independently of vocal mimicry. Therefore,mimicry may have no function in female choice for complex songsand may be weakly selected via interspecific associations. Thesefindings provide little evidence for vocal mimicry having evolvedto serve important functions in most birds.     

Purification and some properties of two polyphenol oxidases from bartlett pears

Two polyphenol oxidases (enzymes A and B) from Bartlett pear (Pyrus communis) peelings were purified to electrophoretic homogeneity according to polyacrylamide gel by a combination of Sephadex gel filtration, diethylaminoethyl cellulose chromatography and hydroxyl apatite chromatography. While the two enzymes differ electrophoretically at pH 9.3, chromatographically on hydroxyl apatite, and in the effect of ionic strength on activity, they are similar with respect to chromatography on diethylaminoethyl cellulose, substrate specificity, pH activity relations, inhibition by p-coumaric and benzoic acids, and heat stability. The two enzymes are o-diphenol oxidases with no detectable monophenolase or laccase activities. Pyrocatechol, 4-methyl catechol, chlorogenic acid, and d-catechin are good substrates of the enzymes with K_m values in the range of 2 to 20 mm. Dependences of activity on oxygen and chlorogenic acid concentrations indicate a sequential mechanism for binding of these substrates to enzyme B. V_max and K_m values for oxygen and chlorogenic acid were 103 μmoles O₂ uptake per minute per milligram of enzyme, 0.11 mm and 7.2 mm, respectively, for enzyme B at pH 4.0. Both enzymes had maximum activity at pH 4.0 on chlorogenic acid. K_m values for chlorogenic acid were independent of pH from 3 to 7; the V_max values for both enzymes gave bell-shaped curves as a function of pH. p-Coumaric acid is a simple, linear noncompetitive inhibitor with respect to chlorogenic acid at pH 6.2 with K_i values of 0.38 and 0.50 mm for enzymes A and B, respectively. Benzoic acid is a linear competitive inhibitor with respect to chlorogenic acid at pH 4.0 with K_i values of 0.04 and 0.11 mm for enzymes A and B, respectively.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.