Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle,Emydura macquarii krefftii,from Australia

The influence of Pleistocene climatic cycles on Southern Hemisphere biotas is not yet well understood. Australia's eastern coastal margin provides an ideal setting for examining the relative influence of landscape development, sea level fluctuation, and cyclic climatic aridity on the evolution of freshwater biodiversity. We examined the impact of climatic oscillations and physical biogeographic barriers on the evolutionary history of the wide‐ranging Krefft's river turtle (Emydura macquarii krefftii), using range‐wide sampling (649 individuals representing 18 locations across 11 drainages) and analysis of mitochondrial sequences (~1.3‐kb control region and ND4) and nuclear microsatellites (12 polymorphic loci). A range of phylogeographic (haplotype networks, molecular dating), demographic (neutrality tests, mismatch distributions), and population genetic analyses (pairwise F_ST, analysis of molecular variance, Bayesian clustering analysis) were implemented to differentiate between competing demographic (local persistence vs. range expansion) and biogeographic (arid corridor vs. drainage divide) scenarios. Genetic data reveal population genetic structure in Krefft's river turtles primarily reflects isolation across drainage divides. Striking north‐south regional divergence (2.2% ND4 p‐distance; c. 4.73 Ma, 95% higher posterior density (HPD) 2.08–8.16 Ma) was consistent with long‐term isolation across a major drainage divide, not an adjacent arid corridor. Ancient divergence among regional lineages implies persistence of northern Krefft's populations despite the recurrent phases of severe local aridity, but with very low contemporary genetic diversity. Stable demography and high levels of genetic diversity are inferred for southern populations, where aridity was less extreme. Range‐wide genetic structure in Krefft's river turtles reflects contemporary and historical drainage architecture, although regional differences in the extent of Plio–Pleistocene climatic aridity may be reflected in current levels of genetic diversity.     

Mutagenic and recombinagenic responses to defective DNA polymerase delta are facilitated by the Rev1 protein in pol3-t mutants of Saccharomyces cerevisiae

Defective DNA replication can result in substantial increases in the level of genome instability. In the yeast Saccharomyces cerevisiae, the pol3-t allele confers a defect in the catalytic subunit of replicative DNA polymerase delta that results in increased rates of mutagenesis, recombination, and chromosome loss, perhaps by increasing the rate of replicative polymerase failure. The translesion polymerases Pol eta, Pol zeta, and Rev1 are part of a suite of factors in yeast that can act at sites of replicative polymerase failure. While mutants defective in the translesion polymerases alone displayed few defects, loss of Rev1 was found to suppress the increased rates of spontaneous mutation, recombination, and chromosome loss observed in pol3-t mutants. These results suggest that Rev1 may be involved in facilitating mutagenic and recombinagenic responses to the failure of Pol delta. Genome stability, therefore, may reflect a dynamic relationship between primary and auxiliary DNA polymerases.     

Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.     

Coupling solid phase microextraction to complementary separation platforms for metabotyping of <Emphasis Type="Italic">E. coli</Emphasis> metabolome in response to natural antibacterial agents

Introduction

Essential oils are known to possess antimicrobial activity; thus, their use has played an important role over the years in medicine and for food preservation purposes.

Objective

The effect of clove oil and its major constituents as bactericidal agents on the global metabolic profiling of E. coli bacteria was assessed by means of metabolic alterations, using solid phase microextraction (SPME) as a sample preparation method coupled to complementary analytical platforms.

Method

E. Coli cultures treated with clove oil and its major individual components were sampled by HS-SPME-GCxGC-ToF/MS and SPME-UPLC–MS. Full factorial design was applied in order to estimate the most effective antibacterial agent towards E. coli. Central composite design and factorial design were applied to investigate parameters influencing metabolite coverage and efficiency by SPME.

Results

The metabolic profile, including 500 metabolites identified by LC–MS and 789 components detected by GCxGC-ToF/MS, 125 of which were identified as dysregulated metabolites, revealed changes in the metabolome provoked by the antibacterial activity of clove oil, and in particular its major constituent eugenol. Analyses of individual components selected using orthogonal projections to latent structures discriminant analysis showed a neat differentiation between control samples in comparison to treated samples in various sets of metabolic pathways.

Conclusions

The combination of a sample preparation method capable of providing cleaner extracts coupled to different analytical platforms was successful in uncovering changes in metabolic pathways associated with lipids biodegradation, changes in the TCA cycle, amino acids, and enzyme inhibitors in response to antibacterial treatment.

     

Effects of Ethanolic Extract of Cynara cardunculus (Artichoke) Leaves on Neuroinflammatory and Neurochemical Parameters in a Diet-Induced Mice Obesity Model

Neurochemical Research - This study aimed to evaluate the effect of Cynara cardunculus leaf ethanol extract on inflammatory and oxidative stress parameters in the hypothalamus, prefrontal cortex,...     

Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana

Species-level genetic diversity and recombination in bacterial pathogens of wild plant populations have been nearly unexplored. Pseudomonas viridiflava is a common natural bacterial pathogen of Arabidopsis thaliana, for which pathogen defense genes and mechanisms are becoming increasing well known. The genetic variation contained within a worldwide sample of P. viridiflava collected from wild populations of A. thaliana was investigated using five genomic sequence fragments totaling 2.3 kb. Two distinct and deeply diverged clades were found within the P. viridiflava sample and in close proximity in multiple populations, each genetically diverse with synonymous variation as high as 9.3% in one of these clades. Within clades, there is evidence of frequent recombination within and between each sequenced locus and little geographic differentiation. Isolates from both clades were also found in a small sample of other herbaceous species in Midwest populations, indicating a possibly broad host range for P. viridiflava. The high levels of genetic variation and recombination together with a lack of geographic differentiation in this pathogen distinguish it from other bacterial plant pathogens for which intraspecific variation has been examined.     

Nutrient limitation and morphological plasticity of the carnivorous pitcher plant Sarracenia purpurea in contrasting wetland environments

* Plasticity of leaf nutrient content and morphology, and macronutrient limitation were examined in the northern pitcher plant, Sarracenia purpurea subsp. purpurea, in relation to soil nutrient availability in an open, neutral pH fen and a shady, acidic ombrotrophic bog, over 2 yr following reciprocal transplantation of S. purpurea between the wetlands. * In both wetlands, plants were limited by nitrogen (N) but not phosphorus (P) (N content < 2% DW(-1), N : P < 14) but photosynthetic quantum yields were high (F(V)/F(M) > 0.79). Despite carnivory, leaf N content correlated with dissolved N availability to plant roots (leaf N vs , r(2) = 0.344, P < 0.0001); carnivorous N acquisition did not apparently overcome N limitation. * Following transplantation, N content and leaf morphological traits changed in new leaves to become more similar to plants in the new environment, reflecting wetland nutrient availability. Changes in leaf morphology were faster when plants were transplanted from fen to bog than from bog to fen, possibly reflecting a more stressful environment in the bog. * Morphological plasticity observed in response to changes in nutrient supply to the roots in natural habitats complements previous observations of morphological changes with experimental nutrient addition to pitchers.     

The effects of geographic origin and antibiotic treatment on the gut symbiotic communities of Bactrocera oleae populations

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is the major insect pest of olive orchards (Olea europaea L.), causing extensive damages on cultivated olive crops worldwide. Due to its economic importance, it has been the target species for a variety of population control approaches including the sterile insect technique (SIT). However, the inefficiency of the current mass‐rearing techniques impedes the successful application of area‐wide integrated pest management programs with an SIT component. It has been shown that insect mass rearing and quality of sterile insects can be improved by the manipulation of the insect gut microbiota and probiotic applications. In order to exploit the gut bacteria, it is important to investigate the structure of the gut microbial community. In the current study, we characterized the gut bacterial profile of two wild olive fruit fly populations introduced in laboratory conditions using next generation sequencing of two regions of the 16S rRNA gene. We compared the microbiota profiles regarding the geographic origin of the samples. Additionally, we investigated potential changes in the gut bacteria community before and after the first exposure of the wild adult flies to artificial adult diet with and without antibiotics. Various genera – such as Erwinia, Providencia, Enterobacter, and Klebsiella – were detected for the first time in B. oleae. The most dominant species was Candidatus Erwinia dacicola Capuzzo et al. and it was not affected by the antibiotics in the artificial adult diet used in the first generation of laboratory rearing. Geographic origin affected the overall structure of the gut community of the olive fruit fly, but antibiotic treatment in the first generation did not significantly alter the gut microbiota community.     

Transferrin receptor 2: a new molecule in iron metabolism

Transferrin receptor 1 (TfR1) which mediates uptake of transferrin-bound iron, is essential for life in mammals. Recently, a close homologue of human transferrin receptor 1 was cloned and called transferrin receptor 2 (TfR2). A similar molecule has been identified in the mouse. Human transferrin receptor 2 is 45% identical with transferrin receptor 1 in the extracellular domain, but contains no iron responsive element in its mRNA and is apparently not regulated by intracellular iron concentration nor by interaction with HFE. Transferrin receptor 2, like transferrin receptor 1, binds transferrin in a pH-dependent manner (but with 25 times lower affinity) and delivers iron to cells. However, transferrin receptor 2 distribution differs from transferrin receptor 1, increasing in differentiating hepatocytes and decreasing in differentiating erythroblasts. Expression of both receptors is cell cycle dependent. Mutations in the human transferrin receptor 2 gene cause iron overload disease, suggesting it has a role in iron homeostasis.