Comparisons between Geographically Diverse Samples of Carried Staphylococcus aureus

Approximately one-third of the human population is asymptomatically colonized by Staphylococcus aureus. However, much of the global diversity within the carriage populations remains uncharacterized, and it is unclear to what degree the variation is geographically partitioned. We isolated 300 carriage isolates from 1,531 adults contemporaneously in four countries: France, Algeria, Moldova, and Cambodia. All strains were characterized by multilocus sequence typing. Six clonal complexes (CCs) were present in all four samples (CC30, -45, -121, -15, -5, and -8). Analyses based on the genotype frequencies revealed the French and Algerian samples to be most similar and the Cambodian sample to be most distinct. While this pattern is consistent with likely rates of human migration and geographic distance, stochastic clonal expansion also contributes to regional differences. Phylogenetic analysis revealed a highly divergent and uncharacterized genotype (ST1223) within Cambodia. This lineage is related to CC75, which has previously been observed only in remote aboriginal populations in northern Australia.Although better known as an important human pathogen, Staphylococcus aureus is typically a commensal species and asymptomatically colonizes approximately one-third of the human population globally (18, 20, 29). This high carriage rate potentially represents a vast reservoir of as-yet-uncharacterized S. aureus diversity, an appreciation of which should shed light on the forces underpinning the diversification and dissemination of S. aureus. There are comparatively few studies examining spatial or temporal genotype distributions within carriage populations, and the extent of biogeographical structure is currently unclear, as is the level of discrimination which might be required to detect such structure.Multilocus sequence typing (MLST) has proved to be very successful as an epidemiological tool in that it delimits S. aureus in to a small number of widespread and discrete clonal complexes (CCs) (6, 8). These can be readily identified as clusters of related genotypes which have diversified radially from “founder” genotypes (9), and because this organism is largely clonal (8), assignments of isolates to these groups is broadly robust to the many different typing methods employed (4, 10, 27). The high level of divergence between these lineages suggests that they are relatively ancient and temporally stable (7), and it is possible that isolated host populations may have been colonized by different S. aureus lineages in the past. However, any footprints of geographical partitioning are likely to have been compromised by high rates of migration in recent times, due largely to the advent of air travel.Previous studies addressing the characterization of carried populations have tended to focus on samples from Western Europe or North America, and these have generally not provided strong evidence for geographical structuring. In a recent study using amplified fragment length polymorphism to compare the carried populations in Holland and North America, the authors noted considerable overlap between the samples, suggesting that they effectively constituted a single unstructured population (17). Similarly, independent MLST studies have revealed regional consistencies in Europe, such as the predominance of CC30 in the United Kingdom (8), Ireland (3), and Switzerland (25). Given the high rates of admixture within Europe and North America, the absence of obvious geographical structuring in the carried S. aureus population in these regions is perhaps not very surprising.Although they are currently scarce, current data from carriage populations outside of Europe or North America point to greater geographical structuring. For example, a sample of carried S. aureus recovered from Bamako, Mali, has recently been characterized, constituting the first such study of an African population (23). Although many of the previously characterized CCs were also present in this sample, the authors noted a high frequency (∼25%) of a single genotype, ST152, which is phylogenetically divergent and noted very rarely in Europe. The high frequency of ST152 in this population raises the possibility that this genotype is endemic to the Malian population and possibly elsewhere in sub-Saharan Africa. This in turn hints at greater geographical partitioning on a global scale, although more representative samples are clearly required. To address this, we generated MLST data from contemporaneous carriage samples recovered from four countries representing three continents: France (Western Europe), Moldova (Eastern Europe), Algeria (North Africa), and Cambodia (Southeast Asia). To our knowledge, this is the first time such a study has been carried out on samples from Eastern Europe, North Africa, or Southeast Asia. These data were therefore generated to uncover diversity within the global carriage population but also to understand further the extent to which geographical distance and host migration can explain regional differences.     

Improvement of an RNA purification method for grapevine (Vitis vinifera L.) suitable for cDNA library construction

A method is described, which consistently yields high quality total RNA from grapevine. Dissolving of crude RNA pellets in borate-containing buffer, instead of normally used water before a selective lithium chloride precipitation, was found to be a critical step, leading to a 2.5-fold increase of yield. The resulting RNA preparations were suitable for standard downstream applications and also for cDNA library construction. The method worked efficiently and reproducibly and could easily be scaled from milligram to gram quantities of plant material grown in hydroponic culture, sandy soil or Perlite. It was applied to different kinds of grapevine tissues (leaves, stem) and, after additional adaptation of the protocol, to roots.     

Serologic Detection of Coccidioidomycosis Antibodies in Northeast Brazil

Coccidioidomycosis is a systemic infection caused by Coccidioides spp. The disease is endemic in Brazil but its incidence is underreported as it is not a notifiable disease. This article presents the results of a serologic survey carried out with 229 volunteers in northeast Brazil by the immunodiffusion (ID) test with commercial Coccidioides spp. antigens. The commercial ID test detected 15 individuals without clinical diagnosis of the disease and two individuals in treatment for coccidioidomycosis. Regarding the epidemiological data, most of the positive individuals were male, between 18 and 65 years of age and were engaged in armadillo hunting. Three women who had never participated in armadillo hunts also displayed positive results for coccidioidal antibodies. Besides armadillo hunts, exposure to environmental dust in endemic areas may account for the serologic response detected in the study. The data from this study suggest the importance of performing epidemiological surveys for coccidioidomycosis in order to understand the prevalence of this disease in Brazil.     

Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin

ABSTRACT: BACKGROUND: Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. RESULTS: According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. CONCLUSIONS: A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.     

Pharmacokinetics, immunogenicity and anticancer efficiency of Aspergillus flavipesl-methioninase

Methionine starvation can powerfully modulate DNA methylation, cell cycle transition, polyamines and antioxidant synthesis of tumor cells, in contrary to normal ones. Aspergillus flavipesl-methioninase was previously characterized by our studies, displaying affordable biochemical properties comparing to Pseudomonas putida enzyme (ONCASE). Thus, the objective of current study was to evaluate the catalytic properties of Af-METase in New Zealand rabbits, exploring its antitumor efficacy. In vivo, Af-METase (40.8U/ml) have T(1/2) 19.8h, elimination constant 0.088U/h and apparent volume distribution 85U/ml. Also, Af-METase has two maxima one at A(280nm) (apo-enzyme) and at A(420nm) (internal Schiff base of PLP), unlike control plasma (without enzyme). The two peaks of absorption spectra were detected maximally at 15min then the absorbance at 420nm was subsequently decreased with circulation time, due to dissociation of the co-enzyme. The A(280/420) ratio was increased from 1.69 to 5.81 with circulation time from 15 to 30h. Rabbits plasma methionine was depleted from 18.7μM (control) to 8.8μM after 1h of enzyme injection and completely omitted after 2h till 19h, assuming the sustainability of negligible levels of methionine (<2μM) in plasma of rabbits, for about 17h. Upon infusion of PLP, the T(1/2) of Af-METase was significantly prolonged by 3.2 fold, assuming the fully reconstitution of the enzyme. The holo-AfMETase still retained its co-enzyme, completely, till 33h of PLP infusion. From spectral studies, the internal aldimine linkage of apo-Af-METase was constructed upon PLP infusion, with fully catalytic structure after less than 4h of its infusion, the A(280/420) ratio being not relatively changed till 45h. After 25 days of last enzyme dose, the titer of IgG was increase by about 1.66 fold comparing to control (without enzyme). However, IgM was not detected along the tested challenge points. In vitro, plasma anti-Af-METase neutralizing antibodies (NAb) were assessed, with no significant reduction on activity of Af-METase by Nab. All the hematological parameters were in normal range, otherwise, the RBCs titer and platelet level was slightly increased, after 25 days of Af-METase injection, comparing to control. There is no obvious negative effect on chemistry of liver, kidney, glucose, lipids, and other electrolytes. Additionally, the anticancer activity of Af-METase was evaluated against five types of human cancer cell lines, in vitro. The enzyme showed a powerful activity against prostate (PC3), liver (HEPG2) and breast (MCF7) cancers, with IC(50) 0.001U/ml, 0.26U/ml and 0.37U/ml, respectively.     

Novel Radiolabeled Peptides for Breast and Prostate Tumor PET Imaging: (64)Cu/and (68)Ga/NOTA-PEG-[d-Tyr(6),βAla(11),Thi(13),Nle(14)]BBN(6-14)

Bombesin (BBN)-based radiolabeled peptides exhibit promising properties for targeted imaging of gastrin-releasing peptide receptors (GRPR)-positive tumors. The aim of this study was to evaluate with positron emission tomography (PET) the pharmacokinetic and imaging properties of two novel BBN-based radiolabeled peptides, (64)Cu/and (68)Ga/NOTA-PEG-BBN(6-14), for diagnosis of breast and prostate cancers using small animal models. Competitive binding assays on T47D breast and PC3 prostate cancer cells showed that the affinity for GRPR depends on the complexed metal and can vary up to a factor of about 3; (64)Cu/NOTA-PEG-BBN(6-14) was found to have the lowest inhibition constant (1.60 ± 0.59 nM). (64)Cu/and (68)Ga/NOTA-PEG-BBN(6-14) presented similar cell uptake on T47D and PC3 cells and were stable in vivo. Biodistribution studies of radiolabeled peptides carried out in Balb/c and tumor-bearing Balb/c nude mice showed that (64)Cu/NOTA-PEG-BBN(6-14) presented higher GRPR-mediated uptake in pancreas and adrenal glands, but comparable PC3 tumor uptake as (68)Ga/NOTA-PEG-BBN(6-14). Finally, receptor-dependent responses were observed during blocking studies with unlabeled peptide in both biodistribution and small-animal PET imaging studies. Our results confirmed the dependence of the affinity and pharmacokinetics of BBN-based radiopeptides on the complexed radiometal. Interspecies differences between mouse and human GRPR binding properties were also noted in these preclinical studies. Considering their good imaging characteristics, both (64)Cu/NOTA-PEG-BBN(6-14) and (68)Ga/NOTA-PEG-BBN(6-14) are promising candidates for GRPR-targeted PET imaging of breast and prostate cancers.     

Sculpting the proteome with AAA(+) proteases and disassembly machines

Machines of protein destruction-including energy-dependent proteases and disassembly chaperones of the AAA(+) ATPase family-function in all kingdoms of life to sculpt the cellular proteome, ensuring that unnecessary and dangerous proteins are eliminated and biological responses to environmental change are rapidly and properly regulated. Exciting progress has been made in understanding how AAA(+) machines recognize specific proteins as targets and then carry out ATP-dependent dismantling of the tertiary and/or quaternary structure of these molecules during the processes of protein degradation and the disassembly of macromolecular complexes.     

Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae

When the yeast Saccharomyces cerevisiae shifts from rapid growth on glucose to slow growth on ethanol, it undergoes profound changes in cellular metabolism, including the destruction of most of the translational machinery. We have examined the effect of this metabolic change, termed the diauxic shift, on the frequency of translational errors. Recoding sites are mRNA sequences that increase the frequency of translational errors, providing a convenient reporter of translational accuracy. We found that the diauxic shift causes no overall change in translational accuracy but does cause a strong reduction in the frequency of one type of programmed error: Ty +1 frameshifting. Genetic data suggest that this effect may be due to changes in the relative amounts of tRNA participating in translation elongation. We discuss possible implications for expression strategies that use recoding.