Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies

Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria

The transcriptional landscape of age in human peripheral blood

Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the 'transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.Peer reviewe

Meal-based intake assessment tool:relative validity when determining dietary intake of Fe and Zn and selected absorption modifiers in UK men

A computer-based dietary assessment tool, the meal-based intake assessment tool (MBIAT), is described. In the current study, dietary intakes of Fe and Zn fractions (total Fe, non-haem Fe, haem Fe, meat Fe, total Zn) and dietary components that influence Fe and Zn absorption (vitamin C, phytate, Ca, grams of meat/fish/poultry, black tea equivalents, phytate:Zn molar ratio) were assessed. The relative validity of the MBIAT was determined in forty-eight UK men aged 40 years and over by comparing its results with those from weighed diet records collected over 12 d. There was good agreement between the MBIAT and the weighed diet records for median intakes of total, non-haem, haem and meat Fe, Zn, vitamin C, phytate, grams of meat/fish/poultry and phytate:Zn molar ratio. Correlations between the two methods ranged from 0.32 (for Ca) to 0.80 (for haem Fe), with 0.76 for total Fe and 0.75 for Zn. The percentage of participants classified by the MBIAT into the same/opposite weighed diet record quartiles ranged from 56/0 for Fe and 60/0 for Zn to 33/10 for Ca. The questionnaire also showed an acceptable level of agreement between repeat administrations (e.g. a correlation for total Fe of 0.74). In conclusion, the MBIAT is appropriate for assessing group dietary intakes of total Fe and Zn and their absorption modifiers in UK men aged 40 years and over

Blood loss is a stronger predictor of iron status in men than C282Y heterozygosity or diet

To determine the relative importance of HFE gene, diet, lifestyle, and blood loss characteristics for predicting iron status in a sample of men aged 40 years or over

Iron absorption in male C282Y heterozygotes

Background: The suggestion that carriers of the HFE C282Y mutation absorb nonheme iron more efficiently than do carriers of the wild type has public health implications for countries where the C282Y mutation is common and foods are fortified with iron. Objective: We investigated the effect of C282Y heterozygosity on nonheme-iron absorption from a diet high in bioavailable iron and from iron-fortified cereals. Design: The subjects were recruited from a parallel study investigating the relation between HFE mutations, habitual diet, and iron status. Iron absorption was measured in 15 wild-type carriers and 15 C282Y heterozygotes aged ≥40 y. Each subject consumed 3 meals of high iron bioavailability (labeled with Fe-57) for 2 d and 2 meals with fortified cereal products (labeled with Fe-54) for the next 3 d. Iron absorption was measured from isotope incorporation into red blood cells 14 d after the last labeled meal and was corrected for utilization of absorbed iron by means of an intravenous infusion of Fe-58. Results: Absorption of Fe-57 with the high-iron-bioavailability diet was 6.8 ± 6.8% (0.6 ± 0.6 mg/d) in the wild-type carriers and 7.6 ± 3.2% (0.7 ± 0.3 mg/d) in the C282Y heterozygotes. Absorption of Fe-54 with cereal products was 4.9 ± 2.0% (0.7 ± 0.3 mg/d) in the wild-type carriers and 5.3 ± 1.3% (0.8 ± 0.2 mg/d) in the C282Y heterozygotes. Conclusions: There was no overall significant difference between C282Y heterozygotes and wild-type men in iron absorption from either dietary nonheme iron or fortified cereal products

Immunodominant Francisella tularensis antigens identified using proteome microarray.

Stimulation of protective immune responses against intracellular pathogens is difficult to achieve using non-replicating vaccines. BALB/c mice immunized by intramuscular injection with killed Francisella tularensis (live vaccine strain) adjuvanted with preformed immune stimulating complexes admixed with CpG, were protected when systemically challenged with a highly virulent strain of F. tularensis (Schu S4). Serum from immunized mice was used to probe a whole proteome microarray in order to identify immunodominant antigens. Eleven out of the top 12 immunodominant antigens have been previously described as immunoreactive in F. tularensis. However, 31 previously unreported immunoreactive antigens were revealed using this approach. Twenty four (50%) of the ORFs on the immunodominant hit list belonged to the category of surface or membrane associated proteins compared to only 22% of the entire proteome. There were eight hypothetical protein hits and eight hits from proteins associated with different aspects of metabolism. The chip also allowed us to readily determine the IgG subclass bias, towards individual or multiple antigens, in protected and unprotected animals. These data give insight into the protective immune response and have potentially important implications for the rational design of non-living vaccines for tularemia and other intracellular pathogens

Galleria mellonella as an alternative infection model for Yersinia pseudotuberculosis

We report that larvae of the wax moth (Galleria mellonella) are susceptible to infection with the human enteropathogen Yersinia pseudotuberculosis at 37 degrees C. Confocal microscopy demonstrated that in the initial stages of infection the bacteria were taken up into haemocytes. To evaluate the utility of this model for screening Y. pseudotuberculosis mutants we constructed and tested a superoxide dismutase C (sodC) mutant. This mutant showed increased susceptibility to superoxide, a key mechanism of killing in insect haemocytes and mammalian phagocytes. It showed reduced virulence in the murine yersiniosis infection model and in contrast to the wild-type strain IP32953 was unable to kill G. mellonella. The complemented mutant regained all phenotypic properties associated with SodC, confirming the important role of this metalloenzyme in two Y. pseudotuberculosis infection models

Dietary patterns and heritability of food choice in a UK female twin cohort

To examine the contribution of genetic factors to food choice, we determined dietary patterns from food frequency questionnaires in 3262 UK female twins aged 18 to 79 years. Five distinct dietary patterns were identified (fruit and vegetable, high alcohol, traditional English, dieting, low meat) that accounted for 22% of the total variance. These patterns are similar to those found in other singleton Western populations, and were related to body mass index, smoking status, physical activity and deprivation scores. Older subjects had higher scores on the fruit and vegetable and traditional English patterns, while lower social deprivation was associated with higher scores for fruit and vegetable, and lower scores for traditional English patterns. All 5 patterns were heritable, with estimates ranging from 41% to 48%. Among individual dietary components, a strongly heritable component was identified for garlic (46%), coffee (41%), fruit and vegetable sources (49%), and red meat (39%). Our results indicate that genetic factors have an important influence in determining food choice and dietary habits in Western populations. The relatively high heritability of specific dietary components implicates taste perception as a possible target for future genetic studies