Distribution of "classic" virulence factors among Salmonella spp

Whether an infection with Salmonella spp. leads to a disease largely depends on the virulence of the strain and the constitution of the host. The virulence of the strain is determined by so-called virulence factors. Whereas a number of virulence factors of Salmonella have been identified only recently, others have been studied for decades. These latter virulence factors i.e., virulence-plasmids, toxins, fimbriae and flagella are therefore referred to as "classic" virulence factors. Here we present an overview on the distribution of (genes coding for) these virulence factors among Salmonella spp. The pathogenicity islands of Salmonella are also reviewed, all be it briefly, since they contain a major part of the virulence genes.     

Modelling energetic costs of fish swimming

The oxygen consumption rates of two cyprinid fishes, carp (Cyprinus carpio L.) and roach (Rutilus rutilus (L.)), were analysed for a wide range of body mass and swimming speed by computerized intermittent-flow respirometry. Bioenergetic models were derived, based on fish mass (M) and swimming speed (U), to predict the minimal speed and mass-specific active metabolic rate (AMR) in these fishes (AMR=aMbUc). Mass and speed together explained more than 90% of the variance in total swimming costs in both cases. The derived models show that carp consume far more oxygen at a specific speed and body mass, thus being less efficient in energy use during swimming than roach. It was further found that in carp (AMR=0.02M0.8U0.95) the metabolic increment during swimming is more strongly effected by speed, whereas in roach (AMR=0.02M0.93U0.6) it is more strongly effected by body mass. The different swimming traits of carp and roach are suitable for their respective lifestyles and ecological demands.     

Transient impairment of the adaptive response to fasting in FXR-deficient mice

The farnesoid X receptor (FXR) has been suggested to play a role in gluconeogenesis. To determine whether FXR modulates the response to fasting in vivo, FXR-deficient (FXR^−/−) and wild-type mice were submitted to fasting for 48 h. Our results demonstrate that FXR modulates the kinetics of alterations of glucose homeostasis during fasting, with FXR^−/− mice displaying an early, accelerated hypoglycaemia response. Basal hepatic glucose production rate was lower in FXR^−/− mice, together with a decrease in hepatic glycogen content. Moreover, hepatic PEPCK gene expression was transiently lower in FXR^−/−mice after 6 h of fasting and was decreased in FXR^−/−hepatocytes. FXR therefore plays an unexpected role in the control of fuel availability upon fasting.     

ApoC-III deficiency prevents hyperlipidemia induced by apoE overexpression

Adenovirus-mediated overexpression of human apolipoprotein E (apoE) induces hyperlipidemia by stimulating the VLDL-triglyceride (TG) production rate and inhibiting the LPL-mediated VLDL-TG hydrolysis rate. Because apoC-III is a strong inhibitor of TG hydrolysis, we questioned whether Apoc3 deficiency might prevent the hyperlipidemia induced by apoE overexpression in vivo. Injection of 2 x 10(9) plaque-forming units of AdAPOE4 caused severe combined hyperlipidemia in Apoe-/- mice [TG from 0.7 +/- 0.2 to 57.2 +/- 6.7 mM; total cholesterol (TC) from 17.4 +/- 3.7 to 29.0 +/- 4.1 mM] that was confined to VLDL/intermediate density lipoprotein-sized lipoproteins. In contrast, Apoc3 deficiency resulted in a gene dose-dependent reduction of the apoE4-associated hyperlipidemia (TG from 57.2 +/- 6.7 mM to 21.2 +/- 18.5 and 1.5 +/- 1.4 mM; TC from 29.0 +/- 4.1 to 16.4 +/- 9.8 and 2.3 +/- 1.8 mM in Apoe-/-, Apoe-/-.Apoc3+/-, and Apoe-/-.Apoc3-/- mice, respectively). In both Apoe-/- mice and Apoe-/-.Apoc3-/- mice, injection of increasing doses of AdAPOE4 resulted in up to a 10-fold increased VLDL-TG production rate. However, Apoc3 deficiency resulted in a significant increase in the uptake of TG-derived fatty acids from VLDL-like emulsion particles by white adipose tissue, indicating enhanced LPL activity. In vitro experiments showed that apoC-III is a more specific inhibitor of LPL activity than is apoE. Thus, Apoc3 deficiency can prevent apoE-induced hyperlipidemia associated with a 10-fold increased hepatic VLDL-TG production rate, most likely by alleviating the apoE-induced inhibition of VLDL-TG hydrolysis.     

Approach for defining endogenous reference genes in gene expression experiments

The quantification of gene expression by real-time polymerase chain reaction (PCR) has revolutionized the field of gene expression analysis. Due to its sensitivity and flexibility it is becoming the method of choice for many investigators. However, good normalization protocols still have to be implemented to facilitate data exchange and comparison. We have designed primers for 10 unrelated genes and developed a simple protocol to detect genes with stable expression that are suitable for use as endogenous reference genes for further use in the normalization of gene expression data obtained by real-time PCR. Using this protocol, we were able to identify human proteosome subunit Y as a reliable endogenous reference gene for human umbilical vein endothelial cells treated for up to 18 h with TNFalpha, IL-4, or IFNgamma and for B cells isolated from healthy controls and patients suffering from IgA nephropathy. Other optional endogenous reference genes that can be considered are phosphomannomutase (PPMM) and actin for endothelial cells and glyceraldehyde-3-phosphate dehydrogenase and PPMM for B cells.     

Circadian rhythms of adult emergence and activity but not eclosion in males of the parasitic wasp Nasonia vitripennis

An endogenous circadian system is responsible for the rhythms observed in many physiological and behavioural traits in most organisms. In insects, the circadian system controls the periodicity of eclosion, egg-laying, locomotor and mating activity. The parasitoid wasp Nasonia vitripennis has been extensively used to study the role of the circadian system in photoperiodism. In this study, behavioural activities expected to be under the control of the endogenous circadian system were characterized in Nasonia. Male emergence from the host puparium is rhythmic under light-darkness conditions while eclosion from the own pupal integument is not rhythmic but continuous. Following entrainment in light-dark conditions, males show robust free-running circadian activity rhythms with a period (τ, tau) of approximately 25.6 h in constant darkness. While the endogenous circadian system is enough to trigger male emergence in Nasonia, light seems to have a modulatory effect: when present it induces more males to emerge. Our results add to the understanding of chronobiological phenotypes in insects and provide a basis towards the molecular characterization of the endogenous circadian system in Nasonia.     

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

Intrinsic flexibility of DNA has hampered the development of efficient protein−DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731–1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor−DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein−DNA complexes from unbound constituents using non-structural experimental data to drive the docking.     

Indicators of erythrocyte formation and degradation in rats with either vitamin A or iron deficiency

Vitamin A deficiency produces anemia and altered iron status. In this study with rats we tested two hypotheses regarding vitamin A deficiency: (1) that it impairs erythropoiesis, leading to an increased red cell turnover, and (2) that it inhibits the glycosylation of transferrin. Erythropoietic activity was assessed indirectly by determining the myeloid:erythroid ratio in bone marrow smears, the number of erythroid colonies in the red pulp of spleen, the blood reticulocyte index, and zinc protoporphyrin and plasma transferrin receptor concentrations. Transferrin glycosylation was assessed by measuring the sialic acid content of transferrin. The effects of vitamin A deficiency were compared with those of iron deficiency. Iron deficiency produced anemia and low iron levels in organs. Vitamin A deficiency produced low levels of plasma and hepatic retinol, and it induced decreased plasma total iron-binding capacity and raised iron levels in tibia and spleen. Short- but not long-term iron deficiency reduced the number of erythroid colonies in spleen; vitamin A deficiency had no influence. Neither iron nor vitamin A deficiency influenced the myeloid:erythroid ratio in bone marrow smears and the blood reticulocyte production. Plasma transferrin receptor and erythrocyte zinc protoporphyrin concentrations were not affected by vitamin A deficiency but increased with iron deficiency. Vitamin A deficiency did not stimulate erythrocyte breakdown, as indicated by unaltered plasma lactate dehydrogenase activity and reduced plasma total bilirubin levels. Both vitamin A and iron deficiencies raised the proportion of multiple sialylated transferrins in plasma. Thus, we have not found evidence that vitamin A deficiency affects erythropoiesis and erythrocyte turnover. The iron accumulation in spleen and bone marrow may be related to reduced iron transport due to inhibition of transferrin synthesis rather than inhibition of transferrin sialylation.