Complete nucleotide sequence of pSCV50, the virulence plasmid of Salmonella enterica serovar Choleraesuis SC-B67

We carried out comparative analysis on the sequences of two 50-kb virulence plasmids of Salmonella enterica serovar Choleraesuis strains SC-B67 (pSCV50) and RF-1 (pKDSC50). The two plasmids share over 99% sequence similarity. Ninety-two nucleotide variations at 42 sites were detected between the two plasmids; pSCV50 contains 24 nucleotide substitutions, 6 deletions, and 62 insertions, compared to pKDSC50. Two regions in pSCV50 appeared to be more susceptible to changes: one is the non-virulence-associated transfer region (27.5-33.0 K) and the other a function-unknown region (9.0-10.5 K). We re-annotated pSCV50 using more advanced tools and the up-to-date databases and corrected the inaccurate annotation in pKDSC50. The results indicate that virulence-related genes on the 50-kb plasmid are under negative selection, suggesting that they play important roles in the expression of virulence during the process of infection, while other genes in this plasmid tend to evolve neutrally.     

Dendroaspis natriuretic peptide protects the post-ischemic myocardial injury

The present study used isolated rat hearts to investigate whether (1) Dendroaspis natriuretic peptide (DNP) is protective against post-ischemic myocardial dysfunction, and (2) whether the cardioprotective effects of DNP is related to alteration of Bcl-2 family protein levels. The excised hearts of Sprague-Dawley rats were perfused on a Langendorff apparatus with Krebs-Henseleit solution with a gas mixture of 95% O2 and 5% CO2. Left ventricular end-diastolic pressure (LVEDP, mmHg), left ventricular developed pressure (LVDP, mmHg) and coronary flow (CF, ml/min) were continuously monitored. In the presence of 50 nM DNP, all hearts were perfused for a total of 100 min consisting of a 20 min pre-ischemic period followed by a 30 min global ischemia and 50 min reperfusion. Lactate dehydrogenase (LDH) activity in the effluent was measured during reperfusion. Treatment with DNP alone improved the pre-ischemic LVEDP and post-ischemic LVEDP significantly comparing with the untreated control hearts during reperfusion. However, DNP did not affect the LVDP, heart rate (HR, beats/min), and CF. Bcl-2, an anti-apoptotic protein expressed in ischemic myocardium of DNP+ischemia/reperfusion (I/R) group, was higher than that in I/R alone group. Bax, a pro-apoptotic protein expressed in ischemic myocardium of DNP+I/R group, has no significant difference compared with I/R alone group. These results suggest that the protective effects of DNP against I/R injury would be mediated, at least in part, through the increased ratio of Bcl-2 to Bax protein after ischemia-reperfusion.     

Soil Properties and their Spatial Pattern in a Degraded Sandy Grassland under Post-grazing Restoration, Inner Mongolia, Northern China

In this study, we use classical and geostatistical methods to identify characteristics of some selected soil properties including soil particle size distribution, soil organic carbon, total nitrogen, pH and electrical conductivity and their spatial variation in a 5-year recovery degraded sandy grassland after two different grazing intensity disturbance: post-heavy-grazing restoration grassland (HGR) and post-moderately grazing restoration grassland (MGR), respectively, in Horqin steppe, Inner Mongolia, northern China. The objective was to examine effect of grazing intensity on spatial heterogeneity of soil properties. One hundred soil samples were taken from the soil layer 0–15 cm in depth of a grid of 10 m×10 m under each treatment. The results showed that soil fine fractions (very fine sand, 0.1–0.05 mm and silt + clay, <0.05 mm), soil organic carbon and total nitrogen concentrations were significant lower and their coefficients of variation significant higher under the HGR than under the MGR. Geostatistical analysis of soil heterogeneity revealed that soil particle size fractions, organic carbon and total nitrogen showed different degree of spatial dependence with exponential or spherical semivariograms on the scale measured under HGR and MGR. The spatial structured variance account for a large proportion of the sample variance in HGR plot ranging from 88% to 97% for soil particle fractions, organic C and total N, however, except for organic C (88.8%), the structured variance only account for 50% of the sample variance for soil particle fractions and total N in the MGR plot. The ranges of spatial autocorrelation for coarse-fine sand, very fine sand, silt + clay, organic C and total N were 13.7 m, 15.8 m, 15.2 m, 22.2 m and 21.9 m in HGR plot, respectively, and was smaller than in MGR plot with the corresponding distance of 350 m, 144.6 m, 45.7 m, 27.3 m and 30.3 m, respectively. This suggested that overgrazing resulted in an increase in soil heterogeneity. Soil organic C and total N were associated closely with soil particle fractions, and the kriging-interpolated maps showed that the spatial distribution of soil organic C and total N corresponded to the distribution patterns of soil particle fractions, indicating that high degree of spatial heterogeneity in soil properties was linked to the distribution of vegetative and bare sand patches. The results suggested that the degree of soil heterogeneity at field scale can be used as an index for indicating the extent of grassland desertification. Also, the changes in soil heterogeneity may in turn influence vegetative succession and restoration process of degraded sandy grassland ecosystem.     

Expression of Helicobacter pylori cag12 gene in Lactococcus lactis MG1363 and its oral administration to induce systemic anti-Cag12 immune response in mice

To develop an oral vaccine against Helicobacter pylori infection, we have expressed the H. pylori cag12 (HP0532) gene, encoding the outer membrane protein Cag12 (31 kDa), in a live delivery vehicle Lactococcus lactis. The cag12 gene was amplified by polymerase chain reaction (PCR) using the genomic DNA of H. pylori K51 isolated from Korean patients. DNA sequence analysis revealed that the cag12 gene of H. pylori K51 has 98.1 and 97.4% identity with individual cag12 genes of the H. pylori 26695 and J99, respectively. The GST–Cag12 fusion protein, produced using the Escherichia coli expression system, was used to raise a rat polyclonal anti-Cag12 antibody. The PCR-amplified cag12 gene of H. pylori K51 was cloned in the E. coli–L. lactis shuttle vector (pMG36e) and transformed into L. lactis. Western blot analysis demonstrated that the Cag12 protein was expressed in the L. lactis transformant, with a maximum level at the log phase without extracelluar secretion. The oral administration of the transformant into mice resulted in the generation of the anti-Cag12 antibody in serum in two out of five cases. These results suggest that the recombinant L. lactis, which expresses Cag12, may be applicable as an oral vaccine to induce protective immunity against H. pylori.     

The effect of an acute elevation of NEFA concentrations on glucagon-stimulated hepatic glucose output

To determine the effect of nonesterified fatty acids (NEFA) on glucagon action, glucagon was infused intraportally (1.65 ng.min(-1).kg(-1)) for 3 h into 18-h-fasted, pancreatic-clamped conscious dogs in the presence [NEFA + glucagon (GGN)] or absence (GGN) of peripheral Intralipid plus heparin infusion. Additionally, hyperglycemic (HG), hyperglycemic-hyperlipidemic (NEFA + HG), and glycerol plus glucagon (GLYC + GGN) controls were studied. Arterial plasma glucagon concentrations rose equally in GGN, NEFA + GGN, and GLYC + GGN but remained basal in hyperglycemic controls. Peripheral infusions of Intralipid and heparin increased arterial plasma NEFA concentrations equally in NEFA + GGN and NEFA + HG and did not change in other protocols. After 15 min, glucagon infusion resulted in a rapid, brief increase in net hepatic glycogenolysis (NHGLY, mg.min(-1).kg(-1)) of approximately 6.0 in GGN and GLYC + GGN but only increased by 3.8 +/- 1.3 in NEFA + GGN. Thus increases in NHGLY, and consequently net hepatic glucose output (NHGO), were blunted by 40%, with no difference between the groups in the last 2.5 h of the study. NHGO and NHGLY did not significantly change in HG and NEFA + HG. Net hepatic gluconeogenic flux did not change in GGN, GLYC + GGN, or HG. However, Intralipid and heparin infusion resulted in similar increases in net hepatic gluconeogenic flux in NEFA + GGN and NEFA + HG. Thus elevated NEFA limit the initial increase in glucagon-stimulated HGO by blunting glycogenolysis, without having any effect on the gluconeogenic or glycogenolytic contributions or NHGO thereafter.     

A homologue of the breast cancer-associated gene BARD1 is involved in DNA repair in plants

hBRCA1 and hBARD1 are tumor suppressor proteins that are involved as heterodimer via ubiquitinylation in many cellular processes, such as DNA repair. Loss of BRCA1 or BARD1 results in early embryonic lethality and chromosomal instability. The Arabidopsis genome carries a BRCA1 homologue, and we were able to identify a BARD1 homologue. AtBRCA1 and the putative AtBARD1 protein are able to interact with each other as indicated by in vitro and in planta experiments. We have identified T-DNA insertion mutants for both genes, which show no visible phenotype under standard growth conditions and are fully fertile. Thus, in contrast to animals, both genes have no indispensable role during development and meiosis in plants. The two single as well as the double mutant are to a similar extent sensitive to mitomycin C, indicating an epistatic interaction in DNA crosslink repair. We could further demonstrate that in Arabidopsis BARD1 plays a prominent role in the regulation of homologous DNA repair in somatic cells.     

Estimating biomarker-based HIV incidence using prevalence data in high risk groups with missing outcomes

The novel two-step serologic sensitive/less sensitive testing algorithm for detecting recent HIV seroconversion (STARHS) provides a simple and practical method to estimate HIV-1 incidence using cross-sectional HIV seroprevalence data. STARHS has been used increasingly in epidemiologic studies. However, the uncertainty of incidence estimates using this algorithm has not been well described, especially for high risk groups or when missing data is present because a fraction of sensitive enzyme immunoassay (EIA) positive specimens are not tested by the less sensitive EIA. Ad hoc methods used in practice provide incorrect confidence limits and thus may jeopardize statistical inference. In this report, we propose maximum likelihood and Bayesian methods for correctly estimating the uncertainty in incidence estimates obtained using prevalence data with a fraction missing, and extend the methods to regression settings. Using a study of injection drug users participating in a drug detoxification program in New York city as an example, we demonstrated the impact of underestimating the uncertainty in incidence estimates using ad hoc methods. Our methods can be applied to estimate the incidence of other diseases from prevalence data using similar testing algorithms when missing data is present.     

Investigation of the Role of a Conserved Glycine Motif in the Saccharomyces cerevisiae Xylose Reductase

All yeast xylose reductases, with the exception of that from Schizosaccharomyces pombe, possess the catalytic and coenzyme-binding elements from both the aldo–keto reductase and short-chain dehydrogenase–reductase (SDR) enzyme families in their primary sequences. In the Saccharomyces cerevisiae xylose reductase (XR), the SDR-like coenzyme-binding GXXXGXG motif (Gly motif) is located between residues 128 and 134, with the third Gly residue being replaced by an Asp. We used site-directed mutagenesis to study the role of this SDR-like Gly motif in the S. cerevisiae xylose reductase. Site-directed mutagenesis of the individual conserved Gly residue positions (G128A, G132A, D134G, and D134A) did not significantly affect the specific activity, kinetic constants (K_m, K_cat, and K_cat/K_m), or dissociation constants (K_d) in any of the variants compared with the wild type. Deletion of the entire Gly motif produced an unstable protein that could not be purified. These results indicate that the SDR-like Gly motif likely provides support to the overall structure of the enzyme, but it does not contribute directly to coenzyme binding in this XR.