Development of a strain-specific molecular method for quantitating individual campylobacter strains in mixed populations

The identification of sites resulting in cross-contamination of poultry flocks in the abattoir and determination of the survival and persistence of campylobacters at these sites are essential for the development of intervention strategies aimed at reducing the microbial burden on poultry at retail. A novel molecule-based method, using strain- and genus-specific oligonucleotide probes, was developed to detect and enumerate specific campylobacter strains in mixed populations. Strain-specific oligonucleotide probes were designed for the short variable regions (SVR) of the flaA gene in individual Campylobacter jejuni strains. A 16S rRNA Campylobacter genus-specific probe was also used. Both types of probes were used to investigate populations of campylobacters by colony lift hybridization. The specificity and proof of principle of the method were tested using strains with closely related SVR sequences and mixtures of these strains. Colony lifts of campylobacters were hybridized sequentially with up to two labeled strain-specific probes, followed by the generic 16S rRNA probe. SVR probes were highly specific, differentiating down to 1 nucleotide in the target sequence, and were sufficiently sensitive to detect colonies of a single strain in a mixed population. The 16S rRNA probe detected all Campylobacter spp. tested but not closely related species, such as Arcobacter skirrowi and Helicobacter pullorum. Preliminary field studies demonstrated the application of this technique to target strains isolated from poultry transport crate wash tank water. This method is quantitative, sensitive, and highly specific and allows the identification and enumeration of selected strains among all of the campylobacters in environmental samples.     

Abscisic acid content at defined levels of bud dormancy and frost tolerance in two contrasting populations of Picea abies grown in a phytotron

Seedlings of a southern (Romanian) and a northern (Swedish) population of Picea abies were cultivated under continuous light and 20°C for 10 weeks. To arrest growth, induce terminal bud dormancy and promote frost tolerance the seedlings were then exposed to 16 h nights for 12 weeks, with gradually lower temperature during the last 6 weeks. Samples for estimating the abscisic acid content of the needles were taken just before the onset of the night treatment, at day 3 of the treatment, and then with one, and later 2 week, intervals. From the second week onwards (third week for frost tolerance) bud dormancy and frost tolerance were assessed at the same time as abscisic acid (ABA) determinations. Phosphate-buffered saline extracts were purified on mini-columns (in some cases immunoaffinity colums) and quantified by HPLC. The degree of dormancy was estimated by transferring the seedlings to growth conditions and determining the number of days until growth was resumed. The frost tolerance of the needles exposed to –10°C and –20°C was classified in 6 classes. The frost tolerance of the terminal buds was estimated as the number of seedlings that showed some growth after 6 weeks in growth conditions. The night treatment rapidly induced terminal bud dormancy in both populations, but the release of dormancy occurred earlier in the northern population. The needles and the terminal buds became highly frost tolerant more rapidly in the northern than in the southern population and before the temperature decrease. The degree of dormancy began to decline before full frost tolerance was obtained in the southern population and this decline continued in both populations, while frost tolerance remained at a high level. The southern population showed a transient peak in ABA content at day 3. Although the ABA content of the northern population was lower than in the southern before the 16-h night treatment, it increased in the northern population during the treatment period, in particular after the temperature decrease.     

Clustering and canonical correspondence analysis of phytoplankton and environmental variables in Swedish lakes

Phytoplankton data consisting of 145 species from a limnological study of lakes from relatively undisturbed areas throughout Sweden were analysed in relation to 11 physical and chemical environmental variables. Three multivariate methods were applied: WPGMA clustering and TWINSPAN for classification, and detrended canonical correspondence analysis (DCCA), a recent technique which extracts ordination axes that can be related directly to variation in the environment. Three types of lakes were recognized consistently: acid humic lakes with Gonyostomum semen as the dominant species, very acid impoverished lakes with rather few, stress-tolerant species, and subarctic lakes with low total biomass but with a varied phytoplankton flora. DCCA allowed a straightforward display of the locations of lakes and species along environmental gradients (including the acidification gradient) reflected in phytoplankton composition. It is suggested that such analyses may be a useful tool for the early detection of environmental change.     

Chlorophyll Formation in Excised Roots of Cucumber and Pea

The effects of red and blue light on the formation of chlorophyll in excised roots of cucumber and pea was investigated and compared with previously reported experiments on wheat roots. All three kinds of roots are similar in that in continuous red light no or very little chlorophyll is formed. and in blue light a considerable amount of chlorophyll is produced. Roots of cucumber and pea differ from those of wheat, in that red light is ineffective (or nearly so) even when combined with blue.     

Molecular tracking, through processing, of Campylobacter strains colonizing broiler flocks

Many of the poultry flocks produced in the United Kingdom are colonized with Campylobacter, and the intensive nature of poultry processing usually results in contaminated carcasses. In this study, a previously reported molecular oligonucleotide probe method was used to track a specific flock-colonizing strain(s) on broiler carcasses during processing in two United Kingdom commercial poultry processing plants. Five Campylobacter-positive flocks were sampled at four points along the processing line, postbleed, postpluck, prechill, and postchill, and two Campylobacter-negative flocks processed immediately after positive flocks were sampled prechill. flaA was sequenced from Campylobacter strains isolated from these flocks, and strain-specific probes were synthesized. Skin and cecal samples were plated onto selective agar to give individual colonies, which were transferred onto membranes. These were then hybridized with the strain- and genus-specific probes. For all the 5 positive flocks, there was a significant reduction in campylobacters postbleed compared to postpluck but no subsequent fall on sampling pre- and postchill, and the strain(s) predominating on the carcasses throughout processing came from the flock being processed. This indicates that strains from the abattoir environment were not a significant cause of carcass contamination in flocks with well-established campylobacter colonization. However, negative flocks that were preceded by positive flocks were contaminated by strains that did not generally originate from the predominating strains recovered from the ceca of the previous positive flocks. This suggests that the abattoir environment has a significant role in the contamination of carcasses from negative but not fully colonized flocks.     

CHK1 activity is required for continuous replication fork elongation but not stabilization of post-replicative gaps after UV irradiation

Ultraviolet (UV)-induced DNA damage causes an efficient block of elongating replication forks. The checkpoint kinase, CHK1 has been shown to stabilize replication forks following hydroxyurea treatment. Therefore, we wanted to test if the increased UV sensitivity caused by the unspecific kinase inhibitor caffeine-inhibiting ATM and ATR amongst other kinases-is explained by inability to activate the CHK1 kinase to stabilize replicative structures. For this, we used cells deficient in polymerase η (Polη), a translesion synthesis polymerase capable of properly bypassing the UV-induced cis-syn TT pyrimidine dimer, which blocks replication. These cells accumulate gaps behind progressing replication forks after UV exposure. We demonstrate that both caffeine and CHK1 inhibition, equally retards continuous replication fork elongation after UV treatment. Interestingly, we found more pronounced UV-sensitization by caffeine than with the CHK1 inhibitor in clonogenic survival experiments. Furthermore, we demonstrate an increased collapse of replicative structures after caffeine treatment, but not after CHK1 inhibition, in UV-irradiated cells. This demonstrates that CHK1 activity is not required for stabilization of gaps induced during replication of UV-damaged DNA. These data suggest that elongation and stabilization of replicative structures at UV-induced DNA damage are distinct mechanisms, and that CHK1 is only involved in replication elongation.     

Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe

Background

Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations.

Principal Findings

In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (F_ST = 0.0040, p<10⁻⁴), also between Eastern and Western Finland (F_ST = 0.0032, p<10⁻³). The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population.

Significance

Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.     

Specific N-terminal CGRP fragments mitigate chronic hypoxic pulmonary hypertension in rats

Chronic hypoxic pulmonary hypertension (HPH) is characterized by elevated pulmonary arterial pressure (P(PA)), right ventricular hypertrophy (RVH), pulmonary vascular remodeling, pulmonary edema and polycythemia. Currently, there is no safe and effective treatment for HPH. Calcitonin gene-related peptide (CGRP) is the most potent peptide vasodilator discovered thus far. We previously demonstrated that exogenous CGRP reversed HPH in rats. However, the CGRP1 receptor antagonist CGRP(8-37) and smaller inhibitory C-terminal CGRP fragments that can be formed by enzymatic cleavage in vivo may compromise the beneficial effects of endogenous or exogenous CGRP. We here examine the agonistic efficacy of N-terminal rat alpha-CGRP peptides containing the disulfide bridge (Cys(2)-Cys(7)) with amidated C-terminal in prevention of HPH. Chronic infusion of CGRP(1-8), CGRP(1-13), or CGRP(1-14) at 7 nmol/h/rat via the right jugular vein during 14 days of hypobaric hypoxia (10% inspired O(2)) significantly decreased the P(PA), RVH and pulmonary arterial medial thickness in comparison with controls, suggesting that these CGRP sequences can mitigate chronic HPH in rats. Systemic pressure was unchanged by infused peptides indicating no carry-over effect. In conclusion, N-terminal CGRP fragments (CGRP(1-8), CGRP(1-13) and CGRP(1-14)) may have a protective role in hypoxic pulmonary hypertension.     

Cutting edge: CD83 regulates the development of cellular immunity

We recently found that human CD83, a marker of mature dendritic cells, is an adhesion receptor that binds to resting monocytes and a subset of activated CD8(+) T cells. We injected CD83-Ig into mice transplanted with the immunogenic P815 mastocytoma and showed that it significantly enhanced the rate of tumor growth and inhibited the development of cytotoxic T cells. In contrast, mice immunized with CD83-transfected K1735 cells, a poorly immunogenic melanoma, could prevent the outgrowth of wild-type K1735 cells. Studies performed in vitro with human PBL showed that coimmobilized CD83-Ig and anti-CD3 enhanced T cell proliferation and increased the proportion of CD8(+) T cells. CD83-transfected B-lymphoblastoid T51 cells stimulated T cell proliferation more effectively than untransfected T51 cells in MLR cultures and increased the generation of cytolytic T cells. We conclude that CD83 is a functionally important receptor that can regulate the development of cellular immunity by interacting with its ligand(s).