Quantifying individual specialization using tracking data: a case study on two species of albatrosses.

Many predictive models of spatial and temporal distribution (e.g. in response to climate change or species introductions) assume that species have one environmental niche that applies to all individuals. However, there is growing evidence that individuals can have environmental preferences that are narrower than the species niche. Such individual specialization has mainly been studied in terms of dietary niches, but a recent increase in the availability of individual movement data opens the possibility of extending these analyses to specialisation in environmental preferences. Yet, no study to date on individual specialisation has considered the environmental niche in its multidimensionality. Here we propose a new method for quantifying individual specialisation in multiple dimensions simultaneously. We compare the hypervolumes in n-dimensional environmental niche space of each individual against that of the population, testing for significant differences against a null model. The same method can be applied to a 2-dimensional geographic space to test for site fidelity. We applied this method to test for individual environmental specialisation (across three dimensions: sea surface temperature, eddy kinetic energy, depth) and for site fidelity among satellite-tracked black-browed albatrosses (Thalassarche melanophris) and grey-headed albatrosses (Thalassarche chrysostoma), during chick-rearing at South Georgia. We found evidence for site fidelity in both species and of environmental specialisation among individual grey-headed but not black-browed albatrosses. Specialisation can affect the resilience of populations affected by natural and anthropogenic changes in the environment, and hence has implications for population dynamics and conservation.

Selenazolidine: a selenium containing proline surrogate in peptide science.

In the search for new peptide ligands containing selenium in their sequences, we investigated l-4-selenazolidine-carboxylic acid (selenazolidine, Sez) as a proline analog with the chalcogen atom in the γ-position of the ring. In contrast to proteinogenic selenocysteine (Sec) and selenomethionine (SeMet), the incorporation within a peptide sequence of such a non-natural amino acid has never been studied. There is thus a great interest in increasing the possibility of selenium insertion within peptides, especially for sequences that do not possess a sulfur containing amino acid (Cys or Met), by offering other selenated residues suitable for peptide synthesis protocols. Herein, we have evaluated selenazolidine in Boc/Bzl and Fmoc/tBu strategies through the synthesis of a model tripeptide, both in solution and on a solid support. Special attention was paid to the stability of the Sez residue in basic conditions. Thus, generic protocols have been optimized to synthesize Sez-containing peptides, through the use of an Fmoc-Xxx-Sez-OH dipeptide unit. As an example, a new analog of the vasopressin receptor-1A antagonist was prepared, in which Pro was replaced with Sez [3-(4-hydroxyphenyl)-propionyl-d-Tyr(Me)-Phe-Gln-Asn-Arg-Sez-Arg-NH2]. Both proline and such pseudo-proline containing peptides exhibited similar pharmacological properties and endopeptidase stabilities indicating that the presence of the selenium atom has minimal functional effects. Taking into account the straightforward handling of Sez as a dipeptide building block in a conventional Fmoc/tBu SPPS strategy, this result suggested a wide range of potential uses of the Sez amino acid in peptide chemistry, for instance as a viable proline surrogate as well as a selenium probe, complementary to Sec and SeMet, for NMR and mass spectrometry analytical purposes.

Evaluation of collected outcome measures in axial spondyloarthritis in daily-care rheumatology settings: the experience of the RHEVER network.

OBJECTIVES: Nowadays, the recommended measures for optimal monitoring of axial Spondyloarthritis (ax-SpA) disease activity are either BASDAI and CRP, or ASDAS-CRP. However, there could be a gap between recommendations and daily practice. We aimed to determine the measures collected by rheumatologists in an ax-SpA follow-up visit, and to determine the impact of a meeting (where rheumatologists reached a consensus on the measures to be collected) on the collection of such measures. METHODS: A consensual meeting of a local network of 32 rheumatologists proposed, four months later, to report at least the BASDAI score in the medical file of every ax-SpA patient at every follow-up visit. An independent investigator reviewed the medical files of 10 consecutive patients per rheumatologist, seen twice during the year (e.g. before and after the meeting). The most frequently collected measures were assessed, and then, the frequency of collection before and after the meeting was compared. RESULTS: A total of 456 medical files from 228 patients were reviewed. Treatment (>60%), CRP (51.3%) and total BASDAI (28.5%) were the most reported measures in medical files. Before/After the meeting, the frequencies of collected measures in medical files were 28.5%/51.7%, 51.3%/52.2%, 16.7%/31.6% and 0.9%/6.1% for BASDAI, CRP, BASDAI + CRP and ASDAS, respectively reaching a statistically significance for BASDAI, ASDAS and BASDAI+CRP (p<0.05). CONCLUSIONS: This study revealed a low rate of systematic report of the recommended outcome measures in ax-SpA. However, it suggests that a consensual meeting involving practicing rheumatologists might be relevant to improve the implementation of such recommendations.

Challenges of cardiovascular risk assessment in the routine rheumatology outpatient setting: an observational study of 110 rheumatoid arthritis patients.

OBJECTIVE: An annual assessment of cardiovascular (CV) risk factors in rheumatoid arthritis (RA) is recommended, but its practical modalities have not been determined. The objective was to assess the feasibility and usefulness of a standardized CV risk assessment in RA, performed by rheumatologists during outpatient clinics. METHODS: We used a cross-sectional design within a network of rheumatologists. Each rheumatologist included 5 consecutive unselected patients with definite RA. Data collection included standardized assessment of CV risk factors: blood pressure, interpretation of glycemia and of lipid levels, and calculation of the Framingham CV risk score. Outcome criteria included feasibility (missing data and time taken to assess the patients) and usefulness (the CV risk assessment was considered useful if at least 1 modifiable and previously unknown CV risk factor was evidenced). RESULTS: Twenty-two rheumatologists (77% in office-based practice) assessed 110 RA patients. The mean ± SD age was 57 ± 10 years, and the mean ± SD RA duration was 11 ± 9 years; 50 patients (45%) were treated with biologic agents, and 76% were women. Regarding feasibility, missing data were most frequent for glycemia (27% of patients) and cholesterolemia (14% of patients). The mean ± SD duration of the CV risk assessment was 15 ± 5 minutes. The CV risk assessment was considered useful in 33 patients (30%), evidencing dyslipidemia (15% of patients) or high blood pressure (9% of patients) as the most frequently previously unknown CV risk factor. CONCLUSION: The assessment of CV risk factors is feasible, but labor intensive, during an outpatient rheumatology clinic. This assessment identified modifiable CV risk factors in 30% of the patients. These results suggest that RA patients are not sufficiently assessed and treated for CV risk factors.

Factors associated with severe skin infections in patients treated with biologic therapies for inflammatory rheumatic diseases.

BACKGROUND: The incidence of severe infections is increased under biologic therapies and the skin is the second localization. OBJECTIVE: To appraise the factors associated with severe skin infections (SSI) in patients under biologic therapies for inflammatory rheumatic diseases (IRD). METHODS: We performed a case-control (ratio 1:3) study nested in a prospective cohort of patients with IRD. SSI was defined as requiring hospitalization or intravenous anti-infectious therapy. We defined two imbedded periods: period A was the time window between the first biologic therapy and the SSI; period B was the last 3 or 12 months (for tumor necrosis factor blockers or rituximab, respectively) before the SSI. RESULTS: Among 4,361 patients with IRD, 29 had a SSI under biologic therapy. In multivariate analyses, SSI were significantly associated with smoking, baseline C-reactive protein and gammaglobulinemia, non-steroidal anti-inflammatory drugs before biologic therapy, cumulative dose of steroids, concomitant steroids during period A, number of different biologic therapies during period A, treatment with infliximab during period A, period B or as first biologic therapy and treatment at high dose during period B. CONCLUSION: In patients under biologic therapies for IRD, the risk of SSI is associated with several factors including tobacco, treatment with infliximab or high dose range.

Non-pathogenic Actinobacillus isolates antigenically and biochemically similar to Actinobacillus pleuropneumoniae: a novel species?

Two unusual Actinobacillus isolates were recovered from pigs with no clinical signs, no lesions and no history of swine pleuropneumonia. Two representative strains (9953L55 and 0347) analyzed in this study were initially biochemically and antigenically identified as A. pleuropneumoniae serotypes 1 and 9, respectively, by traditional identification methods. Both strains presented, however, negative results with three A. pleuropneumoniae-specific PCR tests and revealed in particular the absence of the apxIV toxin genes. However, both strains produced and secreted ApxII toxin although they only harbored the toxin genes apxIICA, which is an uncommon feature for any of the known A. pleuropneumoniae serotypes. Upon experimental inoculation of pigs, these strains proved to be totally non-pathogenic. Animals infected with one of the strains produced antibodies that cross-react with A. pleuropneumoniae serotypes 1-9-11-specific LC-LPS ELISA. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that these strains form a separate phylogenetic group that is distinct from other Actinobacillus species and is particularly different from A. pleuropneumoniae.

Antibody response to an autogenous vaccine and serologic profile for Streptococcus suis capsular type 1/2.

An autogenous vaccine was developed, using sonicated bacteria, with a strain of Streptococcus suis capsular type 1/2. The objectives of this study were to evaluate the antibody response following vaccination and to assess the changes in antibody levels in pigs from a herd showing clinical signs of S. suis capsular type 1/2 infection in 6- to 8-week-old pigs. An enzyme-linked immunosorbent assay using the vaccine antigen was standardized. Results from a preliminary study involving 2 control and 4 vaccinated 4-week-old pigs indicated that all vaccinated pigs produced antibodies against 2 proteins of 34 and 43 kDa, respectively, and, in 3 out of 4 vaccinated pigs, against the 117-kDa muramidase-released protein. For the serologic profile, groups of 30 pigs from the infected herd were blood sampled at 2, 4, 6, 8, and 10 weeks of age. The lowest antibody level was observed between weeks 6 and 8, presumably corresponding to a decrease in maternal immunity. A marked increase was seen at 10 weeks of age, shortly after the onset of clinical signs in the herd. For the vaccination field trial, newly weaned, one-week-old piglets were divided into 2 groups of 200 piglets each (control and vaccinated); blood samples were collected from 36 piglets in each group at 2-week intervals for 12 weeks. A significant increase (P < 0.05) in antibody response was observed 4 weeks following vaccination and the level of antibodies stayed high until the end of the experiment. In the control group, the increase was only observed at 13 weeks of age, probably in response to a natural infection. The response to the vaccine varied considerably among pigs and was attributed, in part, to the levels of maternal antibodies at the time of vaccination. No outbreak of S. suis was observed in the control or vaccinated groups, so the protection conferred by the vaccine could not be evaluated.

Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.

We used molecular modeling to study the optimal conformation of the complex between two p53 DNA-binding domain monomers and a 12 base-pair target DNA sequence. The complex was constructed using experimental data on the monomer binding conformation and a new approach to deform the target DNA sequence. Combined with an internal/helicoidal coordinate model of DNA, this approach enables us to bend the target sequence in a controlled way while respecting the contacts formed with each p53 monomer. The results show that the dimeric complex favors DNA bending towards the major groove at the dimer junction by a value close to experimental findings. In contrast to inferences from earlier models, the calculation of key contributions to the free energy of the complexes indicates a determinant role for DNA in the formation of the complex with the dimer of the p53 DNA-binding domains.

Atypical Actinobacillus pleuropneumoniae isolates that share antigenic determinants with both serotypes 1 and 7.

In the present study, the characterization of 3 atypical isolates of Actinobacillus pleuropneumoniae is presented. Two isolates (1B and 27E) showed positive reactions in coagglutination, immunodiffusion, and indirect hemagglutination tests for serotypes 1 and 7, whereas the third isolate (26B) reacted with antisera to serotypes 1, 4, and 7. These atypical isolates of A. pleuropneumoniae possessed a capsular polysaccharide (CPS) antigenically related to serotype 1 as well as an O-chain lipopolysaccharide antigenically related to serotype 7 or to serotypes 4 and 7, as shown by the use of monoclonal antibodies. Results of toxin profile and virulence assays for mice and pigs showed them to be more related to A. pleuropneumoniae serotype 7 field isolates. All 3 isolates induced antibodies mainly against serotype 7/4 O-long-chain lipopolysaccharide (LC-LPS) and, to a lesser extent, to the CPS of serotype 1, in experimentally infected pigs. Diagnostic laboratories that use a LC-LPS-based enzyme-linked immunosorbent assay (ELISA) for serodiagnosis of A. pleuropneumoniae infection in swine would probably diagnose herds infected with these atypical isolates as being infected by A. pleuropneumoniae serotypes 7 or 4, whereas those that use a CPS-based ELISA would probably consider them as infected by A. pleuropneumoniae serotype 1.

Specific expression of matrix metalloproteinases 1, 3, 9 and 13 associated with invasiveness of breast cancer cells in vitro.

Several matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) were studied in highly invasive (MDA-MB-231) and slightly invasive (MCF-7, T47D, BT-20) breast cancer cell lines. Investigations were carried out at the protein level and/or at the mRNA level, either in cells cultured as monolayers on plastic, or in cells seeded on a thin layer of Matrigel basement membrane matrix. Analysis of MMP expression by RT-PCR showed expression of MMP-1. MMP-3, and MMP-13 in highly invasive MDA-MB-231 cells, but not in slightly invasive cell lines. The extracellular secretion of MMP-1 and MMP-3 by MDA-MB 231 cells could be also shown by ELISA. TIMP-1 and TIMP-2 mRNAs were found in all cell lines, however, the extracellular secretion of both TIMPs was much higher in MDA-MB-231 cells than in the other cell lines. When the cells were cultured on Matrigel matrix, MMP-9 expression was induced in MDA-MB-231 cells only, as assessed by RT-PCR and zymography experiments. The invasive potential of MDA-MB-231 cells evaluated in vitro through Matrigel was significantly inhibited by the MMP inhibitor BB-2516, by 25% and 50% at the concentrations of 2 x 10(-6) M and 10(-5) M, respectively. In conclusion, our data show that highly invasive MDA-MB-231 cells but not slightly invasive T47D, MCF-7 and BT-20 cells express MMP-1, MMP-3, MMP-9 and MMP-13. MMP-9 which is specifically up-regulated by cell contact to Matrigel, may play a key role in the invasiveness of MDA-MB-231 cells through basement membranes.

Identification of Actinobacillus pleuropneumoniae strains of serotypes 7 and 4 using monoclonal antibodies: demonstration of common LPS O-chain epitopes with Actinobacillus lignieresii.

Monoclonal antibodies (Mabs) against Actinobacillus pleuropneumoniae serotype 7 were produced and characterized. Three Mabs directed against surface polysaccharides were selected. One of the Mabs was directed against a capsular polysaccharide epitope (CPS) of A. pleuropneumoniae serotype 7 whereas two other Mabs reacted with different epitopes of the LPS O-chain. One of the latter reacted with the reference strain of serotype 7 and the other one with serotypes 7 and 4. These three Mabs were used to test, by Dot-ELISA, 508 field strains of A. pleuropneumoniae. None of the strains belonging to other serotypes different from serotypes 4 and 7 were positive with the Mabs. Used in combination, the CPS and one of the LPS O-chain directed Mabs were shown to be suitable for serotyping since they detected 100% of serotype 7 strains. In this study, we confirm for the first time that A. pleuropneumoniae serotype 4 is present in North America. Finally, both O-chain specific Mabs also reacted with the O-chain of Actinobacillus lignieresii. The cross-reactivity between the two species was confirmed using sera from pigs experimentally infected with A. pleuropneumoniae serotype 7 and A. lignieresii, using immunoblotting and ELISA. This is the first report of a specific cross-reactivity between the LPS of these bacterial species.

Modeling DNA deformations induced by minor groove binding proteins.

Molecular modeling is used to demonstrate that the major structural deformations of DNA caused by four different minor groove binding proteins, TBP, SRY, LEF-1, and PurR, can all be mimicked by stretching the double helix between two 3'-phosphate groups flanking the binding region. This deformation reproduces the widening of the minor groove and the overall bending and unwinding of DNA caused by protein binding. It also reproduces the principal kinks associated with partially intercalated amino acid side chains, observed with such interactions. In addition, when protein binding involves a local transition to an A-like conformation, phosphate neutralization, via the formation of protein-DNA salt bridges, appears to favor the resulting deformation.

Modelling DNA stretching for physics and biology.

We have used internal coordinate molecular mechanics calculations to study how the DNA double helix deforms upon stretching. Results obtained for polymeric DNA under helical symmetry constraints suggest that two distinct forms, an unwound ribbon and a narrow fibre, can be formed as a function of which ends of the duplex are pulled. Similar results are also obtained with DNA oligomers. These experiments lead to force curves which exhibit a plateau as the conformational transition occurs. This behaviour is confirmed by applying an increasing force to DNA and observing a sudden length increase at a critical force value. It is finally shown some DNA binding proteins can also stretch DNA locally, to conformations related to those created by nanomanipulation.

Production of virulence-related proteins by Canadian strains of Streptococcus suis capsular type 2.

The production of muramidase-released protein (MRP), extracellular protein factor (EF) and hemolysin (suilysin) by 101 Canadian field strains of Streptococcus suis capsular type 2 is described. Most strains (72%) isolated from diseased pigs were MRP-EF- and only 1 strain was MRP+EF+. This strain was also the only 1 to produce the hemolysin. Thirteen strains (15%) were MRP+ EF- and only 3 strains were MRP* EF-. All the strains isolated from clinically healthy pigs as well as a bovine and 2 human isolates had a MRP-EF- phenotype. In addition, 7 strains (8%) had a MRPS phenotype, which had so far been described for S. suis capsular type 1. In conclusion, most Canadian field isolates of S. suis capsular type 2 tested in this study do not produce the virulence-related proteins described so far for this bacterial pathogen.

Modeling the mechanics of a DNA oligomer.

DNA stretching and strand separation have been studied by molecular mechanics using an oligomer which has been the subject of nanomanipulation experiments (Noy et al., Chem. Biol. 4, 519, 1997). Adiabatic mapping of conformational energy carried out as a function of stretching leads to force/extension curves in good correlation with the experimental results. Other types of deformation are also modeled and compared with the experimental results obtained on polymeric DNA. The results highlight overall similarities, but point to thermodynamic differences and also to local base sequence effects which can be expected to play an important role at the level of biologically induced structural deformations.

Unusual DNA conformations.

DNA is on the move across conformational space. Duplexes diversity and, joined by triplexes, quadruplexes, loops, bulges and multiarmed junctions, open the route to a bewildering array of increasingly complex conformations. In addition to this structural growth, DNA has come under increasing scrutiny thanks to the development of chemical and physical techniques for deforming its conformation and probing its properties. These investigations help us to learn more about the mechanics and the activity of this remarkably versatile macromolecule.