Proteomics application exercise of the Swiss Proteomics Society: report of the SPS'02 session

After the success of the mass spectrometry (MS) round table that was held at the first Swiss Proteomics Society congress (SPS'01) in Geneva, the SPS has organized a proteomics application exercise and allocated a full session at the SPS'02 congress. The main objective was to encourage the exchange of expertise in protein identification, with a focus on the use of mass spectrometry, and to create a bridge between the users' questions and the instrument providers' solutions. Two samples were sent to fifteen interested labs, including academic groups and MS hardware providers. Participants were asked to identify and partially characterize the samples. They consisted of a complex mixture of peptide/proteins (sample A) and an almost pure recombinant peptide carrying post-translational modifications (sample B). Sample A was an extract of snake venom from the species Bothrops jararaca. Sample B was a recombinant and modified peptide derived from the shrimp Penaeus vannamei penaeidin 3a. The eight labs that returned results reported the use of a wide range of MS instrumentation and techniques. They mentioned a variety of time and manpower allocations. The origin of sample A was generally identified together with a number of database protein entries. The difficulty of the sample identification lay in the incomplete knowledge of the Bothrops species genome sequence and is discussed. Sample B was generally and correctly identified as penaeidin. However, only one group reported the full primary structure. Interestingly, the approaches were again varied and are discussed in the text.     

Synthesis and antimalarial activity of 2-methoxyprop-2-yl peroxides derivatives

2-Methoxyprop-2-yl peroxides were synthesized and evaluated in vitro against Plasmodium falciparum. These acyclic artemisinin-related peroxides revealed moderate to good activity but were devoid of alkylating property towards the synthetic model of heme Mn(II)-TPP.     

Respective effects of anabolic/androgenic steroids and physical exercise on isometric contractile properties of regenerating skeletal muscles in the rat

We examined the respective effects of anabolic-androgenic steroids and physical exercise on the contractile properties of regenerating fast and slow hindlimb skeletal muscles. Degeneration/regeneration of the left extensor digitorum longus muscles (EDL) and soleus of young Wistar male rats was induced by a snake venom (Notechis scutatus scutatus) injection. During muscle regeneration, experimental rats were either treated with nandrolone (NAN, nortestosterone, im, 2 mg X kg(-1) X week(-1), or endurance exercised on a treadmill (EXE, 60 min x day(-1), 10-40 m X min(-1). Twenty-one days after injury, isometric contractile properties of regenerating muscles were studied in situ. Neither the nandrolone treatment nor the physical exercise program was able to change significantly muscle contraction parameters both in twitch and tetanus in both regenerating EDL and soleus (p > 0.05). However, we observed a greater peak twitch tension in NAN versus grouped control and EXE EDL (p < 0.01). In conclusion, endurance exercise program or anabolic-androgenic steroid (nortestosterone) treatment did not significantly improve isometric contractile properties of regenerating slow and fast muscles in the male young rats.     

Critical Reexamination of Palynological Characters Used to Delimit Asclepiadaceae in Comparison to the Molecular Phylogeny Obtained from PlastidmatK Sequences

The family Asclepiadaceae (Dicotyledones) was created by Brown in 1810 by splitting in two the family Apocynaceae of Jussieu established in 1789. The morphological characters used to make this distinction were mainly palynological, such as presence of tetrads or pollinia and number and orientation of pollinia. Those characters, still used in higher taxonomic delimitation (families, subfamilies, and tribes), are here critically reexamined and compared to a molecular phylogeny obtained with one of the more variable plastid genes (matK) of 46 species in the order Gentianales. In this molecular phylogeny, Asclepiadaceae form a monophyletic group derived from within Apocynaceae. Each of the subfamilies of Asclepiadaceae is monophyletic and based on reliable palynological characters, but palynological characters are not useful to delimit tribes of the subfamily Asclepiadoideae. Based on the molecular data, these tribes have undergone parallelisms in several reproductive traits.     

Evaluation of two new commercial tests for the diagnosis of acute dengue virus infection using NS1 antigen detection in human serum

Background

We compared the performance of two new commercial tests for the detection of dengue NS1 protein during the clinical phase of dengue virus (DENV) infection—an immunochromatographic test allowing rapid detection of the NS1 antigen, Dengue NS1 Ag STRIP (Bio-Rad Laboratories - Marnes La Coquette, France), and a two-step sandwich-format microplate enzyme-linked immunosorbent assay (ELISA), pan-E Dengue Early ELISA (Panbio - Brisbane, Australia)—with a one-step sandwich-format microplate ELISA, the Platelia Dengue NS1 Ag test (Bio-Rad).

Methods

We tested 272 serum samples from patients with dengue disease. Of these, 222 were from patients with acute infection of one of the four dengue serotypes, detected by RT-PCR and/or virus isolation. Forty-eight acute-phase serum samples from patients not infected with dengue virus were also included.

Results

The sensitivity of the Platelia Dengue NS1 Ag test on acute serum samples (n = 222) was 87.4% (95% confidence interval: 82.3% to 91.5%); that of Dengue NS1 Ag STRIP was 81.5% (95% CI: 75.8% to 86.4%) after 15 minutes and 82.4% (95% CI: 76.8% to 87.2%) after 30 minutes. Both tests had a specificity of 100% (97.5% CI, one-sided test: 92.6% to 100.0%). The pan-E Dengue Early ELISA had a sensitivity of 60.4% (95% CI: 53.4% to 66.8%) and a specificity of 97.9% (95% CI: 88.9% to 99.9%).

Conclusion

Our findings support the use of diagnostic tools based on the NS1 antigen detection for the diagnosis of acute DENV infection. The immunochromatographic test, Dengue NS1 Ag STRIP—the first rapid diagnostic test for DENV infection—was highly sensitive and specific, and would therefore be a suitable first-line test in the field. The pan-E Dengue Early ELISA was less sensitive than the Platelia test; this two-step ELISA should be combined with DENV IgM antibody detection for the diagnosis of DENV infection.     

Analysis of the Escherichia coli Tol-Pal and TonB systems by periplasmic production of Tol,TonB, colicin,or phage capsid soluble domains

The aim of this review is to describe an in vivo assay of the interactions taking place in the Tol-Pal or TonB-ExbB-ExbD envelope complexes in the periplasm of Escherichia coli and between them and colicins or g3p protein of filamentous bacteriophages. Domains of colicins or periplasmic soluble domains of Tol or TonB proteins can be artificially addressed to the periplasm of bacteria by fusing them to a signal sequence from an exported protein. These domains interact specifically in the periplasm with the Tol or TonB complexes and disturb their function, which can be directly detected by the appearance of specific tol or tonB phenotypes. This technique can be used to detect new interactions, to characterize them biochemically and to map them or to induce tol or tonB phenotypes to study the functions of these two complexes.     

Small-angle X-ray scattering studies of fibrin film: comparisons of fine and coarse films prepared with thrombin and ancrod

Measurements of small-angle x-ray scattering have been made on films prepared from fine and coarse (i.e., formed at high and low, respectively, pH and ionic strength) clots of bovine fibrin by osmotic shrinkage or compression in one dimension. Intensity profiles were obtained with pinhole geometry on films stretched up to a stretch ratio of 1.43. In unstretched coarse films, repeat spacings were seen at about 245, 120, and 77-80 A. These peaks can probably be identified with the first, second, and third orders of the well-known fibrin repeat of 225 A. In unstretched fine films, only the 77-80 A spacing was seen. In this case, the first two orders may be weak because the half-staggered arrangement of monomer units giving rise to the 225 A reflection is not reinforced by lateral aggregation of protofibrils; the third order may be strong since the molecular subdomains appear to divide the repeat roughly into thirds. After stretching, the 77-80 A spacing persisted in the meridional direction but almost disappeared in the equatorial. Experiments on unstretched films prepared with ancrod substituted for thrombin gave similar results.     

Frailty Markers and Treatment Decisions in Patients Seen in Oncogeriatric Clinics: Results from the ASRO Pilot Study

Background

Comprehensive Geriatric Assessment (CGA) is the gold standard to help oncologists select the best cancer treatment for their older patients. Some authors have suggested that the concept of frailty could be a more useful approach in this population. We investigated whether frailty markers are associated with treatment recommendations in an oncogeriatric clinic.

Methods

This prospective study included 70 years and older patients with solid tumors and referred for an oncogeriatric assessment. The CGA included nine domains: autonomy, comorbidities, medication, cognition, nutrition, mood, neurosensory deficits, falls, and social status. Five frailty markers were assessed (nutrition, physical activity, energy, mobility, and strength). Patients were categorized as Frail (three or more frailty markers), pre-frail (one or two frailty markers), or not-frail (no frailty marker). Treatment recommendations were classified into two categories: standard treatment with and without any changes and supportive/palliative care. Multiple logistic regression models were used to analyze factors associated with treatment recommendations.

Results

217 patients, mean age 83 years (± Standard deviation (SD) 5.3), were included. In the univariate analysis, number of frailty markers, grip strength, physical activity, mobility, nutrition, energy, autonomy, depression, Eastern Cooperative Oncology Group Scale of Performance Status (ECOG-PS), and falls were significantly associated with final treatment recommendations. In the multivariate analysis, the number of frailty markers and basic Activities of Daily Living (ADL) were significantly associated with final treatment recommendations (p<0.001 and p = 0.010, respectively).

Conclusion

Frailty markers are associated with final treatment recommendations in older cancer patients. Longitudinal studies are warranted to better determine their use in a geriatric oncology setting.     

Addition of telomere-associated HeT DNA sequences "heals" broken chromosome ends in Drosophila

Stocks of D. melanogaster X chromosomes carrying terminal deletions (RT chromosomes) have been maintained for several years. Some of the chromosomes are slowly losing DNA from the broken ends (as expected if replication is incomplete) and show no telomere-associated DNA added to the receding ends. Two stocks carry chromosomes that have become "healed" and are no longer losing DNA. In both stocks the broken chromosome end has acquired a segment of HeT DNA, a family of complex repeats found only at telomeres and in pericentric heterochromatin. Although the HeT family is complex, the HeT sequence joined to the broken chromosome end is the same in both stocks. In contrast, the two chromosomes are broken in different places and have no detectable sequence similarity at the junction with the new DNA. Sequence analysis suggests that the new telomere sequences have been added by a specific mechanism that does not involve homologous recombination.