Site localization of sialyl Lewis(x) antigen on alpha1-acid glycoprotein by high performance liquid chromatography-electrospray mass spectrometry

A simple, fast and sensitive method was developed to verify the presence of the sialyl Lewis(x) antigen on an N-linked glycoprotein. High performance liquid chromatography-electrospray mass spectrometry (HPLC-ESI/MS) was used to identify which of the five N-linked glycosylation sites of human plasma alpha1-acid-glycoprotein (orosomucoid, OMD) contain the sialyl Lewis(x) antigen. OMD was digested with proteolytic enzymes and analyzed by reversed phase chromatography coupled with on-line ESI/MS. A tandem mass spectrometry experiment was designed to detect the presence of the sialyl Lewis(x) antigen based on the observation of an 803 mass to charge ratio ( m/z ) ion produced in the intermediate pressure region of the ESI interface. The ESI/MS signal at m/z 803 is consistent with an oxonium ion for a glycan structure containing NeuAc, Gal, GlcNAc, and Fuc. The identity of the m/z 803 ion was confirmed by ESI/MS/MS analysis of the m/z 803 fragment ion and comparison with a sialyl Lewis(x) standard. The stereochemistry and linkage positions were assigned using previous NMR analysis but could be determined with permethylation analysis if necessary. The analysis of OMD gave a pattern showing signal for the sialyl Lewis(x) antigen coeluting with each of the five N-linked glycopeptides. The ability to monitor sialyl Lewis(x) expression at each of the five sites is of interest in the study of OMD's role in inflammatory diseases.      

Cardiovascular risk management in rheumatoid arthritis: are we still waiting for the first step?

Rheumatoid arthritis (RA) is associated with a similar cardiovascular risk to that in diabetes, and therefore cardiovascular risk management (CV-RM) - that is, identification and treatment of cardiovascular risk factors (CRFs) - is mandatory. However, whether and to what extent this is done in daily clinical practice is unknown. In a retrospective cohort investigation, CV-RM was therefore compared between rheumatologists and primary care physicians (PCPs). Remarkably, CRFs in RA were less frequently identified and managed by rheumatologists in comparison with PCPs. In addition, PCPs assessed CRFs less frequently in RA than in diabetes. Obviously, there is a clear need for improvement of CV-RM in RA and this should be a joint effort from the rheumatologist and the PCP.Patients with rheumatoid arthritis (RA) have an increased cardiovascular (CV) risk that appears similar to that in diabetes. This observation highlights the significant CV burden in RA. In 1999, the American Diabetes Association and the American Heart Association published a statement for prevention of CV disease in diabetes. Since then, the CV risk in diabetes has been substantially lower than in earlier decades. Given the increased CV risk in RA, screening, identification of cardiovascular risk factors (CRFs) and cardiovascular risk management (CV-RM) are also highly needed as recommended by the European League Against Rheumatism (EULAR). The increased risk in RA is attributed to systemic inflammation as well as increased prevalence of CRFs. Hence, we should aim for tight disease control and control of CRFs.Presently unknown is whether and to what extent CV-RM is translated into clinical practice. In a retrospective cohort-comprising 251 patients with RA, 251 patients with diabetes, and 251 general population individuals-Desai and colleagues therefore investigated the identification and management of CRFs by rheumatologists and primary care physicians (PCPs) [1]. RA patients had to be registered at the University of Michigan Health System for at least 12 months between June 2007 and April 2012 and had been evaluated both by their rheumatologist as well as the PCP. CRFs of interest were smoking, exercise, weight, blood pressure, lipid profile, and fasting blood glucose.In RA, PCPs identified and managed most CRFs more frequently than rheumatologists. Secondly, identification of CRFs by rheumatologists in RA patients with elevated C-reactive protein levels was not different as compared with those with normal C-reactive protein levels. A third important observation was that PCPs identified and managed CRFs more frequently in patients with diabetes, followed by general population individuals and least often in RA patients. These striking results raise several issues.First, it is hard to believe that the largely absent CV-RM by rheumatologists is explained by under-recognition because the increased CV risk in RA must presently be well known among rheumatologists. A large amount of literature on this topic has been published over the last decade. Additionally, the necessity to screen, identify, and manage CRFs is incorporated into training programmes for rheumatology residents [2]. Against this background, it is important to realise that there is a lag time between the publication of the EULAR guideline and its actual implementation (that is, the guideline was published in 2010 [3] while the current study started in 2007). In other words, CV-RM in today''s clinical practice might have been improved, but not yet recognised.Second, that the CV risk in RA is related to the inflammatory burden is well known. Nevertheless, the present study did not indicate that there is more attention for CV-RM by rheumatologists in patients with a higher inflammatory load.Third, undertreatment of the increased CV risk in RA by PCPs might be explained by under-recognition because CRFs were assessed more frequently in diabetes in comparison with RA.The EULAR guidelines recommend screening and identification of CRFs in all RA patients, and, if indicated according to CV risk-prediction charts, adequate management. As accurate assessment of CV risk depends on RA characteristics, the EULAR favoured individualising risk assessment. Hence, a risk multiplication factor of 1.5 should be used in the presence of two of the following criteria: disease duration >10 years, rheumatoid factor, and/or anti-cyclic citrullinated peptide positivity or the presence of extra-articular manifestations. However, alternative approaches have been suggested - for example, increasing the age of an RA patient by 10 years to obtain a more precise CV risk estimate or to use other risk scores. Perhaps this lack of an RA-specific CV risk-prediction model hampers CV-RM implementation. Obviously, this discussion can only be solved by developing a RA-specific CV risk-prediction model, but this will take several years to complete.One may obviously argue that, due to its retrospective design, the strength of the conclusions of Desai and colleagues may be limited; however, they are in line with other recently published literature and thus confirm extending evidence that CV-RM is poorly conducted in RA, both by rheumatologists and PCPs. Another argument against CV-RM in RA is that we should wait until trials have been conducted that demonstrate the efficacy of statins and antihypertensive agents in RA. However, it will be (many) years before specific risk models are available and withholding cardiopreventive drugs that are very likely to work also in our high-risk population is unethical. Moreover, it is important to realise that, due to the decreased incidence of CV events in the last decades, CV prevention trials are nowadays very difficult to conduct. For instance, the TRACE-RA study [4] - a large placebo-controlled double-blind primary CV prevention trial in RA with atorvastatin - was stopped prematurely owing to the very low number of CV events that occurred.Altogether, the study from Desai and colleagues provides three important clues for improvement of CV-RM in RA. First, more education is urgently needed for both rheumatologists and PCPs. Second, it is important to realise that the contribution of higher prevalence CRFs in RA is one side of the coin, but the other side is effective suppression of the inflammation. The latter is a clear task for the rheumatologist. Third, CV care of a RA patient should be a joint effort by the rheumatologist and the PCP, and they should collaborate and agree on who performs the screening, identification, and, if required, management of CRFs.     

Estimating the rate of evolution of the rate of molecular evolution

A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction with any of the widely used models for nucleotide substitution or amino acid replacement. It is illustrated by analyzing a data set of rbcL protein sequences.      

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

Background  

Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs) are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy.     

Multiple forms of tubulin in the cytoskeletal and flagellar microtubules of polytomella

The alga polytomella contains several organelles composed of microtubules, including four flagella and hundreds of cytoskeletal microtubules. Brown and co-workers have shown (1976. J. Cell Biol. 69:6-125; 1978, Exp. Cell Res. 117: 313-324) that the flagella could be removed and the cytoskeletans dissociated, and that both structures could partially regenerate in the absence of protein synthesis. Because of this, and because both the flagella and the cytoskeletons can be isolated intact, this organism is particularly suitable for studying tubulin heterogeneity and the incorporation of specific tubulins into different microtubule-containing organelles in the same cell. In order to define the different species of tubulin in polytonella cytoplasm, a (35)S- labeled cytoplasmic fraction was subjected to two cycles of assembly and disassembly in the presence of unlabeled brain tubulin. Comparison of the labeled polytomella cytoplasmic tubulin obtained by this procedure with the tubulin of isolated polytomella flagella by two-dimensional gel electrophoresis showed that, whereas the β-tubulin from both cytoplasmic and flagellar tubulin samples comigrated, the two α-tubulins had distinctly different isoelectic points. As a second method of isolating tubulin from the cytoplasm, cells were gently lysed with detergent and intact cytoskeletons obtained. When these cytoskeletons were exposed to cold temperature, the proteins that were released were found to be highly enriched in tubulin; this tubulin, by itself, could be assembled into microtubules in vitro. The predominant α-tubulin of this in vitro- assembled cytoskeletal tubulin corresponded to the major cytoplasmic α-tubulin obtained by coassembly of labeled polytomella cytoplasmic extract with brain tubulin and was quite distinct from the α-tubulin of purified flagella. These results clearly show that two different microtubule-containing organelles from the same cell are composed of distinct tubulins.     

Effect of oxygen tension on human peripheral blood leukocytes: lysosomal enzyme release and metabolic responses during phagocytosis

We found that nonlethal lysosomal enzyme release from human peripheral blood leukocytes during phagocytosis of opsonized zymosan in vitro was modified by the oxygen tension under which the cells were incubated; with decreasing Po(2), zymosan-induced release of lysosomal enzymes was potentiated. The effect on enzyme release could not be attributed secondarily to an effect on phagocytosis, because, as others have reported, Po(2) had little effect on that response. Metabolic responses that accompany phagocytosis were also modified by oxygen tension. Stimulation of oxidation by way of the pentose cycle was further enhanced by increasing Po(2). Conversely, anaerobic glycolysis was promoted by decreasing oxygen tension. ATP levels fell as a function of time and concentration of phagocytic stimulus, mirroring lysosomal enzyme release as modified by Po(2). Cyclic AMP levels fell during phagocytosis and lysosomal enzyme release, a change that could act to facilitate lysosomal enzyme release. However, the fall in nucleotide level was greatest with highest Po(2) (i.e., when lysosomal enzyme release was least). The inverse relationship between oxidative metabolism and enzyme release suggested that a product of oxidative metabolism might adversely influence enzyme release. Sulfhydryl antioxidants (Cysteine, glutathione) and scavengers of oxygen-derived reactants (superoxide dismutase, catalase, benzoate, hypoxanthine, xanthine, histidine, azide) all potentiated zymosan- stimulated enzyme release. These findings are consistent with the interpretation that one or more factors (e.g., superoxide anion, hydrogen peroxide, hydroxyl radical, singlet oxygen), generated in association with the burst of oxidative metabolism which accompanies phagocytosis, acts to inhibit lysosomal enzyme release.