Bioinformatics: living on the edge

A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.     

Expression of CA IX in dysplasia adjacent to surgical resection margins of oral squamous cell carcinoma

Carbonic anhydrase (CA) IX is a hypoxia marker located almost exclusively in tumor cells. We analyzed the expression of this marker in dysplastic lesions adjacent to the surgical resection margin in patients with oral squamous cell carcinoma. We investigated 70 archived tumors, 36 of which showed dysplasia adjacent to the surgical margin. We used tissue microarray technology to perform an immunohistochemical study of CA IX expression. We found 12 (33.3%) cases of mild dysplasia (10 negative, 2 positive for CA IX), five (13.9%) cases of moderate dysplasia (3 negative, 2 positive for CA IX), 1 (2.8%) case of severe dysplasia (negative for CA IX) and 18 (50%) cases of carcinoma in situ (10 negative, 8 positive for CA IX). In cases of intense expression of CA IX in the tumor, the same distribution of positive and negative cases was observed in all degrees of dysplasia (mild, moderate, severe), although cases of carcinoma in situ tended to be CA IX positive.     

Monthly day/night changes and seasonal daily rhythms of sexual steroids in Senegal sole (Solea senegalensis) under natural fluctuating or controlled environmental conditions

In this paper we attempted to investigate the existence of daily fluctuations on plasma sexual steroids (17beta-estradiol, E(2) and testosterone, T) in Senegal sole (Solea senegalensis) females. We described the monthly day/night concentrations and seasonal daily rhythms in animals reared under natural photo- and thermo-period. In addition, the influence of the natural annual fluctuation of the water temperature on the plasma concentration of these steroids was investigated, using one group of Senegal sole under a natural photoperiod, but with an attenuated thermal cycle (around 17-20 degrees C) for one year. Although no significant day/night differences were detected in monthly samplings, the existence of an annual rhythm of E(2) and T (p<0.01) with an acrophase in February was revealed by COSINOR analysis. Maximum values were reached in March for both steroids (6.1+/-1.7 ng mL(-1) at mid-dark, MD and 4.0+/-0.6 ng mL(-1) at mid-light, ML for E2 and 1.4+/-0.4 ng mL(-1) at MD and 0.8+/-0.1 ng mL(-1) at ML for T) in anticipation of the spawning season (May-June). As regards seasonal daily rhythms, the presence of daily oscillations was revealed. At the spring solstice (21st March) a daily rhythm was observed for both steroids (COSINOR, p<0.01), with an acrophase at 20:00 h (E(2)) and at 21:08 h (T). In summer, autumn and winter no daily rhythms were observed due to the low steroid levels at those seasons. When Senegal sole females were submitted to an attenuated annual thermal cycle, the steroid rhythm disappeared (there was no surge in spring, as in the control group) and these fish did not spawn, despite being subjected to natural photoperiod conditions. This result underlined the importance of the natural annual fluctuation of water temperature and photoperiod on the synchronization of the spawning season and on the onset of steroidogenesis.     

Experimental stress in inflammatory rheumatic diseases: a review of psychophysiological stress responses

Introduction  

Stressful events are thought to contribute to the aetiology, maintenance and exacerbation of rheumatic diseases. Given the growing interest in acute stress responses and disease, this review investigates the impact of real-life experimental psychosocial, cognitive, exercise and sensory stressors on autonomic, neuroendocrine and immune function in patients with inflammatory rheumatic diseases.     

Involvement of ethylene and nitric oxide in cell death in mastoparan‐treated unicellular alga Chlamydomonas reinhardtii

This work demonstrates a contribution of ethylene and NO (nitric oxide) in MP (mastoparan)‐induced cell death in the green algae Chlamydomonas reinhardtii. Following MP treatment, C. reinhardtii showed massive cell death, expressing morphological features of PCD (programmed cell death). A pharmacological approach involving combined treatments with MP and ethylene‐ and NO‐interacting compounds indicated the requirement of trace amounts of both ethylene and NO in MP‐induced cell death. By employing a carbon dioxide laser‐based photoacoustic detector to measure ethylene and a QCL (quantum cascade laser)‐based spectrometer for NO detection, simultaneous increases in the production of both ethylene and NO were observed following MP application. Our results show a tight regulation of the levels of both signalling molecules in which ethylene stimulates NO production and NO stimulates ethylene production. This suggests that, in conjunction with the elicitor, NO and ethylene cooperate and act synchronously in the mediation of MP‐induced PCD in C. reinhardtii. To the best of our knowledge, this is the first report on the functional significance of ethylene and NO in MP‐induced cell death.     

The RNA interference pathway: a new target for autoimmunity

Many intracellular macromolecular complexes that are involved in the production or degradation of RNAs are targeted by autoantibodies in systemic autoimmune diseases. RNA interference (RNAi) is a recently characterized gene silencing pathway by which specific mRNAs are either degraded or translationally suppressed. In a recent issue of Arthritis Research and Therapy, Andrew Jakymiw and colleagues reported that the enigmatic Su autoantigen complex contains key components of the RNAi machinery. Anti-Su autoantibodies from both human patients with rheumatic diseases and a mouse model of autoimmunity recognize the endonucleolytic Argonaute and Dicer proteins, both crucial enzymes of the RNAi pathway. These data raise the question of how the anti-Su response is triggered. So far, it is unknown whether molecular modifications may be involved, as has been proposed for other intracellular autoantigens. The implication of RNAi in anti-viral defence may suggest a role for virus infection in this process.     

CD97 neutralisation increases resistance to collagen-induced arthritis in mice

Synovial tissue of rheumatoid arthritis (RA) patients is characterised by an influx and retention of CD97-positive inflammatory cells. The ligands of CD97, CD55, chondroitin sulfate B, and α5β1 (very late antigen [VLA]-5) are expressed abundantly in the synovial tissue predominantly on fibroblast-like synoviocytes, endothelium, and extracellular matrix. Based upon this expression pattern, we hypothesise CD97 expression to result in accumulation of inflammatory cells in the synovial tissue of RA patients. To determine the therapeutic effect of blocking CD97 in an animal model of RA, collagen-induced arthritis was induced in a total of 124 DBA/J1 mice. Treatment was started on day 21 (early disease) or on day 35 (longstanding disease) with the blocking hamster anti-mouse CD97 monoclonal antibody (mAb) 1B2, control hamster immunoglobulin, or NaCl, applied intraperitoneally three times a week. The paws were evaluated for clinical signs of arthritis and, in addition, examined by radiological and histological analysis. Mice receiving 0.5 mg CD97 mAb starting from day 21 had significantly less arthritis activity and hind paw swelling. Furthermore, joint damage and inflammation were reduced and granulocyte infiltration was decreased. When treatment was started on day 35, CD97 mAb treatment had similar effects, albeit less pronounced. The results support the notion that CD97 contributes to synovial inflammation and joint destruction in arthritis.     

Large-scale chromatin de-compaction induced by low light is not accompanied by nucleosomal displacement

Arabidopsis thaliana is widely used as a model to study chromatin compaction dynamics during development and in response to the environment. Signals such as prolonged heat treatment, low light and pathogen infestation are known to induce large-scale de-condensation of nuclear chromatin. Here we demonstrate that the response to different environments varies at the nucleosomal level. Our results show that in contrast to previous reports on heat and biotic infestation, low light intensity signaling does not alter nucleosomal occupancy, despite the marked effects of low light on global chromatin compaction.Key words: Arabidopsis, chromatin, nucleosomes, MNase IThanks to its relatively simple chromatin organization, Arabidopsis thaliana became the model of choice to study dynamics in nuclear chromatin compaction in plants.^1–3 At the microscopic level, highly condensed ‘heterochromatic’ domains (chromocenters), containing compact DNA (mainly repetitive sequences), and less condensed gene-rich ‘euchromatic’ domains can be distinguished upon staining with DAPI (4′,6-diamidino-2-phenylindole). This division however, is not static and compaction changes throughout development (reviewed in ref. ⁴). Chromatin for example de-condensates prior to flowering⁵ and increases with cell differentiation during leaf maturation³ and seedling establishment.⁶ Vice versa, artificially induced cell de-differentiation during protoplastization, results in loosening of compact chromatin.^7,8 Chromatin compaction is also influenced by various environmental signals. These include infestation by pathogenic microorganisms such as Pseudomonas syringae, light and heat signals.^9–11In our recent paper, published in Plant Physiology,¹² we demonstrate that a ∼90% decrease in light intensity (low light) induces a reversible reduction in global chromatin compaction. In addition, also specifically lowering the blue-light wavelengths in the spectrum, or lowering the red-to-far red (R/Fr) ratio induced a significant reduced compaction of the nuclear chromatin. This is interesting from a functional perspective because (1) these are the relevant signals perceived by plants in natural shade conditions occurring in dense-vegetations and (2) because these wavelengths are specifically detected by the light-sensitive photoreceptor proteins. Previously, we demonstrated that the R/Fr-photoreceptor Phytochrome-B (PhyB) is a positive regulator of chromatin compaction in standard light conditions.¹⁰ We now showed that PhyB also controls low light-induced chromatin organization, but that its effect depend on the genetic background of the phyb mutant under study. Likely, PhyB exerts its effects on light-mediated chromatin compaction via stabilization of CRYPTOCHROME 2 (CRY2) protein. This chromatin-associated blue light photoreceptor is a general positive regulator of low light-induced chromatin de-compaction and in addition controls chromatin compaction during floral transition.⁵In addition, we demonstrated that global chromatin de-compaction during floral transition and low light treatment also occurs in euchromatic domains.^5,12 To study possible chromatin changes at the nucleosomal level, we performed Micrococcal Nuclease I (MNase I) analysis. No differences were observed in the nucleosomal occupancy between standard and low light conditions in DNA gels or Southern blots hybridized with different probes for repeated sequences associated to heterochromatin, and dispersed upon low light treatment (Fig. 1). This suggests that the large-scale heterochromatin (de)compaction response observed at the microscopic level under low light conditions is not necessarily accompanied by nucleosomal displacement. These results are in line with the de-condensation conditions induced by protoplastization, where no changes in H3K9Me2 or in DNA methylation (5-mC) levels were found.⁷ However, these results are in contrast to the results of Pecinka and colleagues,¹¹ who demonstrated that prolonged heat stress results in heterochromatin de-condensation and loss of nucleosomes. Moreover, it is in contrast with Pavet and co-workers,⁹ who found reduced 5-mC levels upon infection with P. syringae. Although the results of Pecinka and colleaugues¹¹ were obtained by real-time PCR which may be more sensitive than our Southern blots, we conclude that the response of plants to their environment at the chromatin compaction level may be tailored to the specific signal it is confronted with and that this probably can be dissected at the nucleosomal level.Open in a separate windowFigure 1MNase I analysis of low light treated plants. Southern blots with 3 different probes hybridized to DNA from Col-0 plants cultured under standard (200 µmol m⁻² s⁻¹; control) and low light (15 µmol m⁻² s⁻¹) conditions. For each part, the first two lanes represent control DNA samples (no MNase I), followed by lanes with increasing MNase I concentrations (0.02, 0.1, 0.75 and 3 units MNase I). (A) 5S rDNA probe, (B) 45S rDNA probe, (C) pAl1 probe (180 bp centromeric repeat). M = molecular weight marker.