Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression data

Background

Pterygium is a common ocular surface disease characterized by fibrovascular invasion of the cornea and is sight-threatening due to astigmatism, tear film disturbance, or occlusion of the visual axis. However, the mechanisms for formation and post-surgical recurrence of pterygium are not understood, and a valid animal model does not exist. Here, we investigated the possible mechanisms of pterygium pathogenesis and recurrence.

Methods

First we performed a genome wide expression analysis (human Affymetrix Genechip, >22000 genes) with principal component analysis and clustering techniques, and validated expression of key molecules with PCR. The controls for this study were the un-involved conjunctival tissue of the same eye obtained during the surgical resection of the lesions. Interesting molecules were further investigated with immunohistochemistry, Western blots, and comparison with tear proteins from pterygium patients.

Results

Principal component analysis in pterygium indicated a signature of matrix-related structural proteins, including fibronectin-1 (both splice-forms), collagen-1A2, keratin-12 and small proline rich protein-1. Immunofluorescence showed strong expression of keratin-6A in all layers, especially the superficial layers, of pterygium epithelium, but absent in the control, with up-regulation and nuclear accumulation of the cell adhesion molecule CD24 in the pterygium epithelium. Western blot shows increased protein expression of beta-microseminoprotein, a protein up-regulated in human cutaneous squamous cell carcinoma. Gene products of 22 up-regulated genes in pterygium have also been found by us in human tears using nano-electrospray-liquid chromatography/mass spectrometry after pterygium surgery. Recurrent disease was associated with up-regulation of sialophorin, a negative regulator of cell adhesion, and never in mitosis a-5, known to be involved in cell motility.

Conclusion

Aberrant wound healing is therefore a key process in this disease, and strategies in wound remodeling may be appropriate in halting pterygium or its recurrence. For patients demonstrating a profile of 'recurrence', it may be necessary to manage as a poorer prognostic case and perhaps, more adjunctive treatment after resection of the primary lesion.     

Acute phase reactants add little to composite disease activity indices for rheumatoid arthritis: validation of a clinical activity score

Introduction  

Frequent assessments of rheumatoid arthritis (RA) disease activity allow timely adaptation of therapy, which is essential in preventing disease progression. However, values of acute phase reactants (APRs) are needed to calculate current composite activity indices, such as the Disease Activity Score (DAS)28, the DAS28-CRP (i.e. the DAS28 using C-reactive protein instead of erythrocyte sedimentation rate) and the Simplified Disease Activity Index (SDAI). We hypothesized that APRs make limited contribution to the SDAI, and that an SDAI-modification eliminating APRs – termed the Clinical Disease Activity Index (CDAI; i.e. the sum of tender and swollen joint counts [28 joints] and patient and physician global assessments [in cm]) – would have comparable validity in clinical cohorts.     

The effect of copper supplementation on red blood cell oxidizability and plasma antioxidants in middle-aged healthy volunteers

A multicenter European study (FoodCue) was undertaken to provide data on the significance of increased dietary copper as a pro-oxidant or antioxidant in vivo. The present work describes the effect of Cu supplementation on (2,2'-azo-bis(2-amidinopropane) hydrochloride (AAPH)-induced red blood cell oxidation in middle-aged people. Double-blinded copper supplementation was achieved in 26 healthy volunteers (50-70 years) with pills containing 3 mg CuSO(4), 3 mg Cu glycine chelate (CuG) and 6 mg CuG. Each 6 week supplementation period was preceded and followed by 6 weeks of washout (WO) on placebo. The results show significant increases in time necessary to achieve 50% hemolysis (LT(50)) after 3CuSO(4) and 6CuG compared with values after WO periods. Cu supplementation did not increase the levels of (Cu,Zn)SOD activity in red blood cells. Resistance to hemolysis was significantly and positively correlated (r =.30, p <.01) with alpha- and beta-carotene content in the plasma. Together, these data suggest that intake of copper as high as 7 mg/d has no pro-oxidant activity and may rather result in protection of red blood cells against oxidation. The decreased oxidizability of red blood cells did not result from increased (Cu,Zn)SOD activity and may occur through other mechanisms such as changes in membrane antioxidant content.     

Kelvin-Helmholtz instability on the magnetopause, magnetohydrodynamic waveguide in the outer magnetosphere, and Alfvén resonance deep in the magnetosphere

Oscillations of the “magnetosphere-solar wind” system are studied analytically in the framework of a plane-stratified model of the medium. The properties of oscillations are determined by three phenomena: Kelvin-Helmholtz instability on the tangential discontinuity (magnetopause) separating the magnetosphere and the solar wind, the presence of a waveguide for fast magnetosonic waves in the magnetosphere, and the Alfvén resonance—a sharp increase in the amplitude of oscillations having the properties of Alfvén waves—in the inner magnetosphere. The oscillations of the system form a discrete spectrum of eigenmodes. Analytical expressions are obtained for the frequency and growth rate of instability of each mode, as well as for the functions describing the spatial structure of these modes. All these characteristics of the eigenmodes are shown to depend on the velocity of the solar wind as a parameter. The dependences of the main mode characteristics (such as the instability thresholds, the points of the maximum and minimum growth rate, and the spatial distributions of the oscillation energy) on this parameter are determined for each eigenmode.     

Conservation genetics of highly isolated populations of the xerothermic beetle Crioceris quatuordecimpunctata (Chrysomelidae)

Xerothermic species are rare and threatened in central and eastern Europe. In light of the continuing loss of steppe‐like habitats due to anthropogenic fragmentation and degradation, the evaluation of genetic variation in populations inhabiting them is of immediate importance if appropriate conservation measures are to be undertaken. Here we report on the genetic diversity of the rare leaf beetle Crioceris quatuordecimpunctata, whose populations in central and eastern Europe inhabit highly geographically isolated areas. All of the studied populations (in Poland, Ukraine, and Slovakia) were differentiated at the mitochondrial marker COI. However, with respect to the nuclear marker ITS1, Polish populations were monomorphic, but distinct from all other populations. The distinctiveness of the studied populations was confirmed by Wolbachia screening, which showed that all populations carried different strains (one or two), which were probably transferred independently from other insects. On the other hand, no diversity was found in any marker within particular populations, which could be caused (at least for mtDNA) by a Wolbachia selective sweep. Crioceris quatuordecimpunctata probably consists of isolated populations, which went through narrow bottlenecks leading to a drastic reduction in their genetic diversity. As these populations are reciprocally monophyletic for mtDNA haplotypes and show a significant divergence of allele frequencies at nuclear loci, they could be classified as evolutionarily significant units (ESUs). In addition, DNA barcodes were used to identify Asparagus officinalis as the host plant for members of all studied populations. These data should be valuable in efforts to conserve populations of C. quatuordecimpunctata (e.g., for guiding reintroductions).     

In vivo replication of the hamster polyomavirus genome and generation of specific deletions in the process of lymphomagenesis.

Hamster polyomavirus (HaPV) causes lymphomas when injected into newborn hamsters. These tumors are virus-free but accumulate large amounts of deleted extrachromosomal viral genomes. In order to identify the major sites of virus replication in animals, we have monitored the HaPV DNA present in different organs at various times after injection. The data demonstrate that viral replication preferentially occurs in lymphoid organs. Lymphoma-associated viral genomes display specific deletions. PCR analysis shows that such viral genomes are the only variants detectable in infected animals, suggesting that they are generated by a specific cellular mechanism. We have tested the possible role of the lymphoid cell-specific V(D)J recombination activity in the generation of these specific variants. Our results indicate that this mechanism is not solely responsible for the viral genome rearrangement, if involved at all.     

Temperature and prey quality effects on growth of juvenile walleye pollock Theragra chalcogramma (Pallas): a spatially explicit bioenergetics approach

A bioenergetics model for juvenile age‐0 year walleye pollock Theragra chalcogramma was applied to a spatially distinct grid of samples in the western Gulf of Alaska to investigate the influence of temperature and prey quality on size‐specific growth. Daily growth estimates for 50, 70 and 90 mm standard length (L_S) walleye pollock during September 2000 were generated using the bioenergetics model with a fixed ration size. Similarities in independent estimates of prey consumption generated from the bioenergetics model and a gastric evacuation model corroborated the performance of the bioenergetics model, concordance correlation (r_c) = 0·945, lower 95% CL (transformed) (L₁) = 0·834, upper 95% CL (transformed) (L₂) = 0·982, P < 0·001. A mean squared error analysis (M_SE) was also used to partition the sources of error between both model estimates of consumption into a mean component (M_C), slope component (S_C), and random component (R_C). Differences between estimates of daily consumption were largely due to differences in the means of estimates (M_C= 0·45) and random sources (R_C= 0·49) of error, and not differences in slopes (S_C= 0·06). Similarly, daily growth estimates of 0·031–0·167 g day^?1 generated from the bioenergetics model was within the range of growth estimates of 0·026–0·190 g day^?1 obtained from otolith analysis of juvenile walleye pollock. Temperature and prey quality alone accounted for 66% of the observed variation between bioenergetics and otolith growth estimates across all sizes of juvenile walleye pollock. These results suggest that the bioenergetics model for juvenile walleye pollock is a useful tool for evaluating the influence of spatially variable habitat conditions on the growth potential of juvenile walleye pollock.     

Effect of Osmotic Shock and Low Salt Concentration on Survival and Density of Bacteriophages T4B and T4Bo1

Measurements of survival and buoyant densities of bacteriophages T4B, T4Bo(1), and T4D have demonstrated the following: (a) After suspension in a concentrated salt solution, T4B and T4D are sensitive both to osmotic shock and to subsequent exposure to low monovalent salt concentrations. (b) Sensitivity of T4B to dilution from a concentrated salt solution is dependent on dilution rate, that of T4D is less dependent, and that of T4Bo(1) is independent. (c) Sensitivity of all three phages to low salt concentrations depends on initial salt concentrations to a variable extent. (d) Density gradient profiles indicate that nearly half of osmotically shocked T4B retain their DNA. Similar analysis demonstrates that few, if any, T4Bo(1) lose DNA when subjected to a treatment causing 90% loss of infectivity. (e) The effective buoyant densities of T4B and T4Bo(1) depend significantly on the dilution treatments to which the phages are subjected prior to centrifugation in CsCl gradients. These data are explicable in terms of the different relative permeabilities of the phages to water and solutes, and of alterations in the counterion distribution surrounding the DNA within the phage heads.     

Schematic methods for probabilistic enzyme kinetics.

The theory of steady-state enzyme processes which avoids using the mass action law of chemical kinetics and consistently describes catalytic mechanisms by probabilistic concepts has recently been proposed (Mazur, 1991, J. theor. Biol. 148, 229-242). To facilitate the analysis of complex reaction graphs by this theory the possibility of constructing schematic rules similar to those used in classical kinetics is studied. It is found that due to the similarity of algebraic procedures the popular method of King & Altman can be applied in probabilistic kinetics in addition to the earlier proposed rule based on enumeration of cycles of the reaction graph. This similarity also allows one to adapt many other shortcut methods of classical kinetics for probabilistic reaction graphs. The paper considers separately the possibility of transforming reaction mechanisms so that the initial graph is replaced by a simpler but equivalent one. It is shown that there are few cases when a group of states can be replaced by one united state, with earlier known rules such as the rule of Cha for equilibrium stages being particular cases of a more general procedure. In addition a novel method is proposed which performs step-by-step reduction of any reaction graph. All the new methods can be adapted for traditional kinetics as well. The results obtained demonstrate that many schematic rules of classical kinetics are of probabilistic origin.