The high-level similarity of some disparate gene expression measures

Probe-level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures (GEMs). Disturbingly, the different approaches not only generate quite different measures but they could also yield very different analysis results. Here, we explore the question of how much the analysis results really do differ, first at the gene level, then at the biological process level. We demonstrate that, even though the gene level results may not necessarily match each other particularly well, as long as there is reasonably strong differentiation between the groups in the data, the various GEMs do in fact produce results that are similar to one another at the biological process level. Not only that the results are biologically relevant. As the extent of differentiation drops, the degree of concurrence weakens, although the biological relevance of findings at the biological process level may yet remain.     

Combined effects of zinc and algal food on the competition between planktonic rotifers, <Emphasis Type="Italic">Anuraeopsis fissa</Emphasis> and <Emphasis Type="Italic">Brachionus rubens</Emphasis> (Rotifera)

We evaluated the combined effects of algal (Chlorella vulgaris) food levels (low, 0.5 × 10⁶ (or 2.9 μg C ml⁻¹); and high, 1 × 10⁶ cells ml⁻¹ (or 5.8 μg C ml⁻¹)) and zinc concentrations (0, 0.125, and 0.250 mg l⁻¹ of ZnCl₂) on the competition between two common planktonic rotifers Anuraeopsis fissa and Brachionus rubens using their population growth. Median lethal concentration data (LC₅₀) (mean ± 95% confidence intervals) showed that B. rubens was more resistant to zinc (0.554 ± 0.08 mg l⁻¹) than A. fissa (0.315 ± 0.07 mg l⁻¹). A. fissa when grown alone or with Zn was always numerically more abundant than B. rubens. When grown in the absence of zinc, under low- and high-food levels, the peak abundances of A. fissa varied from 251 ± 24 to 661 ± 77 ind. ml⁻¹, respectively, and the corresponding maxima for B. rubens were 52 ± 3 and 102 ± 18 ind. ml⁻¹. At a given food level, competition for food reduced the peak abundances of both rotifers considerably. Increase in Zn concentration also lowered the rotifer abundances. The impact of zinc on competition between the two-rotifer species was evident at low-food level, mainly for A. fissa. At zinc concentrations of 0 and 0.125 mg l⁻¹, the populations of both rotifers continued to grow for about 10 days, but thereafter B. rubens began to decline. Role of zinc on the competitive outcome of the two species is discussed in relation to the changing algal densities in natural water bodies.     

Progression of early phase diabetic nephropathy in streptozotocin-induced diabetic rats: evaluation of various kidney-related parameters

Diabetic nephropathy (DN) is one of the serious secondary complications of diabetes, which results in end-stage renal failure. Reports on the progressive nature of early phase DN especially with respect to kidney parameters such as kidney weight, type IV collagen excretion, total kidney and urinary glycosaminoglycans (GAGs) are few. This work was undertaken to determine systematically the progression of early phase DN in relation to various kidney-related parameters for a period of four months. Experimentally-induced diabetic rats were grouped based on fasting blood glucose levels. Various basic and kidney-related parameters such as kidney weight, microalbuminuria, urinary excretion of GAGs and type IV collagen, total kidney GAGs, histopathology, glomerular area and glomerular volume were examined in control and diabetic rats. There was a progressive increase in fasting blood sugar, urine sugar, kidney weight, microalbuminuria, urine glycosaminoglycans, urine type IV collagen, glomerular area and glomerular volume but there was a progressive decrease in kidney glycosaminoglycans. Glomerular sclerotic condition was aggravated with the increase in duration of diabetes from 1 to 4 months. Onset of DN in rats begins subtly after one month of diabetes but gets vitiated and more pronounced at the end of four months.     

Evaluating quinacrine as a potential amyloid imaging compound: studies on hen egg white lysozyme as model system

Amyloid plaque is associated with several neuronal and non-neuronal degenerative diseases. More than twenty human proteins can fold abnormally to form pathological deposits like amyloid plaque. Strategies for treating such diseases include therapies designed to decrease protein plaque formation or its complete clearance, but monitoring/clinical trials of these treatments are limited by the lack of effective methods to monitor amyloid deposits in the organs/tissues of living patients. The current study shows binding and staining ability of quinacrine to protein amyloid deposits, using Hen Egg White Lysozyme (HEWL) as model system and characterization of its binding interaction with HEWL, employing several biophysical techniques. Since quinacrine can pass the blood brain barrier, the current report suggests potential application of quinacrine for antemortem diagnostic of amyloid.     

Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end

The heterodimeric actin-capping protein (CP) regulates actin assembly and cell motility by binding tightly to the barbed end of the actin filament. Here we demonstrate that myotrophin/V-1 binds directly to CP in a 1:1 molar ratio with a Kd of 10-50 nm. V-1 binding inhibited the ability of CP to cap the barbed ends of actin filaments. The actin-binding COOH-terminal region, the "tentacle," of the CP beta subunit was important for binding V-1, with lesser contributions from the alpha subunit COOH-terminal region and the body of the protein. V-1 appears to be unable to bind to CP that is on the barbed end, based on the observations that V-1 had no activity in an uncapping assay and that the V-1.CP complex had no capping activity. Two loops of V-1, which extend out from the alpha-helical backbone of this ankyrin repeat protein, were necessary for V-1 to bind CP. Parallel computational studies determined a bound conformation of the beta tentacle with V-1 that is consistent with these findings, and they offered insight into experimentally observed differences between the alpha1 and alpha2 isoforms as well as the mutant lacking the alpha tentacle. These results support and extend our "wobble" model for CP binding to the actin filament, in which the two COOH-terminal regions of CP bind independently to the actin filament, and bound CP is able to wobble when attached only via its mobile beta-subunit tentacle. This model is also supported by molecular dynamics simulations of CP reported here. The existence of the wobble state may be important for actin dynamics in cells.     

Heat stress induced apoptosis in BC-8 cells derived from AK-5 tumor involves downregulation of Bcl-2 and generation of reactive oxygen species

BC-8, a rat histiocytoma undergoes apoptosis after heat shock, which is due to lack of an effective heat shock response. Heat shock induced generation of free radicals, which in turn are involved in the induction of apoptotic death in BC-8 cells. Treatment of BC-8 cells with N-acetylcysteine partially inhibited the heat induced apoptosis. Introduction of Bcl-2 gene in these cells did not protect them from apoptotic death, whereas transfection with hsp-70 gene did render these cells resistant to heat induced apoptosis transiently. Heat shock also downregulated the expression of Bcl-2 and p53 in these cells. These observations suggested that the heat shock induced apoptosis was mediated through reactive oxygen species and controlled upstream of Bcl-2 check point.     

Silencing of TNF-α receptors coordinately suppresses TNF-α expression through NF-κB activation blockade in THP-1 macrophage

Persistently elevated level of TNF-α has been implicated in several inflammatory disorders, however, its autocrine production through TNF-α receptors signaling is poorly understood. Here we report that simultaneous silencing of TNF-receptors, R1 and R2 by DNAzyme or siRNA suppressed TNF-α expression more efficiently than silencing them individually in lipopolysaccharides (LPS) stimulated THP-1 macrophages. Co-silencing of TNF-receptors also inhibited TNF-α induced NF-κB activation to a higher extent. It was further observed that NF-κB inhibitor but not c-Jun N-terminal kinase inhibitor (SP600125) suppressed TNF-α expression. All these results suggest that TNF-α expression is regulated by synergistic signaling of TNF receptors through downstream NF-κB activation.     

Regulation of endocytic trafficking of transferrin receptor by optineurin and its impairment by a glaucoma-associated mutant

Background  

Optineurin is a multifunctional protein involved in several functions such as vesicular trafficking from the Golgi to the plasma membrane, NF-κB regulation, signal transduction and gene expression. Mutations in optineurin are associated with glaucoma, a neurodegenerative eye disease that causes blindness. Genetic evidence suggests that the E50K (Glu50Lys) is a dominant disease-causing mutation of optineurin. However, functional alterations caused by mutations in optineurin are not known. Here, we have analyzed the role of optineurin in endocytic recycling and the effect of E50K mutant on this process.     

Food concentration and temperature effects on the demography of <Emphasis Type="Italic">Latonopsis</Emphasis> cf. <Emphasis Type="Italic">australis</Emphasis> Sars (Cladocera: Sididae)

This study has two main objectives, the first being the determination of net phytoplankton primary production to explain the phytoplankton’s function in a wetland carbon cycle, while the second objective is to relate this function with the phytoplankton assemblage composition. The annual variation in the phytoplankton production was monitored monthly for more than a year (2007–2008) in the semiarid eutrophic, hydrologically-perturbed “Tablas de Daimiel” National Park wetland. The phytoplankton fraction considered in this study comprised all organisms between the size 3 and 100 μm. The total biomass of phytoplankton was obtained by counting algae and calculating their volume, while net primary production and respiration were quantified by in situ incubations with the Winkler method. The respiration ranged from undetectable to 0.07 mgO₂ l⁻¹ h⁻¹; net photosynthesis reached 0.20 mgO₂ l⁻¹ h⁻¹. Net primary production was maximum at the end of the warm period (October 2007), and other peaks occurred at the start of summer (July 2007) or spring (March 2008). When maximum production took place, phytoplankton was mainly composed of small fast-growing chlorophytes (Tetraselmis cf. fontiana or Chlamydomonas sp.), in addition to some of the large, S-strategist algae (Peridinium umbonatum, Microcystis flos-aquae, Euglena sp.). The phytoplankton metabolism in “Tablas de Daimiel” was autotrophic as a whole due to changing contributions of algal groups. Only chlorophyte biomass was statistically related to net primary production. The conclusion reached is that this shallow eutrophic semiarid wetland possessed an annual net autotrophic production of phytoplankton fraction resulting from the small, fast-growing algae enhanced by hydrological perturbations that interrupted the autogenic course of S strategists.