Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

Effects of tricyclohexylhydroxytin on the kinetics of adenosine triphosphatase system and protection by thiol reagents

Tricyclohexylhydroxytin, commonly known as Plictran® inhibited Na⁺, K⁺ -ATPase activity of rat brain synaptosomes in a concentration-dependent manner with median inhibitory concentration (IC-50) of 2 μM. Both K⁺ -stimulated para-nitrophenylphosphatase and [3-H]-ouabain binding to synaptosomes were also inhibited by Plictran with IC-50 values of 11 and 30 μM, respectively. Altered pH and Na⁺, K⁺ -ATPase activity curves demonstrated comparable inhibition in buffered neutral and alkaline pH ranges, and no inhibition was observed in acidic pH. The inhibition of Na⁺, K⁺ -ATPase was independent of temperature. Kinetic studies of substrate (ATP) activation of Na⁺, K⁺ -ATPase indicated uncompetitive inhibition. Results also showed noncompetitive inhibition for p-nitrophenylphosphate and uncompetitive inhibition for K⁺ activations of p-nitrophenylphosphatase. Preincubation of synaptosomes with dithiothreitol, a sulfhydryl (SH) agent, resulted in the complete protection of Plictran inhibition of Na⁺, K⁺ -ATPase, K⁺ -para-nitrophenylphosphatase, and [3-H]-ouabain binding. The protection was specific and concentration dependent since cysteine and glutathione did not afford protection. These results indicate that Plictran inhibited Na⁺, K⁺ -ATPase by interacting with dephosphorylation of the enzyme-phosphoryl complex and exerted a similar effect to that of SH-blocking agents.     

Growth and Endogenous Gibberellin Content of Dormant Groundnut Embryonic-axes as Influenced by Leaching and GA(3)

Leacthing the excised embryonic-axes from dormant groundunt (Arachis hypogaea) seeds resulted in their growth. However, their growth was stunted compared to that of after-ripened ones. It is attributed to (1) the lower amount of gibberellin-like substances in the dry, dormant embryonic-axes than in the after-ripened ones, and (2) the inability of the former to sythesise tbe tibberetllin as indicated by the lower content compared to the after-ripened ones kept in water. Exogenousty supplied GA(3) (0.1 mg/1) increased both the endogenous gibberellin and growth of the dormant, leached embryonic-axes to the level of after-ripened ones.     

Kinetics of succinic dehydrogenase inhibition by methyl parathion and its recovery by oximes and L-cysteine in hepatopancreas of Lamellidens marginalis

Effects in vitro of methyl parathion on some kinetic constants of succinic dehydrogenase (SDH) in hepatopancreas of freshwater mussel, L. marginalis were studied. Altered pH vs. specific activity curves for SDH demonstrated significant inhibition by methyl parathion in buffered acidic, neutral and alkaline ranges. At high pH ranges IC50 (12.5 microM) of methyl parathion did not cause 50% inhibition enzyme as it did at neutral and acidic pHs. Activation energies (delta E) were found to be increased suggesting decreased efficiency of enzyme in presence of methyl parathion. Non-competitive inhibition with respect to activation by succinate was indicated by decreased maximal velocity (V) without change in Michaelis Menten constant (Km). Pyridine-2-aldoxime (25 microM), pyridine-4-aldoxime (15 microM) and L-cysteine (40 microM) neutralized the inhibition of SDH by methyl parathion (12.5 microM). The kinetic data suggests that inhibition of SDH by methyl parathion was pH and temperature independent.     

Effect of sciatectomy and induced ammonia stress on Mg2+_adenosine triphosphatase activity in frog tissues

Mg² + dependent —adenosine triphosphatase activity has been studied in the muscle, brain, kidney and liver tissues of frog,Rana hexadactyla (Lesson) after sciatectomy and induced chronic ammonia stress. The enzyme activity decreased in the tissues of the denervated frog. The activity of the enzyme increased in all the tissues of the normal and denervated frogs except in the denervated muscle when ammonium lactate was infused intraperitoneally.     

Influence of bacterial streak disease development on changes in phenolics,soluble amino acids and carbohydrates of rice leaves

The healthy leaves of rice cultivar ‘BJ 1’ resistant to bacterial leaf streak pathogen (Xanthomonas translucens f. sp.oryzicola) contained higher quantities of total phenolic compounds, reducing and nonreducing sugars than the susceptible cultivar ’IR 8’, while the leaves of cultivar ’IR 8’ possessed larger concentration of total soluble amino acids than the resistant cultivar ’BJ 1’. In the leaves of cultivar ‘BJ 1’, the disease development caused an initial decrease in the concentration of phenols followed by an increase at later stages. As a result of inoculation, soluble carbohydrates and amino acids generally decreased in the leaves of resistant cultivar ‘BJ 1’, in contrast to an increase in their concentration in the leaves of cultivar ‘IR 8’.     

Oxidative dealkylation of a hindered phenol catalyzed by copper (II) bis benzimidazole diamide complex

The oxidative dealkylation of 2,4,6-tri-tert-butylphenol (TTBP) has been investigated using molecular oxygen and [Cu(NO₃(GBHA)](NO₃) as catalyst, where GBHA is N,N′-bis((benzimidazol-2-yl)methyl)hexanediamide [(a) M. Gupta, P. Mathur, R.J. Butcher, Inorg. Chem. 40 (2001) 878; (b) M. Gupta, S.K. Das, P. Mathur, A.W. Cordes, Inorg. Chim. Acta 353 (2003) 197; (c) S. Tehlan, M.S. Hundal, P. Mathur, Inorg. Chem. 43 (2004) 6589; (d) F. Afreen, P. Mathur, A. Rheingold, Inorg. Chim. Acta 358 (2005) 1125.]. X-ray structural characterization of complex [Cu(NO₃)(GBHA)](NO₃) · CH₃OH confirms that the Cu (II) ion is in a distorted square pyramidal geometry (τ = 0.168). The TTBP oxidation reaction proceeds via tri-tert-butylphenoxyl radical producing two products 2,6-di-tert-butyl-1,4-benzoquinone (A) and 4,6-di-tert-butyl-1,2-benzoquinone (B). Both A and B have been well characterized by ¹H NMR, ¹³C NMR, UV-Vis and mass data.     

Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells

TET family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Here, we show that Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem cells (ESCs) and are induced concomitantly with 5hmC during reprogramming of fibroblasts to induced pluripotent stem cells. ESCs depleted of Tet1 by RNAi show diminished expression of the Nodal antagonist Lefty1 and display hyperactive Nodal signaling and skewed differentiation into the endoderm-mesoderm lineage in embryoid bodies in?vitro. In Fgf4- and heparin-supplemented culture conditions, Tet1-depleted ESCs activate the trophoblast stem cell lineage determinant Elf5 and can colonize the placenta in midgestation embryo chimeras. Consistent with these findings, Tet1-depleted ESCs?form aggressive hemorrhagic teratomas with increased endoderm, reduced neuroectoderm, and ectopic appearance of trophoblastic giant cells. Thus, 5hmC is an epigenetic modification associated with the pluripotent state, and Tet1 functions to regulate the lineage differentiation potential of ESCs.