A conserved TN8TCCT motif in the octapeptide-encoding region of Pax genes which has the potential to direct cytosine methylation

Our previous findings have shown that the developmental genes Pax7 and Pax3 are differentially methylated; the gene region that encodes the paired domain is hypomethylated, whereas the region that encodes the homeodomain is hypermethylated. For this reason, the known DNA sequence between the paired and homeoboxes was analysed for the presence of a conserved DNA motif to which a modifying protein could bind in order to direct the methylation or demethylation of surrounding gene sequences. The octapeptide-encoding region was found to contain several nucleotides that were highly conserved throughout the Pax gene family from phylogenetically distant species. The most conserved nucleotides are thought to comprise a motif TN8TCCT where N8=any combination of eight nucleotides. A conserved octapeptide-like-encoding sequence containing the TN8TCCT motif was also found in non-Pax genes of higher eukaryotes and in the non-coding strand of plants. Moreover, differential methylation seems to be associated with the presence of the TN8TCCT motif in p53 and the human oestrogen receptor genes. The presence of the TN8TCCT motif within an octapeptide-like-encoding sequence in human T-cell leukaemia virus type 1 might suggest that the putative recognition motif may have been introduced into various host genomes via some form of retroviral agent.     

Single amino acid substitutions can further increase the stability of a thermophilic L-lactate dehydrogenase

Lactate dehydrogenases are of considerable interest as stereospecificcatalysts in the chemical preparation of enantiomerically pure-hydroxyacid synthons. For such applications in synthetic organicchemistry it would be desirable to have enzymes which tolerateelevated temperatures for prolonged reaction times, to increaseproductivity and to extend then applicability to poor substrates.Here, two examples are reported of significant thermostabilizations,induced by sitedirected mutagenesis, of an already thermostableprotein, the L-lactate dehydrogenase (EC 1.1.1.27 [EC] , 35 kDa permonomer subunit) from Bacillus stearothermophilus. Thermal inactivationof this enzyme is accompanied by irreversible unfolding of thenative protein structure. The replacement of Argl71 by Tyr stabilizesthe enzyme against thermal inactivation and unfolding. Thisstabilizing effect appears to be based on improved interactionsbetween the subunits in the core of the active dimeric or tetramericforms of the enzyme. The thermal stability of L-lactate dehydrogenasevariants with an active site Arg residue, either in the 171(wild-type) or in the 102 position, is further increased bysulfate ions. The two stabilizing effects are additive, as foundfor the Argl71Tyr/ Gln1O2Arg double mutant, for which the stabilityof the protein in 100 mM sulfate solution reaches that of L-lactatedehydrogenases from extreme thermophiles. All mutant proteinsretain significant catalytic activity, both in the presenceand absence of stnhilfoing salts, and are viable catalysts inpreparative scale reactions.     

Fractional brownian motion: a maximum likelihood estimator and its application to image texture

Fractals have been shown to be useful in characterizing texture in a variety of contexts. Use of this methodology normally involves measurement of a parameter H, which is directly related to fractal dimension. In this work the basic theory of fractional Brownian motion is extended to the discrete case. It is shown that the power spectral density of such a discrete process is only approximately proportional to |f|a instead of in direct proportion as in the continuous case. An asymptotic Cramer-Rao bound is derived for the variance of an estimate of H. Subsequently, a maximum likelihood estimator (MLE) is developed to estimate H. It is shown that the variance of this estimator nearly achieves the minimum bound. A generation algorithm for discrete fractional motion is presented and used to demonstrate the capabilities of the MLE when the discrete fractional Brownian process is contaminated with additive Gaussian noise. The results show that even at signal-to-noise ratios of 30 dB, significant errors in estimation of H can result when noise is present. The MLE is then applied to X-ray images of the human calcaneus to demonstrate how the line-to-line formulation can be applied to the two-dimensional case. These results indicate that it has strong potential for quantifying texture.     

Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell

DNA methylation is a prevalent regulatory modification in prokaryotes and eukaryotes. N¹-methyladenine (m¹A) and N⁶-methyladenine (m⁶A) have been found to be capable of altering DNA structures via disturbing Watson–Crick base pairing. However, little has been known about their influences on non-B DNA structures, which are associated with genetic instabilities. In this work, we investigated the effects of m¹A and m⁶A on both the structure and thermodynamic stability of a newly reported DNA minidumbbell formed by two TTTA tetranucleotide repeats. As revealed by the results of nuclear magnetic resonance spectroscopic studies, both m¹A and m⁶A favored the formation of a T·m¹A and T·m⁶A Hoogsteen base pair, respectively. More intriguingly, the m¹A and m⁶A modifications brought about stabilization and destabilization effects on the DNA minidumbbell, respectively. This work provides new biophysical insights into the effects of adenine methylation on the structure and thermodynamic stability of DNA.     

Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

Water sorption of poly(vinyl alcohol)/ poly(diallyldimethylammonium chloride) interpenetrating polymer network hydrogels

Temperature‐responsive interpenetrating polymer network (IPN) hydrogels constructed with poly(vinyl alcohol) and poly(diallyldimethylammonium chloride) using the sequential IPN method were studied. The characteristics of IPN hydrogels were investigated using the dynamic vapor sorption system. IPN hydrogels exhibited a relatively high sorption ratio, 180–360% at room temperature. The sorption ratio of hydrogels depended on temperature. Diffusion coefficients were calculated according to the Fickian Law at several temperatures. The apparent activation energy was 5.43 kJ mol^?1, which corresponds to typical diffusion processes. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 1389–1392, 2003     

Evidence for the involvement of quinone rings in reactions of some coals with tetralin

Model compounds representing a variety of hydrocarbon groups and most of the oxygen-containing functional groups have been tested for reactivity with tetralin at 400° C. Only the quinones were capable of oxidizing tetralin to naphthalene. Anthraquinone is completely deoxygenated to anthracene. Evidence for homolysis of carbon-carbon bonds was found only in the case of dibenzyl, and this was not accompanied by oxidation of tetralin. The extractability of subbituminous coals with the non-reducing solvent, diphenyl-diphenyl ether eutectic, is correlated with oxygen content and depth of burial. It is suggested that oxidized coals near the surface contain quinone rings, and that dissolution by tetralin is primarily then due to lowering of the solvent parameter as a consequence of deoxygenation.     

Adsorption of aroma chemicals on cotton fabric from aqueous systems

The adsorption of aroma chemicals on cotton fabric was studied relative to the surfactant concentration, surfactant type, water solubility, and fiber morphology. The adsorption increased with increasing surfactant concentration to a maximum near the critical micelle concentration, then decreased with further increases in surfactant concentration. The adsorption also was found to be highly dependent on the fiber surface area and pore structure; dramatic differences were observed between untreated and mercerized cotton fabric and are believed to be due to morphological differences. Cationic and anionic surfactants increased the aroma chemical adsorption, which varied with surfactant type, with cetyltrimethylammonium chloride (CTAC)>sodium dodecyl sulfate (SDS)>H₂O. Water solubility also influenced adsorption; in most cases, adsorption increased with water solubility. In addition, adsorption was also influenced by chemical structure and hydrophobic interactions. The adsorption of aroma chemicals on cotton fabric can be attributed to the aqueous solution being physically held in capillaries and pore structures within the fibular structure of cotton fiber and also to molecular interactions among the aroma chemical molecules, surfactants, and cotton substrate.     

Preparation and characterizations of interpenetrating polymer network hydrogels of poly(ethylene oxide) and poly(methyl methacrylate)

Interpenetrating polymer network (IPN) hydrogels based on poly(ethylene oxide) and poly(methyl methacrylate) were prepared by radical polymerization using 2,2‐dimethyl‐2‐phenylacetophenone and ethylene glycol dimethacrylate as initiators and crosslinkers, respectively. The IPN hydrogels were analyzed for sorption behavior at 25°C and at a relative humidity of 95% using dynamic vapor sorption. The IPN hydrogels exhibited a relatively high equilibrium water content in the range of 13–68%. The state of water in the swollen IPN hydrogels was investigated using differential scanning calorimetry. The free water in the hydrogels increased as the hydrophilic content increased. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 258–262, 2003