Genome-wide integrative analysis revealed a correlation between lengths of copy number segments and corresponding gene expression profile

Microarray analysis has been applied to comprehensively reveal the abnormalities of DNA copy number (CN) and gene expression in human cancer research during the last decade. These analyses have individually contributed to identify the genes associated with carcinogenesis, progression, metastasis of tumor cells and poor prognosis of cancer patients. However, it is known that the correlation between profiles of CN and gene expression does not highly correlate. Factors which determine the degree of correlation remain largely unexplained. To investigate one such factor, we performed trend analyses between the lengths of CN segments and corresponding gene expression profiles from microarray data in hepatocellular carcinoma (HCC) and colorectal carcinoma (CRC). Significant correlations were observed in CN gain of HCC and CRC (p<0.05). The trend of the CN loss showed a significant correlation in HCC although there was no correlation between the length of CN loss segments and gene expression in CRC. Our findings suggest that the influence of CN on gene expression highly depends on the length of CN region, especially in the case of CN gain. To the best of our knowledge, this is the first study describing the correlation between lengths of CNA segments and expression profiles of corresponding genes.     

Distinct mechanisms of tumor invasion and metastasis

Most cancer deaths are caused by metastasis rather than the primary tumor. Cancer cells invade normal tissue as epithelial sheets or single cells by inducing expression of programs characteristic of developmental processes. Depending on their tissue of origin, cancer cells subsequently spread to distinct target organs where they seed secondary tumors (metastasis). Recent experimental evidence suggests that metastasis requires changes not only in cancer cells but also in the tumor microenvironment and in the metastatic target site. For example, a premetastatic niche is formed in target organs that attract cancer cells. Understanding the distinct mechanisms used by cancer cells to form metastasis will enable better patient evaluation and the design of innovative therapeutic approaches.     

Enantioselective recognition of ammonium perchlorate salts by optically active monoaza-15-crown-5 ethers

Chiral monoaza-15-crown-5 ethers (1, 2) were prepared from (R)-(-)-2-amino-1-butanol in high yield. The chiral monoaza-15-crown-5 ethers were purified directly as NaClO(4) complexes. Molecular recognition by these chiral monoaza-crown ethers of (R)- and (S)-PhEtHClO(4) and (R)- and (S)-NapEtHClO(4) as characterized by UV-vis spectroscopy. The order of enantiomeric selectivity is (R)- > (S)- PhEtHClO(4) and (S)- > (R)-NapEtHClO(4) for 1. In the case of 2 it was (R)- > (S)-PhEtHClO(4) and (R)- > (S)- NapEtHClO(4). The cavity of macrocycle and steric hindrance of the benzene units appears to play an important role in recognition.     

Determination of degradation of radioactivity and its kinetics in aerobic composting

In this study, the kinetics of disappearance of radioactivity in aerobic composting was investigated. For this purpose, compost materials were prepared by mixing sugar beet wastes, wine factory wastes (grape wastes), straw and biological treatment sludge in different amounts. While alpha-radioactivity was not initially detected in all composting materials, the composting materials had some beta-radioactivity. In the mixtures of sugar beet wastes--straw-biological treatment sludge (1), sugar beet wastes-wine factory wastes (grape wastes)-biological treatment sludge (II) and wine factory wastes (grape wastes)-biological treatment sludge (III), the beta-radioactivity reduced by 82%, 58%, 85% respectively of initial values after 52 d. The beta-radioactivity degradation in the composting process could be represented by first-order kinetics and reaction rate constants of mixtures of I, II and III were k = 0.0693 d(-1) (R2 - 0.84), k = 0.0453 d(-1) (R2 = 0.98), k = 0.0234 d(-1) (R2 = 0.97), respectively.     

A newFerulago (Apiaceae) species from Turkey

Ferulago antiochia Saya & Miski is newly described: it is known only from the type locality in Hatay province and has affinities toF. trachycarpa Boiss. of sect.Anisotaenia.     

Adsorption of metal complex dyes from aqueous solutions by pine sawdust

An attempt to alleviate the problem caused by the presence of metal complex dyes, mostly used in textile industries, in the textile effluents was undertaken. The effects of adsorbent particle size, pH, adsorbent dose, contact time and initial dye concentrations on the adsorption of metal complex dyes by pine sawdust was investigated. Acidic pH was favorable for the adsorption of metal complex dyes. A contact time of 120 min was required to reach the equilibrium. The experimental isotherm data were analyzed using the Langmuir, Freundlich and Temkin equations. The equilibrium data fit well the Langmuir isotherm. The monolayer adsorption capacities are 280.3 and 398.8 mg dye per g of pine sawdust for Metal Complex Blue and Metal Complex Yellow, respectively. The results indicate that pine sawdust could be employed as low-cost alternative to commercial activated carbon in aqueous solution for the removal of metal complex dyes.     

A comparative tool for the validity of rate kinetics in ion channels by Onsager reciprocity theorem

The precise form of the rate constant functions of ion channels is very crucial for reproducing the electrophysiological behavior. Therefore, how well they account for experimental data plays an important role in the behavior of the model. In this study, we derive kinetic coefficients of activation and inactivation gates in ion channels by Onsager reciprocity theorem for an ensemble of gating particles, and propose that the obtained kinetic coefficients can be used as a comparative tool for the empirical validity of fitted rate constant functions to experimental data. We also illustrate its applicability based on the activation and inactivation kinetics of T-type calcium channel in thalamic relay neurons. We show that the shape of the steady-state curve by itself seems to be a poor indicator of the functional form of the rate functions, but the time constant curves reflect considerable variation depending on the particular form of the rate functions, and that the kinetic coefficients related to the time constants provide a powerful tool to determine the empirical validity of the fitted rate constants.     

The effect of L-NAME administrations after oral mucosal incision on wound NO level in rabbit

The aim of the current study was to comparatively investigate the effect of inhibition of nitric oxide (NO) production by N-nitro-L-arginine methyl ester (L-NAME), an isoform non-specific inhibitor of nitric oxide synthase (NOS), after oral mucosal incision on wound tissue NO levels. A standard incision was applied to the oral mucosa of rabbits. After oral mucosal incision, rabbits were divided into five groups as follows: (1) Untreated incisional group (control); (2) Titanium (Ti) implanted group; (3) Ti + Polyethylene glycol (PEG) 4000 implanted group; (4) Ti + PEG 4000 + L-NAME (2 × 10⁻⁴ M) implanted group and (5) i.p. L-NAME administrated group (10 mg/kg). At 5 days after oral incision operations, wound tissue strips and plasma were obtained from rabbits. Oral wound tissue and plasma nitric oxide, plasma thiobarbituric acid reactive substances (TBARS) and total sulfhydryl group (RSH) levels were investigated. Plasma TBARS and NOx levels decreased after i.p. L-NAME administration. Total RSH group levels were not changed in all groups (p>0.05). This means that L-NAME inhibits the deteriorating effects of free radicals without affecting healing. L-NAME in PEG and titanium also has no effect on tissue and plasma NOx levels. These findings indicate that NO generation will not be affected both Ti and local nitric oxide synthase (NOS) inhibitor. (Mol Cell Biochem 278: 65–69, 2005)     

The agnoprotein of polyomaviruses: a multifunctional auxiliary protein

The late region of the three primate polyomaviruses (JCV, BKV, and SV40) encodes a small, highly basic protein known as agnoprotein. While much attention during the last two decades has focused on the transforming proteins encoded by the early region (small and large T-antigens), it has become increasingly evident that agnoprotein has a critical role in the regulation of viral gene expression and replication, and in the modulation of certain important host cell functions including cell cycle progression and DNA repair. The importance of agnoprotein is underscored by its expression during lytic infection of glial cells by JCV that occurs in progressive multifocal leukoencephalopathy (PML), and also in some JCV-associated human neural tumors particularly medulloblastoma. In this review, we will discuss the structure and function of agnoprotein in the viral life cycle during the course of lytic infection and the consequences of agnoprotein expression for the host cell.