Cytogenetic analysis of myxoid liposarcoma and myxofibrosarcoma by array-based comparative genomic hybridisation

AIM

To investigate overall chromosomal alterations using array-based comparative genomic hybridisation (CGH) of myxoid liposarcomas (MLSs) and myxofibrosarcomas (MFSs).

MATERIALS AND METHODS

Genomic DNA extracted from fresh-frozen tumour tissues was labelled with fluorochromes and then hybridised on to an array consisting of 1440 bacterial artificial chromosome clones representing regions throughout the entire human genome important in cytogenetics and oncology.

RESULTS

DNA copy number aberrations (CNAs) were found in all the 8 MFSs, but no alterations were found in 7 (70%) of 10 MLSs. In MFSs, the most frequent CNAs were gains at 7p21.1-p22.1 and 12q15-q21.1 and a loss at 13q14.3-q34. The second most frequent CNAs were gains at 7q33-q35, 9q22.31-q22.33, 12p13.32-pter, 17q22-q23, Xp11.2 and Xq12 and losses at 10p13-p14, 10q25, 11p11-p14, 11q23.3-q25, 20p11-p12 and 21q22.13-q22.2, which were detected in 38% of the MFSs examined. In MLSs, only a few CNAs were found in two sarcomas with gains at 8p21.2-p23.3, 8q11.22-q12.2 and 8q23.1-q24.3, and in one with gains at 5p13.2-p14.3 and 5q11.2-5q35.2 and a loss at 21q22.2-qter.

CONCLUSIONS

MFS has more frequent and diverse CNAs than MLS, which reinforces the hypothesis that MFS is genetically different from MLS. Out-array CGH analysis may also provide several entry points for the identification of candidate genes associated with oncogenesis and progression in MFS.

The application of wavelet and feature vectors to ECG signals

The Electrocardiogram (ECG) is one of the most commonly known biological signals. Traditionally ECG recordings are analysed in the time-domain by skilled physicians. However, pathological conditions may not always be obvious in the original time-domain signal. Fourier analysis provides frequency information but has the disadvantage that time characteristics will be lost. Wavelet analysis, which provides both time and frequency information, can overcome this limitation. Here a new method, the combination of wavelet analysis and feature vectors, is applied with the intent to investigate its suitability as a diagnostic tool. ECG signals with normal and abnormal beats were examined. There were two stages in analysing ECG signals: feature extraction and feature classification. To extract features from ECG signals, wavelet decomposition was first applied and feature vectors of normalised energy and entropy were constructed. These feature vectors were used to classify signals. The results showed that normal beats and abnormal beats composed different clusters in most cases. In conclusion, the combination of wavelet transform and feature vectors has shown potential in detecting abnormalities in an ECG recording. It was also found that normalised energy and entropy are features, which are suitable for classification of ECG signals.

Plasma ghrelin levels in healthy elderly volunteers: the levels of acylated ghrelin in elderly females correlate positively with serum IGF-I levels and bowel movement frequency and negatively with systolic blood pressure

Aging is associated with a decrease in growth hormone (GH) secretion, appetite and energy intake. As ghrelin stimulates both GH secretion and appetite, reductions in ghrelin levels may be involved in the reductions in GH secretion and appetite observed in the elderly. However, only preliminary studies have been performed on the role of ghrelin in elderly subjects. In this study, we sought to clarify the physiologic implications of the age-related alterations in ghrelin secretion by determining plasma ghrelin levels and other clinical parameters in healthy elderly subjects. Subjects were > or = 65 years old, corresponding to the SENIEUR protocol, had not had a resection of the upper gastrointestinal tract and had not been treated with hormones. One hundred and five volunteers (49 men and 56 women) were admitted to this study (73.4 +/- 6.3 years old). Plasma levels of acylated ghrelin in elderly female subjects positively correlated with serum IGF-I levels and bowel movement frequency and negatively with systolic blood pressure. In elderly men, desacyl ghrelin levels correlated only weakly with bowel movement frequency. These findings suggest that the plasma levels of the acylated form of ghrelin may influence the age-related alterations in GH/IGF-I regulation, blood pressure and bowel motility. These observational associations warrant further experimental studies to clarify the physiologic significance of these effects.

A novel NADH-dependent carbonyl reductase from Kluyveromyces aestuarii and comparison of NADH-regeneration system for the synthesis of ethyl (S)-4-chloro-3-hydroxybutanoate

To compare NADH-regeneration systems for the synthesis of (S)-4-chloro-3-hydroxybutanoate (ECHB), a novel NADH-dependent carbonyl reductase (KaCR1), which reduced ethyl 4-chloroacetoacetate (ECAA) to form (S)-ECHB, was screened and purified from Kluyveromyces aestuarii and a gene encoding KaCR1 was cloned. Glucose dehydrogenase (GDH) and formate dehydrogenase (FDH) were compared as enzymes for NADH regeneration using Escherichia coli cells coexpressing each enzyme with KaCR1. E. coli cells coexpressing GDH produced 45.6 g/l of (S)-ECHB from 50 g/l of ECAA and E. coli cells coexpressing FDH, alternatively, produced only 19.0 g/l. The low productivity in the case of FDH was suggested to result from the low activity and instability of FDH.

Comprehensive gene expression analysis of the response to straight-chain alcohols in Saccharomyces cerevisiae using cDNA microarray

AIMS

The purpose of this study was to examine the gene expression profiles of yeast Saccharomyces cerevisiae subjected to straight-chain alcohols.

METHODS AND RESULTS

Lipophilic alcohols with high log Pow values were more toxic to yeast than those with low log Pow values. Morphological changes after exposure to ethanol, 1-pentanol, 1-octanol were observed, whereas n-pentane as a model hydrocarbon affected the surface of the outer membrane, with little change in organelles. Using cDNA microarrays, quite a few up-regulated gene categories were classified into the category 'cell rescue, defence and virulence' by ethanol, and the category 'energy' and 'metabolism' by 1-pentanol. Meanwhile, the characteristic genes up-regulated by n-pentane were not observed, and the expression profile was distantly related to ethanol, 1-pentanol and 1-octanol.

CONCLUSIONS

This study suggests that gene expression profiles at the whole genome level were intimately associated with the cell growth inhibition and morphological changes by straight-chain alcohols with differing log Pow values.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study of comprehensive gene expression profiles by cDNA microarrays elucidates the straight-chain alcohol adaptation mechanisms.

Common fragile genes

Common chromosome fragile sites show susceptibility to DNA damage, leading to alterations that contribute to cancer development. The cloning and characterization of fragile sites have demonstrated that fragile sites are associated with genes that relate to tumorigenesis. Identification of the basis of instability at fragile sites and the related genes provides an entree to understanding of important aspects of chromosomal instability, a prominent feature of neoplastic genomes. FHIT/FRA3B and WWOX/FRA16D, the most sensitive common fragile genes in the human genome, function as tumor suppressor genes. The common features of these two common fragile genes are summarized, and suggest clues to understanding the relation between genomic instability and tumor biology.

Synthesis of ethyl ( S)-4-chloro-3-hydroxybutanoate using fabG-homologues

This paper is a report on the successful application of bioinformatics to enzyme screening. The synthesis of ethyl ( S)-4-chloro-3-hydroxybutanoate (ECHB) by asymmetric reduction of ethyl 4-chloroacetoacetate (ECAA) using fabG-homologues was studied. beta-Ketoacyl-acyl carrier protein reductases from both Escherichia coli and Bacillus subtilis, which are components of type II fatty acid synthase, could reduce ECAA to ( S)-ECHB with 94-98% ee. Furthermore, acetoacetyl-CoA reductases (ARs) from both Ralstonia eutropha and Zoogloea ramigera, whose genes are significantly similar to fabG genes and play a physiological role in the biosynthesis of poly-beta-3-hydroxybutyrate, could also catalyze the asymmetric reduction of ECAA to ( S)-ECHB with >99% ee. ( S)-ECHB was synthesized to 48.7 g/l with an optical purity of 99.8% ee, using recombinant E. coli cells coexpressing AR from R. eutropha and glucose dehydrogenase from B. subtilis for the regeneration of NADPH.

Non-uniformities in polymer/liquid crystal mixtures I. Interfacial tension

We theoretically study interfacial properties between two coexisting phases in mixtures of a flexible polymer and a low-molecular-weight liquid crystal. By numerically solving Euler equations for compositional and orientational order parameter fields, we calculate the order parameter profiles and interfacial tensions for nematic-isotropic and isotropic-isotropic phase equilibria. We find that the order parameter profiles are non-monotonic at some temperatures. The nematic-isotropic interfacial tension increases with decreasing temperature and is approximately proportional to (T - T(NI))(n) at temperatures below the nematic-isotropic transition temperature (T(NI)) of the pure nematogen. The value of the exponent n is strongly affected by the existence of a triple point.

Non-uniformities in polymer/liquid crystal mixtures II. Nematic nucleation

We theoretically model the nucleation of nematic droplets during phase ordering in mixtures of a flexible polymer and a low-molecular-weight liquid crystal. By appealing to classical nucleation theory (CNT), we calculate the energy barrier to nucleation and the size of a critical nucleus. We study the influence of a metastable intermediate phase on the nucleation of the nematic. Below a triple point in the phase diagram, there are two distinct mechanisms for the formation of a nematic nucleus: 1) direct nucleation from the isotropic phase and 2) nucleation via a precursor metastable isotropic phase. We calculate the crossover concentration as a function of temperature, delineating the regions of the phase diagram in which each mechanism prevails. In the latter case, the presence of a hidden metastable isotropic-isotropic binodal may either promote or delay the nucleation of a nematic phase.

Purification and properties of a carbonyl reductase useful for production of ethyl (S)-4-chloro-3-hydroxybutanoate from Kluyveromyces lactis

A novel carbonyl reductase (KLCR1) that reduced ethyl 4-chloroacetoacetate (ECAA) to synthesize ethyl (S)-4-chloro-3-hydroxybutanoate ((S)-ECHB) was purified from Kluyveromyces lactis. KLCR1 catalyzed the NADPH-dependent reduction of ECAA enantioselectively but not the oxidation of (S)-ECHB. From partial amino acid sequences, KLCR1 was suggested to be an alpha subunit of fatty acid synthase (FAS) but did not have FAS activity.

Synthesis of (R)-1,3-butanediol by enantioselective oxidation using whole recombinant Escherichia coli cells expressing (S)-specific secondary alcohol dehydrogenase

The synthesis of (R)-1,3-butanediol (BDO) from its racemate was studied using whole cells of recombinant Escherichia coli expressing an (S)-specific secondary alcohol dehydrogenase (CpSADH) from Candida parapsilosis by enantioselective oxidation. Under the optimized conditions, the yield of (R)-1,3-BDO reached 72.6 g/l, with a molar recovery yield of 48.4% from a racemate of 15% and an optical purity of 95% ee.