CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?

Background: CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. ( 2006) recently developed a new algorithm, CpGcluster, which uses a completely diffe

Interaction between phycobilisomes from Porphyridium cruentum and thylakoid membranes from Gymnodinium sp or spinach

Thylakoid membranes were isolated from Gymnodinium sp. and spinach, whereas the phycobilisomes were isolated and purified from red alga Porphyridium cruentum. The absorption spectra of the purified phycobilisomes (PBS) showed three peaks at 548, 564, and 624 nm, respectively, and the ratio of the fluorescence intensity at the lambda(680)(em) to lambda(80)(em5) that at was about 7.3. All these results demonstrated that the purified PBS remained intact. The thylakoid membranes were incubated with the purified phycobilisomes, and the thylakoid membranes, which harbored the phycobilisomes, were purified by sucrose density gradient centrifugation. Meantime, the conjugates of phycobilisome-thylakoid membranes were constructed using glutaraldehyde and further purified. Their characteristics were studied by measuring the absorption spectra and fluorescence emission spectra. The results showed that the phycobilisomes from Porphyridium cruentum can attach to the thylakoid membranes from Gymnodinium sp. and spinach without covalent cross-linking, but the excited energy transfer did not occur. The conjugate of phycobilisome-thylakoid. membranes with covalent cross-linking exhibits the excited energy transfer between the phycobilisomes and the thylakoid membranes.

Effects of acute temperature or salinity stress on the immune response in sea cucumber, Apostichopus japonicus

Invertebrates are increasingly raised in mariculture, where it is important to monitor immune function and to minimize stresses that could suppress immunity. The activities of phagocytosis, superoxide dismutase (SOD), catalase (CAT), myeloperoxiclase (MPO), and lysozyme (LSZ) were measured to evaluate the immune capacities of the sea cucumber, Apostichopus japonicus, to acute temperature changes (from 12 degrees C to 0 degrees C, 8 degrees C, 16 degrees C, 24 degrees C, and 32 degrees C for 72 h) and salinity changes (from 30 parts per thousand to 20 parts per thousand, 25 parts per thousand, and 35 parts per thousand for 72 h) in the laboratory. Phagocytosis was significantly affected by temperature increases in 3 h, and by salinity (25 parts per thousand and 35 parts per thousand) changes in 1 h. SOD activities decreased significantly in 0.5 h to 6 h samples at 24 degrees C. At 32 degrees C, SOD activities decreased significantly in 0.5 h and 1 h exposures, and obviously increased for 12 h exposure. CAT activities decreased significantly at 24 degrees C for 0.5 h exposure, and increased significantly at 32 degrees C in 3 h to 12 h exposures. Activities of MPO increased significantly at 0 degrees C in 0.5 h to 6 In exposures and at 8 degrees C for 1 h. By contrast, activities of MPO decreased significantly in 24 degrees C and 32 degrees C treatments. In elevated-temperature treatments, activities of LSZ increased significantly except at 32 degrees C for 6 h to 12 h exposures. SOD activity was significantly affected by salinity change. CAT activity decreased significantly after only 1 h exposure to salinity of 20 parts per thousand.. Activities of MPO and LSZ showed that A. japonicus tolerates limited salinity stress. High-temperature stress had a much greater effect on the immune capacities of A. japonicus than did low-temperature and salinity stresses. Crown Copyright (C) 2008 Published by Elsevier Inc. All rights reserved.

LC determination of amino acids in rat plasma with fluorescence detection: Application to exercise physiology

An LC method for the determination of 20 amino acids (AAs), using 1,2-Benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC) as fluorescent labeling reagent, has been validated and applied for the analysis of AAs in rat plasma at three different states concerning exercise physiology. Identification of AA derivatives was carried out by LC-MS with electrospray ion (ESI), and the MS-MS cleavage mode of the representative tyrosine (Tyr) derivative was analyzed. Gradient elution on a Hypersil BDS C-18 column gave good separation of the derivatives. Excellent linear responses were observed and good compositional data could be obtained from as little as 50-200 mu L of plasma samples. The contents of 20 AAs in rat plasma of three groups (24 rats, group A: quiet state, group B: at exercising exhaust, group C: 12 h after exercising exhaust) exhibited evident difference corresponding to the physiological states. Facile BCEOC derivatization coupled with LC-FLD-ESI-MS analysis allowed the development of a highly sensitive method for the quantitative analysis of trace level of AAs from plasma or other biochemical samples.