Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.     

Hypochlorous acid-induced stress on human spermatozoa. A model for inflammation in the male genital tract

The fertilising ability of human spermatozoa may be impaired by inflammations of the genital tract, although details of these processes are still unknown. Hypochlorous acid (HOCl), an important product of myeloperoxidase released from stimulated neutrophils, induces a concentration-dependent increase in externalisation of phosphatidylserine in ejaculated human spermatozoa as revealed by fluorescence-activated cell sorting (FACS) analysis. The increase of annexin-V binding cells starts already at about 10(-5) mol/l HOCl, while a formation of lysophosphatidylcholines as detected by matrix-assisted laser desorption and ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is only found at HOCl concentrations higher than 10(-4) mol/l. Thus, changes in lipid composition of spermatozoa are unlikely responsible for the phosphatidylcholine (PS)-externalisation. These data gave concomitant evidence that HOCl itself leads to a dramatic damage of the cell membrane. Thus, the neutrophil-derived HOCl contributes to the deterioration of spermatozoa leading to diminished fertilisation ability.     

Requirement of c-Jun NH2-terminal kinase activation in interferon-alpha-induced apoptosis through upregulation of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) in Daudi B lymphoma cells

Interferon alpha (IFN-alpha) inhibits growth, at least in part, through induction of apoptosis. However, the molecular mechanisms underlying IFN-alpha-induced apoptosis are not completely understood. In the present study, we found that IFN-alpha induced a sustained activation of c-Jun N-terminal kinase 1 (JNK1), but not extracellular kinases (ERKs), in Daudi B lymphoma cells, as assessed by Western blotting using phospho-specific antibodies. Several lines of evidence support the notion that the IFN-alpha-induced activation of JNK is responsible for IFN-alpha-induced apoptosis, at least in part, through upregulation of TNF-related apoptosis-inducing ligand (TRAIL). First, pretreatment of Daudi cells with a JNK inhibitor reduced IFN-alpha-induced upregulation of TRAIL and loss of mitochondrial membrane potential (DeltaPsim) and annexin-positive cells, which was assessed by flow cytometry. Second, a dominant-negative form of JNK1 (dnJNK1) also reduced these apoptotic events, while a constitutively active form of JNK1, MKK7-JNK1beta, enhanced them. Finally, treatment with IFN-alpha enhanced the promoter activity of the TRAIL gene, which was partially abrogated by either JNK inhibitor or dnJNK1, while it was moderately enhanced by MKK7-JNK1beta. These findings are useful for understanding molecular mechanisms of IFN-alpha-induced apoptosis and also for development of treatment modalities of some tumors with IFN-alpha.     

Evaluation of three methods for effective extraction of DNA from human hair

In this paper we evaluate three different methods for extracting DNA from human hair i.e. the Chelex method, the QIAamp DNA Mini Kit method and the ISOHAIR method. Analysis of DNA prepared from dyed hairs with the ISOHAIR method suggested that the DNA extracts contained PCR inhibitors. On the other hand, few inhibition was observed when DNA from dyed hairs were extracted using the Chelex method and the QIAamp DNA Mini Kit method. In conclusion, the Chelex method is recommended for PCR experiments in view of its simplicity and cost-effectiveness. To assess the reliability of the Chelex method for the extraction of genomic DNA from both natural and dyed hair samples, minisatellite variant repeat (MVR)-polymerase chain reaction (PCR) patterns of Chelex-extracted DNA were compared using hairs (three natural black hairs and three dyed hairs) with buccal swabs from six individuals. Complete agreement was observed between hair and swab samples in each individual, proving the utility of the Chelex method.     

Changes of enzyme activity in lipid signaling pathways related to substrate reordering

The static fluid mosaic model of biological membranes has been progressively complemented by a dynamic membrane model that includes phospholipid reordering in domains that are proposed to extend from nanometers to microns. Kinetic models for lipolytic enzymes have only been developed for homogeneous lipid phases. In this work, we develop a generalization of the well-known surface dilution kinetic theory to cases where, in a same lipid phase, both domain and nondomain phases coexist. Our model also allows understanding the changes in enzymatic activity due to a decrease of free substrate concentration when domains are induced by peptides. This lipid reordering and domain dynamics can affect the activity of lipolytic enzymes, and can provide a simple explanation for how basic peptides, with a strong direct interaction with acidic phospholipids (such as beta-amyloid peptide), may cause a complex modulation of the activities of many important enzymes in lipid signaling pathways.     

Synthesis of 2,3-unsaturated C-glycosides by HClO4-SiO2 catalyzed Ferrier rearrangement of glycals

Alkyl 2,3-unsaturated C-glycopyranosides have been prepared by Ferrier rearrangement of acyl or alkyl protected glycals catalyzed by HClO(4)-SiO(2).     

Direct one-pot conversion of acylated carbohydrates into their alkylated derivatives under heterogeneous reaction conditions using solid NaOH and a phase transfer catalyst

A convenient one-pot protocol for the direct conversion of acyl-protected carbohydrates into their alkylated counterparts has been developed by using alkyl halides in the presence of solid sodium hydroxide and a phase transfer catalyst. These economically convenient, mild, two-phase reaction conditions allow the preparation of a variety of monosaccharide intermediates for use in the synthesis of complex oligosaccharides.     

Reactions of D-glucose with phenolic amino acids: further insights into the competition between Maillard and Pictet-Spengler condensation pathways

The reactions of 5-S-cysteinyldopa, L-alpha-methyldopa and DL-m-tyrosine with D-glucose were investigated at 90 degrees C in phosphate buffer at pH ranging from 5.0 to 9.0. Whereas gave mainly the double Maillard condensation product N,N'-bis(1'-deoxy-D-fructos-1'-yl)-5-S-cysteinyldopa, as an inseparable mixture of beta-D-fructopyranosyl and alpha,beta-D-fructofuranosyl derivatives, 2 and 3 gave both Maillard and Pictet-Spengler products, although to different extents and with different regio- and stereochemistry. A peculiar pattern of reactivity was displayed by which gave, besides the Maillard product and the expected 6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline C-1 diastereoisomeric pairs, the unprecedented 7,8-dihydroxy-1,2,3,4-tetrahydroisoquinoline derivative via the ortho cyclization pathway. Pictet-Spengler cyclization of 2 and 3 proceeded with Felkin-Anh-type asymmetric induction, favouring the 1R isomer throughout the pH range 5.0-9.0. These results, which highlight the first example of carbohydrate-derived 7,8-dihydroxytetrahydroisoquinoline, provide new insights into the factors governing competition between Maillard and Pictet-Spengler condensation pathways.