Cloning and gene map assignment of the Xiphophorus DNA ligase 1 gene

Fishes represent the stem vertebrate condition and have maintained several gene arrangements common to mammalian genomes throughout the 450 Myr of divergence from a common ancestor. One such syntenic arrangement includes the GPI-PEPD enzyme association on Xiphophorus linkage group IV and human chromosome 19. Previously we assigned the Xiphophorus homologue of the human ERCC2 gene to linkage group U5 in tight association with the CKM locus. CKM is also tightly linked to the ERCC2 locus on human chromosome 19, leading to speculation that human chromosome 19 may have arisen by fusion of two ancestral linkage groups which have been maintained in fishes. To investigate this hypothesis further, we isolated and sequenced Xiphophorus fish genomic regions exhibiting considerable sequence similarity to the human DNA ligase 1 amino acid sequence. Comparison of the fish DNA ligase sequence with those of other species suggests several modes of amino acid conservation in this gene. A 2.2-kb restriction fragment containing part of an X. maculatus DNA ligase 1 exon was used in backcross hybrid mapping with 12 enzyme or RFLP loci. Significant linkage was observed between the nucleoside phosphorylase (NP2) and the DNA ligase (LIG1) loci on Xiphophorus linkage group VI. This assignment suggests that the association of four DNA repair-related genes on human chromosome 19 may be the result of chance chromosomal rearrangements.      

An Electron Microscope Study of Autoinfection in Neogregarines (Sporozoa, Neogregarinida)

SYNOPSIS. In an electron microscope study of the neogregarine Farinocystis tribolii Weiser 1953 in the fat body of the larvae of the flour beetle Tribolium castaneum , empty oocysts and adjacent sporozoites of the gregarine were found. The empty oocysts contained host cell cytoplasm, a residuum only slightly larger than that in mature oocysts, and some remnants of the oocyst membrane pressed tightly against the inner surface of the wall. Apparently normal sporozoites were found near the empty oocysts and no damaged ones were seen. It is assumed that the sporozoites go on developing in the host, i.e., that autoinfection takes place.     

A nonlinear method for estimating nucleotide polymorphism from restriction maps

Restriction mapping is used to estimate nucleotide sequence polymorphism when the regions to be studied are too long or too numerous to be sequenced. Restriction mapping is less costly than DNA sequencing, but it does not allow direct measurement of underlying nucleotide polymorphism. It is therefore useful to be able to estimate underlying nucleotide polymorphism from observations of polymorphism in restriction maps, as this offers some of the resolution afforded by DNA sequencing at a reduced cost. Previous estimators of underlying nucleotide polymorphism have assumed that each restriction-enzyme- binding site contains, at most, a single polymorphic nucleotide position (the low-polymorphism-frequency assumption), and this assumption has placed an upper limit on the level of polymorphism that can be resolved by these estimators. The present study documents an estimator which allows relaxation of this assumption. The new estimator more accurately estimates underlying nucleotide polymorphism when the polymorphism level is high enough to falsify the low-polymorphism- frequency assumption. The new estimator therefore yields good results for data sets that are too divergent for analysis by present methods.      

Moss synusiae in South Estonian forests

On the Karula Upland, South Estonia, the forest moss layer was analysed using a transect of 726 contiguous 0.2×0.2 m plots. The sample plots were classified according to a multistage clustering procedure based on the sequential use of algorithms with different criteria. Several obtained clusters are rather similar in species composition, but abundance relationships among dominant species are distinctly different. For detailed analysis of mutual relations among societies a formal definition of adjacency is proposed, and two aspects of the cluster continuum — transitionality and distinctness — are estimated. It appears that almost all resulting societies are very distinct (P<0.05), but at the same time can be continual in the sense of transitionality. Spatial changes in vegetation along transects are also discontinuous. The null hypothesis assuming the independency of neighbouring sample plots type was refuted withP=0.01. The spatial extent of different synusiae is typically several times larger than it should be if there were no structure in moss vegetation.     

Whole Genome Amplification for Sequencing and Applications in Conservation Genetics

Abstract: We describe a method for rapidly amplifying whole genomes via a Phi29 DNA polymerase-mediated strand displacement reaction (SDR). Genomic amplification products derived from the SDR reaction resulted in high quantities of DNA suitable for polymerase chain reaction (PCR) amplification and sequencing of mitochondrial genomes. Control region sequences of DNA derived directly from PCR amplicons of extracted DNA were identical to those derived from PCR amplification of SDR genomic DNA. Effective SDR amplification and subsequent sequencing was successful across tissues sources ranging in age from 1 year to 19 years. Strand replacement reaction genomic amplification offers a means of obtaining large quantities of DNA from small amounts of tissue.     

Prospective study of interaction between alcohol, NSAID use and polymorphisms in genes involved in the inflammatory response in relation to risk of colorectal cancer

Inflammatory bowl disease predisposes to cancer of the colorectum, and the use of non-steroidal anti-inflammatory drugs (NSAIDs) decreases the risk; hence genetic variations that modify the inflammatory response may alter the risk of colorectal cancer (CRC). The purpose of this study was to determine if polymorphisms associated with an altered inflammatory response are associated with colorectal cancer risk, and to investigate the possible interaction with lifestyle factors such as alcohol use, smoking and NSAID use. We studied 355 adenocarcinoma cases and 753 control persons, nested within the prospective "Diet, Cancer and Health" study. None of the polymorphisms were associated with risk of colorectal cancer. A statistically significant interaction between PPARgamma2 Pro(12)Ala and alcohol was found, where alcohol use was associated with a 22% increased risk of CRC per 10g alcohol/day among carriers of the variant allele but not among homozygous wild type allele carriers (P for interaction=0.02). Moreover, an interaction between DLG5 R30Q and NSAID use was found (P for interaction=0.02). Our results do not suggest that inborn variations in the inflammatory response play any major role in risk of colorectal cancer.     

Mutations in the Kv1.5 channel gene KCNA5 in cardiac arrest patients

Mutations in one of the ion channels shaping the cardiac action potential can lead to action potential prolongation. However, only in a minority of cardiac arrest cases mutations in the known arrhythmia-related genes can be identified. In two patients with arrhythmia and cardiac arrest, we identified the point mutations P91L and E33V in the KCNA5 gene encoding the Kv1.5 potassium channel that has not previously been associated with arrhythmia. We functionally characterized the mutations in HEK293 cells. The mutated channels behaved similarly to the wild-type with respect to biophysical characteristics and drug sensitivity. Both patients also carried a D85N polymorphism in KCNE1, which was neither found to influence the Kv1.5 nor the Kv7.1 channel activity. We conclude that although the two N-terminal Kv1.5 mutations did not show any apparent electrophysiological phenotype, it is possible that they may influence other cellular mechanisms responsible for proper electrical behaviour of native cardiomyocytes.     

Paclitaxel binding to the fatty acid-induced conformation of human serum albumin--automated docking studies

Paclitaxel (Taxol^®) binding to the conformation of human serum albumin assumed in the presence of long-chain fatty acids was studied by automated docking. Reduced binding affinities at both the primary and secondary sites were predicted, compared to those characterizing the interaction with the fatty acid-free protein. The baccatin core of paclitaxel was found to play a more important role than its C13 side chain in determining the ligand binding mode as well as in contributing to the overall binding energy at the primary site.     

Paclitaxel binding to human serum albumin--automated docking studies

A computational approach was used to study the interaction of the potent anticancer drug paclitaxel (Taxol) with human serum albumin. The primary and secondary binding sites were located at the interface of subdomains IIA and IIIA, and in the cleft between domains I and III of the protein, respectively. The C13 side chain and the baccatin core of paclitaxel were found to contribute approximately equally to the binding energy at the primary site, whereas the binding mode appears to be governed by the C13 side chain.     

Salivary alpha amylase and salivary cortisol response to fluid consumption in exercising athletes

The objective of the study was to examine salivary biomarker response to fluid consumption in exercising athletes. Exercise induces stress on the body and salivary alpha amylase (sAA) and salivary cortisol are useful biomarkers for activity in the sympathoadrenal medullary system and the hypothalamic pituitary adrenal axis which are involved in the stress response. Fifteen college students were given 150 ml and 500 ml of water on different days and blinded to fluid condition. The exercise protocol was identical for both fluid conditions using absolute exercise intensities ranging from moderate to high. Saliva was collected prior to exercise, post moderate and post high intensities and analyzed by Salimetrics assays. Exercise was significant for sAA with values different between pre-exercise (85 ± 10 U · ml⁻¹) and high intensity (284 ± 30 U · ml⁻¹) as well as between moderate intensity (204 ± 32 U · ml⁻¹) and high intensity. There was no difference in sAA values between fluid conditions at either intensity. Exercise intensity and fluid condition were each significant for cortisol. Cortisol values were different between pre-exercise (0.30 ± 0.03 ug · dL⁻¹) and high intensity (0.45 ± 0.05 ug · dL⁻¹) as well as between moderate intensity (0.33 ± 0.04 ug · dL⁻¹) and high intensity. Moderate exercise intensity cortisol was lower in the 500 ml condition (0.33 ± 0.03 ug · dL⁻¹) compared with the 150 ml condition (0.38 ± 0.03 ug · dL⁻¹). This altered physiological response due to fluid consumption could influence sport performance and should be considered. In addition, future sport and exercise studies should control for fluid consumption.