T296→M,a common mutation causing mild hemophilia B in the Amish and others: founder effect,variability in factor IX activity assays,and rapid carrier detection

Summary By direct genomic sequencing, we have delineated the causative mutation in 64 families of European descent with hemophilia B. Six (9%) had a CT transition at base 31008, which substitutes methionine for threonine 296 (T²⁹⁶M) in the catalytic domain of factor IX. Five of the patients had the same haplotype (frequency of 16% in the northern European population). These individuals are of Amish/German descent and they are likely to share a common ancestor. The sixth patient had a different haplotype, which indicates that his mutation had an independent origin. The data highlight the importance of clinical criteria for the classification of hemophilia B. All six patients had clinically mild disease and their factor IX coagulant activities were in the range of 3%–6% when tested simultaneously in one laboratory, yet the factor IX activities provided with patient records varied 40-fold. Due to the high frequency of this mutation, we have utilized the technique of polymerase chain reaction amplification of specific alleles (PASA) to perform rapid and inexpensive carrier diagnoses in the families with this mutation. This is of particular importance for the Amish since the mutation should account for much of, if not all, the mild hemophilia B that is commonly found in this population.     

Sterol methylation in Saccharomyces cerevisiae.

Various nystatin-resistant mutants defective in S-adenosylmethionine: delta 24-sterol-C-methyltransferase (EC 2.1.1.41) were shown to possess alleles of the same gene, erg6. The genetic map location of erg6 was shown to be close to trp1 on chromosome 4. Despite the single locus for erg6, S-adenosylmethionine: delta 24-sterol-C-methyltransferase enzyme activity was found in three separate fractions: mitochondria, microsomes, and the "floating lipid layer." The amount of activity in each fraction could be manipulated by assay conditions. The lipids and lipid synthesis of mutants of Saccharomyces cerevisiae defective in the delta 24-sterol-C-methyltransferase were compared with a C5(6) desaturase mutant and parental wild types. No ergosterol (C28 sterol) could be detected in whole-cell sterol extracts of the erg6 mutants, the limits of detection being less than 10(-11) mol of ergosterol per 10(8) cells. The distribution of accumulated sterols by these mutants varied with growth phase and between free and esterified fractions. The steryl ester concentrations of the mutants were eight times higher than those of the wild type from exponential growth samples. However, the concentration of the ester accumulated by the mutants was not as great in stationary-phase cells. Whereas the head group phospholipid composition was the same between parental and mutant strains, strain-dependent changes in fatty acids were observed, most notably a 40% increase in the oleic acid content of phosphatidylethanolamine of one erg6 mutant, JR5.     

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant ( P  <   0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.     

A palynological study of the Acheulian site of Gesher Benot Ya’aqov, Israel

The results are discussed of the palynological (pollen-analytical) examination of a sediment section in the Hula Valley of northern Israel, with evidence of Acheulian occupation dated to 700,000–800,000 b.p. In general there is a fair agreement between the palynological data and the wood remains identified from the site, but there are also discrepancies, some of which can be explained and others not. Although relatively well represented in the pollen record, Pinus (pine) most probably did not occur in the Hula area. Some pollen types are thought to have been carried in from hundreds of kilometres away (long-distance transport). Together the pollen and wood evidence suggests that Quercus ithaburensis–Pistacia atlantica (Tabor oak–Atlantic terebinth) woodland (open forest) was found in the Hula Valley (other than the lake and marshes) and on the lower reaches of the mountains flanking the valley on both sides. In addition to deciduous Tabor oak, evergreen Kermes oak (Quercus calliprinos) must have been an important component of this woodland. Wild olive (Olea europaea var. oleaster) may also have been quite common here. The suggestion of open forest, with fairly widely spaced trees, is based upon the high non-arboreal pollen frequencies and indicates fairly dry climatic conditions. Various stream-bank trees and shrubs are represented in the pollen and/or wood records, such as Fraxinus (ash), Ulmus (elm), Salix (willow) and Platanus (plane tree). During the period represented by the upper section of the pollen diagram, Cedrus (cedar) must have reached the Hula area, indicating increased humidity. In the steppe-like field layer (undergrowth of the woodland) grasses (Gramineae) must have played a prominent role in addition to a great number of other species. In particular Compositae and Umbelliferae include a large variety of species (many different pollen types). Two Chenopodiaceae maxima, coinciding with Gramineae minima, are thought to be indicative of periods of increased climatic dryness. The local lake and marsh vegetation is fairly well represented in the pollen record, but interpretation in terms of vegetation succession is only possible to some degree. Mention is made here of Trapa natans (water chestnut), the nuts of which were consumed by the Acheulian inhabitants. Sytze Bottema: Deceased in 2005.     

Mouse model of skeletal muscle adiposity: A glycerol treatment approach

Fat cell accumulation in skeletal muscle is a major characteristic of various disorders, such as obesity, sarcopenia and dystrophies. Moreover, these fat cells could be involved in muscle homeostasis regulation as previously described for adipocytes in bone marrow. Despite recent advances on the topic, no clearly characterized mouse model is currently available to study fat accumulation within skeletal muscle. Here, we report a detailed characterization of a mouse model of skeletal muscle fat cell accumulation after degeneration induced by intra-muscular injection of glycerol. Information is provided on the kinetics of degeneration/fat deposition, including the quantity of fat deposited based on various parameters such as glycerol concentration, age, sex and strain of mice. Finally, these fat cells are characterized as true white adipocytes morphologically and molecularly. Our study shows that the mouse adipocyte accumulation within skeletal muscle after glycerol degeneration is a reproducible, transposable and easy model to use. This mouse model should allow a more comprehensive understanding of the impact of adipocyte accumulation in skeletal muscle pathophysiology.     

Role of sterol structure in the thermotropic behavior of plasma membranes of Saccharomyces cerevisiae

Plasma membranes from Saccharomyces cerevisiae were prepared by a new procedure involving lyticase treatment of the yeast cells. The plasma membranes were right-side-out, closed vesicles of uniform appearance with a sterol to phospholipid molar ratio of 0.365. The thermotropic behavior of these plasma membranes from wild-type yeast and from sterol mutants was examined by differential scanning calorimetry, fluorescence anisotropy and Arrhenius kinetics of plasma membrane enzymes. While differential scanning calorimetry failed to demonstrate any lipid transition, fluorescence anisotropy data indicated that lipid transitions were occurring in the plasma membranes of the yeast sterol mutants but not the sterol wild-type. The temperature dependence of the plasma membrane enzymes, chitin synthase and Mg²⁺-ATPase, was also investigated. The Arrhenius kinetics of chitin synthase did not reveal any transitions in either the sterol mutant or wild-type plasma membranes, yet the Arrhenius kinetics of the Mg²⁺-ATPase suggested that lipid transitions were occurring in both cases.     

Delta14-sterol reductase in Saccharomyces cerevisiae.

An in vitro assay for delta14-sterol reductase from yeast was developed, using ergosta-8,14-dien-3beta-ol as the substrate. The kinetics and localization of the enzyme were examined. The inhibition of the enzyme by the antimycotic agent, 15-azasterol, was verified.     

Metal enrichment in water and fish in a semi-urban Nigerian lake,and their associated risks

Trace metal (Zn, Pb, Cu, Cr and Cd) concentrations in the water column and in the liver, muscle and gill tissues of Parachanna obscura and Clarias gariepinus in Agulu Lake, Nigeria, were investigated in June 2014 and compared with WHO and FAO safe limits for water and fish. Hazard index (HI) values were estimated to assess the potential public health risk of consuming contaminated fish. Lead and cadmium exceeded WHO guideline values for drinking water. In most cases, variations in concentration of the metals in organs were liver > muscle > gill. Differences in tissue-specific concentrations between species were not significant, except for zinc in muscles and gills. Cadmium and chromium were not detected in the fish, but lead was above the FAO maximum value for consumption. Hazard index values were below 1, indicating a low risk to public health. However, trace metal contamination in Agulu Lake is increasing.     

Selection of haplotype variables from a high-density marker map for genomic prediction

Background

Using haplotype blocks as predictors rather than individual single nucleotide polymorphisms (SNPs) may improve genomic predictions, since haplotypes are in stronger linkage disequilibrium with the quantitative trait loci than are individual SNPs. It has also been hypothesized that an appropriate selection of a subset of haplotype blocks can result in similar or better predictive ability than when using the whole set of haplotype blocks. This study investigated genomic prediction using a set of haplotype blocks that contained the SNPs with large effects estimated from an individual SNP prediction model. We analyzed protein yield, fertility and mastitis of Nordic Holstein cattle, and used high-density markers (about 770k SNPs). To reach an optimum number of haplotype variables for genomic prediction, predictions were performed using subsets of haplotype blocks that contained a range of 1000 to 50 000 main SNPs.

Results

The use of haplotype blocks improved the prediction reliabilities, even when selection focused on only a group of haplotype blocks. In this case, the use of haplotype blocks that contained the 20 000 to 50 000 SNPs with the highest effect was sufficient to outperform the model that used all individual SNPs as predictors (up to 1.3 % improvement in prediction reliability for mastitis, compared to individual SNP approach), and the achieved reliabilities were similar to those using all haplotype blocks available in the genome data (from 0.6 % lower to 0.8 % higher reliability).

Conclusions

Haplotype blocks used as predictors can improve the reliability of genomic prediction compared to the individual SNP model. Furthermore, the use of a subset of haplotype blocks that contains the main SNP effects from genomic data could be a feasible approach to genomic prediction in dairy cattle, given an increase in density of genotype data available. The predictive ability of the models that use a subset of haplotype blocks was similar to that obtained using either all haplotype blocks or all individual SNPs, with the benefit of having a much lower computational demand.