An analysis of linkage disequilibrium in the interleukin-1 gene cluster, using a novel grouping method for multiallelic markers.

In population- and family-based association studies, it is useful to have some knowledge of the patterns of linkage disequilibrium that exist between markers in candidate regions. When such studies are carried out with multiallelic markers, it is often convenient to group the alleles into a biallelic system, for analysis. In this study, we specifically examined the interleukin-1 (IL-1) gene cluster on chromosome 2, a region containing candidates for many inflammatory and autoimmune disorders. Data were collected on eight markers, four of which were multiallelic. Using these data, we investigated the effect of three allele-grouping strategies, including a novel method, on the detection of linkage disequilibrium. The novel approach, termed the "delta method," measures the deviation from the expected haplotype frequencies under linkage equilibrium, for each allelic combination. This information is then used to group the alleles, in an attempt to avoid the grouping together of alleles at one locus that are in opposite disequilibrium with the same allele at the second locus. The estimate haplotype frequencies (EH) program was used to estimate haplotype frequencies and the disequilibrium measure. In our data it was found that the delta method compared well with the other two strategies. Using this method, we found that there was a reasonable correlation between disequilibrium and physical distance in the region (r=-.540, P=.001, one-tailed). We also identified a common, eight-locus haplotype of the IL-1 gene cluster.     

Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences

Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes.     

Catabolite Inactivation in the Methylotrophic Yeast Pichia pastoris

Inactivation of the alcohol oxidase enzyme system of Pichia pastoris, during the whole-cell bioconversion of ethanol to acetaldehyde, was due to catabolite inactivation. Electron microscopy showed that methanol-grown cells contained peroxisomes but were devoid of these microbodies after the bioconversion. Acetaldehyde in the presence of O₂ was the effector of catabolite inactivation. The process was initiated by the appearance of free acetaldehyde, and was characterized by an increase in the level of cyclic AMP, that coincided with a rapid 55% drop in alcohol oxidase activity. Further enzyme inactivation, believed to be due to proteolytic degradation, then proceeded at a constant but slower rate and was complete 21 h after acetaldehyde appearance. The rate of catabolite inactivation was dependent on acetaldehyde concentration up to 0.14 mM. It was temperature dependent and occurred within 24 h at 37°C and by 6 days at 15°C but not at 3°C. Alcohol oxidase activity was psychrotolerant, with only a 17% decrease in initial specific activity over a temperature drop from 37 to 3°C. In contrast, protease activity was inhibited at temperatures below 15°C. When the bioconversion was run at 3°C, catabolite inactivation was prevented. In the presence of 3 M Tris hydrochloride buffer, 123 g of acetaldehyde per liter was produced at 3°C, compared with 58 g/liter at 30°C. By using 0.5 M Tris in a cyclic-batch procedure, 140.6 g of acetaldehyde was produced.     

A soluble binding protein specific for interleukin 1 beta is produced by activated mononuclear cells

Soluble interleukin 1 (IL 1) binding proteins were identified by gel filtration and covalent cross-linking of 125I IL 1 in normal human serum and inflammatory exudate. High molecular weight 125I IL 1 protein complexes occurred with both IL 1 alpha and IL 1 beta, however, high molecular weight binding appeared to be non-specific. One specific IL 1 beta binding protein was observed to elute at approximately 100 kDa on gel filtration when bound to 125I IL 1 beta. This complex migrated as a broad band at 60 kDa when covalently cross-linked and analyzed by SDS-PAGE. The protein did not bind 125I IL 1 alpha and 125I IL 1 beta binding was only displaceable by excess cold IL-1 beta. The production of the specific IL 1 beta binding protein was assessed in a number of cell populations. Unstimulated peripheral blood mononuclear cells (PBMNC) did not produce the binding protein, but stimulation with phytohemagglutinin (PHA) caused production within 24 hr and binding protein levels remained elevated for up to 7 days. Stimulation with lipopolysaccharide (LPS) and IL 1 alpha did not consistently induce synthesis of the binding protein. Ligand-binding studies were performed to compare solubilized EL 4 NOB.1 cell membrane IL 1 receptor (sIL 1R) with semi-purified IL 1 beta binding protein from pooled synovial fluid. The sIL 1R preparation bound ligand with an affinity of 168 pM while the IL 1 beta binding protein bound 125I IL 1 beta with an affinity of 370 pM. This protein may function as an important carrier molecule for IL 1 beta and determine its distribution and kinetics in vivo.     

Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato

Negative correlations between quality traits and fruit size may hamper the breeding of fresh market tomato varieties for better organoleptic qualities. In a recent QTL analysis, QTLs with large effects on fruit weight, locule number and several quality traits were detected in the distal 50 cM of chromosome 2, but favorable alleles for fruit weight and locule number were unfavorable to quality traits. Substitution mapping was undertaken to determine whether the effects were due to a single QTL or to several tightly linked QTLs. Several chromosomal segments were characterized using near-isogenic lines. Five of them appeared to be involved in one or several traits. Considering the five segments from the top to the bottom of the region, the QTLs detected in each segment controlled the variation of: (1) fruit weight, (2) soluble solids content and dry matter weight, (3) fruit weight, (4) locule number and (5) fruit weight, dry matter weight, total sugars, titratable acidity and soluble solids content. This last cluster illustrates an antagonism between fruit weight and four quality traits, as favorable alleles are not conferred by the same parent in both cases. Nevertheless, several antagonistic QTLs were separated from each other in the first four segments, holding the promise for marker-assisted improvement of fruit quality traits without compromising the fruit size.     

Effects of increasing crude protein concentrations on performance and carcass characteristics of growing and finishing steers and heifers

A 2 × 3 factorial design was utilized to ascertain the effects of three dietary crude protein (CP) concentrations on performance, carcass characteristics, and serum urea nitrogen (SUN) concentration in steers and heifers. Animals were blocked by gender (n = 9) and body weight (BW; n = 3/gender), randomly assigned to a diet containing 110, 125 or 140 g/kg dietary CP (n = 6), subjected to a growing period of 56, 84 or 112 d, depending on start BW, and a finishing period of 84 d. Animals were weighed and bled at 28 d intervals and daily dry matter intake (DMI), average daily gain (ADG), and gain to feed (G:F) were calculated and SUN was analyzed as a repeated measure throughout the study. Following slaughter, carcass data was collected for hot carcass weight (HCW), dressing percent (DP), kidney, pelvic and heart fat (KPH), 12th rib backfat (BF), loin muscle (LM) area, marbling score (MS), and yield grade (YG). Growing steers and heifers were programmed to gain 1.02 and 0.91 kg/d, respectively. Therefore, heifers consumed less than steers and steers gained more than heifers (P<0.01) with no differences in feed efficiency. Dietary CP treatment did not effect DMI, but did result in a quadratic (P=0.04) increase in ADG; thereby quadratically (P=0.06) and linearly (P=0.08) increasing final BW, and G:F, respectively. Finishing heifers consumed and gained less than steers (P<0.01), had lighter HCW (P<0.01) and greater DP (P=0.01) and LM area (P=0.01) than steers. DMI (P=0.02), ADG (P=0.05), HCW (P=0.08), and DP (P=0.06) reacted quadratically with increasing dietary CP. HCW (P=0.02) increased linearly with increasing dietary CP. G:F, KPH, BF, LM area, MS and YG was not affected by dietary CP concentration and G:F, KPH, BF, MS, and YG did not differ between genders. However, there was a gender × dietary CP interaction (P=0.01) for G:F. Steers were the most efficient at 125 g/kg dietary CP, while heifers were most efficient at 140 g/kg dietary CP. Gender had no effect on SUN concentrations, but SUN increased linearly (P<0.01) with increasing dietary CP concentrations. In conclusion, quadratic responses in DMI and ADG indicate that a 125 g/kg dietary CP concentration is optimal for either steers or heifers during the finishing period.     

Modulation of Aβ peptides by estrogen in mouse models

Clinical studies have shown that estrogen deprivation through menopause is a risk factor in both the initiation and progression of Alzheimer's disease (AD) and that estrogen replacement therapy may be protective. One of the major pathological features in the human AD brain is the senile plaque, a proteinaceous structure composed mainly of heterogeneous peptides collectively known as A-beta (A(beta)). In vitro studies have linked estrogen with A(beta) modulation, suggesting that one-way that estrogen depletion at menopause may exacerbate the features of AD is through A(beta) accumulation. To test this, two studies were performed on transgenic models of amyloidosis. Firstly, transgenic mice without detectable amyloid aggregates were subjected to ovariectomy and estradiol supplementation, and A(beta) levels were assessed. Secondly, the effects of estrogen modulation were assessed in mice at an age when plaques would be forming initially. Overall, A(beta) levels were higher in estrogen-deprived mice than intact mice, and this effect could be reversed through the administration of estradiol. These data suggest that, in vivo, estrogen depletion leads to the accumulation of A(beta) in the CNS, which can be reversed through replacement of estradiol. These results provide evidence that post-menopausal estrogen depletion may be linked to an increased risk of AD through A(beta) modulation.     

Histological Co-Localization of Iron in Aß Plaques of PS/APP Transgenic Mice

This study confirms the presence of iron, co-localized with A plaques, in PS/APP mouse brain, using Perls stain for Fe³⁺ supplemented by 3,3-diaminobenzidine (DAB) and A immunohistochemistry in histological brains sections fixed with formalin or methacarn. In this study, the fixation process and the slice thickness did not interfere with the Perls technique. The presence of iron in ß-amyloid plaques in PS/APP transgenic mice, a model of Alzheimers disease (AD) pathology, may explain previous reports of reductions of transverse relaxation time (T₂) in MRI studies and represent the source of the intrinsic Aß plaque MR contrast in this model.