Comparison of sequence repetitiveness of human cDNA and genomic DNA using the miniplasmid vector, piVX

We studied the sequence repetitiveness of human cDNA and genomic DNA fragments inserted in the miniplasmid piVX. Sequence repetitiveness was assayed by the frequency with which a given insert mediated recombination between the chimeric miniplasmid and a recombinant bacteriophage library constructed from large random human genomic fragments. The methodology allows rapid analysis and isolation of sequences of a given copy number in the genome: few (1 to 10 copies), low order-repeated (10 to 100 copies) and a more highly repeated (over 100 copies). In a model application of the method, the distribution of these classes of sequences was compared in cDNA and genomic DNA libraries constructed in piVX. The major difference observed between cDNA and genomic DNA repeat structure was the paucity of highly repeated elements in cDNA copies from high-molecular-weight cytoplasmic poly(A) + RNA.     

Formation of intracellular lumina in dispersed pig thyroid cells

Intracellular cavities characterized by the presence of microvilli have been identified in dispersed thyroid cells. These structures resembling follicular lumina were called intracellular lumina or ICL. Freshly dispersed cells did not contain ICL. At 37 degrees C, ICL formation was a rapid process. After 60 min of incubation, ICL were present in 15 to 20% of the cells; the number of ICL remained rather constant during 3 to 4 h of incubation. In the presence of thyrotropin, the number of ICL increased with time to reach a value ranging from 40 to 60 ICL per 100 cells after 4 h of incubation. ICL formation was also increased in the presence of dibutyryl cyclic AMP (2 mM). Vinblastine (30 microM), a microtubule-disrupting agent and monensin (30 microM), an ionophore inhibiting Golgi functions blocked the formation of ICL in control and thyrotropin-stimulated cells. Cycloheximide (0.5 mM) and puromycin (0.5 mM) did not inhibit ICL formation in either control or thyrotropin stimulated cells. The iodination capacity of ICL was studied by quantitative electron microscopic autoradiography after incubation of thyroid cells with 125 I-iodide for 2 to 60 min. Radioiodinated products appeared first in ICL. After 1 h of labeling autoradiographic grains were found mainly in ICL (60-70%) and over the cytoplasm. The labeling of ICL was heterogeneous; ICL contained either few or numerous overlapping grains. Whatever the labeling time, a high proportion of ICL (70-80%) were labeled. The labeling of ICL as well as the labeling over the cytoplasm was increased in the presence of thyrotropin and almost completely inhibited in the presence of an iodide trapping inhibitor: sodium perchlorate. Pulse-chase experiments revealed that thyrotropin stimulated the discharge of 125 I-labeled material from ICL.     

On the interpretation of the hazard ratio in Cox regression

We argue that the term “relative risk” should not be used as a synonym for “hazard ratio” and encourage to use the probabilistic index as an alternative effect measure for Cox regression. The probabilistic index is the probability that the event time of an exposed or treated subject exceeds the event time of an unexposed or untreated subject conditional on the other covariates. It arises as a well known and simple transformation of the hazard ratio and nicely reveals the interpretational limitations. We demonstrate how the probabilistic index can be obtained using the R-package Publish.     

The BAM H1 Restriction Site in the Bacteriophage T4 Chromosome Is Located in or near Gene 8

Bacteriophage T4 cytosine-containing DNA is cleaved at a single site by the restriction endonuclease, Bam H1. The site lies within the late region of the T4 genome, close to, or within, gene 8, one of the structural genes of the phage particle baseplate.     

Assembly of an antibody and its derived antibody fragment inNicotiana andArabidopsis

The yield and assembly of an IgG1 antibody and its derived F_ab fragment were compared inNicotiana andArabidopsis. The results obtained showed a lot of interclonal variability. For 45% of the primary transgenic calluses, antigen-binding entities represented less than 0.1% of the total soluble protein (TSP). Only two of the 103 analysed transformants contained more than 1% of antigen-binding protein, with 1.26% being the highest yield. Analogous amounts of complete antibody and F_ab accumulated in primary callus tissue. Moreover, yields were in the same range for both species as far as primary callus tissue is concerned. However, the accumulation of the F_ab fragment in leaf tissue of regenerated plants differed significantly betweenNicotiana andArabidopsis. The F_ab fragment accumulated to only 0.044% of TSP inNicotiana leaves but up to 1.3% inArabidopsis leaves. Furthermore, both species showed differences in the assembly pattern of the complete antibody. WhereasArabidopsis contained primarily fully assembled antibodies of 150 kDa,Nicotiana showed an abundance of fragments in the 50 kDa range.     

The microtubule binding domain of tau protein

Tau protein is a microtubule-associated protein implicated in the spatial and temporal specification of microtubules and has been found in the neurofibrillary tangles of Alzheimer's disease. Determination of tau protein structure has revealed three 18 amino acid repeated sequences hypothesized to be tubulin binding sites. Using tau cDNA clones from human fetal brain, we employed E. coli expression systems to synthesize tau protein and fragments of tau protein in order to identify the microtubule binding site. A fragment containing the three repeated sequences binds microtubules, while the amino-terminal half of the protein does not bind. Fragments containing two or one repeat are also capable of binding, indicating that the basic tubulin interacting unit is one repeat.     

Gene silencing results in instability of antibody production in transgenic plants

The stability of antibody and F_ab expression was assessed in five different homozygous transgenic Arabidopsis lines. Each of these lines showed silencing of the transgenes that encode the antibody polypeptides, leading to instability of antibody production. However, each line had a different and specific instability profile. The characteristic variation in the level of antibody accumulation in each line as a function of developmental stage indicated that the T-DNA integration pattern played a role in triggering silencing, and also that the history and the integration position of simple transgene loci can influence the susceptibility to epigenetic silencing. In different lines with low antibody accumulation levels, methylation was found either in the promoter alone, in both the promoter and the transcribed region, in the transcribed region only, or in the transcribed region and downstream sequences. In conclusion, our data suggest that epigenetic effects result in different transgene expression profiles in each of the five Arabidopsis lines analyzed. Received: 27 July 1998 / Accepted: 12 October 1998     

Expression and Function of mARC: Roles in Lipogenesis and Metabolic Activation of Ximelagatran

Recently two novel enzymes were identified in the outer mitochondrial membrane, mARC1 and mARC2. These molybdenum containing enzymes can reduce a variety of N-hydroxylated compounds, such as N-hydroxy-guanidines and sulfohydroxamic acids, as well as convert nitrite into nitric oxide (NO). However, their endogenous functions remain unknown. Here we demonstrate a specific developmental pattern of expression of these enzymes. mARC1, but not mARC2, was found to be expressed in fetal human liver, whereas both, in particular mARC2, are abundant in adult liver and also expressed in omental and subcutaneous fat. Caloric diet restriction of obese patients caused a decreased expression of mARC2 in liver, similar to that seen in the livers of starved rats. Knock down of mARC2 expression by siRNA in murine adipocytes had statistically significant effect on the level of diglycerides and on the fatty acid composition of some triglycerides, concomitantly a clear trend toward the reduced formation of most of triglyceride and phospholipid species was observed. The involvement of mARC2 in the metabolism of the hepatotoxic drug ximelagatran was evaluated in hepatocytes and adipocytes. Ximelagatran was shown to cause oxidative stress and knock down of mARC2 in adipocytes prevented ximelagatran induced inhibition of mitochondrial respiration. In conclusion, our data indicate that mARC1 and mARC2 have different developmental expression profiles, and that mARC2 is involved in lipogenesis, is regulated by nutritional status and responsible for activation of ximelagatran into a mitotoxic metabolite(s).