Apolipoprotein E gene mapping and expression: localization of the structural gene to human chromosome 19 and expression of ApoE mRNA in lipoprotein- and non-lipoprotein-producing tissues

Apolipoprotein E (apoE) binds to specific cell-surface receptors and appears to be an important determinant in lipoprotein metabolism in man. Cloned human apoE cDNA (pAE155) was used as a probe in chromosome mapping studies to detect the structural gene sequences in human--Chinese hamster cell hybrids. Southern blot analysis of HincII-digested DNAs from 13 hybrids localized the gene to human chromosome 19. This observation indicates that apoE is syntenic to at least two other genes related to lipid metabolism, those for the low-density lipoprotein (LDL) receptor (the LDLR) and apoC-II. The cloned apoE cDNA was further used to detect the presence of apoE mRNA in RNA extracts of various human and baboon tissues. Northern gel analysis using the 32P-labeled pAE155 as a probe demonstrated the presence of hybridizable apoE mRNAs in human liver and in baboon liver, intestine, spleen, kidney, adrenal gland, and brain but not in baboon skeletal muscle. The apoE mRNAs appear to be intact and migrate on an agarose gel under denaturing conditions at approximately 18 S. To assay for the biological activity of the apoE mRNAs in these tissues, they were translated in a reticulocyte lysate system in vitro. Immunoprecipitation with an apoE-specific antiserum followed by sodium dodecyl sulfate gel electrophoresis and fluorography demonstrated that immunoreactive apoE with the expected apparent size was a product of translation of mRNAs from baboon liver, intestine, kidney, spleen, and brain but not that from baboon skeletal muscle.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular characterization and differential mRNA tissue distribution of rabbit apolipoprotein D

We report for the first time the quantification of relative apolipoprotein D (apoD) mRNA concentrations in a wide selection of organs and a detailed characterization of the rabbit protein. ApoD cDNA clones were isolated from a rabbit testis cDNA library by screening with a human apoD cDNA-derived RNA probe. The 912 nucleotide sequence of rabbit apoD cDNA contains a unique reading frame coding for a protein sharing 80% homology with human apoD. The two sequences have two potential asparagine-linked glycosylation sites at the same positions, almost superimposable hydrophobicity plot, and the antigenic proteins show similar charge polymorphism, Mr, and lipoprotein distribution. This high degree of similarity shows that the rabbit system can be used as a model for apoD studies. Moreover, the two consensus sequences of the hydrophobic ligand carrier (alpha 2-microglobulin) family present in human apoD are also found in the rabbit protein and these sequences coincide with the most conserved regions. The distribution of apoD mRNA among rabbit organs was determined by Northern blot and quantitative dot blot analysis. The highest levels of mRNA were found in spleen, adrenal glands, lungs, brain, testis, and kidneys. Moderate or low concentrations were detected in all the other organs tested including liver and small intestine. Thus, our results show that the apoD gene is expressed mainly in peripheral organs, with levels as high as 59-fold that of the liver, unlike other apolipoproteins. We suggest that apoD exerts its main function locally in peripheral organs.     

Apolipoprotein E gene expression is reduced in apolipoprotein A-I transgenic mice

The levels of plasma apolipoprotein (apo) E, an anti-atherogenic protein involved in mammalian cholesterol transport, were found to be 2-3 fold lower in mice over-expressing human apoA-I gene. ApoE is mainly associated with VLDL and HDL-size particles, but in mice the majority of the apoE is associated with the HDL particles. Over-expression of the human apoA-I in mice increases the levels of human apoA-I-rich HDL particles by displacing mouse apoA-I from HDL. This results in lowering of plasma levels of mouse apoA-I. Since plasma levels of apoE also decreased in the apoA-I transgenic mice, the mechanism of apoE lowering was investigated. Although plasma levels of apoE decreased by 2-3 fold, apoB levels remained unchanged. As expected, the plasma levels of human apoA-I were almost 5-fold higher in the apoAI-Tg mice compared to mouse apoA-I in WT mice. If the over-expression of human apoA-I caused displacement of apoE from the HDL, the levels of hepatic apoE mRNA should remain the same in WT and the apoAI-Tg mice. However, the measurements of apoE mRNA in the liver showed 3-fold decreases of apoE mRNA in apoAI-Tg mice as compared to WT mice, suggesting that the decreased apoE mRNA expression, but not the displacement of the apoE from HDL, resulted in the lowering of plasma apoE in apoAI-Tg mice. As expected, the levels of hepatic apoA-I mRNA (transgene) were 5-fold higher in the apoAI-Tg mice. ApoE synthesis measured in hepatocytes also showed lower synthesis of apoE in the apoAI-Tg mice. These studies suggest that the integration of human apoA-I transgene in mouse genome occurred at a site that affected apoE gene expression. Identification of this locus may provide further understanding of the apoE gene expression.     

Angiotensin receptor subtypes in rat, rabbit and monkey tissues: relative distribution and species dependency

The displacement of [125I]Sar1, Ile8 angiotensin II binding by the receptor subtype selective angiotensin II antagonists, DuP-753 and WL-19 (PD121981) was used to define the relative proportion of angiotensin subtype AT1 and subtype AT2 receptors, respectively in various tissues (aorta, heart, adrenal cortex, kidney cortex and brain) of the rat, rabbit and monkey. The relative abundance of these receptor subtypes varied greatly not only among different tissues of the same species but also within the same tissue of different species. The relative affinity of the DuP-753 and WL-19 for the angiotensin receptor subtypes did not vary markedly suggesting that the two angiotensin receptor subtypes in these tissues and species are similar.     

Coral in Alaska: distribution,abundance, and species associations

To help identify fishery management actions that minimize the adverse impacts of fishing activities on corals in Alaska, the distribution and abundance of corals were analyzed based on trawl survey data collected during 1975–1998. We also examined the species of commercially managed fish that are associated with coral. Soft corals, primarily Gersemia sp. (=Eunephthya sp.), were the most frequently encountered corals in the Bering Sea. In the Aleutian Islands gorgonian corals, primarily in the genera Callogorgia, Primnoa, Paragorgia, Thouarella, and Arthrogorgia were the most common corals. In the Gulf of Alaska, gorgonian corals, primarily in the genera Callogorgia and Primnoa, and cup corals, primarily `Scleractinia unidentified', occurred most frequently. The Aleutian Islands area appears to have the highest abundance and diversity of corals. Some fish groups are associated with particular types of coral. Rockfish (Sebastes spp. and Sebastolobus alascanus) and Atka mackerel (Pleurogrammus monopterygius) were the most common fish captured with gorgonian, cup, and hydrocorals, whereas flatfish and gadids were the most common fish captured with soft corals.     

Progesterone receptor mRNA expression and distribution in the female rabbit brain

Progesterone regulates diverse functions in the rabbit brain through the interaction with its nuclear receptor (PR). Although PR protein has been detected in some regions of the rabbit forebrain, PR mRNA expression and distribution in the rabbit brain are unknown. Hence, we investigated these issues by in situ hybridization. New Zealand adult female rabbits were ovariectomized and treated with vehicle or estradiol (5 μg/(kg day)) for 3 days. The results show an extended distribution of PR mRNA expression in the rabbit brain. The highest expression was detected in preoptic area and hypothalamic anterior nuclei such as paraventricular, periventricular and arcuate nuclei. A high expression was also detected in thalamic and telencephalic areas, including hippocampus and cerebral cortex. Estradiol treatment induced an increase in PR mRNA expression in many brain areas, particularly in the hippocampus and the hypothalamic and preoptic area regions. The wide distribution of PR mRNA in the rabbit brain suggests that progesterone through PR activation is involved in several functions apart from reproductive behavior in rabbits, and that PR expression is up-regulated by estradiol in the rabbit brain.     

Apolipoprotein B mRNA editing: a new tier for the control of gene expression.

Two forms of apolipoprotein (apo) B are found in mammals. The shorter form is translated from an edited mRNA in which a specific cytidine base is deaminated to a uridine, creating a new stop codon. Apo B mRNA editing is mediated by a site-specific cytidine deaminase that recognizes a downstream target sequence in the RNA. The enzyme has no energy or cofactor requirements and no RNA component, and thus bears no obvious relationship to RNA processing events such as splicing or polyadenylation. While apo B mRNA editing activity may have arrived late in evolution to target dietary lipid to the liver in mammals, the discovery of the editing activity in tissues and cells that do not express apo B suggests a more widespread role in the generation of RNA and protein diversity.     

Elevational partitioning in species distribution,abundance and body size of Australian alpine grasshoppers (Kosciuscola)

Changes in the physical environment with elevation can influence species distributions and their morphological traits. In mountainous regions, steep temperature gradients can result in patterns of ecological partitioning among species that potentially increases their vulnerability to climate change. We collected data on species distributions, relative abundance and body size for three grasshopper species of the genus Kosciuscola (K. usitatus, K. tristis and K. cognatus) at three locations within the mountainous Kosciuszko National Park in Australia (Thredbo, Guthega and Jagungal). All three species showed differences in their distributions according to elevation, with K. usitatus ranging from 1400 to 2000 m asl, K. tristis from 1600 to 2000 m asl and K. cognatus from 1550 to 1900 m asl. Decreasing relative abundance with increasing elevation was found for K. usitatus, but the opposite pattern was found for K. tristis. The relative abundance of K. cognatus did not change with elevation but was negatively correlated with foliage cover. Body size decreased with elevation in both male and female K. usitatus, which was similarly observed in female K. tristis and male K. cognatus. Our results demonstrate spatial partitioning of species distributions and clines in body size in relation to elevational gradients. Species‐specific sensitivities to climatic gradients may help to predict the persistence of this grasshopper assemblage under climate change.     

Rabbit apolipoprotein A-I mRNA and gene. Evidence that rabbit apolipoprotein A-I is synthesized in the intestine but not in the liver

In order to study the tissue-specific expression of rabbit apolipoprotein (apo) A-I, a 923-base-pair clone, pRBA-502, complementary to rabbit apo A-I mRNA was identified from a rabbit intestinal cDNA library by hybrid-select translation and immunoprecipitation methods. Northern blot and dot-blot hybridization, utilizing 32P-labeled pRBA-502, revealed that the rabbit apo A-I gene is expressed in the intestine, not in the liver and that rabbit apo A-I mRNA is about 950 nucleotides in length. The entire nucleotide sequence of pRBA-502 has been determined and the complete amino acid sequence of the corresponding apo A-I has been deduced. The mRNA codes for a protein comprising 265 amino acids. Amino acids 1-18 and 19-24 of the primary translation product represent the presegment and prosegment, respectively, of apo A-I. Matured rabbit apo A-I contains 241 amino acids and has a molecular mass of 27612 Da. Using pRBA-502 as a probe, a 15.5-kb genomic fragment, which contains the entire apo A-I gene, was isolated from a rabbit liver genomic library. Sequence analysis of the gene shows that the 200 base pairs of the 5' upstream flanking region of the rabbit and human apo A-I genes showed 78% sequence homology. Like the human apo A-I gene, the rabbit apo A-I gene is interrupted by three intervening sequences. Except for two nucleotides in the fourth exon, the coding sequence of the rabbit liver apo A-I gene is identical to that of pRBA-502. Our data showed that the lack of expression of apo A-I gene in rabbit liver is not due to the alternation of rabbit liver apo A-I gene sequence and suggest that the expression of apo A-I gene in rabbit liver is regulated by a trans-acting regulating element(s).     

The distribution of glucosamine in mammalian glycogen from different species, organs and tissues

The reasons for the occurrence of trace amounts of glucosamine in animal liver glycogens have been explored. Human liver glycogen is now shown to contain this amino sugar. Galactosamine, known to be the source of the incorporated glucosamine, is found to give rise to glucosamine in glycogen when administered orally, or as the N-acetyl derivative. The rabbit can also incorporate glucosamine into kidney glycogen but not into glycogen in heart or skeletal muscle. These experiments led to the discovery that glucosamine is incorporated into rabbit liver glycogen in such a way that there is intermolecular heterogeneity in the content of glucosamine, suggesting that there exists more than one pool of liver glycogen.     

How species richness and total abundance constrain the distribution of abundance

The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow‐curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R² values > 75%), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.     

Connecting species richness, abundance and body size in deep-sea gastropods

Aim This paper examines species richness, abundance, and body size in deep‐sea gastropods and how they vary over depth, which is a strong correlate of nutrient input. Previous studies have documented the empirical relationships among these properties in terrestrial and coastal ecosystems, but a full understanding of how these patterns arise has yet to be obtained. Examining the relationships among macroecological variables is a logical progression in deep‐sea ecology, where patterns of body size, diversity, and abundance have been quantified separately but not linked together. Location 196–5042 m depth in the western North Atlantic. Method Individuals analysed represent all Vetigastropoda and Caenogastropoda (Class Gastropoda) with intact shells, excluding Ptenoglossa, collected by the Woods Hole Benthic Sampling Program (3424 individuals representing 80 species). Biovolume was measured for every individual separately (i.e. allowing the same species to occupy multiple size classes) and divided into log₂ body size bins. Analyses were conducted for all gastropods together and separated into orders and depth regions (representing different nutrient inputs). A kernel smoothing technique, Kolmogorov‐Smirnov test of fit, and OLS and RMA were used to characterize the patterns. Results Overall, the relationship between the number of individuals and species is right skewed. There is also a positive linear relationship between the number of individuals and the number of species, which is independent of body size. Variation among these relationships is seen among the three depth regions. At depths inferred to correspond with intermediate nutrient input levels, species are accumulated faster given the number of individuals and shift from a right‐skewed to a log‐normal distribution. Conclusion A strong link between body size, abundance, and species richness appears to be ubiquitous over a variety of taxa and environments, including the deep sea. However, the nature of these relationships is affected by the productivity regime and scale at which they are examined.     

On the expression of cytokeratins and their distribution in some rabbit gland tissues.

The composition and distribution of cytokeratins were studied in a series of exocrine and endocrine glands in the rabbit, by means of anti-human monoclonal antibodies. Rabbit cytokeratins are known to be homologous to those in man, and their in situ distribution was also found to be similar. In acinic cells of the exocrine glands, only cytokeratins 8 and 18 were detected, whereas in ductal cells 1, 5, 10, 11 and 13, 19 were also present. The myoepithelial cells surrounding acini and basal duct cells were stained with the antibodies directed against cytokeratins 13 and 1, 5, 10, 11. Among the endocrine glands, a higher reactivity was observed in the thyroid gland and pancreatic islets, while pituitary and adrenal gland often remained unstained. Although the expression of cytokeratins was found to be almost homogeneous in each glandular cell type, a certain variability was observed, depending on the organ examined and the treatment carried out.     

Apolipoprotein C-III displacement of apolipoprotein E from VLDL: effect of particle size.

ApoC-III and apoE are important determinants of intravascular lipolysis and clearance of triglyceride-rich chylomicrons and VLDL from the blood plasma. Interactions of these two apolipoproteins were studied by adding purified human apoC-III to human plasma at levels observed in hypertriglyceridemic subjects and incubating under specific conditions (2 h, 37 degrees C). As plasma concentrations of apoC-III protein were increased, the contents in both VLDL and HDL were also increased. Addition of apoC-III at concentrations up to four times the intrinsic concentration resulted in the decreasing incremental binding of apoC-III to VLDL while HDL bound increasing amounts without evidence of saturation. No changes were found in lipid content or in particle size of any lipoprotein in these experiments. However, distribution of the intrinsic apoE in different lipoprotein particles changed markedly with displacement of apoE from VLDL to HDL. The fraction of VLDL apoE that was displaced from VLDL to HDL at these high apoC-III concentrations varied among individuals from 20% to 100% its intrinsic level. The proportion of VLDL apoE that was tightly bound (0% to 80%) was found to be reproducible and to correlate with several indices of VLDL particle size. In the group of subjects studied, strongly adherent apoE was essentially absent from VLDL particles having an average content of less than 50,000 molecules of triglyceride.Addition of apoC-III to plasma almost completely displaces apoE from small VLDL particles. Larger VLDL contain tightly bound apoE which are not displaced by increasing concentration of apoC-III.     

Regulation of adeno-associated virus gene expression in 293 cells: control of mRNA abundance and translation.

We studied the effects of the adeno-associated virus (AAV) rep gene on the control of gene expression from the AAV p40 promoter in 293 cells in the absence of an adenovirus coinfection. AAV vectors containing the chloramphenicol acetyltransferase (cat) gene were used to measure the levels of cat expression and steady-state mRNA from p40. When the rep gene was present in cis or in trans, cat expression from p40 was decreased 3- to 10-fold, but there was a 2- to 4-fold increase in the level of p40 mRNA. Conversely, cat expression increased and the p40 mRNA level decreased in the absence of the rep gene. Both wild-type and carboxyl-terminal truncated Rep proteins were capable of eliciting both effects. These data suggest two roles for the pleiotropic AAV rep gene: as a translational inhibitor and as a positive regulator of p40 mRNA levels. We also provide additional evidence for a cis-acting negative regulatory region which decreases RNA from the AAV p5 promoter in a fashion independent of rep.     

Intron size, abundance, and distribution within untranslated regions of genes

Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species, Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5' UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5' UTRs than in CDSs. Introns in 5' UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5' UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5' UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5' UTRs, so long as a minimum required exon size was assumed. Introns in 3' UTRs were much less abundant than in 5' UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3' UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.