Rat Genome Database (RGD): mapping disease onto the genome

The Rat Genome Database (RGD, http://rgd.mcw.edu) is an NIH-funded project whose stated mission is ‘to collect, consolidate and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community’. In a collaboration between the Bioinformatics Research Center at the Medical College of Wisconsin, the Jackson Laboratory and the National Center for Biotechnology Information, RGD has been created to meet these stated aims. The rat is uniquely suited to its role as a model of human disease and the primary focus of RGD is to aid researchers in their study of the rat and in applying their results to studies in a wider context. In support of this we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature and bulk dataset curation. RGD version 2.0, released in June 2001, includes curated data on rat genes, quantitative trait loci (QTL), microsatellite markers and rat strains used in genetic and genomic research. VCMap, a dynamic sequence-based homology tool was introduced, and allows researchers of rat, mouse and human to view mapped genes and sequences and their locations in the other two organisms, an essential tool for comparative genomics. In addition, RGD provides tools for gene prediction, radiation hybrid mapping, polymorphic marker selection and more. Future developments will include the introduction of disease-based curation expanding the curated information to cover popular disease systems studied in the rat. This will be integrated with the emerging rat genomic sequence and annotation pipelines to provide a high-quality disease-centric resource, applicable to human and mouse via comparative tools such as VCMap. RGD has a defined community outreach focus with a Visiting Scientist program and the Rat Community Forum, a web-based forum for rat researchers and others interested in using the rat as an experimental model. Thus, RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.     

Rat pineal gland phosducin: cDNA isolation, nucleotide sequence, and chromosomal assignment in the mouse

The pineal gland contains a soluble phosphoprotein, phosducin, which is homologous to that of retinal photoreceptors. Phosducin has been shown to bind the beta, gamma subunits of the retinal G-protein transducin. Retinal phosducin has been cloned and now we report a rat pineal cDNA encoding phosducin. A 1217-nucleotide cDNA was isolated from a rat pineal library by DNA-DNA hybridization with a polymerase chain reaction-amplified cDNA of bovine retina mRNA for phosducin. Northern blot analysis demonstrates that the mRNA for phosducin is approximately 1.3 kb in both rat pineal and rat retina. The translated mRNA from rat pineal encodes a protein with 246 amino acids, compared to the 245 amino acids of bovine retina phosducin. The predicted molecular weight of rat pineal phosducin is 28,201. Immunoblot analysis with affinity-purified antibodies against bovine retina phosducin identify a single immunoreactive protein of approximately 33 kDa in both rat retina and rat pineal. The amino acid sequence of rat pineal phosducin is homologous to that of bovine retina phosducin, revealing 89% identity and another 5.7% similarity. Both rat pineal and bovine retina phosducins are acidic proteins with pIs of 4.3 and 4.5, respectively. The translated protein lacks hydrophobic domains that would suggest an integral membrane protein. Rat pineal phosducin has a single consensus phosphorylation domain for protein kinase A that is nearly identical to that of retinal phosducin, which is phosphorylated by protein kinase A in situ. Rat phosducin also contains three potential phosphorylation domains for protein kinase C and nine for casein kinase II as well as a predicted site for N-glycosylation. The cDNA encoding phosducin was used to localize the gene within a linkage group to a large segment of mouse chromosome 1 in a conserved region with the long arm of human chromosome 1 with a panel of DNA samples from an interspecific cross. In keeping with a proposed role of retinal phosducin in down-regulation of the photo-transduction cascade, a modulatory role in signal transduction is proposed for pineal phosducin.     

Rat corticosteroid binding globulin: primary structure and messenger ribonucleic acid levels in the liver under different physiological conditions

Rat corticosteroid binding globulin (CBG) cDNAs were isolated from a lambda gt11 liver cDNA library. When rat hepatic mRNA was hybrid selected and translated in vitro, a major product reacted with antibodies against rat CBG and its Mr (approximately 43,000) was consistent with a nonglycosylated, CBG precursor polypeptide. Two overlapping cDNAs produced a 1,432 nucleotide sequence with an open reading frame comprising 396 amino acids. This includes a potential signal peptide of 22 residues followed by the amino terminus of purified rat CBG. Rat CBG therefore contains 374 amino acids (Mr = 42,196), and has six consensus sites for N-glycosylation. There is 60% identity in the primary structures of rat and human CBG over 383 residues that comprise the human sequence. Furthermore, the single cysteine in rat CBG corresponds to one of two cysteines in human CBG, and this may be significant because a cysteine is located in the human CBG steroid binding site. Northern analysis of RNA from various rat tissues revealed an approximate 1.8 kilobase CBG mRNA only in the liver. Its relative abundance in a pregnant rat was only 30% higher than in an adult female; approximately 3-fold higher than in an adult male, and 25-fold higher than in the fetuses from the same animal. Southern analysis of rat genomic DNA suggests the presence of a single gene for CBG.     

Cloning and analysis of cDNA clones for rat kidney alpha-spectrin

We have isolated a 3922-base pair (bp) cDNA clone for rat nonerythroid alpha-spectrin from a rat kidney lambda gt11 cDNA library. Sequence analysis revealed that this cDNA contains an open reading frame of 3090 bp encoding for the C-terminal 1030 amino acid sequence of rat kidney alpha-spectrin. The 3'-untranslated region (including a 38-bp poly(A+) tail) contains an 832-bp sequence. A single mRNA of about 8 kilobase pairs was detected in rat liver, kidney, brain, heart, intestine, lung, testis, stomach, spleen, and muscle with varying abundances, which is consistent with and further confirms the presence of spectrins in nonerythroid tissues as demonstrated previously by immunoblot analysis. Southern blot analysis suggested that there is a single gene for nonerythroid alpha-spectrin. The derived amino acid sequence contains sequence from the spectrin 106-residue internal repeat 12 to the C terminus of rat kidney alpha-spectrin. Sequence comparison with human and chicken nonerythroid alpha-spectrin showed that nonerythroid alpha-spectrin is well conserved during evolution. The rat kidney alpha-spectrin sequence, when compared to rat brain alpha-spectrin, contains an extra 76-amino-acid sequence at the C terminus. Sequence comparison of all the internal repeats available revealed that the internal repeat 3, 4, 5, 6, 7, and 8 has highest sequence similarity with internal repeat 12, 13, 14, 15, 16, and 17, respectively. Therefore, internal repeats 3-8 and 12-17 are most likely derived from an ancestral gene through gene duplication, suggesting that the spectrin gene is derived from a half-spectrin gene by gene duplication and divergence during evolution.     

Rat ear reattachment as an animal model

The external ear of the rat is an excellent model for practicing microsurgical dissection and for the refinement of microvascular anastomoses, techniques that are crucial for microvascular en bloc tissue transfer and replantation. Preparation of the rat ear for replantation requires familiarity with the vascular anatomy and gentle tissue handling with atraumatic dissection of arterial and venous pedicles, steps similarly crucial in raising free flaps for microvascular transfer. The strategy of performing accurate reduction and stabilization of the tubal cartilage prior to vessel repairs, anastomosing the more deeply seated external carotid artery prior to the more superficial posterior facial vein, is as critical to rat ear replantation as for digital reattachment. In addition, the rat ear as compared to other animal models such as the rabbit ear or canine hindlimbs is much less expensive. Compared to the rat hindlimb model, rat ears are much easier to observe, which is a distinct advantage when used as a model for long-term study of replantation, revascularization, or transplantation.     

Molecular cloning of actin filament-associated protein: a putative adaptor in stretch-induced Src activation

Mechanical stretch-induced activation of c-Src is an important step for signal transduction of stretch-induced fetal rat lung cell proliferation. This process appears to be mediated through actin filament-associated protein (AFAP), encoded by a gene originally cloned from the chicken. In the present study, we cloned the rat AFAP gene from fetal rat lungs. Its mRNA and protein are differentially expressed among various tissues. The protein is colocalized with actin filaments in fetal rat lung epithelial cells and fibroblasts. Mechanical stretch increased tyrosine phosphorylation of rat AFAP and its binding to c-Src within the initial several minutes. Src SH2 and SH3 binding motifs are highly conserved in the AFAP proteins (from chicken, rat to human). On the basis of the molecular structure of AFAP protein, we speculate that it is an adaptor in mechanical stretch-induced activation of c-Src. A novel model of mechanoreception is proposed.     

Nucleotide sequence divergence and functional constraint in VIP precursor mRNA evolution between human and rat

The nucleotide sequence analysis of cloned cDNA for VIP precursor from rat cerebral cortex reveals that the precursor contains both rat VIP and PHI-27. The deduced primary structure of rat VIP is identical with human VIP. The amino acid sequence of rat PHI-27 differs by 4 amino acids from human PHM-27. When each VIP precursor is divided functionally into 6 domains, the amino acid sequence homology between rat and human precursors ranges from 69 to 100%. In contrast, any domain exhibits an essentially equal degree of nucleotide sequence homology.     

Physical and biological properties of an epsilon-heavy chain mRNA and a kappa-light chain mRNA coding for rat immunoglobulin E

The mRNA coding for epsilon-heavy chain and kappa-light chain have been highly enriched from a rat IgE-producing myeloma, IR-162. Based on denaturing gel analyses, the 20 S epsilon-heavy chain mRNA has an estimated molecular weight of 850,000, equivalent to about 2500 nucleotides. The 14S rat kappa-light chain mRNA has an estimated molecular weight of 410,000, equivalent to about 1200 nucleotides. Only about two-thirds of the length of these mature cytoplasmic rat mRNA code for protein. The 20 S mRNA stimulates the in vitro synthesis of a single major serologically related protein which is large enough to be epsilon-heavy chain. It is unglycosylated and has an apparent molecular weight of about 62,000. The in vivo unglycosylated epsilon-heavy chain, obtained in the presence of tunicamycin, has an apparent molecular weight of about 59,000, compared with about 76,000 for the glycosylated heavy chain of the secreted rat IgE. Therefore, the in vitro synthesized epsilon-heavy chain protein is about Mr = 3000 larger than the in vivo unglycosylated epsilon-heavy chain, equivalent to about 25 extra amino acids. This is consistent with the synthesis of an epsilon-heavy chain putative precursor. Likewise, the 14 S mRNA stimulates the in vitro synthesis of a single putative precursor protein, which is serologically related to kappa chain, is unglycosylated, and is about an extra 20 amino acids. This is the first report on the physical and biological properties of an epsilon-heavy chain mRNA, as well as any rat immunoglobulin mRNA.     

Expression of IGF-binding protein-1 phosphoisoforms in fasted rat skin and its role in regulation of collagen biosynthesis

Insulin-like growth factor-I (IGF-I) is an important stimulator of collagen and glycosaminoglycan (GAG) biosynthesis in tissues. IGF-I activity is modulated by a family of IGF-binding proteins (IGFBPs) with different IGF-I binding affinities. At least IGFBP-1 and IGFBP-2 are known as inhibitors of IGF functions. Some IGFBPs (IGFBP-1, IGFBP-3 and IGFBP-5) may undergo phosphorylation that dramatically increase their affinity for IGF. During fasting of animals there is a significant decrease of the collagen and GAG content of the skin, accompanied by a reduction of plasma IGF-I levels. However, in previous studies we showed that in the skin of fasted rats IGF-I as well as IGFBP-1 and IGFBP-2 expressions were not different, compared to control rat skin, although collagen content was significantly decreased. In the present study we show that fasted rat skin contains similar amounts of IGF-I, IGFBP-3 and IGFBP-1, although extract from fasted rat skin induced inhibition of collagen biosynthesis in cultured fibroblasts, compared to control rat skin extract. Western immunoblot analysis of control and fasted rat skin extracts, using anti-phosphoserine antibodies for immunoprecipitated IGFBP-1 and IGFBP-3, revealed that both proteins are present in phosphorylated form. Although no differences were found in the expression of phosphorylated IGFBP-3 between control and fasted rat skins, that of phosphorylated IGFBP-1 in fasted rat skin extract was higher than in control one. We suggest that there is an increased level of IGFBP-1 phosphoisoform in fasted rat skin, associated with increased affinity for IGF-I. The increase of phosphorylated IGFBP-1 in fasted rat skin tissue may augment IGF-I binding affinity for IGF and decrease its bioavailability for receptor interaction. This mechanism may prevent IGF-I dependent stimulation of fibroblasts to produce extracellular matrix components. The specific expression of IGFBPs and their phosphoisoforms in tissues may play an important role in regulation of IGF-I action during physiologic and pathologic responses.     

Binding of epidermal growth factor from man, rat and mouse to the human epidermal growth factor receptor

Human, rat and mouse epidermal growth factors (EGF) bind to the same receptor on human placenta, but the binding characteristics differ. The apparent affinity constant (KA) for human EGF is higher (15 X 10(9) l/mol) than KA for rat EGF (10 X 10(9) l/mol). Mouse EGF binds with the lowest KA (5 X 10(9) l/mol). The pH optimum differs so that human and rat EGF bind with a pH optimum of 8.0, whereas mouse EGF binds with an optimum of pH 7.4. Half maximal dissociation is 130, 50 and 25 min for human, rat and mouse EGF, respectively. The structures of human, rat and mouse EGF differ somewhat. At least 11 of the first 24 residues differ. The N-terminal sequence of rat EGF is: Ala/Ser-Gly-X-Pro-Pro-Ser-Tyr-Asp-Gly-Tyr-X-Lys-Asp-Gly-Gly-Val-X-Met-Ty r-Val -Glu.     

Simultaneous blockade of Fc gamma receptors and indirect labeling of mouse lymphocytes by the selective detection of allotype-restricted epitopes on the kappa chain of rat monoclonal antibodies

BACKGROUND: Incubation of mouse hemopoietic cells with rat monoclonal antibodies (mAbs) of the IgG class sometimes results in Fc-region mediated binding of immunoglobulins by Fc-receptors. This unwanted binding can be prevented by preincubation of target cells with the rat anti-mouse anti-CD16/32 (2.4G2) mAb. METHODS: To avoid the cross-reactivity of fluorochrome-conjugated secondary anti-rat antibodies with the Fc-receptor blocking 2.4G2, direct fluorochrome-conjugated immunoglobulins need to be used. However, we report that a mouse mAb (MRC OX12) with a strong rat Igk(a) allotype preference can be used for flow cytometric measurements in conjunction with unlabeled rat mAbs with the simultaneous blockade of Fc gamma receptors by the 2.4G2 mAb. Results and Discussion This lack of reactivity of OX12 against the 2.4G2 mAb is remarkable, as it could efficiently detect another Sprague-Dawley-derived rat mAb. This staining procedure (unlabeled rat mAb of the appropriate strain detected by OX12 mAb in the presence of 2.4G2 IgG) is an attractive alternative to using direct antibody conjugates, while satisfying the need for an effective Fc gamma-receptor blockade.     

Properties and biochemical characterization of NADH 5 alpha-reductase from rat liver microsomes

NADH 5 alpha-reductase is present in microsomes of various rat organs: heart and skeletal muscle, liver, adrenal glands, kidney, testes and prostate. The enzyme from rat liver microsomes utilizes B-hydrogen from the coenzyme NADH for steroid reduction. After solubilization of the enzyme with the nonionic detergent lubrol, phosphatidylcholine is necessary to restore the activity. This reactivation of the enzyme activity is paralleled by a corresponding increase of Vmax for testosterone (17 beta-hydroxy-4-androsten-3-one). Km and Vmax for testosterone change, Km and Vmax for the coenzyme NADH remain constant with an alteration of phosphate concentration in the incubation medium. The NADH 5 alpha-reductase is inhibited by numerous substances: amytal, phenobarbital, mepacrin, thenoyltrifluoracetone, gallic acid propyl ester, dicoumarol, pentachlorophenol, NADP and antibodies against rat liver NADPH ferrihemoprotein reductase. Antibodies against rat liver cytochrome-b5 reductase cause an activation of NADH 5 alpha-reductase.     

Alteration in skeletal muscle mitochondria of cold-acclimated rats: Association with enhanced metabolic response to noradrenaline

This paper reports a search for structural changes in skeletal muscle mitochondria of cold-acclimated rats. Histochemical studies (succinic dehydrogenase) show that there appears to be a higher proportion of red fibers in the semitendinosus muscle of the cold-acclimated rat and that the white region of this muscle contains fibers which resemble intermediate fibers. Electron micrographs show an apparently larger number of small mitochondria in both red and white fibers. Counts of mitochondria isolated from skeletal muscle show that there are more mitochondria per gram of both red and white muscle in the cold-acclimated rat than in the non-acclimated control rat. Each mitochondrion contains less protein and less cytochrome oxidase. Thus the mitochondrial mass per gram of red and white muscle is not altered, as indicated by the unchanged content of mitochondrial protein and of cytochrome oxidase per gram of muscle. Thus there appears to be a repackaging of mitochondrial material into smaller units in the skeletal muscle of the cold-acclimated rat. The alteration is shown to be associated with the adaptive state of the rat. No change occurs in muscle mitochondria of cold-acclimated rats in which the development of the enhanced metabolic response to noradrenaline, a measure of the extent of adaptation, is inhibited by treatment with oxytetracycline. The change in skeletal muscle mitochondria disappears when the enhanced metabolic response to noradrenaline in rats which are already cold-climated is reversed by treating the rats with oxytetracycline while they continue to live in the cold. The change in muscle mitochondria also disappears when the cold-acclimated rat undergoes deacclimation after return to room temperature. The alteration in muscle mitochondria is thus not associated either with shivering or with a high metabolic rate. Skeletal muscle of the cold-acclimated rat is known to be an important site of heat production in the course of nonshivering thermogenesis; that is, it can undergo a considerable increase in metabolic rate in the absence of shivering on exposure of the cold-acclimated rat to cold. The metabolic basis of nonshivering thermogenesis is in an enhanced capacity of the tissues of the cold-acclimated rat, principally skeletal muscle, to respond by an increase in metabolic rate to the large amounts of noradrenaline secreted by the nerve endings of the sympathetic nervous system as a consequence of cold-exposure. The mechanism by which the metabolic response to noradrenaline in the cold-acclimated rat can be enhanced is unknown. The structural alteration observed in the skeletal muscle mitochondria of the cold-acclimated rat may indicate a functional alteration responsible for the enhanced capacity of the muscle to respond to noradrenaline by an increase in metabolic rate.     

A 50 kDa, actin-binding protein in plasma membranes of rat hepatocytes and of rat liver tumors

Plasma membranes from normal rat livers and rat liver tumors were compared by SDS-gel electrophoresis, and analyzed for actin-binding proteins by an 125I-labelled actin gel-overlay assay and by actin-affinity blotting. After treatment of rats with alpha-hexachlorocyclohexane and after induction of liver tumors by combined treatment with N-nitrosomorpholine and phenobarbital, liver plasma membranes prepared from these animals were found to be highly enriched in an actin-binding, 50 kDa polypeptide. This polypeptide seemed to be an integral protein of the plasma membrane as judged by Triton X-114-phase separation. Microsomes did not contain an actin-binding polypeptide in the 50 kDa region. Therefore, the 50 kDa protein is a candidate for interaction of actin with the liver cell plasma membrane. A possible relationship of this protein with the multi-specific, cholate transporting system of the rat liver plasma membrane is discussed.     

Predictions based on the rat–mouse comparative map provide mapping information on over 6000 new rat genes

For identification of ECS (``evolutionarily conserved segments') between rat and mouse, 893 rat–mouse orthologous gene-pairs were brought together with zoo-FISH analysis. In total, 59 autosomal ECS and 4 X-chromosomal ones were detected. Combining FISH and zoo-FISH data, the segments were anchored on the rat chromosomes, providing an improved comparative map between the two species. Since chromosomal evolution is a slow process, it is reasonable to assume that the genome organization, including gene order, is essentially conserved within the ECS. In this way we assigned tentative subchromosomal map positions to 303 rat genes, for which no regional mapping information was available. Furthermore, the concept of prediction mapping was extended to unmapped rat homologs of genes, which in the mouse are situated inside or in the vicinity of an ECS. For a total of 6669 genes, we predicted a single rat chromosomal position, whereas for another 448 genes we could predict that they were located in one of two possible positions. Thus, our study has increased the number of genes for which there is positional mapping information in the rat almost fivefold.     

Immunocytochemical distribution of E-cadherin in normal and injured lung tissue of the rat

Affinity purified rabbit anti-mouse E-cadherin antibodies, reacting with diverse rat epithelia, were used to characterize epithelial changes in a radiation-induced fibrosis model of rat lung by immunoblotting techniques, immunoperoxidase and immunofluorescence microscopy. Immunostaining of normal rat lung tissues revealed a predominant staining of type II pneumocytes. Immunoelectron microscopy confirmed the immunohistochemical data of normal lung tissue obtained at the light microscopic level. In severely injured rat lung, we found enhanced immunoreactivity for E-cadherin at the surface of type I alveolar epithelial cells. The results suggest that E-cadherin is an adhesion molecule that is modulated after pathological alteration of the alveolar epithelium and that the antiserum may be useful for the characterization of normal and diseased rat epithelia.     

The thigh flap: an osteomyocutaneous free-flap model in the rat

A new experimental model for free-flap transfer has been developed in the rat. This "thigh flap" is an osteomyocutaneous free flap of bone (femur), muscle (thigh), and skin (groin) based on the femoral vessels. The flap is harvested from the left groin and thigh of an inbred female rat and is transferred to a subcutaneous pocket in the left groin of a male rat of the same inbred strain. The femoral vessels supplying the flap are anastomosed end-to-end with the femoral vessels of the recipient. Thirty flaps have been transferred, with 5 technical failures. Three of the remaining 25 flaps developed necrosis within 24 hours. The other 22 flaps remained viable until the rat was sacrificed at 7 days. The survival rate of the thigh flap was thus 88 percent. The model is suitable for use in metabolic, vascular, and immunologic studies of composite free flaps.