bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutation of p53 in primary biopsy material and cell lines from Hodgkin disease.
Authors: Gupta R K , Patel K , Bodmer W F , Bodmer J G
Published: May 2006

The p53 tumor-suppressor gene encodes a nuclear phosphoprotein that arrests cell cycle progress at G1. It may facilitate DNA damage repair and is frequently mutated in many human tumors. Hodgkin disease, a malignant condition of the lymphoid system, is characterized by the presence of Reed-Sternberg cells and mononuclear variants (Hodgkin cells), whose etiology remains unknown. The large multinucleated Reed-Sternberg cells often comprise < 1% of the total cell population within a biopsy specimen and are thought to be the neoplastic component in an admixture of reactive cells. It has been shown in the large majority of cases that up to 60% of these multinucleated cells react with CM-1, an anti-p53 antibody. However, whether this "overexpression" of p53 protein reflects abnormality at the DNA level can no longer be assumed by immunocytochemistry alone. p53 from six Hodgkin disease-derived cell lines was examined by immunoprecipitation, polymerase chain reaction (PCR)-single-strand conformation polymorphism analysis, and sequencing. In one cell line, point mutations were identified in exons 5 and 8 of p53. Sequencing of cloned PCR products confirmed the mutations to be on different alleles. A strategy involving extraction of nuclei followed by enrichment by flow cytometry was used to determine whether p53 overexpression in the Reed-Sternberg cells from patient biopsy material was due to mutations in this gene. Single-strand conformation polymorphism revealed additional bands in the polyploid nuclear preparations, suggesting abnormalities, and sequence analysis confirmed the presence of point mutations.
The APC gene product in normal and tumor cells.
Authors: Smith K J , Johnson K A , Bryan T M , Hill D E , Markowitz S , Willson J K , Paraskeva C , Petersen G M , Hamilton S R , Vogelstein B
Published: May 2006

The APC gene has been found to be mutated during the development of sporadic colorectal tumors as well as in the germ line of familial adenomatous polyposis patients. To facilitate the characterization of both normal and mutant APC protein, a series of monoclonal and polyclonal antibodies specific for the APC protein was produced. When lymphoblastoid cell lines derived from seven familial adenomatous polyposis patients with known mutations were analyzed by Western blot, an approximately 300-kDa protein corresponding to the predicted size of full-length APC was detected in all 7 cell lines. In addition, truncated APC proteins corresponding to the product of the known mutated alleles could be detected in 4 of the 7 lines. Similar analysis of 23 colon carcinoma and 9 adenoma cell lines revealed truncated proteins in 24 (75%) of the cell lines. Moreover, 26 (81%) of the colon tumor lines were totally devoid of the normal, full-length protein. In contrast, Western blot analysis of 40 cell lines derived from sporadic tumors of other organs detected only full-length APC. Immunohistochemical analysis of APC in normal colonic mucosa revealed cytoplasmic staining with more intense staining in the basolateral margins of the epithelial cell. This staining was markedly increased in the upper portions of the crypts, suggesting an increased level of expression with maturation. These studies provide some initial clues to the function of the cytoplasmic protein APC and demonstrate the feasibility of identifying APC mutations by direct analysis of the APC protein.
Rhabdomyosarcoma arising in transgenic mice harboring the beta-globin locus control region fused with simian virus 40 large T antigen gene.
Authors: Teitz T , Chang J C , Kitamura M , Yen T S , Kan Y W
Published: May 2006

The beta-globin locus control region (LCR) confers a high level of erythroid-specific and copy-number-dependent expression to human globin genes in transgenic mice. Simian virus 40 T (tumor) antigen (Tag) with its own natural enhancer causes choroid plexus tumors in mice. We investigated the effect of the LCR on Tag gene expression, reasoning that mice harboring a LCR-Tag fusion gene might develop hematopoietic malignancies. To test this hypothesis we introduced an enhancerless Tag gene downstream of a LCR cassette into the germ lines of mice. The phenotypes of the transgenic mice depended on the copy number of the transgene. While mice with 1-2 copies matured normally, those with 3-7 copies developed rhabdomyosarcomas in different anatomic sites at high frequency and showed hyperplasia of the pancreatic islet cells which progressed to pancreatic islet tumors. In addition, the mice bearing 7 copies of the transgene had hypoglycemia and were stunted in growth. Mice with more than 10 copies were markedly stunted in growth and died within 2-4 weeks. Tag expression was detected at high levels in the mouse tumors but not in any other tissues, including the hematopoietic cells.
Electrophysiological tests of neural models: evidence for nonlinear binocular interactions in humans.
Authors: Zemon V , Pinkhasov E , Gordon J
Published: May 2006

Evoked cortical potentials were used to test neural models of binocular interactions in humans. The critical feature that distinguished between basic models was whether the two monocular signals combined linearly or nonlinearly. Stimuli were presented separately and simultaneously to two eyes with the relative temporal phase parametrically varied. Fourier analysis was applied to the recorded electroencephalogram to measure the frequency response of the visual cortex to this stimulation. Comparisons of the models' predictions with the experimental results indicate that the greatest contribution to the cortical response originates in a neural pathway that contains nonlinear binocular combination, and a smaller contribution originates in a pathway with linear binocular combination. Current models, based on psychophysical studies of humans and on single-cell neurophysiological investigations of cats, are inadequate to explain these results. A model of binocular interaction is proposed that does account for the present findings and is also supported by neurophysiological studies on monkeys. This model, which contains both nonlinear and linear binocular interactions, has profound implications for perceptual processing.
The sluggish-A gene of Drosophila melanogaster is expressed in the nervous system and encodes proline oxidase, a mitochondrial enzyme involved in glutamate biosynthesis.
Authors: Hayward D C , Delaney S J , Campbell H D , Ghysen A , Benzer S , Kasprzak A B , Cotsell J N , Young I G , Miklos G L
Published: May 2006

Certain gene mutations in Drosophila melanogaster cause sluggish motor activity. We have localized the transcription unit of the sluggish-A gene to a 14.7-kb region at the base of the X chromosome and have cloned corresponding cDNAs. The predicted protein product has significant sequence similarity to Saccharomyces cerevisiae proline oxidase (EC 1.5.99.8), a mitochondrial enzyme which catalyzes the first step in the conversion of proline to glutamate. In the mutant fly, mitochondrial proline oxidase activity is reduced and has kinetic properties different from those of the wild type, providing further evidence that the gene encodes proline oxidase. Indeed, the free proline level in mutant flies is elevated. When the mutant is rescued by transformation, the proline oxidase and free proline levels, as well as the motor and phototactic behavior, are restored to normal. During embryonic development the sluggish-A transcript is predominantly expressed in the nervous system. Significantly, it has previously been reported that a mouse mutant, PRO/Re, which has reduced proline oxidase activity and elevated free proline levels, also exhibits sluggish behavior.
Direction of handedness linked to hereditary asymmetry of a sensory system.
Authors: Barnéoud P , Van der Loos H
Published: May 2006

Studies on the role of heredity in the transmission of handedness in nonhuman mammals have, so far, led to the isolation of mouse strains that differed in the lateralized versus ambidextrous use of the forepaw in a food-retrieval task (strength of paw preference). Here we report that left versus right use of the forepaw (direction of paw preference) is associated with a genetically expressed structural asymmetry of a sensory system, the whisker-to-barrel pathway. Mice that express whisker pad asymmetry of a direction that corresponds with the asymmetry for which they were bred demonstrate an opposite shift in the distribution of handedness: a right or left dominance of the whisker pad predicts a high proportion of left-handers or right-handers, respectively. Is an altered brain circuit--that is, a consequence of the asymmetry of the whisker pad--associated with a change in the circuitry that governs handedness? Or, alternatively, are there two gene sets responsible for the phenomena that we report--one that causes "whiskeredness" and another that causes handedness?
Genes for a microaerobically induced oxidase complex in Bradyrhizobium japonicum are essential for a nitrogen-fixing endosymbiosis.
Authors: Preisig O , Anthamatten D , Hennecke H
Published: May 2006

We report the discovery of a Bradyrhizobium japonicum gene cluster (fixNOQP) in which mutations resulted in defective soybean root-nodule bacteroid development and symbiotic nitrogen fixation. The predicted, DNA-derived protein sequences suggested that FixN is a heme b and copper-binding oxidase subunit, FixO a monoheme cytochrome c, FixQ a polypeptide of 54 amino acids, and FixP a diheme cytochrome c and that they are all membrane-bound. The isolation and analysis of membrane proteins from B. japonicum wild-type and mutant cells revealed two c-type cytochromes of 28 and 32 kDa as the likely products of the fixO and fixP genes and showed that both were synthesized only under oxygen-limited growth conditions. Furthermore, fixN insertion and fixNO deletion mutants grown microaerobically or anaerobically (with nitrate) exhibited a strong decrease in whole-cell oxidase activity as compared with the wild type. The data suggest that the fixNOQP gene products are induced at low oxygen concentrations and constitute a member of the bacterial heme/copper cytochrome oxidase superfamily. The described features are compatible with the postulate that this oxidase complex is specifically required to support bacterial respiration in endosymbiosis.
Signal sequence region of mitochondrial precursor proteins binds to mitochondrial import receptor.
Authors: Murakami H , Blobel G , Pain D
Published: May 2006

An integral mitochondrial membrane protein (p32) of yeast has previously been molecularly cloned and sequenced and suggested to function as a mitochondrial import receptor. However, this protein has also been proposed to function as phosphate translocator [Guérin, B., Bukusoglu, C., Rakotomanana, F. & Wohlrab, H. (1990) J. Biol. Chem. 265, 19736-19741; Phelps, A., Schobert, C.T. & Wohlrab, H. (1991) Biochemistry 30, 248-252]. Here we have purified p32 after expression of its gene in Escherichia coli and assayed its ability to bind to various preproteins containing signal sequences for protein translocation into mitochondria, chloroplasts, or the endoplasmic reticulum. Our data suggest that p32 contains a binding site specific for the signal sequence region of mitochondrial preproteins. These data are consistent with the previous assignment of p32 as an import receptor and are discussed with regard to the apparently conflicting assignment of this protein as phosphate translocator.
Structure of the human 3-methyladenine DNA glycosylase gene and localization close to the 16p telomere.
Authors: Vickers M A , Vyas P , Harris P C , Simmons D L , Higgs D R
Published: May 2006

We recently reported the presence of four genes lying between the human alpha-globin gene cluster and the telomere of the short arm of chromosome 16 (16p). We now report that one of these genes encodes 3-methyladenine DNA glycosylase, an enzyme important in the repair of DNA after damage by alkylating agents. The gene comprises five exons, representation of which differs in independently isolated cDNA clones. Although the gene is widely expressed, the abundance of its mRNA is considerably higher in a colon adenocarcinoma cell line (HT29) than in other cell lines that were tested. The major positive erythroid-specific regulatory element controlling alpha-globin gene expression lies equidistant between the promoters of the alpha-globin genes and the 3-methyladenine DNA glycosylase gene. Interestingly, in contrast to the alpha-globin genes, expression of the 3-methyladenine DNA glycosylase gene is not influenced by the regulatory element in the human erythroleukemia cell line K562.
Transforming growth factor beta as a virulence mechanism for Leishmania braziliensis.
Authors: Barral A , Barral-Netto M , Yong E C , Brownell C E , Twardzik D R , Reed S G
Published: May 2006

Transforming growth factor beta (TGF-beta) has potent down-regulating effects on macrophages and is thus capable of influencing the fate of intramacrophage parasites, including leishmanias. We report the development of a mouse model for the study of the human pathogen Leishmania braziliensis and demonstrate, both in vitro and in vivo, a key regulatory role for TGF-beta in the pathogenesis of infection with this parasite. Recombinant TGF-beta added to cultures of murine peritoneal macrophages led to increased intracellular L. braziliensis replication, whereas addition of neutralizing anti-TGF-beta monoclonal antibody decreased levels of infection. Macrophages infected with L. braziliensis produced biologically active TGF-beta, with a direct correlation between amounts of TGF-beta induced by two parasite isolates and their relative virulence. In vivo, treatment with recombinant TGF-beta rendered avirulent parasites virulent and activated latent L. braziliensis infection. Activation of parasite replication was observed in mice which had been infected with L. braziliensis 15 weeks previously but had not developed lesions or had healed lesions, depending on the parasite isolate used to infect the mice. The exacerbation of L. braziliensis infection in vivo was associated with an increase of interleukin 10 mRNA in the draining lymph node. These results demonstrate that TGF-beta is able to alter the course of in vitro and in vivo infections with L. braziliensis, the latter being characterized by an increase in interleukin 10, an important Th2 helper-T-cell cytokine.
Decreased expression of Mac-2 (carbohydrate binding protein 35) and loss of its nuclear localization are associated with the neoplastic progression of colon carcinoma.
Authors: Lotz M M , Andrews C W , Korzelius C A , Lee E C , Steele G D , Clarke A , Mercurio A M
Published: May 2006

The Mac-2 lectin (carbohydrate binding protein 35) is a soluble, 32- to 35-kDa phosphoprotein that binds galactose-containing glycoconjugates. We report here that the colonic epithelium is a major site of Mac-2 expression in vivo based on immunohistochemistry of human tissue specimens. In this epithelium, proliferating cells at the base of the crypts do not express Mac-2 but its expression increases with differentiation along the crypt-to-surface axis. Mac-2 expression is concentrated in the nuclei of these differentiated epithelial cells. The progression from normal mucosa to adenoma to carcinoma is associated with significant changes in Mac-2 nuclear localization and expression. In all adenomas (9/9) and carcinomas (13/13) examined, Mac-2 was not present in the nucleus but was localized in the cytoplasm. Sequencing of Mac-2 cDNAs from normal mucosa and carcinoma revealed no specific mutations that could account for this loss of nuclear localization. We also observed a 5- to 10-fold decrease in Mac-2 mRNA levels in cancer compared to normal mucosa as well as a significant reduction in the amount of Mac-2 protein expressed. These observations suggest that Mac-2 exclusion from the nucleus and its decreased expression may be related to the neoplastic progression of colon cancer.
Role of RNA structure in arginine recognition of TAR RNA.
Authors: Puglisi J D , Chen L , Frankel A D , Williamson J R
Published: May 2006

The human immunodeficiency virus Tat protein binds specifically to an RNA stem-loop structure (TAR) that contains two helical stem regions separated by a three-nucleotide bulge. A single arginine within the basic region of Tat mediates specific binding to TAR, and arginine as the free amino acid also binds specifically to TAR. We have previously proposed a model in which interaction of the arginine guanidinium group with guanosine-26 (G26) and with a pair of phosphates is stabilized by formation of a base triple between U23 in the bulge and A27.U38 in the upper helix. Here we show by NMR spectroscopy that formation of the base triple is critical for arginine binding to TAR. Mutants of TAR that cannot form the base triple or that remove the guanine contact do not bind arginine specifically. These mutants also showed reduced transactivation by Tat. A triple mutant designed to form an isomorphous base triple between C23 and G27.C38 binds arginine and adopts the same conformation as wild-type TAR. These results demonstrate the importance of RNA structure for arginine binding and further demonstrate the direct correspondence between arginine and Tat binding.
Replacement of germ-line epsilon promoter by gene targeting alters control of immunoglobulin heavy chain class switching.
Authors: Xu L , Gorham B , Li S C , Bottaro A , Alt F W , Rothman P
Published: May 2006

Recent work has shown that the ability of cytokines to direct immunoglobulin heavy chain class-switch recombination to particular heavy chain constant (C) region (CH) genes correlates with the induction of specific germ-line CH transcripts. To test the role of germ-line transcripts in class switching, we have used homologous recombination to mutate the immunoglobulin heavy chain locus of the 18.81A20 murine pre-B-cell line. In the parent cell line, the combination of interleukin-4 (IL-4) and lipopolysaccharide (LPS) induces germ-line epsilon locus transcription prior to class switching to epsilon. The heavy chain locus of the mutated cell line contains the immunoglobulin heavy chain enhancer and variable region gene promoter in place of the LPS/IL-4-responsive germ-line epsilon promoter. The mutant cell line constitutively transcribes the epsilon locus in the absence of IL-4. Strikingly, the mutant cell line also switches to epsilon in the absence of IL-4. This result demonstrates that, at least in the 18.81A20 cell line, germ-line epsilon transcription plays a direct role in class switching to the epsilon locus. In addition, the ability to change the pattern of class switching by altering transcriptional activity indicates that transcription of germ-line CH is mechanistically important in regulation of class switching.
Interleukin 13 induces interleukin 4-independent IgG4 and IgE synthesis and CD23 expression by human B cells.
Authors: Punnonen J , Aversa G , Cocks B G , McKenzie A N , Menon S , Zurawski G , de Waal Malefyt R , de Vries J E
Published: May 2006

Recently the cDNA encoding interleukin 13 (IL-13), a T-cell-derived cytokine, was cloned and expressed. The present study demonstrates that IL-13 induces IgG4 and IgE synthesis by human B cells. IL-13-induced IgG4 and IgE synthesis by unfractionated peripheral blood mononuclear cells and highly purified B cells cultured in the presence of activated CD4+ T cells or their membranes. IL-13-induced IgG4 and IgE synthesis is IL-4-independent, since it was not affected by neutralizing anti-IL-4 monoclonal antibody. Highly purified, surface IgD+ B cells could also be induced to produce IgG4 and IgE by IL-13, indicating that the production of these isotypes reflected IgG4 and IgE switching and not a selective outgrowth of committed B cells. IL-4 and IL-13 added together at optimal concentrations had no additive or synergistic effect, suggesting that common signaling pathways may be involved. This notion is supported by the observation that IL-13, like IL-4, induced CD23 expression on B cells and enhanced CD72, surface IgM, and class II major histocompatibility complex antigen expression. In addition, like IL-4, IL-13 induced germ-line IgE heavy-chain gene transcription in highly purified B cells. Collectively, our data indicate that IL-13 is another T-cell-derived cytokine that, in addition to IL-4, efficiently directs naive human B cells to switch to IgG4 and IgE production.
Activated estrogen receptor mediates growth arrest and differentiation of a neuroblastoma cell line.
Authors: Ma Z Q , Spreafico E , Pollio G , Santagati S , Conti E , Cattaneo E , Maggi A
Published: May 2006

Several reports demonstrate estrogen receptor involvement in specific brain functions. In addition, estrogen receptors are expressed at early stages of brain development, suggesting that estrogens or related molecules may play an instructive role in the differentiation of specific brain areas. The lack of model systems in which these phenomena could be studied prompted us to develop a neuroblastoma cell line expressing the estrogen receptor. The cell line expresses the hormone receptor at levels compatible with a physiological activity. The activated estrogen receptor is capable of blocking proliferation of the cells without exerting toxic effects. Following growth arrest, the cells display a neuron-like morphology and express tau and synaptophysin, two proteins synthesized in differentiating neurons. The cell line generated will provide a valuable model system for molecular and biochemical studies of the activity of estrogens in neural-derived cells.
Efficient transplantation of BCR-ABL-induced chronic myelogenous leukemia-like syndrome in mice.
Authors: Gishizky M L , Johnson-White J , Witte O N
Published: May 2006

Lethally irradiated mice reconstituted with bone marrow expressing P210 BCR-ABL can develop myeloproliferative syndromes that resemble the initial phase of human chronic myelogenous leukemia (CML). Mice that develop the CML-like syndrome can be segregated into two groups based on the latency with which the granulocytic disease appears--early onset (< 20 weeks) and late onset (> 20 weeks). Only cells from mice exhibiting the late-onset CML-like syndrome can efficiently propagate the disease when transplanted into sublethally irradiated syngeneic recipients. Mice engrafted with late-onset murine CML cells develop a range of hematopoietic disorders that originate from multipotent stem cells. The chronic granulocytic hyperplasia can be propagated by serial transplantation into secondary and tertiary recipient mice. The majority of transplanted mice succumb to acute myeloid and B- and T-lymphoid leukemias. These data support the idea that late-onset murine CML originates from a multipotent progenitor cell with a high replicating capacity. The inability to transplant the disease from mice developing the early-onset CML-like syndrome suggests that this disorder may originate from more differentiated progenitor cells with limited replication capacity that have undergone clonal expansion but are not immortalized. Although both early- and late-onset CML-like syndromes exhibit granulocytic hyperplasia, these disorders represent distinct diseases that appear to originate from different hematopoietic cell types. The late-onset CML-like disease and transfer to secondary recipients provides a useful murine model with features of the chronic and acute phases of human CML.
Actin is a surface component of calf pulmonary artery endothelial cells in culture.
Authors: Moroianu J , Fett J W , Riordan J F , Vallee B L
Published: May 2006

An angiogenin binding protein isolated previously from endothelial cells has been shown to be a member of the actin family. Calf pulmonary artery endothelial (CPAE) cells were investigated for the presence of surface actin by immunoblotting of isolated surface proteins and by immunofluorescence. CPAE cell surface proteins were isolated by selective apical biotinylation and recovery of biotinylated proteins by avidin affinity chromatography. Immunoblotting with a specific smooth muscle alpha-actin antibody detected the presence of this type of actin among the isolated cell surface proteins. Immunofluorescence confirmed that smooth muscle alpha-actin is localized at the surface of nonpermeabilized CPAE cells. Exposure of CPAE cells to angiogenin prior to cell surface immunostaining diminished the signal. When CPAE and rat aortic smooth muscle cells were made permeable before staining, stress fibers could be recognized by the antibody in smooth muscle cells but not CPAE cells. The results indicate that a smooth muscle type of alpha-actin is localized specifically on the surface of cultured CPAE cells where it might interact with angiogenin and other actin binding proteins present in the extracellular environment.
Ligand-dependent transformation by the receptor for human granulocyte/macrophage colony-stimulating factor and tyrosine phosphorylation of the receptor beta subunit.
Authors: Areces L B , Jücker M , San Miguel J A , Mui A , Miyajima A , Feldman R A
Published: May 2006

The receptor for human granulocyte/macrophage colony-stimulating factor (hGMR) is composed of two subunits, alpha and beta, which are both required for high-affinity binding of the ligand. To examine the transforming potential of hGMR, we have transfected cDNAs encoding the receptor alpha and beta subunits into NIH 3T3 cells, which normally do not express GMRs. Introduction of the receptor subunits into these cells resulted in focal transformation, which was dependent on the presence of human granulocyte/macrophage colony-stimulating factor (hGM-CSF) in the culture medium. No transformation was observed when hGM-CSF was replaced with other growth factors such as human epidermal growth factor or human interleukin 3 or when cells were transfected with the alpha or beta subunit alone. Individual conditional transformants isolated after transfection expressed functional hGMRs, were susceptible to transformation by picomolar levels of the ligand, and were capable of anchorage-independent growth in soft agar in the presence but not in the absence of hGM-CSF. Biochemical analysis showed that treatment of these cells with hGM-CSF caused a rapid phosphorylation of the beta subunit and other cellular proteins on tyrosine residues, recapitulating some of the events that take place during GM-CSF signaling in myeloid cells. We conclude that coexpression of the alpha and beta subunits of hGMR in established murine fibroblasts is sufficient to reconstitute a functional receptor, which is capable of causing ligand-dependent transformation. The oncogenic potential of hGMR lends support to the hypothesis that its deregulated or abnormal expression may play a role in leukemogenesis.
Photoisomerization mechanism of the rhodopsin chromophore: picosecond photolysis of pigment containing 11-cis-locked eight-membered ring retinal.
Authors: Mizukami T , Kandori H , Shichida Y , Chen A H , Derguini F , Caldwell C G , Biffe C F , Nakanishi K , Yoshizawa T
Published: May 2006

The primary photochemical event in rhodopsin is an 11-cis to 11-trans photoisomerization of its retinylidene chromophore to form the primary intermediate photorhodopsin. Earlier picosecond studies have shown that no intermediate is formed when the retinal 11-ene is fixed through a bridging five-membered ring, whereas a photorhodopsin-like intermediate is formed when it is fixed through a flexible seven-membered ring. Results from a rhodopsin analog formed from a retinal with locked 11-ene structure through the more flexible eight-membered ring (Ret8) are described. Incubation of bovine opsin with Ret8 formed two pigments absorbing at 425 nm (P425) and 500 nm (P500). P425, however, is an artifact because it formed from thermally denatured opsin or other proteins and Ret8. Excitation of P500 with a picosecond green pulse led to formation of two intermediates corresponding to photo- and bathorhodopsins. These results demonstrate that an appearance of early intermediates is dependent on the flexibility of the 11-ene and that the photoisomerization of P500 proceeds by stepwise changes of chromophore-protein interaction, which in turn leads to a relaxation of the highly twisted all-trans-retinylidene chromophore in photorhodopsin.
Structure from function: screening structural models with functional data.
Authors: Jin L , Cohen F E , Wells J A
Published: May 2006

Structural constraints derived from different antibody epitopes on human growth hormone (hGH) were used to screen three-dimensional models of hGH that were generated by computer algorithms. Previously, alanine-scanning mutagenesis defined the residues that modulate binding to 21 different monoclonal antibodies to hGH. These functional epitopes were composed of 4-14 side chains whose alpha-carbons clustered within 4-23 A. Distance and topographic constraints for these functional epitopes were virtually the same as constraints derived from known x-ray structures of protein-antigen complexes. The constraints were used to evaluate about 1400 models of hGH that were computer-generated by a secondary-structure prediction and packing algorithm. On average each functional epitope reduced the number of models in the pool by a factor of 2, so that 8 monoclonal antibodies could reduce the number of possible models to < 10. The average root-mean-square deviation of alpha-carbon coordinates between the x-ray structure and either the pool of starting models or final models ranged from 13 to 16 A or 4 to 7 A, respectively, depending on the pool of starting models and the level of constraints imposed. All of the final models had the correct folding topography, and the best model was within 3.8 A root-mean-square deviation of the x-ray coordinates. This model was as close as it could have been because the models were built by using ideal helices and those in the x-ray structure are not. Our studies suggest that epitope mapping data can effectively screen structural models and, when coupled to predictive algorithms, can help to generate low-resolution models of a protein.
Sialokinin I and II: vasodilatory tachykinins from the yellow fever mosquito Aedes aegypti.
Authors: Champagne D E , Ribeiro J M
Published: May 2006

The saliva of the mosquito Aedes aegypti has previously been reported to contain a 1400-Da peptide with pharmacological properties typical of a tachykinin. In the present study this vasodilator has been purified to homogeneity and found to consist of two peptides: sialokinin I, with the sequence Asn-Thr-Gly-Asp-Lys-Phe-Tyr-Gly-Leu-Met-NH2, and sialokinin II, identical to sialokinin I except for an Asp in position 1. These peptides are present in amounts of 0.62 and 0.16 pmol (711 and 178 ng), respectively, per salivary gland pair. When assayed on the guinea pig ileum, both peptides are as active as the mammalian tachykinin substance P, with K0.5 values of 5.07, 6.58, and 4.94 nM for sialokinin I, sialokinin II, and substance P, respectively.
The frequency of gene targeting in yeast depends on the number of target copies.
Authors: Wilson J H , Leung W Y , Bosco G , Dieu D , Haber J E
Published: May 2006

We have compared the efficiency of transformation by linear DNA fragments in yeast strains carrying different numbers of homologous targets for recombination. In strains carrying dispersed copies of a target and in strains carrying tandem arrays, the frequency of transformation is proportional to the number of targets. This result is in contrast to previous studies of transformation in mammalian cells, where targeted integration was insensitive to the number of targets. We conclude that, in yeast, the search for a homologous partner is a rate-limiting step in the successful recombination of linearized DNA fragments. Furthermore, the fact that we obtain the same results with both dispersed and clustered targets argues against models of homology searching in which DNA becomes nonspecifically associated with a chromosome and then slides along the DNA until homology is encountered.
Tissue distribution of glycine N-methyltransferase, a major folate-binding protein of liver.
Authors: Yeo E J , Wagner C
Published: May 2006

Glycine N-methyltransferase (GNMT; S-adenosyl-L-methionine:glycine N-methyltransferase, EC 2.1.1.20) is a major protein in rat liver that binds 5-methyltetrahydrofolate polyglutamate in vivo. This enzyme is believed to function in the regulation of the availability of S-adenosylmethionine, the primary donor of methyl groups in the body. The distribution of GNMT in a variety of rat tissues was examined immunohistochemically. In liver, GNMT was most abundant in the periportal region, whereas in kidney it was seen primarily in the proximal convoluted tubules. In pancreas, GNMT was abundant, principally in the exocrine tissue. GNMT was present in the striated duct cells of the submaxillary gland. In the jejunum, GNMT was found in the epithelial cells of the villi. Close examination of the liver indicated GNMT in the nucleus; this site was confirmed by purification of the nuclei and measurement of enzyme activity. The location of GNMT in the liver and kidney suggests that this enzyme plays a role in gluconeogenesis, while its presence in the exocrine cells suggests it may also be a factor in secretion.
Stochastic component to development of class I major histocompatibility complex-specific T cells.
Authors: Itano A , Kioussis D , Robey E
Published: May 2006

The mechanism by which an initially uncommitted cell chooses between alternative fates is a central issue in developmental biology. In the mammalian thymus, CD4 helper T cells and CD8 cytotoxic T cells arise from a common precursor that expresses both CD4 and CD8. The choice between the CD4 and CD8 lineage is linked to the specificity of the T-cell antigen receptor expressed by a thymocyte, but whether lineage commitment is stochastic or instructed has not been definitively resolved. We present evidence that expression of a constitutive CD8 transgene during thymic selection permits development of mature CD4 cells bearing the class I-restricted F5 T-cell antigen receptor. These results suggest that there is a stochastic component to the development of class I major histocompatibility complex-restricted T cells.
A minority of carcinoma cells producing acidic fibroblast growth factor induces a community effect for tumor progression.
Authors: Jouanneau J , Moens G , Bourgeois Y , Poupon M F , Thiery J P
Published: May 2006

It is generally accepted that primary tumors become heterogeneous as a consequence of tumor-cell genetic instability. Clonal dominance has been shown to occur in some experimental models allowing a subpopulation of cells to overgrow the primary heterogeneous tumor and to metastasize. Alternatively, interactions among coexisting tumor subpopulations may contribute to the emergence of a malignant invasive primary solid tumor. We asked the question whether emergence of carcinoma cells producing a growth/dissociating factor within a tumor cell population may be a determinant for tumor progression and for clonal dominance. To mimic such a situation, we have investigated the impact of tumor subpopulation heterogeneity in an in vivo model in which mixtures of carcinoma cells that differ in their ability to produce acidic fibroblast growth factor are injected into nude mice. Our data indicate that a growth-factor-producing cell subpopulation can confer increased tumorigenicity to an entire cell population and subsequently elicit a shorter delay for appearance of metastasis. A community effect via cell interactions may account for a heterogeneous tumor cell population rather than clonal dominance during progression of certain tumor types.
Topography of a binding site for small amnestic peptides deduced from structure-activity studies: relation to amnestic effect of amyloid beta protein.
Authors: Flood J F , Roberts E , Sherman M A , Kaplan B E , Morley J E
Published: May 2006

Four peptides homologous to amyloid beta protein containing the Val-Phe-Phe (VFF) sequence administered intracerebroventricularly after training caused amnesia for footshock active avoidance training in mice. Results with VFF and other peptides containing VFF or portions thereof were used to generate a topographic map for a hypothetical binding surface for amnestic peptides, termed Z. Effects on retention of footshock active avoidance training were rationalized in terms of fit to Z, making possible design of potential memory-modulating peptidic and nonpeptidic substances. Three peptides that neither improved nor impaired retention blocked the amnestic effects of beta-(12-28), a peptide homologous to amyloid beta protein, opening the way to development of substances that can antagonize the neurotoxic effects of amyloid beta protein on neural structures and thus attenuate symptoms and progression of Alzheimer disease.
Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.
Authors: Cruse W B , Saludjian P , Biala E , Strazewski P , Prangé T , Kennard O
Published: May 2006

The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.
Direct evidence linking expression of matrix metalloproteinase 9 (92-kDa gelatinase/collagenase) to the metastatic phenotype in transformed rat embryo cells.
Authors: Bernhard E J , Gruber S B , Muschel R J
Published: May 2006

Members of the matrix metalloproteinase (MMP) family have been implicated in the metastasis of tumor cells, but no direct evidence linking any given member of the MMP family to metastatic behavior has been presented. Rat embryo cells transformed by the Ha-ras and v-myc oncogenes or by Ha-ras alone are metastatic in nude mice and release the 92-kDa gelatinase/collagenase (MMP-9), whereas those transformed by Ha-ras plus the adenovirus E1A gene are not metastatic and do not release MMP-9. Here we demonstrate that MMP-9 expression can be induced in these tumorigenic but nonmetastatic rat cells by transfection with an MMP-9 expression vector. Transfection of a MMP-9 expression vector, but not control DNAs, conferred metastatic capacity on the nonmetastatic cells. The majority of colonies isolated after continued passage either in vivo or in vitro had lost the MMP-9 expression vector. However, occasional cells were isolated from metastases which retained MMP-9 expression after passage. These cells retained metastatic capacity. In contrast, cells isolated after losing MMP-9 expression also lost the ability to metastasize. These results provide direct evidence that MMP-9 has a role in tumor metastasis.
Structural similarity of a developmentally regulated bacterial spore coat protein to beta gamma-crystallins of the vertebrate eye lens.
Authors: Bagby S , Harvey T S , Eagle S G , Inouye S , Ikura M
Published: May 2006

The solution structure of Ca(2+)-loaded protein S (M(r) 18,792) from the Gram-negative soil bacterium Myxococcus xanthus has been determined by multidimensional heteronuclear NMR spectroscopy. Protein S consists of four internally homologous motifs, arranged to produce two domains with a pseudo-twofold symmetry axis, overall resembling a triangular prism. Each domain consists of two topologically inequivalent "Greek keys": the second and fourth motifs form standard Greek keys, whereas the first and third motifs each contain a regular alpha-helix in addition to the usual four beta-strands. The structure of protein S is similar to those of the vertebrate eye lens beta gamma-crystallins, which are thought to be evolutionarily related to protein S. Both protein S and the beta gamma-crystallins function by forming stable multimolecular assemblies. However, protein S possesses distinctive motif organization and domain packing, indicating a different mode of oligomerization and a divergent evolutionary pathway from the beta gamma-crystallins.
Activation of protein kinases and inhibition of protein phosphatases play a central role in the regulation of exocytosis in mouse pancreatic beta cells.
Authors: Ammälä C , Eliasson L , Bokvist K , Berggren P O , Honkanen R E , Sjöholm A , Rorsman P
Published: May 2006

The mechanisms that regulate insulin secretion were investigated using capacitance measurements of exocytosis in single beta cells maintained in tissue culture. Exocytosis was stimulated by voltage-clamp depolarizations to activate the voltage-dependent Ca2+ channels that mediate Ca2+ influx into the beta cell. Under basal conditions, the exocytotic responses were small despite large Ca2+ currents. The exocytotic responses were dramatically increased (10- to 20-fold) by conditions that promote protein phosphorylation, such as activation of protein kinases A and C or inhibition of protein phosphatases. The stimulation of secretion was not due to an enhancement of Ca2+ influx and both peak and integrated Ca2+ currents were largely unaffected. Our data indicate that exocytosis in the insulin-secreting pancreatic beta cell is determined by a balance between protein phosphorylation and dephosphorylation. They further suggest that although Ca2+ is required for the initiation of exocytosis, modulation of exocytosis by protein kinases and phosphatases, at a step distal to the elevation of Ca2+, is of much greater quantitative importance. Thus an elevation of Ca2+ may represent a permissive rather than a decisive factor in the regulation of the insulin secretory process.
Anergic self-reactive B cells present self antigen and respond normally to CD40-dependent T-cell signals but are defective in antigen-receptor-mediated functions.
Authors: Eris J M , Basten A , Brink R , Doherty K , Kehry M R , Hodgkin P D
Published: May 2006

B-cell tolerance to soluble protein self antigens such as hen egg lysozyme (HEL) is mediated by clonal anergy. Anergic B cells fail to mount antibody responses even in the presence of carrier-primed T cells, suggesting an inability to activate or respond to T helper cells. To investigate the nature of this defect, B cells from tolerant HEL/anti-HEL double-transgenic mice were incubated with a membrane preparation from activated T-cell clones expressing the CD40 ligand. These membranes, together with interleukin 4 and 5 deliver the downstream antigen-independent CD40-dependent B-cell-activating signals required for productive T-B collaboration. Anergic B cells responded to this stimulus by proliferating and secreting antibody at levels comparable to or better than control B cells. Furthermore, anergic B cells presented HEL acquired in vivo and could present the unrelated antigen, conalbumin, targeted for processing via surface IgD. In contrast, the low immunoglobulin receptor levels on anergic B cells were associated with reduced de novo presentation of HEL and a failure to upregulate costimulatory ligands for CD28. These defects in immunoglobulin-receptor-mediated functions could be overcome in vivo, suggesting a number of mechanisms for induction of autoantibody responses.
Identification of a B2 bradykinin receptor expressed by PC12 pheochromocytoma cells.
Authors: Nardone J , Gerald C , Rimawi L , Song L , Hogan P G
Published: May 2006

We have used rat PC12 pheochromocytoma cells, a clonal cell line closely related to sympathetic neurons, to investigate reports that the bradykinin receptor expressed in the peripheral nervous system is distinct from the well-characterized B2 bradykinin receptor of smooth muscle. Although there have been reports that [Thi5,8,D-Phe7]bradykinin [where Thi is beta-(2-thienyl)alanine] is a full agonist at some sites in the peripheral nervous system, we find that in PC12 cells [Thi5,8,D-Phe7]bradykinin behaves as a competitive antagonist of bradykinin-stimulated phosphatidylinositol turnover. In particular, sufficient concentrations of [Thi5,8,D-Phe7]bradykinin completely block the increase in inositol bisphosphate and trisphosphate in response to 100 nM bradykinin; [Thi5,8,D-Phe7]bradykinin alone, at up to 10 microM, does not appreciably increase inositol bisphosphate and trisphosphate. In contrast to the absence of evidence for a distinctive neuronal receptor, we have found convincing evidence that the bradykinin receptor previously identified in smooth muscle is present in PC12 cells. Using the polymerase chain reaction, we have isolated a full-length cDNA encoding a bradykinin receptor that is expressed in PC12 cells and verified that its nucleotide sequence is identical except at a single position to that of the rat uterine B2 bradykinin receptor. When expressed in COS cells this uterine bradykinin receptor exhibits the same high affinity for [3H]bradykinin (Kd 4.4 nM), the same relative affinities for a series of kinin antagonists, and the same efficient coupling to phosphatidylinositol turnover (EC50 2.5 nM) as the receptor in PC12 cells. We interpret our data, and the findings of a number of pharmacological studies, as strengthening the view that the B2 receptor expressed in PC12 cells and in certain cells of the peripheral nervous system is identical to the receptor in rat uterine smooth muscle.
An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.
Authors: Bowie J U , Eisenberg D
Published: May 2006

Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected from a database of known protein structures. A fragment was selected if it was compatible with a segment of the sequence to be folded, as judged by three-dimensional profile scores. By linking the selected fragment conformations together, hundreds of trial structures were generated of the same length and sequence as the protein to be folded. These starting trial structures were then improved by an evolutionary algorithm. Selection pressure for improving the structures was provided by an energy function that was designed to guide the conformational search procedure toward the correct structure. We find that by evolution of only 400 structures for fewer than 1400 generations, the overall fold of some small helical proteins can be computed from the sequence, with deviations from observed structures of 2.5-4.0 A for C alpha atoms.