bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical mechanics of kinetic proofreading in protein folding in vivo.
Authors: Gulukota K , Wolynes P G
Published: May 2006

The statistical energy landscape picture of protein folding has led to the understanding that the energy landscape must have guiding forces leading to a protein folding funnel in order to avoid the Levinthal paradox in vitro. Since folding in vivo often requires the action of chaperone molecules and ATP hydrolysis, we must ask whether folding in a system maintained away from equilibrium can avoid the Levinthal paradox in other ways. We describe a model of the action of chaperone molecules in protein folding in vivo on the basis of a repetitive cycle of binding and unbinding, allowing the possibility of kinetic proofreading. We also study models in which chaperone binding is locally biased, depending on the similarity of the conformation to the native one. We show that while kinetic proofreading can modestly facilitate folding, it is insufficient by itself to overcome the Levinthal paradox. On the other hand, such kinetic proofreading with biasing can provide the nonequilibrium analog of a folding funnel and greatly enhance folding yields and speed up folding.
High-efficiency synthesis of human alpha-endorphin and magainin in the erythrocytes of transgenic mice: a production system for therapeutic peptides.
Authors: Sharma A , Khoury-Christianson A M , White S P , Dhanjal N K , Huang W , Paulhiac C , Friedman E J , Manjula B N , Kumar R
Published: May 2006

Chemical synthesis of peptides, though feasible, is hindered by considerations of cost, purity, and efficiency of synthesizing longer chains. Here we describe a transgenic system for producing peptides of therapeutic interest as fusion proteins at low cost and high purity. Transgenic hemoglobin expression technology using the locus control region was employed to produce fusion hemoglobins in the erythrocytes of mice. The fusion hemoglobin contains the desired peptides as an extension at the C end of human alpha-globin. A protein cleavage site is inserted between the C end of the alpha-globin chain and the N-terminal residue of the desired peptide. The peptide is recovered after cleavage of the fusion protein with enzymes that recognize this cleavage signal as their substrate. Due to the selective compartmentalization of hemoglobin in the erythrocytes, purification of the fusion hemoglobin is easy and efficient. Because of its compact and highly ordered structure, the internal sites of hemoglobin are resistant to protease digestion and the desired peptide is efficiently released and recovered. The applicability of this approach was established by producing a 16-mer alpha-endorphin peptide and a 26-mer magainin peptide in transgenic mice. Transgenic animals and their progeny expressing these fusion proteins remain health, even when the fusion protein is expressed at > 25% of the total hemoglobin in the erythrocytes. Additional applications and potential improvements of this methodology are discussed.
c-Krox, a transcriptional regulator of type I collagen gene expression, is preferentially expressed in skin.
Authors: Galéra P , Musso M , Ducy P , Karsenty G
Published: May 2006

We have cloned a mouse cDNA that is a member of the Krox gene family and encodes a protein we have named c-Krox. The c-Krox protein contains three zinc fingers of the Cys2His2 type. c-Krox binds specifically to a guanine-rich cis-acting element present twice in the promoter element of the mouse alpha 1(I) collagen gene. Study of c-Krox gene expression shows that c-Krox is markedly enriched in skin, one of the two major sites of type I collagen synthesis, but is absent in bone, the other main type I collagen-producing tissue, indicating that type I collagen gene expression is differentially regulated in skin and bone. DNA transfection experiments in mouse NIH 3T3 fibroblasts, cells that express the c-Krox gene, or in Drosophila S2 cells, which do not express c-Krox, reveal that c-Krox can activate transcription of a reporter gene linked to several copies of its binding site in the alpha 1(I) collagen promoter. Thus, c-Krox is only the second member of the Krox family for which a target gene has been identified. The selective spatial pattern of expression of its mRNA and its transcription activation ability suggest that c-Krox may be an important regulator of type I collagen skin specific expression in physiologic conditions and in fibrotic diseases such as scleroderma.
Identification of prosaposin as a neurotrophic factor.
Authors: O'Brien J S , Carson G S , Seo H C , Hiraiwa M , Kishimoto Y
Published: May 2006

Prosaposin was identified as a neurotrophic factor stimulating neurite outgrowth in murine neuroblastoma (NS20Y) cells and choline acetyltransferase (ChAT) activity in human neuroblastoma (SK-N-MC) cells. The four naturally occurring saposins, which are derived by proteolytic processing of prosaposin, were tested for activity. Saposin C was found to be active, whereas saposins A, B, and D were inactive as neurotrophic factors. Dose-response curves demonstrated that nanomolar concentrations of prosaposin and saposin C stimulated neurite outgrowth and increased ChAT activity. Prosaposin and saposin C exerted activity by a mechanism independent of nerve growth factor, brain-derived neurotrophic factor, and neurotrophin 3. Binding assays utilizing saposin C as a ligand gave two saturable binding constants, a high-affinity (Kd = 19 pM) and a low-affinity (Kd = 1 nM) constant, with 2000 and 15,000 sites per NS20Y cell, respectively. Phosphorylation stimulation experiments demonstrated that brief treatment with prosaposin or saposin C enhanced phosphorylation of a variety of proteins, some of which contained phosphorylated tyrosine(s). Since both cell lines were also stimulated by ciliary neurotrophic factor (CNTF) as well as prosaposin, inhibition was tested by utilizing an anti-gp130 monoclonal antibody, which specifically inhibited CNTF stimulation; this antibody did not inhibit prosaposin or saposin C stimulation. These results indicate that prosaposin and saposin C are neurotrophic factors which initiate signal transduction by binding to a high-affinity receptor that induces protein phosphorylation.
Axotomy induces the expression of vasopressin receptors in cranial and spinal motor nuclei in the adult rat.
Authors: Tribollet E , Arsenijevic Y , Marguerat A , Barberis C , Dreifuss J J
Published: May 2006

8-L-Arginine vasopressin ([Arg8]VP) receptors are expressed transiently in the rat facial nucleus during the perinatal period. Electrophysiological studies suggest that at least part of these receptors is located on facial motoneurones. In the present study we report that, in the adult rat, unilateral section of a facial nerve results in a massive and transient reexpression of [Arg8]VP receptors in the deeferented facial nucleus. Data were obtained by quantitative film autoradiography. During the first 2 postoperative weeks, binding of an iodinated ligand selective for V1a-type receptors increased about 10-fold. Maximal levels of binding were maintained for 1-2 weeks and then started to decrease. Binding was not strictly restricted to the facial nucleus but included the neuropile between motoneuronal pools and the perifacial area, which may indicate a dendritic localization of [Arg8]VP receptors. To investigate whether other motor nuclei also react to axotomy by up-regulating [Arg8]VP receptors, we sectioned either a hypoglossal nerve or a sciatic nerve. Two weeks after surgery, the hypoglossal nucleus or sciatic motoneuronal pools ipsilateral to the lesion were intensely labeled with the iodinated ligand. In contrast, nerve section had no effect on oxytocin binding sites in facial, hypoglossal, or sciatic motor nuclei. The results suggest that [Arg8]VP receptor expression in motor nuclei may depend upon neuromuscular contacts and, thus, that [Arg8]VP may be involved in the establishment of neuromuscular connections during development and in their reestablishment after nerve injury.
Interaction of proteins with transcriptionally active estrogen receptors.
Authors: Cavaillès V , Dauvois S , Danielian P S , Parker M G
Published: May 2006

The ligand binding domain of the estrogen receptor contains a hormone-dependent transcriptional activation function. To investigate the mechanism by which it stimulates transcription, we have expressed fusion proteins containing either the wild-type or a transcriptionally defective form of this domain fused to glutathione-S-transferase and searched for proteins that specifically interact in vitro. By far-Western blotting, three proteins of 160, 140, and 80 kDa expressed in different mammalian cells (HeLa, ZR75-1, and COS-1) were shown to associate directly with the wild-type receptor in the presence of estrogen. Two additional proteins appeared to interact indirectly with the hormone binding domain since they were detected only by a pull-down assay. All of these interactions were abolished by antiestrogens, such as 4-hydroxytamoxifen, ICI 164384, or ICI 182780, which inhibit hormone-dependent transcription. Moreover, they were not observed with the transcriptionally defective form of the receptor even in the presence of estrogen. Thus, since the ability of these proteins to interact with the hormone binding domain correlates with its transcriptional activity, one or more of them may contribute to hormone-dependent transcriptional activation by the estrogen receptor.
Myocardial expression of a constitutively active alpha 1B-adrenergic receptor in transgenic mice induces cardiac hypertrophy.
Authors: Milano C A , Dolber P C , Rockman H A , Bond R A , Venable M E , Allen L F , Lefkowitz R J
Published: May 2006

Transgenic mice were generated by using the alpha-myosin heavy chain promoter coupled to the coding sequence of a constitutively active mutant alpha 1B-adrenergic receptor (AR). These transgenic animals demonstrated cardiac-specific expression of this alpha 1-AR with resultant activation of phospholipase C as shown by increased myocardial diacylglycerol content. A phenotype consistent with cardiac hypertrophy developed in adult transgenic mice with increased heart/body weight ratios, myocyte cross-sectional areas, and ventricular atrial natriuretic factor mRNA levels relative to nontransgenic controls. These transgenic animals may provide insight into the biochemical triggers that induce hypertrophy in cardiac disease and serve as a convenient experimental model for studies of this condition.
Association of focal adhesion kinase with its potential substrate phosphatidylinositol 3-kinase.
Authors: Chen H C , Guan J L
Published: May 2006

The focal adhesion kinase (FAK) has been implicated in signal transduction pathways initiated by cell adhesion receptor integrins and by neuropeptide growth factors. To gain insight into FAK function, we examined the potential interaction of FAK with intracellular signaling molecules containing the Src homology 2 domains. We report here the stable association of FAK with phosphatidylinositol 3-kinase (PI3-kinase; EC 2.7.1.137) in NIH 3T3 mouse fibroblasts. This interaction was stimulated by cell adhesion concomitant with FAK activation. We also found that recombinant FAK bound to the p85 subunit of PI 3-kinase directly in vitro and that autophosphorylation of recombinant FAK in vitro increased its binding to PI 3-kinase. We detected increased tyrosine phosphorylation of the p85 subunit of PI 3-kinase during cell adhesion and observed direct phosphorylation of p85 by FAK in vitro. Together, these results suggest that PI 3-kinase may be a FAK substrate in vivo and serve as an effector of FAK.
In vivo diagnosis of cervical intraepithelial neoplasia using 337-nm-excited laser-induced fluorescence.
Authors: Ramanujam N , Mitchell M F , Mahadevan A , Warren S , Thomsen S , Silva E , Richards-Kortum R
Published: May 2006

Laser-induced fluorescence at 337-nm excitation was used in vivo to differentiate neoplastic [cervical intraepithelial neoplasia (CIN)], nonneoplastic abnormal (inflammation and human papilloma viral infection), and normal cervical tissues. A colposcope (low-magnification microscope used to view the cervix with reflected light) was used to identify 66 normal and 49 abnormal (5 inflammation, 21 human papilloma virus infection, and 23 CIN) sites on the cervix in 28 patients. These sites were then interrogated spectroscopically. A two-stage algorithm was developed to diagnose CIN. The first stage differentiated histologically abnormal tissues from colposcopically normal tissues with a sensitivity, specificity, and positive predictive value of 92%, 90%, and 88%, respectively. The second stage differentiated preneoplastic and neoplastic tissues from nonneoplastic abnormal tissues with a sensitivity, specificity, and positive predictive value of 87%, 73%, and 74%, respectively. Spectroscopic differences were consistent with a decrease in the absolute contribution of collagen fluorescence, an increase in the absolute contribution of oxyhemoglobin attenuation, and an increase in the relative contribution of reduced nicotinamide dinucleotide phosphate [NAD(P)H] fluorescence as tissue progresses from normal to abnormal in the same patient. These results suggest that in vivo fluorescence spectroscopy of the cervix can be used to diagnose CIN at colposcopy.
Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria.
Authors: Nelson K , Selander R K
Published: May 2006

The gnd gene, encoding 6-phosphogluconate dehydrogenase (EC 1.1.1.44), was sequenced in 87 strains of 15 species assigned to five nominal genera of the Enterobacteriaceae, including 36 isolates of Salmonella enterica and 32 strains of Escherichia coli. In S. enterica, the effective (realized) rate of recombination of horizontally transferred gnd sequences is only moderately higher than the rates for other chromosomal housekeeping genes. In contrast, recombination at gnd has occurred with such high frequency in Escherichia coli that the indicated evolutionary relationships among strains are not congruent with those estimated by sequence analysis of other genes and by multilocus enzyme electrophoresis. E. coli and S. enterica apparently have not exchanged gnd sequences, but those of several strains of E. coli have been imported from species of Citrobacter and Klebsiella. The relatively frequent exchange of gnd within and among taxonomic groups of the Enterobacteriaceae, compared with other housekeeping genes, apparently results from its close linkage with genes that are subject to diversifying selection, including those of the rfb region determining the structure of the O antigen polysaccharide.
Peptides corresponding to a predictive alpha-helical domain of human immunodeficiency virus type 1 gp41 are potent inhibitors of virus infection.
Authors: Wild C T , Shugars D C , Greenwell T K , McDanal C B , Matthews T J
Published: May 2006

To define the role of the human immunodeficiency virus type 1 (HIV-1) envelope proteins in virus infection, a series of peptides were synthesized based on various regions of the HIV-1 transmembrane protein gp41. One of these peptides, DP-178, corresponding to a region predictive of alpha-helical secondary structure (residues 643-678 of the HIV-1LAI isolate), has been identified as a potent antiviral agent. This peptide consistently blocked 100% of virus-mediated cell-cell fusion at < 5 ng/ml (IC90 approximately 1.5 ng/ml) and gave an approximately 10 times reduction in infectious titer of cell-free virus at approximately 80 ng/ml. The inhibitory activity was observed at peptide concentrations approximately 10(4) to 10(5) times lower than those at which cytotoxicity and cytostasis were detected. Peptide-mediated inhibition is HIV-1 specific in that approximately 10(2) to 10(3) times more peptide was required for inhibition of a human immunodeficiency virus type 2 isolate. Further experiments showed that DP-178 exhibited antiviral activity against both prototypic and primary HIV-1 isolates. As shown by PCR analysis of newly synthesized proviral DNA, DP-178 blocks an early step in the virus life cycle prior to reverse transcription. Finally, we discuss possible mechanisms by which DP-178 may exert its inhibitory activity.
Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30.
Authors: Tan S , Garrett K P , Conaway R C , Conaway J W
Published: May 2006

The C terminus of mammalian transcription factor RAP30 has been found to be a cryptic DNA-binding domain strikingly similar to the C-terminal DNA-binding domain present in conserved region 4 of members of the sigma 70 family of bacterial sigma factors. This RAP30 domain shares strongest sequence similarity with the DNA-binding domain present in region 4 of Bacillus subtilis sporulation-specific sigma K. Like the region 4 DNA-binding activity of Escherichia coli sigma 70, the RAP30 C-terminal DNA binding activity is masked in intact RAP30 but is readily detectable when the RAP30 C terminus is expressed as a fusion protein. Consistent with a role for RAP30 DNA-binding activity in transcription, mutations that abolish DNA binding also abolish transcription. Therefore, RAP30 may function at least in part through the action of an evolutionarily ancient DNA-binding domain that first appeared prior to the divergence of bacteria and eukaryotes.
The Reed-Sternberg cells of Hodgkin disease are clonal.
Authors: Inghirami G , Macri L , Rosati S , Zhu B Y , Yee H T , Knowles D M
Published: May 2006

Relatively little progress has been made in understanding the nature of the Reed-Sternberg (RS) cell and its morphologic variants in Hodgkin disease (HD). This is primarily due to the fact that RS cells represent a minute subpopulation within HD lesions. To investigate the clonal origin of RS cells and variants, we studied 27 HD lesions obtained from 11 patients. Using an image analyzer (CAS 200) we were able to demonstrate that CD30-positive RS cells are clonal elements with unique and individualized DNA profiles and that the DNA content of any given patient RS cell population is constant over time and in different pathologic sites. Using 1, 9, 11, and X alpha satellite chromosome probes and interphase cytogenetics, we also demonstrated that RS cells obtained from different tissue samples of the same patient have a unique and often abnormal chromosomal pattern. To definitively prove the hypothesis that CD30-positive RS cells are clonal elements, we investigated the presence of point mutations within p53 gene exons 5 through 9 and found that only a single patient possessed a nonsense p53 somatic point mutation (Arg to His). This same mutation could be identified in all of his available biopsies. Altogether, these findings demonstrate that RS cells and variants in HD are clonal and represent the neoplastic elements of this entity.
Molecules vs. morphology in avian evolution: the case of the "pelecaniform" birds.
Authors: Hedges S B , Sibley C G
Published: May 2006

The traditional avian Order Pelecaniformes is composed of birds with all four toes connected by a web. This "totipalmate" condition is found in ca. 66 living species: 8 pelicans (Pelecanus), 9 boobies and gannets (Sula, Papasula, Morus), ca. 37 cormorants (Phalacrocorax), 4 anhingas or darters (Anhinga), 5 frigatebirds (Fregata), and 3 tropicbirds (Phaethon). Several additional characters are shared by these genera, and their monophyly has been assumed since the beginning of modern zoological nomenclature. Most ornithologists classify these genera as an order, although tropicbirds have been viewed as related to terns, and frigatebirds as relatives of the petrels and albatrosses. DNA.DNA hybridization data indicated that the pelicans are most closely related to the Shoebill (Balaeniceps rex), a stork-like bird that lives in the swamps of central Africa; the boobies, gannets, cormorants, and anhingas form a closely related cluster; the tropicbirds are not closely related to the other taxa; and the frigatebirds are closest to the penguins, loons, petrels, shearwaters, and albatrosses (Procellarioidea). Most of these results are corroborated by DNA sequences of the 12S and 16S rRNA mitochondrial genes, and they provide another example of incongruence between classifications derived from morphological versus genetic traits.
A determination of the frequency of gene conversion in unmanipulated mouse sperm.
Authors: Högstrand K , Böhme J
Published: May 2006

Gene conversion, sometimes also called micro gene conversion or gene conversion-like events, has been proposed to act on a number of genes in higher eukaryotes, such as gamma-globin, beta-tubulin, major urinary protein, and amyloid A genes. In the immune system, immunoglobulin genes and major histocompatibility complex class I and class II genes have been implicated. The notion that integral segments of DNA have been transferred from one gene to another in these cases has, however, met considerable resistance. We have devised a PCR assay detecting only the molecule that results if the E beta d-derived fragment analogous to that introduced in the bm12 mutation is transferred to the A beta k gene. We have proceeded to analyze sperm from the F1 cross C3H/HeJ (haplotype k) x BALB/c (haplotype d). In our assay, we find that the frequency for conversion of this particular DNA segment is 2 x 10(-6). This frequency is relevant only in the germ line; when liver cells were tested as an example of somatic cells, no events were observed, implying a frequency of < 2 x 10(-8) in liver. Fragments > 100 bp seem to be possible to transfer in this conversion.
Galanin-containing neurons in the paraventricular nucleus: a neurochemical marker for fat ingestion and body weight gain.
Authors: Akabayashi A , Koenig J I , Watanabe Y , Alexander J T , Leibowitz S F
Published: May 2006

The physiological function of the peptide galanin (Gal) remains to be established. It is known to exist in high concentrations within the hypothalamus and to modulate the secretion of specific hormones, as well as to potentiate food consumption. Our study provides evidence for an essential function of neuronal Gal, within a specific hypothalamic area, in stimulating the behavioral process of fat ingestion and body weight gain. Through analyses of peptide levels via RIA and of gene expression via in situ hybridization, a close positive association is established between Gal in the paraventricular nucleus (PVN), particularly its midlateral region, and fat ingestion. No such relationship is detected for Gal in other brain areas or between PVN Gal and ingestion of carbohydrate or protein, supporting the behavioral and anatomical specificity of this relationship. Through PVN injection studies with antisense oligonucleotides to Gal mRNA, a dramatic decline in fat ingestion and body weight suggests that endogenous Gal contributes to the natural appetite for fat. Thus, Gal in the PVN is identified as a neurochemical marker for fat ingestion and, consequently, body weight gain.
Oncogenic potential of guanine nucleotide stimulatory factor alpha subunit in thyroid glands of transgenic mice.
Authors: Michiels F M , Caillou B , Talbot M , Dessarps-Freichey F , Maunoury M T , Schlumberger M , Mercken L , Monier R , Feunteun J
Published: May 2006

Transgenic mice have been used to address the issue of the oncogenic potential of mutant guanine nucleotide stimulatory factor (Gs) alpha subunit in the thyroid gland. The expression of the mutant Arg-201-->His Gs alpha subunit transgene has been directed to murine thyroid epithelial cells by bovine thyroglobulin promoter. The transgenic animals develop hyperfunctioning thyroid adenomas with increased intracellular cAMP levels and high uptake of [125I]iodine and produced elevated levels of circulating triiodothyronine and thyroxine. These animals demonstrate that the mutant form of Gs alpha subunit carries an oncogenic activity, thus supporting the model that deregulation of cAMP level alters growth control in thyroid epithelium. These animals represent models for humans with autonomously functioning thyroid nodules.
Selection-based learning in bird song development.
Authors: Nelson D A , Marler P
Published: May 2006

Bird song is a model system for study of the neurobiology, development, and functions of learned vocal communication signals. Research on avian song learning has been dominated by an instructive model of learning--the sensorimotor model. Developmental plasticity is assumed to be based on the incorporation of novel material into the song repertoire. Experimental evidence now indicates an alternative form of plasticity operating in harmony with sensorimotor learning, based on principles of selection, rather than instruction. Song dialects, a common consequence of vocal learning, can be achieved by overproduction of previously memorized songs and selective attrition of those that fail to match the dialect of interacting males. These distinct processes of learning have important implications for study of the neural substrates underlying song production and perception and for efforts to interpret patterns of geographic variation in song.
d(G3T4G3) forms an asymmetric diagonally looped dimeric quadruplex with guanosine 5'-syn-syn-anti and 5'-syn-anti-anti N-glycosidic conformations.
Authors: Smith F W , Lau F W , Feigon J
Published: May 2006

The structure formed by the DNA oligonucleotide d(G3T4G3) has been studied by one- and two-dimensional 1H NMR spectroscopy. In NaCl solution, d(G3T4G3), like d(G4T4G4) (Oxy-1.5), forms a dimeric quadruplex with the thymines in loops across the diagonal of the end quartets. Unlike Oxy-1.5, the dimer is not symmetric, and both monomer strands are observed in NMR spectra. Three quartets are formed from the GGG tracts. Glycosidic conformations of the guanines are 5'-syn-syn-anti-(loop)-syn-anti-anti in one strand and 5'-syn-anti-anti-(loop)-syn-syn-anti in the other strand. Thus, the stacking of the quartets (tail-to-tail, head-to-tail) is unlike all previously described fold-back (tail-to-tail, head-to-head) and parallel-stranded (head-to-tail, head-to-tail) quadruplexes.
Oxidative damage and mitochondrial decay in aging.
Authors: Shigenaga M K , Hagen T M , Ames B N
Published: May 2006

We argue for the critical role of oxidative damage in causing the mitochondrial dysfunction of aging. Oxidants generated by mitochondria appear to be the major source of the oxidative lesions that accumulate with age. Several mitochondrial functions decline with age. The contributing factors include the intrinsic rate of proton leakage across the inner mitochondrial membrane (a correlate of oxidant formation), decreased membrane fluidity, and decreased levels and function of cardiolipin, which supports the function of many of the proteins of the inner mitochondrial membrane. Acetyl-L-carnitine, a high-energy mitochondrial substrate, appears to reverse many age-associated deficits in cellular function, in part by increasing cellular ATP production. Such evidence supports the suggestion that age-associated accumulation of mitochondrial deficits due to oxidative damage is likely to be a major contributor to cellular, tissue, and organismal aging.
Ubiquitous receptor: a receptor that modulates gene activation by retinoic acid and thyroid hormone receptors.
Authors: Song C , Kokontis J M , Hiipakka R A , Liao S
Published: May 2006

The cDNA for a member of the nuclear receptor family was cloned and named ubiquitous receptor (UR), since UR protein and mRNA are detected in many cell types. Rat UR/human retinoid X receptor alpha (hRXR alpha) heterodimers bound preferentially to double-stranded oligonucleotide direct repeats having the consensus half-site sequence AGGTCA and 4-nt spacing (DR-4). Coexpression of UR in COS-1 cells inhibited the stimulation of chloramphenicol acetyltransferase (CAT) reporter gene expression by hRXR alpha and human retinoic acid receptor alpha in the presence of all-trans-retinoic acid when DR-4 (but not DR-5) was present upstream of the promoter of a CAT reporter gene (DR-4-CAT). UR expression also inhibited the activation of a DR-4-CAT reporter gene by hRXR alpha and 9-cis-retinoic acid or by thyroid hormone receptor beta in the presence of thyroid hormone. However, in the absence of 9-cis-retinoic acid, UR in combination with hRXR alpha stimulation DR-4-CAT expression. Coexpression of thyroid hormone receptor markedly reduced this stimulation in the absence of thyroid hormone. UR may play an important role in normal growth and differentiation by modulating gene activation in retinoic acid and thyroid hormone signaling pathways.
Interchain binding at the tail end of the Drosophila spectrin molecule.
Authors: Viel A , Branton D
Published: May 2006

Spectrin's function as an actin-crosslinking protein and membrane skeleton component involves the tail end of the molecule, where multiple interactions between two spectrin chains and between these chains and other proteins give rise to complexes that form membrane skeleton network junctions. To determine whether the sequences that contribute to interchain binding can be distinguished from sequences that are involved in other spectrin tail end functions, we mapped the regions in each Drosophila spectrin chain that are required for interchain binding in vitro. Segments 20 and 21 of the alpha chain and 2 and 3 of the beta chain are required for binding. Binding appears to be very dependent on the lateral register of segments in the two apposed chains. Domains of the nonrepetitive segments, 22 of alpha chain and 1 of beta chain, are also involved in associating the two chains. Required sequences within these nonrepetitive segments are interspersed within domains that are known to be involved in associations with other structural proteins, such as actin, and regulatory components, such as protein 4.1 and calcium.
Specific tolerance across a discordant xenogeneic transplantation barrier.
Authors: Lee L A , Gritsch H A , Sergio J J , Arn J S , Glaser R M , Sablinski T , Sachs D H , Sykes M
Published: May 2006

Successful induction of tolerance across disparate (discordant) species barriers could overcome the organ shortage that presently limits clinical transplantation. We demonstrate here that xenogeneic swine thymic transplants can induce tolerance to swine antigens in mice, while positively selecting functional host CD4+ T cells. Immunologically normal C57BL/10 mice were thymectomized and depleted of T and natural killer cells; then they received transplants of fetal pig thymus and liver fragments. Mature mouse CD4+ T cells developed in the pig thymus grafts and migrated to the periphery. Swine grafts grew markedly and no anti-pig IgG response was produced. Mixed lymphocyte reactions confirmed that the new T cells were functional and were tolerant to pig antigens.
Serum Vpr regulates productive infection and latency of human immunodeficiency virus type 1.
Authors: Levy D N , Refaeli Y , MacGregor R R , Weiner D B
Published: May 2006

In human immunodeficiency virus (HIV)-positive individuals, the vast majority of infected peripheral blood cells and lymph node cells may be latently or nonproductively infected. The vpr open reading frame of HIV-1 encodes a 15-kDa virion-associated protein, Vpr. The vpr gene has been shown to increase virus replication in T cells and monocyte/macrophages in vitro. We have previously reported that vpr expression in various tumor lines leads to growth inhibition and differentiation, indicating that Vpr may function as a regulator of cellular permissiveness to HIV replication. Here we show that Vpr protein is present in significant amounts in the serum of AIDS patients. Purified serum Vpr activated virus expression from five latently infected cell lines, U1, OM.10.1, ACH-2, J1.1, and LL58. Serum Vpr also activated virus expression from resting peripheral blood mononuclear cells of HIV-infected individuals. Together, these findings implicate serum Vpr in the activation of HIV replication in vivo and in the control of latency. Anti-Vpr antibodies inhibited Vpr activity, suggesting that humoral immunity modulates Vpr activity in vivo. These results have broad implications for the virus life cycle and for the prospective control of HIV replication and pathogenesis.
Regulation of expression of cAMP response element-binding protein in the locus coeruleus in vivo and in a locus coeruleus-like cell line in vitro.
Authors: Widnell K L , Russell D S , Nestler E J
Published: May 2006

Expression of the cAMP response element (CRE)-binding protein (CREB) has been thought to be constitutive and not subject to regulation. In the course of investigating effects of chronic morphine on the cAMP pathway in the locus coeruleus, a brain region important for opiate addiction, we found that levels of CREB immunoreactivity and CRE binding were increased by chronic morphine administration. To further investigate possible mechanisms underlying this unexpected finding, we studied the regulation of CREB expression in a cell line (CATH.a) that exhibits many properties of locus coeruleus neurons. Agents that activate the cAMP pathway led to a > 60% decrease in CREB mRNA in this cell line. Moreover, these alterations in CREB mRNA levels were associated with changes in levels of CREB immunoreactivity and CRE-binding activity. In contrast, the same treatments fail to alter CREB expression in PC12 pheochromocytoma cells.
Long-term production and delivery of human growth hormone in vivo.
Authors: Heartlein M W , Roman V A , Jiang J L , Sellers J W , Zuliani A M , Treco D A , Selden R F
Published: May 2006

The application of somatic cell gene therapy to large patient populations will require the development of safe and practical approaches to the generation and characterization of genetically manipulated cells. Transkaryotic implantation is a gene therapy system based on the production of clonal strains of engineered primary and secondary cells, using non-viral methods. We demonstrate here that, on implantation, these clonal cell strains stably and reproducibly deliver pharmacologic quantities of protein for the lifetime of the experimental animals.
An alternatively spliced form of the nerve growth factor receptor TrkA confers an enhanced response to neurotrophin 3.
Authors: Clary D O , Reichardt L F
Published: May 2006

TrkA, a member of the receptor tyrosine kinase family, binds nerve growth factor (NGF) and subsequently activates intracellular signaling pathways. Previous studies have found variable and weak interaction of the TrkA receptor with neurotrophin 3 (NT-3), another member of the NGF family. TrkA is expressed in two splice forms, differing in the presence of an 18-bp exon in the extracellular domain. The biological responses of each isoform of the TrkA receptor were tested after transfection into the cell line PC12nnr5, a variant of PC12 cells lacking functional TrkA protein. NGF was found to activate each form of the receptor comparably. However, the TrkA isoform containing the variable exon showed significantly higher activation by NT-3, which was detected by stimulation of TrkA autophosphorylation, induction of ZIF268 transcription, and cellular differentiation. Function-perturbing antibodies to the p75 low-affinity NGF receptor potentiated the NT-3 responses of both forms of TrkA in the transfected PC12nnr5 cell lines, suggesting that the low-affinity NGF receptor suppresses the ability of TrkA to respond to NT-3.
Selective and asymmetric molecular transport across electroporated cell membranes.
Authors: Tekle E , Astumian R D , Chock P B
Published: May 2006

Transport of a divalent cation (Ca2+) and three DNA indicators [ethidium bromide (EB), propidium iodide (PI), and ethidium homodimer (EthD-1)] across electroporated membranes of several mammalian cell lines was found to be selective and asymmetrical. In low salt medium, Ca2+ and EB were preferentially transported across the anodefacing cell membrane while PI and EthD-1 predominately entered at the site facing the cathode. In high salt medium, the entry site for Ca2+ and EB was reversed to the cathode-facing hemisphere while it remained unchanged for PI and EthD-1. In all these experiments, the observed transport patterns remained unaffected whether the dyes (or ion) were present during or added after the electroporating pulse. The data suggest that asymmetric pores are created on both sides of the membrane facing the electrodes, with smaller pore size (but greater in number) on the anode side and larger pores (with a lower population) on the cathode side. Furthermore, the rate of resealing of the membrane pores is significantly enhanced in high ionic strength medium, thus affecting the entry site. The asymmetric transport pattern is neither caused by electrophoresis induced by the externally applied electric field nor due to one-sided membrane breakdown as previously believed.
Separation of oxidant-initiated and redox-regulated steps in the NF-kappa B signal transduction pathway.
Authors: Anderson M T , Staal F J , Gitler C , Herzenberg L A , Herzenberg L A
Published: May 2006

Studies presented here show that overall NF-kappa B signal transduction begins with a parallel series of stimuli-specific pathways through which cytokines (tumor necrosis factor alpha), oxidants (hydrogen peroxide and mitomycin C), and phorbol ester (phorbol 12-myristate 13-acetate) individually initiate signaling. These initial pathways culminate in a common pathway through which all of the stimulating agents ultimately signal NF-kappa B activation. We distinguish the stimuli-specific pathways by showing that the oxidative stimuli trigger NF-kappa B activation in only one of two human T-cell lines (Wurzburg but not Jurkat), whereas tumor necrosis factor alpha and phorbol 12-myristate 13-acetate readily stimulate in both lines. We propose the common pathway as the simplest way of accounting for the common requirements and properties of the signaling pathway. We include a redox-regulatory mechanism(s) in this common pathway to account for the previously demonstrated redox regulation of NF-kappa B activation in Jurkat cells (in which oxidants don't activate NF-kappa B); we put tyrosine phosphorylation in the common pathway by showing that kinase activity (inhibitable by herbimycin A and tyrphostin 47) is required for NF-kappa B activation by all stimuli tested in both cell lines. Since internal sites of oxidant production have been shown to play a key role in the cytokine-stimulated activation of NF-kappa B, and since tyrosine kinase and phosphatase activities are known to be altered by oxidants, these findings suggest that intracellular redox status controls NF-kappa B activation by regulating tyrosine phosphorylation event(s) within the common step of the NF-kappa B signal transduction pathway.
Detection and classification of mutagens: a set of base-specific Salmonella tester strains.
Authors: Gee P , Maron D M , Ames B N
Published: May 2006

A detection and classification system for mutagens has been developed that identifies the six possible base-pair substitution mutations. A set of six Salmonella typhimurium (TA7001 to TA7006) strains has been constructed, each of which carries a unique missense mutation in the histidine biosynthetic operon. In addition to the his mutation, these strains carry different auxiliary features that enhance the mutability of the target his mutation. These include the R factor pKM101, which has the SOS-inducible mucAB system; a deletion of the uvrB component of excision repair; and rfa mutations to increase the accessibility of bulky chemicals to the bacteria. Another set of strains (TA7041 to TA7046) contain a wild-type rfa gene. Reversion via the base substitution unique to each strain was verified by sequence analyses of > 800 revertants obtained from different types of mutagens. The strains have considerably lower spontaneous reversion frequencies and detect a variety of mutagens at a sensitivity comparable to the Salmonella tester strains TA100, TA102, and TA104. The low spontaneous frequency of reversion of a mixture of the six tester strains (approximately 10 revertants per plate) enables a single mutation assay with the mixture that is followed by classification of the type of mutation with the individual strains.
Connectional topography in the zebrafish olfactory system: random positions but regular spacing of sensory neurons projecting to an individual glomerulus.
Authors: Baier H , Rotter S , Korsching S
Published: May 2006

It is unknown how neuronal connections are specified in the olfactory system. To define rules of connectivity in this system, we investigated whether the projection of sensory neurons from the olfactory epithelium to the olfactory bulb is topographically ordered. By backtracking with 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI), we find that neurons projecting into a single identified glomerulus are widely dispersed over the olfactory epithelium. Their positions in the sensory surface do not predict their glomerulus specificity and are probably random. A statistical analysis reveals that neurons connected to the same glomerulus are spaced at distances of several cell diameters from each other. The convergence of projections to one point in the target area from neurons that are widely and evenly distributed in the sensory surface constitutes an unusual type of connectional topography that contrasts with the precise topological (neighborhood-preserving) maps found in other sensory systems. It may maximize the probability to detect odorants that activate a single glomerular unit.
Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer.
Authors: Gohlke C , Murchie A I , Lilley D M , Clegg R M
Published: May 2006

Fluorescence resonance energy transfer (FRET) has been used to demonstrate the bending of DNA and RNA helices for three series of double-stranded molecules containing bulge loops of unopposed adenosine nucleotides (An, n = 0-9). Fluorescein and rhodamine were covalently attached to the 5' termini of the two component strands. Three different methods were applied to measure the FRET efficiencies. The extent of energy transfer within each series increases as the number of bulged nucleotides varies from 1 to 7, indicating a shortening of the end-to-end distance. This is consistent with a bending of DNA and RNA helices that is greater for larger bulges. The FRET efficiency for DNA molecules with A9 bulges is lower than the efficiency for the corresponding A7 bulged molecules, although the A9 molecules exhibit increased electrophoretic retardation. Ranges of bending angles can be estimated from the FRET results.
Differentiation of receptor subtypes by thermodynamic analysis: application to opioid delta receptors.
Authors: Wild K D , Porreca F , Yamamura H I , Raffa R B
Published: May 2006

The temperature dependence of the dissociation constant for the interaction of an opioid delta selective ligand and its receptor was evaluated in three tissues. The change in free energy of this interaction was similar in mouse brain, mouse spinal cord, and NG 108-15 mouse neuroblastoma-rat glioma hybrid cells (delta G(o)' = -13.44, -13.34, and -13.66 kcal.mol-1, respectively). However, the reaction was endothermic and occurred with an increase in entropy in mouse brain and NG 108-15 cells, but it was exothermic and occurred with a negligible change in entropy in mouse spinal cord. These data are consistent with the existence of multiple subtypes of opioid delta receptor, and they further suggest that the opioid delta receptor recently cloned from the NG 108-15 cell line is of the brain subtype. Subtypes of opioid delta receptors may mediate analgesia, but not side-effects, of opiates and thus could be targets for future drug design.
Establishment of an adherent cell feeder layer from human umbilical cord blood for support of long-term hematopoietic progenitor cell growth.
Authors: Ye Z Q , Burkholder J K , Qiu P , Schultz J C , Shahidi N T , Yang N S
Published: May 2006

Previous attempts to establish a stromal cell feeder layer from human umbilical cord blood (HUCB) have met with very limited success. It has been suggested that there is an insufficient number of stromal precursor cells in HUCB to form a hematopoietic-supporting feeder layer in primary cultures. The present study shows that HUCB does contain a significant accessory cell population that routinely develops into a confluent, adherent cell layer under defined primary culture conditions. HUCB-derived adherent layers were shown to support long-term hematopoietic activity for an average of 4 months. This was achieved by using a customized coverslip with a modified surface structure as the cell attachment substratum and using a specialized culture feeding regime. We have characterized the various cell types (including fibroblasts, macrophages, and endothelial cells) and extracellular matrix proteins (including fibronectin, collagen III, and laminin) that were present in abundance in the HUCB-derived adherent cell layer. In contrast, oil red O-staining fat cells were rarely detected. ELISA and bioassays showed that stem cell factor and interleukin 6 were produced by the HUCB stromal cell cultures, but interleukin 3 or granulocyte/macrophage colony-stimulating factor was not detected. Application of this hematopoietic culture system to transgenic and gene therapy studies of stem cells is discussed.
Pancreatic beta cells express a diverse set of homeobox genes.
Authors: Rudnick A , Ling T Y , Odagiri H , Rutter W J , German M S
Published: May 2006

Homeobox genes, which are found in all eukaryotic organisms, encode transcriptional regulators involved in cell-type differentiation and development. Several homeobox genes encoding homeodomain proteins that bind and activate the insulin gene promoter have been described. In an attempt to identify additional beta-cell homeodomain proteins, we designed primers based on the sequences of beta-cell homeobox genes cdx3 and lmx1 and the Drosophila homeodomain protein Antennapedia and used these primers to amplify inserts by PCR from an insulinoma cDNA library. The resulting amplification products include sequences encoding 10 distinct homeodomain proteins; 3 of these proteins have not been described previously. In addition, an insert was obtained encoding a splice variant of engrailed-2, a homeodomain protein previously identified in the central nervous system. Northern analysis revealed a distinct pattern of expression for each homeobox gene. Interestingly, the PCR-derived clones do not represent a complete sampling of the beta-cell library because no inserts encoding cdx3 or lmx1 protein were obtained. Beta cells probably express additional homeobox genes. The abundance and diversity of homeodomain proteins found in beta cells illustrate the remarkable complexity and redundancy of the machinery controlling beta-cell development and differentiation.
Bootstrap hypothesis tests for evolutionary trees and other dendrograms.
Authors: Brown J K
Published: May 2006

The bootstrap computer-intensive statistical technique is frequently applied to statistical analyses of phylogenetic trees. The widely used rule that a group is supported significantly if it appears in at least 95% of bootstrap trees is conservative in most situations. This paper describes three ways of using the bootstrap to carry out statistical inference on phylogenies. The first method tests whether there is nonrandom support for a single group or tree. The second method compares the support for two groups or trees. The third method tests whether a single group or tree has better support than the set of all possible alternatives; this may be a replacement for the "95% rule." These tests generally require fewer bootstrap trees to be estimated than do other methods of bootstrapping phylogenies. A simple, sequential statistical method can be used to increase the efficiency further. These methods can be applied to tests of multiple hypotheses about a single phylogeny. Parsimony analyses of 5S rRNA sequences of plants and cluster analyses of randomly amplified polymorphic DNA bands in three pathotypes of the cereal eyespot fungus are used as illustrative examples. The tests can be used to analyze dendrograms in subjects other than taxonomy.