bluuebunny/crossref_metadata_2025 huggingface dataset:
The complete sequence of Drosophila beta-spectrin reveals supra-motifs comprising eight 106-residue segments.
Authors: Byers T J , Brandin E , Lue R A , Winograd E , Branton D
Published: May 2006

The alpha and beta chains of spectrin are homologous, yet they have acquired different structural features that work in synergy to give the multimer its overall properties. The primary amino acid sequence of each spectrin subunit is dominated by tandemly repeated 106-residue motifs. By comparing the complete Drosophila beta-spectrin sequence with other spectrins we have discovered evidence that a higher-order, 848-amino acid supra-motif is tandemly repeated in both alpha- and beta-spectrin. These data argue that alpha- and beta-spectrin, rather than evolving independently from sequences encoding the ancestral 106-residue motifs, must have arisen after the establishment of a large supra-motif composed of eight of the 106-residue motifs. Our data suggest the segment structure of a progenitor gene that gave rise to both alpha- and beta-spectrin as well as dystrophin. The structural differences that evolved after the split between the alpha- and beta-spectrin genes confer the independent functions that exist in their products today.
Rapid decline of chronic myeloid leukemic cells in long-term culture due to a defect at the leukemic stem cell level.
Authors: Udomsakdi C , Eaves C J , Swolin B , Reid D S , Barnett M J , Eaves A C
Published: May 2006

In this report we describe a quantitative in vitro assay for the most primitive type of leukemic precursors yet defined in patients with chronic myeloid leukemia (CML). This assay is based on the recently described "long-term culture-initiating cell" (LTC-IC) assay for primitive normal human hematopoietic cells. Such cells, when cocultured with competent fibroblast feeder layers, give rise after a minimum of 5 weeks to multiple single and multilineage clonogenic progenitors detectable in secondary semisolid assay cultures. Similar cultures initiated by seeding a highly enriched source of leukemic cells from patients onto normal feeders showed the clonogenic cell output after 5 weeks to be linearly related to the input innoculum over a wide range down to limiting numbers of input cells, thus allowing absolute frequencies of leukemic LTC-ICs to be determined using standard limiting dilution analysis techniques. Leukemic LTC-IC concentrations in CML marrow were found to be decreased, on average to less than 10% of the normal LTC-IC concentration in normal marrow, but were greatly increased (up to greater than 10(5) times) in CML blood. Assessment of the number of clonogenic cells produced per leukemic LTC-IC by comparison to normal blood or marrow LTC-IC values showed this function to be unchanged in leukemic LTC-ICs [i.e., 3.1 +/- 0.4 clonogenic cells per CML LTC-IC (mean +/- SEM, n = 6) versus 3.7 +/- 1.2 (n = 3) and 4.3 +/- 0.4 (n = 5), respectively, for normal blood and marrow LTC-ICs]. In contrast, leukemic LTC-IC maintenance in LTC proved to be highly defective by comparison to normal LTC-IC of either blood or marrow origin. Thus, when cells from primary LTC were subcultured into secondary LTC-IC assays, leukemic LTC-IC rapidly declined (greater than 30-fold) within the first 10 days of culture, whereas normal LTC-IC numbers remained unchanged during this period. These findings illustrate how self-maintenance and differentiation events in primitive human hematopoietic cells can be differentially modulated by an oncogenic process and provide a framework for further studies of their manipulation, analysis, and therapeutic exploitation.
Selective stimulation of prostatic carcinoma cell proliferation by transferrin.
Authors: Rossi M C , Zetter B R
Published: May 2006

Aggressive prostatic carcinomas most frequently metastasize to the skeletal system. We have previously shown that cultured human prostatic carcinoma cells are highly responsive to growth factors found in human bone marrow. To identify the factor(s) responsible for the increased prostatic carcinoma cell proliferation, we fractionated crude bone marrow preparations by using hydroxylapatite HPLC. The major activity peak contained two high molecular weight bands (M(r) = 80,000 and 69,000) that cross-reacted with antibodies to human transferrin and serum albumin, respectively. Bone marrow transferrin, purified to apparent homogeneity by using DEAE-Affi-Gel Blue chromatography, anti-transferrin affinity chromatography, and hydroxylapatite HPLC, markedly stimulated prostatic carcinoma cell proliferation, whereas human serum albumin showed no significant growth factor activity. Marrow preparations, depleted of transferrin by passage over an anti-transferrin affinity column, lost greater than 90% of their proliferative activity. In contrast to the response observed with the prostatic carcinoma cell lines, a variety of human malignant cell lines, derived from other primary sites and metastatic to sites other than bone marrow, showed a reduced response to purified marrow-derived transferrin. These results suggest that rapid growth of human prostatic carcinoma metastases in spinal bone may result from a combination of conditions that include (i) drainage of prostatic carcinoma cells into the paravertebral circulation, (ii) high concentrations of available transferrin in bone marrow, and (iii) increased sensitivity of prostatic carcinoma cells to the mitogenic activity of transferrin.
Reversion of recombinant toxoids: mutations in diphtheria toxin that partially compensate for active-site deletions.
Authors: Killeen K P , Escuyer V , Mekalanos J J , Collier R J
Published: May 2006

Deleting an important active-site residue of diphtheria toxin, glutamic acid-148, reduces the toxin's ADP-ribosyltransferase activity by a factor of greater than 10(4). We considered using this mutation to construct a recombinant toxoid for expression by live attenuated vaccines and explored second-site mutations that might cause reversion. Activity was partially restored by substituting glutamic acid for valine-147 or by extending the deletion by five residues toward the NH2 terminus, thereby placing glutamic acid-142 immediately adjacent to tyrosine-149. In both mutants the indicated glutamic acid may occupy a spatial locus similar to that of glutamic acid-148 in the unmutated protein. Simply deleting a crucial residue does not, therefore, provide confidence that a second-site mutation could not readily restore activity to a toxoid.
The LIM family transcription factor Isl-1 requires cAMP response element binding protein to promote somatostatin expression in pancreatic islet cells.
Authors: Leonard J , Serup P , Gonzalez G , Edlund T , Montminy M
Published: May 2006

Many eukaryotic genes are regulated by cAMP through a conserved cAMP response element (CRE). Here we show that, in the pancreatic islet cell line Tu6, a well-characterized CRE in the somatostatin gene does not provide cAMP responsiveness but functions as an essential element for its basal activity. DNA-binding and functional analyses indicate that the cAMP-responsive factor CREB regulates somatostatin expression in these cells without requirement for phosphorylation at the protein kinase A-regulated Ser-133 phosphorylation site. In addition to the CRE site, cell-specific expression of the somatostatin gene requires a second promoter element, which binds the recently characterized LIM family protein Isl-1. Thus, Isl-1 and CREB appear to synergize on the somatostatin promoter to stimulate high-level expression in Tu6 cells. The ability of CREB to function in a phosphorylation-independent manner suggests a mechanism by which this protein can regulate gene transcription.
Protein-induced bending and DNA cyclization.
Authors: Kahn J D , Crothers D M
Published: May 2006

We have applied T4 ligase-mediated DNA cyclization kinetics to protein-induced bending in DNA. The presence and direction of a static bend can be inferred from J factors for cyclization of 150- to 160-base-pair minicircles, which include a catabolite activator protein binding site phased against a sequence-directed bend. We demonstrate a quasi-thermodynamic linkage between cyclization and protein binding; we find that properly phased DNAs bind catabolite activator protein approximately 200-fold more tightly as circles than as linear molecules. The results unambiguously distinguish DNA bends from isotropically flexible sites and can explain cooperative binding by proteins that need not contact each other.
Conservation of the organization of five tightly clustered genes over 600 million years of divergent evolution.
Authors: Colombo P , Yon J , Garson K , Fried M
Published: May 2006

The organization of the mouse surfeit locus is unusual in that it contains six housekeeping genes (Surf-1-Surf-6), which are unrelated by sequence homology, in the tightest mammalian gene cluster thus far described. A maximum of only 73 base pairs separates any two of the four well-characterized genes, and two of the genes overlap at their 3' ends. The direction of transcription of each of the five surfeit genes, Surf-1-Surf-5, alternates with respect to that of its neighbor, suggesting cis-interaction or coregulation between the genes by mechanisms such as the sharing of regulatory elements and/or antisense regulation. The Surf-3 gene has been identified as encoding the ribosomal protein L7a (Rpl7a). We have used the high conservation of the Rpl7a gene to clone the chicken gene and surrounding genomic DNA. The tight clustering and juxtaposition of at least five of the surfeit genes (Surf-1-Surf-5) and their associated CpG-rich islands have been found to be conserved over the 600 million years of divergent evolution that separates birds and mammals. This strongly suggests that the surfeit locus represents a different form of gene cluster in which gene organization may play both a positive and negative regulatory role in gene expression possibly via cis-interactions between the closely spaced genes.
Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core.
Authors: Ogata K , Hojo H , Aimoto S , Nakai T , Nakamura H , Sarai A , Ishii S , Nishimura Y
Published: May 2006

The DNA-binding domain of the c-myb protooncogene product consists of three imperfect tandem repeats of 51 or 52 amino acids, each of which contains three conserved tryptophans, spaced 18 or 19 amino acids apart. The structure of the third repeat, which is essential for sequence-specific DNA binding, has been determined by NMR with distance geometry calculation. It includes three well-defined helices (residues 149-162, 166-172, and 178-187) maintained by a hydrophobic core that includes the three conserved tryptophans, together with two histidines. Helices 2 and 3 form a structure related to but distinct from a canonical helix-turn-helix motif. In particular, the turn between these helices is one amino acid longer than the corresponding turn in bacterial repressors and homeodomains and contains a proline residue. In addition, the architecture of the three helices is different from those of homeodomains and DNA-binding domains of bacterial repressors. Based on the present structure, the binding mode of Myb repeat 3 with a specific DNA is also discussed.
T cells expressing variable elements of T-cell receptor beta 8 and beta 2 chain regulate murine IgE production.
Authors: Renz H , Bradley K L , Marrack P , Gelfand E W
Published: May 2006

After sensitization to ovalbumin (Ova) by inhalation of nebulized antigen, BALB/c mice respond with an early rise in IgE but not in IgG anti-Ova antibody production. Our purpose here was to analyze the repertoire of T cells that may contribute to regulating this IgE response. Initial study of Ova-reactive T-cell hybridomas showed that they selectively express the T-cell receptor variable beta-chain (V beta) elements 2, 8.1/8.2, and 14. The frequency of T cells bearing these V beta elements in local draining lymph nodes of the airways and lungs (peribronchial-draining lymph nodes) after Ova inhalation was examined. Local sensitization increased the proportion of V beta 8.1/8.2 T cells in the peribronchial-draining lymph nodes, whereas expression of V beta 2 or V beta 14 was similar in sensitized and nonsensitized animals. In the presence of increased antigen concentrations, V beta 8 and V beta 2 T cells were equally reactive to Ova when cell proliferation was assayed. Coculture of Ova-selected V beta 8 T cells from peribronchial-draining lymph nodes and spleens of sensitized animals with primed splenic B cells increased IgE but not IgG production. The V beta 8 increase in IgE production was related to an increase in numbers of IgE-secreting B cells. In contrast, coculture of Ova-selected V beta 2 T cells with sensitized B cells had no stimulatory effect on either IgE or IgG production. Further, addition of V beta 2 cells to V beta 8 cells inhibited the V beta 8-induced augmentation of IgE production. These data indicate that T cells expressing different T cell receptors or, perhaps, different V beta elements may play different roles in IgE production in sensitized mice.
Evolution of major histocompatibility complex class II allelic diversity: direct descent in mice and humans.
Authors: Lundberg A S , McDevitt H O
Published: May 2006

The high degree of polymorphism seen at major histocompatibility complex (MHC) class II loci is a feature unique to the MHC. Most of the beta-chain polymorphism is localized in "hypervariable" regions (HVRs). HVR amino acid sequence similarity between distantly related species has recently been found. We have employed a Monte-Carlo statistic to show that shared HVR polymorphism between beta-chain genes of humans and mice represents direct descent of ancestral sequences rather than convergent evolution. Furthermore, half the sequence polymorphism seen in class II beta-chain genes of mice persists in evolution and is encoded by the same DNA sequence in humans. No evidence for increased mutation rate within the HVR was found. We postulate that the HVR can be considered the genetic unit of recombination, with selection for HVR sequences and combinations of HVRs constrained by functional considerations.
Active nuclear import of human immunodeficiency virus type 1 preintegration complexes.
Authors: Bukrinsky M I , Sharova N , Dempsey M P , Stanwick T L , Bukrinskaya A G , Haggerty S , Stevenson M
Published: May 2006

After cell infection by the human immunodeficiency virus type 1 (HIV-1), nascent viral DNA in the form of a high molecular weight nucleoprotein preintegration complex must be transported to the nucleus of the host cell prior to integration of viral DNA with the host genome. The mechanism used by retroviruses for nuclear targeting of preintegration complexes and dependence on cell division has not been established. Our studies show that, after infection, the preintegration complex of HIV-1 was rapidly transported to the nucleus of the host cell by a process that required ATP but was independent of cell division. Functional HIV-1 integrase, an essential component of the preintegration complex, was not required for nuclear import of these complexes. The ability of HIV-1 to use host cell active transport processes for nuclear import of the viral preintegration complex obviates the requirement for host cell division in establishment of the integrated provirus. These findings are pertinent to our understanding of early events in the life cycle of HIV-1 and to the mode of HIV-1 replication in terminally differentiated nondividing cells such as macrophages (monocytes, tissue macrophages, follicular dendritic cells, and microglial cells).
Structure-function relationships of the yeast fatty acid synthase: negative-stain, cryo-electron microscopy, and image analysis studies of the end views of the structure.
Authors: Stoops J K , Kolodziej S J , Schroeter J P , Bretaudiere J P , Wakil S J
Published: May 2006

The yeast fatty acid synthase (M(r) = 2.5 x 10(6)) is organized in an alpha 6 beta 6 complex. In these studies, the synthase structure has been examined by negative-stain and cryo-electron microscopy. Side and end views of the structure indicate that the molecule, shaped similar to a prolate ellipsoid, has a high-density band of protein bisecting its major axis. Stained and frozen-hydrated average images of the end views show an excellent concordance and a hexagonal ring having three each alternating egg- and kidney-shaped features with low-protein-density protrusions extending outward from the egg-shaped features. Images also show that the barrel-like structure is not hollow but has a Y-shaped central core, which appears to make contact with the three egg-shaped features. Numerous side views of the structure give good evidence that the beta subunits have an archlike shape. We propose a model for the synthase that has point-group symmetry 32 and six equivalent sites of fatty acid synthesis. The protomeric unit is alpha 2 beta 2. The ends of each of the two archlike beta subunits interact with opposite sides of the two dichotomously arranged disclike alpha subunits. Three such protomeric units form the ring. We propose that the six fatty acid synthesizing centers are composed of two complementary half-alpha subunits and a beta subunit, an arrangement having all the partial activities of the multifunctional enzyme required for fatty acid synthesis.
Vicariance biogeography in the Pleistocene and speciation in North American wood warblers: a test of Mengel's model.
Authors: Bermingham E , Rohwer S , Freeman S , Wood C
Published: May 2006

It is widely believed that habitat fragmentation during the Pleistocene initiated speciation events in many songbird genera. One such vicariance model for avian speciation in the Pleistocene was developed by R. M. Mengel for North American birds. This model suggests that the first Pleistocene glacial advance reduced the area of an extensive, eastern North American deciduous forest, forcing adaptation by some species to boreal forest. This, in turn, facilitated the development of transcontinental range expansions during interglacials. Subsequent glacial advances repeatedly fragmented the ranges of these species into eastern and western populations; western isolates speciated to form the multispecies groups observed among various North American birds. We used mtDNA restriction site data to reconstruct the phylogeny of the black-throated green warbler complex-the group that Mengel considered the best fit to his model. Contrary to Mengel's model, the phylogeny indicates that not all western endemics were derived from an eastern ancestor. Instead, our results imply a mix, wherein some western endemics were budded off an eastern source, as Mengel posits, while others probably resulted from intermontane isolations in the west.
Mutational analysis of the human immunodeficiency virus type 1 Eli Nef function.
Authors: Zazopoulos E , Haseltine W A
Published: May 2006

The studies presented here define an internally consistent experimental system that permits systematic analysis of the effect of nef on the rate of the human immunodeficiency virus type 1 (HIV-1) replication in a CD4+ tumor T-cell line and in primary peripheral blood mononuclear cells. The parental full-length Nef protein, derived from the Eli strain of HIV-1, accelerates virus replication in both cell types. Mutations that destabilize or alter the intracellular location of the protein affect the ability of the Nef protein to accelerate virus replication. A set of mutants was made in amino acids proposed to be required for Nef function, including threonine and serine residues proposed to be targets for phosphorylation, and in sequences thought to resemble the G-1, G-3, and G-4 sites of the family of G proteins. In most cases alterations of the critical amino acids yield stable Nef proteins of parental phenotype. These results challenge the existing theories for the mechanism of Nef function. The results also identify two residues in the carboxyl half of the protein that are important for Nef function.
Evolution of the major histocompatibility complex: isolation of class II A cDNA clones from the cartilaginous fish.
Authors: Kasahara M , Vazquez M , Sato K , McKinney E C , Flajnik M F
Published: May 2006

Along with the T-cell receptor and immunoglobulin, the major histocompatibility complex (MHC) plays a key role in mounting immune responses to foreign antigen. To gain insights into the evolution of the MHC, class II A cDNA clones were isolated from nurse sharks, a member of the class of cartilaginous fish. Two closely related cDNA clones, which might encode allelic products, were identified; of the three amino acid substitutions found in the alpha 1 domain, two were located at positions postulated to interact with processed peptides. The deduced nurse shark MHC class II alpha chains showed conspicuous structural similarity to their mammalian counterparts. Isolation of cDNA clones encoding typical MHC class II alpha chains was unexpected since no direct evidence for T-cell-mediated immune responses has been obtained in the cartilaginous fish. The cartilaginous fish is phylogenetically the most primitive class of vertebrates from which any MHC gene has been isolated.
Attenuation of sensory receptor signaling by covalent modification.
Authors: Borkovich K A , Alex L A , Simon M I
Published: May 2006

The Tar receptor is a transmembrane protein that regulates bacterial chemotaxis in response to changes in the level of aspartic acid in the medium. The extracellular portion of the protein can bind aspartate, and the cytoplasmic portion modulates CheA kinase activity. The receptor can either activate or inhibit the kinase. The cytoplasmic portion of the receptor can be modified by carboxymethylation of specific glutamic acid residues. To test the effects of differential methylation on receptor function, we prepared membranes from cells that have specifically modified forms of the receptor and tested the relative ability of each of these forms to activate or inhibit CheA kinase. Completely demethylated receptor was a potent inhibitor and poor activator of the kinase, while the fully modified receptor was an excellent activator but an inefficient inhibitor. Partially modified receptor could act both as an effective inhibitor and as an activator. Reversible modification provides a mechanism that allows the cell to accumulate a population of receptor molecules capable of generating a wide range of signaling intensities.
Antisense oligodeoxynucleotides to the cystic fibrosis transmembrane conductance regulator inhibit cAMP-activated but not calcium-activated chloride currents.
Authors: Wagner J A , McDonald T V , Nghiem P T , Lowe A W , Schulman H , Gruenert D C , Stryer L , Gardner P
Published: May 2006

Phosphorylation of the cystic fibrosis transmembrane conductance regulator (CFTR) by cAMP-dependent protein kinase leads to chloride flux in epithelial cells. Is CFTR also required for the calcium-dependent activation of chloride channels? We used antisense oligodeoxynucleotides to CFTR to reduce the expression of CFTR in colonic and tracheal epithelial cells. The antisense oligomers were a pair of adjacent 18-mers complementary to nucleotides 1-18 and 19-36 of CFTR mRNA. Sense and misantisense oligomers served as controls. A 48-h antisense treatment reduced the expression of CFTR protein as assayed by immunoprecipitation and autoradiography to 26% of the level in sense-treated T84 cells. Whole-cell patch clamp revealed that a 48-h antisense treatment of T84 and 56FHTE-8o- fetal tracheal epithelial cells reduced the cAMP-activated chloride current to approximately 10% of that in sense-treated cells. The half-life of functional CFTR is less than 24 h in these cells. In contrast, the calcium-activated chloride current was not affected by antisense treatment. Hence, the cAMP and calcium pathways are separate. CFTR is required for the cAMP pathway but not for the calcium pathway.
One-step generation of cytoplasmic male sterility by fusion of mitochondrial-inactivated tomato protoplasts with nuclear-inactivated Solanum protoplasts.
Authors: Melchers G , Mohri Y , Watanabe K , Wakabayashi S , Harada K
Published: May 2006

Mesophyll protoplasts of Lycopersicon esculentum were treated with iodoacetamide to inactivate mitochondria, and protoplasts of Solanum acaule and Solanum tuberosum were irradiated with gamma- or x-rays to inactivate nuclei. Mixtures of protoplasts thus modified were treated with Ca2+ and polyethylene glycol to obtain heterologous fusion products. Among the fusion products were some tomato plants that were indistinguishable from the original cultivars with respect to morphology, physiology, and chromosome number (2N = 24) but exhibited various degrees of male sterility (MS): complete lack or malformation of anthers, shrunken pollen, and normal-looking stainable pollen that could not germinate. The MS thus induced in five cultivars of different growth types, including one of subspecies L. esculentum cerasiforme, was inherited maternally over several generations and is, therefore, cytoplasmically determined MS (CMS). Analysis of mitochondrial DNA revealed that the mitochondrial genome of the CMS hybrids does not contain all elements of the mitochondrial DNA of either parent but includes sequences of a recombinational nature not present in either parent. The CMS hybrids, therefore, possess a true hybrid mitochondrial genome. The same procedure applied to fusion of tomato with Solanum lycopersicoides and Nicotiana tabacum cells did not produce CMS phenotypes. The advantages of this method over others for generating MS are as follows: (i) only one step is required; (ii) the nuclear genotype of the cultivar is unaffected; (iii) the prospect that cytoplasmic determination allows generation of 100% CMS progenies. The normal-appearing but nonfunctional pollen of certain CMS types might render them attractive to pollinating bumblebees that thus would facilitate production of hybrid seed.
Intracellular neutralization of virus by immunoglobulin A antibodies.
Authors: Mazanec M B , Kaetzel C S , Lamm M E , Fletcher D , Nedrud J G
Published: May 2006

IgA is thought to neutralize viruses at the epithelial surface of mucous membranes by preventing their attachment. Since IgA, a polymeric immunoglobulin, is transported through the lining of epithelial cells by the polymeric-immunoglobulin receptor and since viruses are obligate intracellular parasites, we hypothesized that IgA antibodies may also interfere with viral replication by binding to newly synthesized viral proteins within infected cells. Polarized monolayers of Madin-Darby canine kidney epithelial cells expressing the polymeric-immunoglobulin receptor were infected on the apical surface with Sendai virus. Anti-Sendai virus IgA monoclonal antibody delivered from the basolateral surface colocalized with viral protein within the cell, as documented by immunofluorescence. More importantly, anti-viral IgA reduced virus titers greater than 1000-fold (P less than 0.0001) in apical supernatants and greater than 10-fold (P less than 0.0001) in cell lysates from monolayers treated with anti-viral IgA compared with those treated with either anti-viral IgG or an irrelevant IgA monoclonal antibody. We believe that the differences in viral titers between cell layers treated with specific IgA, which enters the epithelial cell by binding to the polymeric-immunoglobulin receptor, and those treated with specific IgG, which does not enter the cells, or irrelevant IgA indicate that specific intracellular IgA antibodies can inhibit viral replication. Thus, in addition to the classical role of humoral antibodies in extracellular defense, IgA antibody may be able to neutralize microbial pathogens intracellularly, giving IgA a role in host defense that has traditionally been reserved for cell-mediated immunity.
Identification and isolation of the polyferredoxin from Methanobacterium thermoautotrophicum strain delta H.
Authors: Steigerwald V J , Pihl T D , Reeve J N
Published: May 2006

Sequencing the genes encoding the methyl viologen-reducing hydrogenase, cloned from Methanobacterium thermoautotrophicum strain delta H and Methanothermus fervidus, revealed the presence of tightly linked genes, designated mvhB, which were predicted to encode proteins containing six tandemly arranged bacterial ferrodoxin-like domains. A lacZ-mvhB gene fusion has been constructed and expressed in Escherichia coli. Rabbit antibodies raised against the fusion polypeptide purified from E. coli have been used to identify and isolate the polyferrodoxin from Mb. thermoautotrophicum strain delta H. The polyferredoxin accumulates in cells of the methanogen during exponential growth but decreases rapidly on entry into stationary phase. It is not processed into monoferredoxins and is located primarily in the soluble fraction of cell lysates of Mb. thermoautotrophicum. Metronidazole reduction by crude extracts of Mb. thermoautotrophicum strain delta H cells, dependent on the presence of hydrogen and the heterodisulfide CoM-S-S-HTP [formed from the two coenzymes 2-mercaptoethanesulfonic acid (coenzyme M, HS-CoM) and N-(7-mercaptoheptanoyl)threonine O3-phosphate (HS-HTP)], was not inhibited by the antibodies raised against the LacZ-MvhB fusion polypeptide.
dOct2, a Drosophila Oct transcription factor that functions in yeast.
Authors: Prakash K , Fang X D , Engelberg D , Behal A , Parker C S
Published: May 2006

Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Here we report the cDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20% to 40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in 14 stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. Our data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.
Dermorphin-related peptides from the skin of Phyllomedusa bicolor and their amidated analogs activate two mu opioid receptor subtypes that modulate antinociception and catalepsy in the rat.
Authors: Negri L , Erspamer G F , Severini C , Potenza R L , Melchiorri P , Erspamer V
Published: May 2006

Three naturally occurring dermorphin-like peptides from the skin of the frog Phyllomedusa bicolor, the related carboxyl-terminal amides, and some substituted analogs were synthesized, their binding profiles to opioid receptors were determined, and their biological activities were studied in isolated organ preparations and intact animals. The opioid binding profile revealed a very high selectivity of these peptides for mu sites and suggested the existence of two receptor subtypes, of high and low affinity. The peptides tested acted as potent mu opioid agonists on isolated organ preparations. They were several times more active in inhibiting electrically evoked contractions in guinea pig ileum than in mouse vas deferens. When injected into the lateral brain ventricle or peritoneum of rats, the high-affinity-site-preferring ligand, [Lys7-NH2]dermorphin, behaved as a potent analgesic agent. By contrast, the low-affinity-site-preferring ligand, [Trp4,Asn7-NH2]dermorphin, produced a weak antinociception but an intense catalepsy.
Conformation for a beta-cyclodextrin monosubstituted with a cyclic dipeptide.
Authors: Di Blasio B , Pavone V , Nastri F , Isernia C , Saviano M , Pedone C , Cucinotta V , Impellizzeri G , Rizzarelli E , Vecchio G
Published: May 2006

The structural characterization of a beta-cyclodextrin monosubstituted with the peptide cyclo(L-His-L-Leu) is reported. This work provides an x-ray example of a covalently bound group that folds in such a way that the terminal apolar side chain is retained in the hydrophobic interior of the cone-shaped cyclodextrin cavity. 6-Deoxy-6-cyclo(L-histidyl-L-leucyl)-beta-cyclodextrin crystallizes in the space group P1 with cell dimensions a = 14.728(8) A, b = 15.084(7) A, c = 18.182(10) A, alpha = 94.36(6) degrees, beta = 95.81(5) degrees, gamma = 116.08(9) degrees; overall isotropic agreement R = 10.6% for 5703 observed reflections (Fo greater than 3 sigma). The molecular structure consists of two independent molecules with the formula C54H86N4O36.7.25H2O. Each molecule assumes a "sleeping swan"-like overall shape with the hydrophobic leucine side chain inserted inside the cavity of the macrocycle. The two independent units give rise to a head-to-tail dimer linked by hydrogen bonds occurring between primary and secondary hydroxyl groups of the two monomers. The packing of the dimers produces cavities containing water molecules. There are infinite hydrophilic channels running in the crystal, which is similar to what is found in the structures of cyclic peptides.
Brefeldin A affects early events but does not affect late events along the exocytic pathway in pancreatic acinar cells.
Authors: Hendricks L C , McClanahan S L , Palade G E , Farquhar M G
Published: May 2006

Brefeldin A (BFA) blocks protein export from the endoplasmic reticulum (ER) to Golgi complex and causes dismantling of the Golgi complex with relocation of resident Golgi proteins to the ER in some cultured cells. It is not known whether later steps in the secretory process are affected. We previously have shown that in BFA-treated rat pancreatic lobules, there is no detectable relocation of Golgi proteins to the ER and, although Golgi cisternae are rapidly dismantled, clusters of small smooth vesicles consisting of both bona fide Golgi remnants and associated vesicular carriers persist even with prolonged BFA exposure. We now report the effects of BFA on transport of proteins through the secretory pathway in exocrine pancreatic cells; we pulse-labeled pancreatic lobules with [35S]methionine and then chased for various times before adding BFA. When BFA was added at pulse, treated lobules released less than 10% of radioactive protein in comparison with controls, regardless of whether or not the lobule cultures were stimulated with carbamoylcholine. However, when lobules were pulsed and then chased for 30, 45, or 60 min before BFA addition, the amount of labeled protein released was comparable in both BFA-treated and untreated cultures. Furthermore, the kinetics and amounts of basal and carbamoylcholine-stimulated release of unlabeled alpha-amylase from storage in zymogen granules were similar in both control and BFA-treated lobules. Therefore, in the rat pancreas, BFA blocks ER to Golgi transport but does not affect later stages along the secretory pathway, including intra-Golgi transport, exit from the Golgi complex, formation and concentration of secretory granules, and exocytosis.
Phorbol ester-induced amino-terminal phosphorylation of human JUN but not JUNB regulates transcriptional activation.
Authors: Franklin C C , Sanchez V , Wagner F , Woodgett J R , Kraft A S
Published: May 2006

Phorbol ester tumor promoters activate gene transcription by regulating both the synthesis and posttranslational modification of the activator protein 1 (AP-1) transcription factor, c-Jun and JunB are components of the mammalian AP-1 complex. Here we demonstrate that in U-937 human leukemic cells, phorbol esters stimulate the phosphorylation of the amino terminus of human c-Jun (JUN) but not human JunB (JUNB). Mutational analysis indicates that serine-63 and -73, which reside within the putative regulatory domain of JUN, are required for both constitutive and phorbol 12-myristate 13-acetate-inducible N-terminal JUN phosphorylation. To determine the functional role of this N-terminal phosphorylation, we prepared several chimeric proteins containing the N-terminal 84 amino acids (positions 5-89) of human JUN or murine JUNB fused to the yeast GAL4 DNA-binding domain. This region was found to be sufficient for the phorbol ester-inducible transcriptional activity of JUN, but not JUNB. This induction was abolished by the mutation of serine-63 and -73 to leucine residues. Thus, we propose that phorbol esters enhance the trans-activation potential of JUN, but not JUNB, by the phosphorylation of the N-terminal regulatory domain of JUN.
Stimulation of adenosine A1 receptors and bradykinin receptors, which act via different G proteins, synergistically raises inositol 1,4,5-trisphosphate and intracellular free calcium in DDT1 MF-2 smooth muscle cells.
Authors: Gerwins P , Fredholm B B
Published: May 2006

We have examined the cross talk between adenosine and bradykinin receptors in DDT1 MF-2 smooth muscle cells. Both adenosine and bradykinin mobilized intracellular free calcium via the formation of inositol 1,4,5-trisphosphate in a time- and dose-dependent manner. Adenosine exerted its actions via adenosine A1 receptors as demonstrated by the observations that N6-cyclopentyladenosine, a selective A1 receptor agonist, had an EC50 in the low nanomolar range and that a selective adenosine A1 receptor antagonist, 8-cyclopentyl-1,3-dipropylxanthine, counteracted adenosine-mediated responses at concentrations typical for signaling via adenosine A1 receptors. Adenosine A1 receptors were coupled to phospholipase C via pertussis toxin-sensitive guanine nucleotide-binding regulatory protein(s) [G protein(s)], whereas bradykinin responses were unaffected by pertussis toxin. When adenosine or N6-cyclopentyladenosine was combined with bradykinin, the resulting formation of inositol 1,4,5-triphosphate was more than additive, and the EC50 value for adenosine and N6-cyclopentyladenosine was shifted to the left by bradykinin, the affinity of which was unaltered. Combining N6-cyclopentyladenosine and bradykinin also synergistically raised intracellular free calcium both at subthreshold levels and at maximal concentrations of the two agonists. The interaction was not dependent upon cAMP. In conclusion, stimulation of adenosine A1 receptors coupled to pertussis toxin-sensitive G protein(s) and bradykinin receptors coupled to pertussis toxin-insensitive G protein(s) synergistically mobilizes intracellular free calcium and inositol 1,4,5-trisphosphate formation.
Involvement of endogenous tumor necrosis factor alpha and transforming growth factor beta during induction of collagen type II arthritis in mice.
Authors: Thorbecke G J , Shah R , Leu C H , Kuruvilla A P , Hardison A M , Palladino M A
Published: May 2006

Both tumor necrosis factor alpha (TNF-alpha) and transforming growth factor beta (TGF-beta) are found in synovial fluid from arthritic joints of humans and of rodents with experimental arthritis. The role of endogenously produced TGF-beta and TNF in the pathogenesis of collagen type II-induced arthritis (CIA) in DBA/1 mice was examined by determining the effect of neutralizing monoclonal antibodies to these factors on the course of the disease. Endogenously produced as well as systemically administered TGF-beta 1 and TNF-alpha had opposite effects, since TGF-beta 1 and anti-TNF protected against CIA, whereas anti-TGF-beta and TNF-alpha increased CIA incidence and/or severity. Intraperitoneally injected TGF-beta 1 at a dose of 2 micrograms per day for 14 days significantly ameliorated arthritis, even when started at the time of arthritis development, although it did not reverse established disease. The resistance to CIA induction caused by a prior intravenous injection of collagen type II was not significantly influenced by the simultaneous injection of TGF-beta 1, TNF-alpha, or interleukin 1 alpha. It is concluded that the endogenous production of TNF and TGF-beta is important in determining the course of CIA.
Identification of the naturally processed form of hen egg white lysozyme bound to the murine major histocompatibility complex class II molecule I-Ak.
Authors: Nelson C A , Roof R W , McCourt D W , Unanue E R
Published: May 2006

A murine B-cell lymphoma bearing the class II major histocompatibility complex molecule I-Ak was cultured with the protein antigen hen egg white lysozyme (HEL). The I-Ak molecules were purified, and their associated peptides were extracted for characterization. Five HEL peptides were identified. Four contained the 10 amino acid residues HEL 52-61 (DYGILQINSR) but were heterogeneous in length and flanking residues. This core sequence is known to confer a high binding affinity for I-Ak. One additional peptide contained the amino acid residues HEL 48-60. These data demonstrate that the HEL epitope containing residues 52-61 is the most abundant HEL epitope presented on the major histocompatibility complex of the antigen-presenting cells and consequently explains its immunodominance.
Yeast FKBP-13 is a membrane-associated FK506-binding protein encoded by the nonessential gene FKB2.
Authors: Nielsen J B , Foor F , Siekierka J J , Hsu M J , Ramadan N , Morin N , Shafiee A , Dahl A M , Brizuela L , Chrebet G
Published: May 2006

The immunosuppressants FK506 and rapamycin prevent T-cell activation and also inhibit the growth of certain strains of the yeast Saccharomyces cerevisiae. It has previously been shown that yeast contains a 12-kDa cytosolic FK506-binding protein (yFKBP-12), which also possesses peptidylprolyl cis-trans isomerase activity, and that fkb1 strains lacking yFKBP-12 are resistant to rapamycin and sensitive to FK506. The absence of yFKBP-12 permitted the detection and isolation of a second FK506- and rapamycin-binding protein, which is about 13 kDa in size (yFKBP-13) and membrane-associated. Purified yFKBP-13 binds FK506 with 15-fold lower affinity than yFKBP-12 and has peptidylprolyl cis-trans isomerase activity with a similar substrate profile. The sequence of the first 37 N-terminal amino acids was determined, and the yFKBP-13 gene (FKB2) was cloned and sequenced. A hydrophobic putative signal sequence precedes the N terminus of the mature protein. yFKBP-13 most closely resembles the membrane-associated human FKBP-13, which also possesses a signal peptide, whereas yFKBP-12 most closely resembles human FKBP-12. fkb2 and fkb1 fkb2 mutants are viable and unaltered in their sensitivity to FK506, suggesting that yeast possesses an additional target for this drug. Furthermore, fkb2 null mutations confer no change in rapamycin sensitivity. These findings show that yFKBP-13 and yFKBP-12 have distinct functions within the cell.
The evolutionary selection of DNA base pairs in gene-regulatory binding sites.
Authors: Berg O G
Published: May 2006

The DNA base-pair sequences that serve as gene-regulatory sites have been selected during evolution to provide an appropriate functional binding for a particular protein. In most cases, the function depends on the binding probability, which can be influenced both by the binding strength and by the abundance of the protein in the cell. As a consequence, the same function can be achieved with strong binding sites and a small amount of protein as with weak binding sites and a large amount of protein. However, increasing the protein burden will decrease the growth rate of the cells, even when all functions remain the same. Thus, for maximal growth, the protein levels should be as low as possible and the binding correspondingly strong. On the other hand, sequences with a weaker binding can be formed in many more ways and are, therefore, more probable, and random mutations are more likely to produce them. Thus, the selection pressure against an increased protein burden can be balanced against the random mutational drift in the recognition sequences, thereby tying together the statistics of base-pair choice, the binding strength, and the protein burden. In terms of this model, the selection pressure can be estimated from the properties of a gene-regulatory protein and its recognition sites. A key feature is the mutational randomization pressure that appears as a fundamental force shaping the optimal solutions that provide maximal growth. The model is tested on a number of gene-regulatory systems in Escherichia coli. The same principles should hold for all proteins for which overall activity in the cell is proportional to abundance; then the selective pressure to increase the efficiency of an individual protein cannot be larger than the selective pressure to decrease the total protein burden.
Reciprocal control of RNA-binding and aconitase activity in the regulation of the iron-responsive element binding protein: role of the iron-sulfur cluster.
Authors: Haile D J , Rouault T A , Tang C K , Chin J , Harford J B , Klausner R D
Published: May 2006

Several mechanisms of posttranscriptional gene regulation are involved in regulation of the expression of essential proteins of iron metabolism. Coordinate regulation of ferritin and transferrin receptor expression is produced by binding of a cytosolic protein, the iron-responsive element binding protein (IRE-BP) to specific stem-loop structures present in target RNAs. The affinity of this protein for its cognate RNA is regulated by the cell in response to changes in iron availability. The IRE-BP demonstrates a striking level of amino acid sequence identity to the iron-sulfur (Fe-S) protein mitochondrial aconitase. Moreover, the recombinant IRE-BP has aconitase function. The lability of the Fe-S cluster in mitochondrial aconitase has led us to propose that the mechanism by which iron levels are sensed by the IRE-BP involves changes in an Fe-S cluster in the IRE-BP. In this study, we demonstrate that procedures aimed at altering the IRE-BP Fe-S cluster in vitro reciprocally alter the RNA binding and aconitase activity of the IRE-BP. The changes in the RNA binding of the protein produced in vitro appear to match the previously described alterations of the protein in response to iron availability in the cell. Furthermore, iron manipulation of cells correlates with the activation or inactivation of the IRE-BP aconitase activity. The results are consistent with a model for the posttranslational regulation of the IRE-BP in which the Fe-S cluster is altered in response to the availability of intracellular iron and this, in turn, regulates the RNA-binding activity.
Adenovirus-human immunodeficiency virus (HIV) envelope recombinant vaccines elicit high-titered HIV-neutralizing antibodies in the dog model.
Authors: Natuk R J , Chanda P K , Lubeck M D , Davis A R , Wilhelm J , Hjorth R , Wade M S , Bhat B M , Mizutani S , Lee S
Published: May 2006

Recombinant human adenoviruses (Ads) (types 4, 5, and 7) expressing the HIV-1 envelope membrane glycoprotein (gp160) were tested for immunogenicity in the dog. Administration of recombinant Ad7-env by intratracheal inoculation resulted in a low serum antibody response to gp160, which developed over several weeks. A strong neutralizing antibody response to the Ad7 vector developed within 1 week of infection. A subsequent booster inoculation 12 weeks later with the heterotypic Ad4-env recombinant virus resulted in significantly enhanced humoral responses directed at the envelope antigen, as measured by both ELISA and Western blot analysis as well as high-titer type-specific neutralizing antibodies, with some animals achieving neutralization titers approaching 1000. Recombinant HIV envelope glycoprotein derived from Ad-HIV-infected cell cultures was used as a subunit booster injection for dogs that had previously received sequential immunizations with heterotypic recombinant Ads. Significant immune responses against the envelope developed as measured by ELISA, Western blot analysis, and neutralization assays. These data indicate that live recombinant Ad-HIV vaccines are capable of inducing high-titer type-specific neutralizing antibodies to gp160 in vivo. Recombinant HIV envelope glycoprotein subunit vaccines, prepared from Ad-env-infected cells, are capable of boosting these responses.