bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional transfer RNAs with modifications in the 3'-CCA end: differential effects on aminoacylation and polypeptide synthesis.
Authors: Liu M , Horowitz J
Published: May 2006

The trinucleotide CCA sequence is present at the 3' terminus of all mature tRNAs. Despite this high degree of conservation, we have been able to prepare in vitro transcripts of Escherichia coli tRNA(Val) with altered 3' termini that are readily aminoacylated and can function in polypeptide synthesis. Replacement of the 3'-terminal adenosine with either cytidine or uridine yields a tRNA(Val) variant that retains almost full aminoacylation activity, having specificity constants (Vmax/Km) 40-50% that of wild-type tRNA(Val). The tRNA(Val) variant with a 3'-terminal guanosine remains fully chargeable but is a poor substrate for valyl-tRNA synthetase, largely as the result of a decrease in the catalytic constant. End-group analysis revealed the absence of adenosine at the 3' end of the tRNA(Val) mutants and identified the nucleotide expected from the sequence of the DNA template as the predominant 3'-terminal residue; Val-cytidine was isolated from the aminoacylated C76 mutant. Val-tRNA(Val) with 3'-CCG is active in poly(U,G)-directed (Val, Phe) copolypeptide synthesis, whereas the tRNA(Val) mutants terminating in 3'-CCC and 3'-CCU, which are readily aminoacylated, are inactive. The differential effects of nucleotide substitution on aminoacylation and polypeptide synthesis suggest that the universally conserved 3'-CCA end of tRNAs is monitored at two or more steps in protein synthesis that have different nucleotide recognition specificities.
HMG-domain proteins specifically inhibit the repair of the major DNA adduct of the anticancer drug cisplatin by human excision nuclease.
Authors: Huang J C , Zamble D B , Reardon J T , Lippard S J , Sancar A
Published: May 2006

The most frequent DNA adduct made by the anticancer drug cisplatin, the 1,2-intrastrand d(GpG) cross-link, as well as the minor 1,3-intrastrand d(GpTpG) adduct, were both repaired by an in vitro human excision repair system. Fragments of 27-29 nt containing the platinum damage were excised. The high mobility group (HMG)-domain proteins HMG1 and human mitochondrial transcription factor specifically inhibited repair of the 1,2-intrastrand cross-link by the human excision nuclease. These results suggest that the types and levels of HMG-domain proteins in a given tumor may influence the responsiveness of that cancer to cisplatin chemotherapy and they provide a rational basis for the synthesis of new platinum anticancer drug candidates.
Mammal extinctions, body size, and paleotemperature.
Authors: Bown T M , Holroyd P A , Rose K D
Published: May 2006

There is a general inverse relationship between the natural logarithm of tooth area (a body size indicator) of some fossil mammals and paleotemperature during approximately 2.9 million years of the early Eocene in the Bighorn Basin of northwest Wyoming. When mean temperatures became warmer, tooth areas tended to become smaller. During colder times, larger species predominated; these generally became larger or remained the same size. Paleotemperature trends also markedly affected patterns of local (and, perhaps, regional) extinction and immigration. New species appeared as immigrants during or near the hottest (smaller forms) and coldest (larger forms) intervals. Paleotemperature trend reversals commonly resulted in the ultimate extinction of both small forms (during cooling intervals) and larger forms (during warming intervals). These immigrations and extinctions mark faunal turnovers that were also modulated by sharp increases in sediment accumulation rate.
Isolation of GD3 synthase gene by expression cloning of GM3 alpha-2,8-sialyltransferase cDNA using anti-GD2 monoclonal antibody.
Authors: Haraguchi M , Yamashiro S , Yamamoto A , Furukawa K , Takamiya K , Lloyd K O , Shiku H , Furukawa K
Published: May 2006

For the isolation of ganglioside GD3 synthase (EC 2.4.99.8) cDNA, we developed an expression cloning approach that used an anti-GD2 monoclonal antibody for selection. A host recipient cell line that we have named KF3027-Hyg5 was also utilized. This cell line expresses high levels of GM2 as well as GM3 but no GD3 or GD2 and was constructed from mouse B16 melanoma cells transfected with the polyoma large tumor antigen gene (KF3027) and the previously cloned beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.92) cDNA. Four rounds of transfection, monoclonal antibody 3F8 panning, and Hirt extraction resulted in the isolation of two cDNA clones, transfection of which directed the expression of GD3 in KF3027 and B16 melanoma cells and GD3 and GD2 in KF3027-Hyg5 cells. The cDNA contained a 1650-bp insert and a single open reading frame. The deduced amino acid predicted a type II membrane topology consisting of cytoplasmic (14 aa), transmembrane (18 aa), and catalytic (309 aa) domains. The sequence also predicted the presence of a sialyl motif similar to that found in the other sialyltransferases cloned so far. As expected, mRNA of this gene (2.6 kb) was strongly expressed in human melanoma lines.
Assembly of the phagocyte NADPH oxidase: binding of Src homology 3 domains to proline-rich targets.
Authors: Leto T L , Adams A G , de Mendez I
Published: May 2006

The NADPH oxidase responsible for generation of superoxide anion and related microbicidal oxidants by phagocytes is assembled from at least five distinct proteins. Two are cytosolic components (p47-phox and p67-phox) that contain Src homology 3 (SH3) domains and associate with a transmembrane cytochrome b558 upon activation. We show here that the SH3 domains of p47-phox bind to proline-rich sequences in p47-phox itself and the p22-phox subunit of cytochrome b558. Binding of the p47-phox SH3 domains to p22-phox was abolished by a mutation in one proline-rich sequence (Pro156-->Gln) noted in a distinct form of chronic granulomatous disease and was inhibited by a short proline-rich synthetic peptide corresponding to residues 149-162 of p22-phox. Expression of mutated p22-phox did not restore oxidase activity to p22-phox-deficient B cells and did not enable p22-phox-dependent translocation of p47-phox to membranes in phorbol ester-stimulated cells. We also show that the cytosolic oxidase components associate with one another through the C-terminal SH3 domain of p67-phox and a proline-rich C-terminal sequence in p47-phox. These SH3 target sites conform to consensus features deduced from SH3 binding sites in other systems. We propose a model in which the oxidase complex assembles through a mechanism involving SH3 domains of both cytosolic proteins and cognate proline-rich targets in other oxidase components.
Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli.
Authors: Jeanteur D , Schirmer T , Fourel D , Simonet V , Rummel G , Widmer C , Rosenbusch J P , Pattus F , Pagès J M
Published: May 2006

A strain of Escherichia coli, selected on the basis of its resistance to colicin N, reveals distinct structural and functional alterations in unspecific OmpF porin. A single mutation [Gly-119-->Asp (G119D)] was identified in the internal loop L3 that contributes critically to the formation of the construction inside the lumen of the pore. X-ray structure analysis to a resolution of 3.0 A reveals a locally altered peptide backbone, with the side chain of residue Asp-119 protruding into the channel, causing the area of the constriction (7 x 11 A in the wild type) to be subdivided into two intercommunicating subcompartments of 3-4 A in diameter. The functional consequences of this structural modification consist of a reduction of the channel conductance by about one-third, of altered ion selectivity and voltage gating, and of a decrease of permeation rates of various sugars by factors of 2-12. The structural modification of the mutant protein affects neither the beta-barrel structure nor those regions of the molecule that are exposed at the cell surface. Considering the colicin resistance of the mutant, it is inferred that in vivo, colicin N traverses the outer membrane through the porin channel or that the dynamics of the exposed loops are affected in the mutant such that these may impede the binding of the toxin.
Sex-specific processing of the Drosophila exuperantia transcript is regulated in male germ cells by the tra-2 gene.
Authors: Hazelrigg T , Tu C
Published: May 2006

The Drosophila exuperantia (exu) gene encodes overlapping sex-specific, germline-dependent mRNAs. In this work, the structural differences between these sex-specific exu mRNAs were determined by sequence analysis of 9 ovary and 10 testis cDNAs. The transformer 2 (tra-2) gene functions in sex determination of female somatic cells through its role in regulating female-specific splicing of doublesex (dsx) RNA. We report here that tra-2 is required in male germ cells for efficient male-specific processing of exu RNA; in the absence of tra-2, X/Y males produce a new mRNA which is processed at its 3' end so that it contains sequences normally specific to the female 3' untranslated region. Although the processing event that requires tra-2 occurs in an untranslated region of the exu transcript, the isolation and characterization of a male-specific exu allele which deletes male 3' untranslated sequence indicate that this processing is biologically significant.
Tagged versus untagged libraries: methods for the generation and screening of combinatorial chemical libraries.
Authors: Janda K D
Published: May 2006

Over the past two decades the pharmaceutical industry has been driven by the biological sciences. The discovery and description of the biological mechanisms that underlie disease states accompanied by an unraveling of these mechanisms has provided drug, and more recently biotechnological, companies with a barrage of new therapeutic targets. Paradoxically, as a result of such biological and biochemical advances, new sources of drug leads are in short supply. Considerable efforts in trying to create potential drug candidates has led to the parturition of combinatorial chemical libraries. In this review I will examine some of the main technologies for generating and deducing active components from combinatorial libraries that have been segregated into two schools of thought: (i) the creation and decoding of combinatorial libraries by so-called tagged methodologies, and (ii) the production and deconvolution of chemical libraries by untagged protocols.
Autoantibodies to the alpha/beta T-cell receptors in human immunodeficiency virus infection: dysregulation and mimicry.
Authors: Lake D F , Schluter S F , Wang E , Bernstein R M , Edmundson A B , Marchalonis J J
Published: May 2006

Autoimmune reactivity is a consequence of infection with human immunodeficiency virus (HIV). We studied serological cross-reactions of purified pooled IgG from sera of HIV-infected individuals by using nested sets of synthetic overlapping peptides duplicating the covalent structures of T-cell receptors (TCRs) and immunoglobulin light chains and report that two processes of autoantibody production occur. (i) IgG autoantibodies to putative regulatory variable domain CDR1 and FR3 epitopes (where CDR is complementarity-determining region and FR is framework region) are present in pooled IgG from HIV-infected individuals at levels 10-fold greater than that in pooled IgG from healthy humans. (ii) Anti-TCR autoimmunization involves antigenic mimicry between a conserved peptide stretch of the major neutralizing V3 loop determinant of HIV-1 gp120 and the conserved FR4 segment of the TCR V beta. Affinity-purified antibodies to the synthetic V3 loop peptide bound to a recombinant single-chain TCR and to a synthetic TCR joining segment peptide containing the FR4 sequence. Conversely, affinity-purified autoantibodies from pooled IgG from HIV-infected individuals to the TCR peptide bound the V3 loop peptide and a single-chain TCR. Inhibition studies indicated that the cross-reactive immunizing antigen was the V3 loop. These results bear upon the impact of HIV infection on immune regulation and on the selection of peptides for vaccine development.
Adenovirus E3 14.7-kilodalton protein, an antagonist of tumor necrosis factor cytolysis, increases the virulence of vaccinia virus in severe combined immunodeficient mice.
Authors: Tufariello J M , Cho S , Horwitz M S
Published: May 2006

The adenovirus (Ad) 14.7-kDa protein, which is called "14.7K," has been shown to function as a general inhibitor of tumor necrosis factor alpha (TNF) cytolysis in tissue culture assays, and the effect of this antagonism on viral pathogenesis in vivo has recently been explored. In infections of immunocompetent BALB/c mice, we have shown previously that Ad type 2 (Ad2) 14.7K, when cloned into a vaccinia virus (VV) vector in combination with the gene for murine TNF, is able to counteract much of the attenuating effect of TNF on VV virulence. In the present study we utilized VV constructs expressing various combinations of Ad 14.7K and TNF in infections of T- and B-cell-deficient C.B-17 severe combined immunodeficient (SCID) mice to determine whether these cells are directly necessary for 14.7K's reversal of TNF-mediated viral attenuation. The mice were infected by the intranasal route, and mortality, morbidity, histopathology, and virus replication in selected organs were evaluated at various times after infection. We found that, in the SCID murine pneumonia model, neither the attenuation by TNF nor its reversal by Ad 14.7K require the participation of T or B lymphocytes or their secreted products. SCID mice infected with VV expressing both 14.7K and TNF [VV 14.7(+)/TNF] were generally well clinically for the first 7-10 days after infection; however, they developed a subacute or chronic illness, succumbing to diseminated VV infection at least 3 weeks earlier than mice infected with VV expressing TNF alone [VV 14.7(-)/TNF]. Animals infected with VV 14.7(+)/TNF were shown to have higher initial titers of virus and delayed clearance from the lungs as well as more rapid spread of virus to internal organs than animals infected with VV 14.7(-)/TNF. SCID mice infected intranasally with VV without TNF showed a dramatic increase in acute disease and succumbed within the first 1-2 weeks after infection, independent of Ad 14.7K expression.
Formation of free nitric oxide from l-arginine by nitric oxide synthase: direct enhancement of generation by superoxide dismutase.
Authors: Hobbs A J , Fukuto J M , Ignarro L J
Published: May 2006

Although nitric oxide (NO) appears to be one of the oxidation products of L-arginine catalyzed by NO synthase (NOS; EC 1.14.13.39), past studies on the measurement of NO in cell-free enzymatic assays have not been based on the direct detection of the free NO molecule. Instead, assays have relied on indirect measurements of the stable NO oxidation products nitrite and nitrate and on indirect actions of NO such as guanylate cyclase activation and oxyhemoglobin oxidation. Utilizing a specific chemiluminescence assay, we report here that the gaseous product of L-arginine oxidation, catalyzed by both inducible macrophage and constitutive neuronal NOS, is indistinguishable from authentic NO on the basis of their physicochemical properties. NO gas formation by NOS was dependent on L-arginine, NADPH, and oxygen and inhibited by NG-methyl-L-arginine and cyanide anion. Superoxide dismutase (SOD) caused a marked, concentration-dependent increase in the production of free NO by mechanisms that were unrelated to the dismutation of superoxide anion or activation of NOS. These observations indicate that free NO is formed as a result of NOS-catalyzed L-arginine oxidation and that SOD enhances the generation of NO without directly affecting NO itself. SOD appears to elicit a novel biological action, perhaps accelerating the conversion of an intermediate in the L-arginine-NO pathway such as nitroxyl (HNO) to NO.
Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney.
Authors: Echevarria M , Windhager E E , Tate S S , Frindt G
Published: May 2006

The terminal part of the inner medullary collecting duct exhibits a high degree of water permeability that is independent of increased intracellular cAMP and not accounted for by the activity of the known renal epithelial water channels CHIP28 (28-kDa channel-forming integral protein) and WCH-CD (collecting duct water channel protein). Starting with rat kidney papilla mRNA, reverse transcription PCR was performed with degenerate primers assuming that the putative channel would be a member of the major intrinsic protein (MIP) family of proteins. A cDNA fragment was identified and used to screen a rat kidney cDNA library. A 1.9-kb cDNA clone was isolated. The open reading frame of 876 bp coded for a protein of 292 amino acids (M(r), 31,431). Aquaporin 3 (AQP3; 31.4-kDa water channel protein) is a newly discovered member of the MIP family. Northern blot analysis showed a single transcript for AQP3 of approximately 1.9 kb present in the renal medulla, predominantly in the inner medulla. With in situ hybridization, abundant message was found in the cells of the medullary collecting ducts. Injection of the complementary RNA of AQP3 into Xenopus oocytes markedly increased the osmotic water permeability. This permeability had an energy of activation of 3.0 kcal/mol (1 cal = 4.184 J), it was fully blocked by 1 mM p-chloromercuriphenylsulfonate, and this inhibition was reversed by 5 mM dithiothreitol. cAMP did not increase this water permeability. AQP3 did not permit passage of monovalent ions (Na, K, Cl); however, it is slightly permeable to urea. The present study demonstrates the existence of an additional water channel, AQP3, in epithelial cells of the medullary collecting duct.
Localization of an aminoacridine antitumor agent in a type II topoisomerase-DNA complex.
Authors: Freudenreich C H , Kreuzer K N
Published: May 2006

Type II topoisomerases are the targets of several classes of chemotherapeutic agents that stabilize an intermediate of the catalytic cycle with the enzyme covalently linked to cleaved DNA. We have used 3-azido-AMSA [4'-(3-azido-9-acridinylamino)methanesulfon-m-anisidide], a photo-activatible analog of the inhibitor m-AMSA [4'-(9-acridinylamino)methanesulfon-m-anisidide], to localize the inhibitor binding site in a cleavage complex consisting of an oligonucleotide substrate and the bacteriophage T4 type II DNA topoisomerase. Upon photoactivation, the inhibitor covalently attached to the substrate only in the presence of topoisomerase. Sites of inhibitor attachment were detected by primer-extension analysis and by piperidine-induced cleavage of the covalently modified substrate. 3-Azido-AMSA reacted with bases immediately adjacent to the two phosphodiester bonds cleaved by the enzyme. Therefore, topoisomerase creates or stabilizes preferential binding sites for the inhibitor precisely at the two sites of DNA cleavage.
The purification of megapoietin: a physiological regulator of megakaryocyte growth and platelet production.
Authors: Kuter D J , Beeler D L , Rosenberg R D
Published: May 2006

The circulating blood platelet is produced by the bone marrow megakaryocyte. In response to a decrease in the platelet count, megakaryocytes increase in number and ploidy. Although this feedback loop has long been thought to be mediated by a circulating hematopoietic factor, no such factor has been purified. Using a model of thrombocytopenia in sheep, we have identified an active substance called megapoietin, which stimulated an increase in the number and ploidy of megakaryocytes in bone marrow culture. Circulating levels of this factor could be quantified with this assay and were found to be inversely proportional to the platelet count of the sheep. Levels increased from < 0.26 pM in normal sheep to 25-40 pM in thrombocytopenic sheep. From large amounts of thrombocytopenic sheep plasma we have purified a 31,200-Da protein and found that it retained the ability to stimulate both megakaryocyte number and ploidy in vitro. Injection of partially purified megapoietin into rats stimulated a 24% increase in megakaryocyte number and a 60% increase in mean ploidy as well as a 77% increase in the platelet count. Sheep platelets bound megapoietin and the amount of platelets required to eliminate half the activity in vitro was close to the amount associated with this same level of activity in vivo. We believe that megapoietin is the physiologically relevant mediator of megakaryocyte growth and platelet production. Moreover, our data suggest that the level of megapoietin is directly determined by the ability of platelets to remove megapoietin from the circulation.
Expression of a functional human complement inhibitor in a transgenic pig as a model for the prevention of xenogeneic hyperacute organ rejection.
Authors: Fodor W L , Williams B L , Matis L A , Madri J A , Rollins S A , Knight J W , Velander W , Squinto S P
Published: May 2006

The serious shortage of human organs available for transplantation has engendered a heightened interest in the use of animal organs (xenografts) for transplantation. However, the major barrier to successful discordant xenogeneic organ transplantation is the phenomenon of hyperacute rejection. Hyperacute rejection results from the deposition of high-titer preformed antibodies that activate serum complement on the luminal surface of the vascular endothelium, leading to vessel occlusion and graft failure within minutes to hours. Although endogenous membrane-associated complement inhibitors normally protect endothelial cells from autologous complement, they are species restricted and thus confer limited resistance to activated xenogeneic complement. To address the pathogenesis of hyperacute rejection in xenotransplantation, transgenic mice and a transgenic pig were engineered to express the human terminal complement inhibitor hCD59. High-level cell surface expression of hCD59 was achieved in a variety of murine and porcine cell types, most importantly on both large vessel and capillary endothelium. hCD59-expressing porcine cells were significantly resistant to challenge with high-titer anti-porcine antibody and human complement. These experiments demonstrate a strategy for developing a pig-to-primate xenogeneic transplantation model to test whether the expression of a human complement inhibitor in transgenic pigs could render xenogeneic organs resistant to hyperacute rejection.
Requirement of posttranslational modifications for the generation of biologic activity of glycosylation-inhibiting factor.
Authors: Liu Y C , Nakano T , Elly C , Ishizaka K
Published: May 2006

Secretion of bioactive glycosylation-inhibiting factor (GIF) appears to be restricted to suppressor T (Ts) cells, although various human and murine cell line cells secrete the 13-kDa peptide that reacts with anti-GIF. Nucleotide sequences of GIF cDNA from the Ts and non-Ts cells are identical, indicating that bioactive GIF and inactive GIF have an identical amino acid sequence. A stable transfectant of human GIF (hGIF) cDNA in BMT10 cells secretes inactive GIF peptide, whereas transfection of a chimeric cDNA encoding a fusion protein consisting of the N-terminal region of procalcitonin precursor and hGIF into the same cells results in secretion of bioactive GIF. Evidence was obtained that the fusion protein goes into the endoplasmic reticulum and is cleaved for the secretion of mature GIF peptide, whereas the inactive 13-kDa peptide synthesized by the former transfectant does not go through the endoplasmic reticulum. However, a stable transfectant of hGIF cDNA in mouse Ts hybridoma contains inactive GIF in the cytosol and secretes bioactive hGIF without participation of the endoplasmic reticulum-Golgi system. Heterogeneity of the 13-kDa hGIF from the transfectant was detected in two-dimensional electrophoresis. The results suggested that Ts cells have a machinery that converts a portion of inactive cytosolic GIF peptide to bioactive GIF during secretion.
Prostate and mammary adenocarcinoma in transgenic mice carrying a rat C3(1) simian virus 40 large tumor antigen fusion gene.
Authors: Maroulakou I G , Anver M , Garrett L , Green J E
Published: May 2006

A transgenic mouse model for prostate and mammary cancer has been developed in mice containing a recombinant gene expressing the simian virus 40 early-region transforming sequences under the regulatory control of the rat prostatic steroid binding protein [C3(1)] gene. Male transgenic mice develop prostatic hyperplasia in early life that progresses to adenoma or adenocarcinoma in most animals surviving to longer than 7 months of age. Prostate cancer metastases to lung have been observed. Female animals from the same founder lines generally develop mammary hyperplasia by 3 months of age with subsequent development of mammary adenocarcinoma by 6 months of age in 100% of the animals. The development of tumors correlates with the expression of the transgene as determined by Northern blot and immunohistochemical analyses. The results of these experiments demonstrate that the C3(1) regulatory region used in these experiments is useful for targeting expression to the prostate and mammary gland. To our knowledge, this experimental system is the first reported transgenic mouse model for prostate cancer. These transgenic animals offer the opportunity to study hormone response elements in vivo and the multistage progression from normal tissue to carcinoma in the prostate and mammary glands.
Activity-dependent current distributions in model neurons.
Authors: Siegel M , Marder E , Abbott L F
Published: May 2006

The electrical activity of a neuron can affect its intrinsic physiological characteristics through a wide range of processes. We study a computer-simulated multicompartment model neuron in which channel density depends on local Ca2+ concentrations. This has three interesting consequences for the spatial distribution of conductances and the physiological behavior of the neuron: (i) the model neuron spontaneously develops a realistic, nonuniform distribution of conductances that is linked both to the morphology of the neuron and to the pattern of synaptic input that it receives, (ii) the response to synaptic input reveals a form of intrinsic localized plasticity that balances the synaptic contribution from dendritic regions receiving unequal stimulation, and (iii) intrinsic plasticity establishes a biophysical gain control that restores the neuron to its optimal firing range after synapses are strengthened by "Hebbian" long-term potentiation.
NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain.
Authors: Szyperski T , Pellecchia M , Wall D , Georgopoulos C , Wüthrich K
Published: May 2006

DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution.
Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips.
Authors: Woolley A T , Mathies R A
Published: May 2006

Capillary electrophoresis arrays have been fabricated on planar glass substrates by photolithographic masking and chemical etching techniques. The photolithographically defined channel patterns were etched in a glass substrate, and then capillaries were formed by thermally bonding the etched substrate to a second glass slide. High-resolution electrophoretic separations of phi X174 Hae III DNA restriction fragments have been performed with these chips using a hydroxyethyl cellulose sieving matrix in the channels. DNA fragments were fluorescently labeled with dye in the running buffer and detected with a laser-excited, confocal fluorescence system. The effects of variations in the electric field, procedures for injection, and sizes of separation and injection channels (ranging from 30 to 120 microns) have been explored. By use of channels with an effective length of only 3.5 cm, separations of phi X174 Hae II DNA fragments from approximately 70 to 1000 bp are complete in only 120 sec. We have also demonstrated high-speed sizing of PCR-amplified HLA-DQ alpha alleles. This work establishes methods for high-speed, high-throughput DNA separations on capillary array electrophoresis chips.
Microtubule dynamics in vitro are regulated by the tubulin isotype composition.
Authors: Panda D , Miller H P , Banerjee A , Ludueña R F , Wilson L
Published: May 2006

The growing and shortening dynamics of individual bovine brain microtubules at their plus ends at steady state in vitro, assembled from isotypically pure alpha beta II, alpha beta III, or alpha beta IV tubulin dimers, were determined by differential interference contrast video microscopy. Microtubules assembled from the purified alpha beta III isotype were considerably more dynamic than microtubules made from the alpha beta II or alpha beta IV isotypes or from unfractionated phosphocellulose-purified tubulin. Furthermore, increasing the proportion of the alpha beta II isotype in a mixture of the alpha beta II and alpha beta III isotypes suppressed microtubule dynamics, demonstrating that microtubule dynamics can be influenced by the tubulin isotype composition. The data support the hypothesis that cells might determine the dynamic properties and functions of its microtubules in part by altering the relative amounts of the different tubulin isotypes.
Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences.
Authors: Escalante A A , Ayala F J
Published: May 2006

Malaria is among mankind's worst scourges, affecting many millions of people, particularly in the tropics. Human malaria is caused by several species of Plasmodium, a parasitic protozoan. We analyze the small subunit rRNA gene sequences of 11 Plasmodium species, including three parasitic to humans, to infer their evolutionary relationships. Plasmodium falciparum, the most virulent of the human species, is closely related to Plasmodium reichenowi, which is parasitic to chimpanzee. The estimated time of divergence of these two Plasmodium species is consistent with the time of divergence (6-10 million years ago) between the human and chimpanzee lineages. The falciparum-reichenowi clade is only remotely related to two other human parasites, Plasmodium malariae and Plasmodium vivax, which are also only remotely related to each other. Thus, the parasitic associations of the Plasmodium species with their human hosts are phylogenetically independent. The remote phylogenetic relationship between the two bird parasites, Plasmodium gallinaceum and Plasmodium lophurae, and any of the human parasites provides no support for the hypothesis that infection by Plasmodium falciparum is a recent acquisition of humans, possibly coincident with the onset of agriculture.
AtVPS34, a phosphatidylinositol 3-kinase of Arabidopsis thaliana, is an essential protein with homology to a calcium-dependent lipid binding domain.
Authors: Welters P , Takegawa K , Emr S D , Chrispeels M J
Published: May 2006

The cDNA encoding phosphatidylinositol (PI) 3-kinase was cloned from Arabidopsis thaliana, and the derived amino acid sequence (AtVPS34) has a significantly higher homology to yeast PI 3-kinase (VPS34) than to the mammalian (p110). The protein has two conserved domains: a catalytic site with the ATP-binding site near the C terminus and a calcium-dependent lipid-binding domain near the N terminus. The plant cDNA does not rescue a yeast vps34 deletion mutant, but a chimeric gene in which the coding sequence for the C-terminal third of VPS34 is replaced by the corresponding sequence from the plant gene does rescue the yeast mutant. PI 3-kinase activity is detectable in extracts from plants that overexpress the plant PI 3-kinase. Expression of antisense constructs gives rise to second-generation transformed plants severely inhibited in growth and development.
Recursive deconvolution of combinatorial chemical libraries.
Authors: Erb E , Janda K D , Brenner S
Published: May 2006

A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a solid support. After each coupling, a portion of the resin from each of the four reaction vials was set aside and catalogued. The solid support from each vial is then combined, mixed, and redivided. The steps of (i) coupling, (ii) saving and cataloging, and (iii) randomizing were repeated until a pentapeptide library was obtained. The four pentapeptide libraries where the N-terminal amino acid is defined were screened against the beta-endorphin antibody and quantitated via an ELISA. The amino acid of the four pools that demonstrated the most binding was then coupled to the four tetrapeptide partial libraries that had been set aside and catalogued during the split synthesis. This recursive deconvolution was repeated until the best binders were deduced. Besides the anticipated native binder, two other members of the library displayed significant binding. This recursive method of deconvolution does not use a molecular tag, requires only one split synthesis, and can be applied to the deconvolution of nonlinear small-molecule combinatorial libraries and linear oligomeric combinatorial libraries, since it is based only on the procedure of the synthesis.
Drosophila PS1 integrin is a laminin receptor and differs in ligand specificity from PS2.
Authors: Gotwals P J , Fessler L I , Wehrli M , Hynes R O
Published: May 2006

We have expressed Drosophila position-specific (PS) integrins on the surfaces of Schneider S2 cells and tested for adhesion and spreading on various matrix molecules. We report that PS1 integrin is a laminin receptor and that PS1 and PS2 integrins promote cell spreading on two different Drosophila extracellular matrix molecules, laminin and tiggrin, respectively. The differing ligand specificities of these two integrins, combined with data on the in vivo expression patterns of the integrins and their ligands, lead to a model for the structure of integrin-dependent attachments in the pupal wings and embryonic muscles of Drosophila.
Purification and characterization of a ubiquitin carrier protein kinase from HeLa cells.
Authors: Kong S K , Chock P B
Published: May 2006

Protein ubiquitination plays an important role in ATP-dependent protein turnover, and it also may regulate other cellular events. Covalent attachment of ubiquitin to other proteins is catalyzed by three different enzymes, E1, E2, and E3. We have previously shown that protein ubiquitination can be regulated by phosphorylation. In the present study, we show that 20-kDa E2, an E2 molecular mass isoform, is phosphorylated by a protein kinase from the cytosolic fraction of HeLa cells. This protein kinase was purified by a procedure involving ammonium sulfate precipitation and three column chromatographies (phenyl-Sepharose, Superose gel filtration, and DEAE-Sephacel). Gel-filtration chromatography indicated that the molecular mass of this protein kinase was about 300 kDa. However, SDS/PAGE showed that the purified protein kinase consists of three subunits with molecular masses of 120, 105, and 70 kDa, respectively. The stoichiometry of the phosphorylated 20-kDa E2 isozyme was found to be 0.45 mol of phosphate per mol of protein. The phosphorylation of 20-kDa E2 occurred only at the serine residue. The activity of this protein kinase required the presence of Mg2+; however, the enzyme was inhibited by a high concentration of Mg2+.
Regulatory elements and transcription factors controlling basal and cytokine-induced expression of the gene encoding intercellular adhesion molecule 1.
Authors: Hou J , Baichwal V , Cao Z
Published: May 2006

The gene encoding intercellular adhesion molecule 1 (ICAM-1) is transcriptionally induced in response to inflammatory and immunomodulatory cytokines. To investigate the mechanisms controlling ICAM-1 gene expression, we have identified regulatory DNA sequences responsible for maintaining basal and mediating induced transcription in response to tumor necrosis factor alpha (TNF-alpha) and interferon gamma (IFN-gamma). Regulatory elements centered 115, 60, and 40 bp upstream from the ICAM-1 transcription start site were implicated in cytokine-independent gene expression. Regulatory elements dedicated to TNF-alpha and IFN-gamma were identified 190 and 90 bp, respectively, upstream from the ICAM-1 transcription start site. A combination of mutagenesis and DNA-binding assays revealed that the TNF-alpha response element is composite, consisting of binding sites for both C/EBP and NF-kappa B. The IFN-gamma response element behaved as a simple regulatory element that selectively binds to an IFN-gamma-inducible activity composed, at least in part, of p91. These observations provide a framework for understanding how extracellular signals dynamically regulate the adhesive properties of mammalian cells.
Antigenic implications of human immunodeficiency virus type 1 envelope quaternary structure: oligomer-specific and -sensitive monoclonal antibodies.
Authors: Broder C C , Earl P L , Long D , Abedon S T , Moss B , Doms R W
Published: May 2006

A majority of monoclonal antibodies (mAbs) raised against soluble oligomeric human immunodeficiency virus type 1 isolate IIIB (HIV-1IIIB) envelope (env) glycoprotein reacted with conformational epitopes within the gp120 or gp41 subunits. Of 35 mAbs directed against gp41, 21 preferentially reacted with oligomeric env. A subset of these mAbs reacted only with env oligomers (oligomer-specific mAbs). In contrast, only 1 of 27 mAbs directed against the gp120 subunit reacted more strongly with env oligomers than with monomers, and none were oligomer-specific. However, 50% of anti-gp120 mAbs preferentially recognized monomeric env, suggesting that some epitopes in gp120 are partially masked or altered by intersubunit contacts in the native env oligomer. Two mAbs to oligomer-dependent epitopes in gp41 neutralized HIV-1IIIB and HIV-1SF2, and binding of these mAbs to env was blocked by preincubation with HIV-1-positive human serum. Thus, immunization with soluble, oligomeric env elicits antibodies to conserved, conformational epitopes including a newly defined class of neutralizing antibodies that bind to oligomer-specific epitopes in gp41, and may also minimize the production of antibodies that preferentially react with monomeric env protein.
Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis.
Authors: Lee W H , Morton R A , Epstein J I , Brooks J D , Campbell P A , Bova G S , Hsieh W S , Isaacs W B , Nelson W G
Published: May 2006

Hypermethylation of regulatory sequences at the locus of the pi-class glutathione S-transferase gene GSTP1 was detected in 20 of 20 human prostatic carcinoma tissue specimens studied but not in normal tissues or prostatic tissues exhibiting benign hyperplasia. In addition, a striking decrease in GSTP1 expression was found to accompany human prostatic carcinogenesis. Immunohistochemical staining with anti-GSTP1 antibodies failed to detect the enzyme in 88 of 91 prostatic carcinomas analyzed. In vitro, GSTP1 expression was limited to human prostatic cancer cell lines containing GSTP1 alleles with hypomethylated promoter sequences; a human prostatic cancer cell line containing only hypermethylated GSTP1 promoter sequences did not express GSTP1 mRNA or polypeptides. Methylation of cytidine nucleotides in GSTP1 regulatory sequences constitutes the most common genomic alteration yet described for human prostate cancer.
Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation.
Authors: Jüttermann R , Li E , Jaenisch R
Published: May 2006

The deoxycytidine analog 5-aza-2'-deoxycytidine (5-azadCyd) has been widely used as a DNA methylation inhibitor to experimentally induce gene expression and cellular differentiation. Prior to the availability of mutant mice with altered DNA methyltransferase levels, treatment of cells with drugs has been the only means to experimentally manipulate the level of genomic DNA methylation in mammalian cells. Substitution of DNA with 5-azadCyd leads to covalent trapping of the enzyme, thereby depleting the cells of enzyme activity and resulting in DNA demethylation. 5-AzadCyd or 5-azacytidine treatment causes multiple changes in treated cells, including activation of silent genes, decondensation of chromatin, and induction of cellular differentiation, all of which are believed to be consequences of drug-induced demethylation. 5-AzadCyd is highly toxic in cultured cells and animals and is utilized as a potent antitumor agent for treatment of certain human cancers. It has been postulated that the toxicity of the drug in mammalian cells is also due to its inhibition of DNA methylation. The chemistry of the methylation reaction is consistent, however, with an alternative mechanism: the cytotoxic effect of 5-azadCyd may be directly mediated through the covalent binding of DNA methyltransferase to 5-azadCyd-substituted DNA. We have tested this possibility by using embryonic stem cells and mice with reduced levels of DNA methyltransferase due to a targeted mutation of the gene. When exposed to 5-azadCyd mutant embryonic stem cells or embryos were significantly more resistant to the toxic effects of the drug than wild-type cells and embryos, respectively. These results strongly suggest that the cellular DNA methyltransferase itself, rather than the secondary demethylation of genomic DNA, is the primary mediator of 5-azadCyd cytotoxicity. In light of our results, some conclusions from previous studies using 5-azadCyd in order to experimentally manipulate cellular methylation levels may have to be reassessed. Also, our data make clear predictions for cancer treatment: tumor cells with elevated DNA methyltransferase levels would be expected to be susceptible to treatment with 5-azadCyd, whereas tumors with reduced levels of the enzyme would be resistant.
Stepwise immortalization and transformation of adult human prostate epithelial cells by a combination of HPV-18 and v-Ki-ras.
Authors: Rhim J S , Webber M M , Bello D , Lee M S , Arnstein P , Chen L S , Jay G
Published: May 2006

Recent investigations have shown the presence of ras gene mutations and human papillomavirus (HPV) DNA in prostate carcinomas. In the present study, secondary adult human prostatic epithelial cells, upon transfection with a plasmid containing the entire HPV-18 genome, acquired an indefinite life-span in culture but did not undergo malignant conversion. Subsequent infection of these immortalized cells with the Kirsten murine sarcoma virus, which contains an activated Ki-ras oncogene, induced morphological transformation that led to the acquisition of neoplastic properties. These findings demonstrate the malignant transformation of adult human prostate epithelial cells in culture by a combination of viral oncogenes and the successive roles of HPV infection and Ki-ras activation in a multistep process responsible for prostate carcinogenesis.
Excessive production of amyloid beta-protein by peripheral cells of symptomatic and presymptomatic patients carrying the Swedish familial Alzheimer disease mutation.
Authors: Citron M , Vigo-Pelfrey C , Teplow D B , Miller C , Schenk D , Johnston J , Winblad B , Venizelos N , Lannfelt L , Selkoe D J
Published: May 2006

The 39- to 43-amino acid amyloid beta-protein (A beta), which is progressively deposited in cerebral plaques and blood vessels in Alzheimer disease (AD), is secreted by cultured human cells during normal metabolism. In studies of cell lines transfected with beta-amyloid precursor protein (beta APP) cDNAs, the beta APP mutation K670N/M671L found in a Swedish familial AD (FAD) pedigree has previously been shown to cause a marked augmentation of A beta secretion. Here, we have conducted blinded analyses of beta APP metabolism in primary skin fibroblasts from affected members of the Swedish FAD pedigree and their unaffected siblings or spouses. These fibroblasts continuously secrete a homogenous population of A beta molecules starting at Asp-1 (D672 of beta APP). We found a consistent and significant approximately 3-fold elevation of A beta release from all biopsied skin fibroblasts bearing the FAD mutation. No significant alterations of other metabolic derivatives of beta APP were detected. The elevated A beta levels were found in cells from both patients with clinical AD and presymptomatic subjects. Thus, A beta overproduction in this FAD pedigree is not a secondary event but is consistent with a causal role in the development of the disease. Increased A beta secretion can begin many years prior to onset of symptoms, even in peripheral tissues, indicating that it does not require preexisting neural abnormalities.
Disruption of a topoisomerase-DNA cleavage complex by a DNA helicase.
Authors: Howard M T , Neece S H , Matson S W , Kreuzer K N
Published: May 2006

The type II DNA topoisomerases are targets for a variety of chemotherapeutic agents, including the antibacterial quinolones and several families of antitumor drugs. These agents stabilize an enzyme-DNA cleavage complex that consists of the topoisomerase covalently linked to the 5' phosphates of a double-stranded DNA break. Although the drug-stabilized cleavage complex is readily reversible, it can result in cell death by a mechanism that remains uncertain. Here we demonstrate that the action of a DNA helicase can convert the cleavage complex into a nonreversible DNA break by displacing DNA strands from the complex. Formation of a nonreversible DNA break, induced by a DNA helicase, could explain the cytotoxicity of these topoisomerase poisons.