bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleotide sequence of the genetic loci encoding subunits of Bradyrhizobium japonicum uptake hydrogenase.
Authors: Sayavedra-Soto L A , Powell G K , Evans H J , Morris R O
Published: May 2006

An indispensable part of the hydrogen-recycling system in Bradyrhizobium japonicum is the uptake hydrogenase, which is composed of 34.5- and 65.9-kDa subunits. The gene encoding the large subunit is located on a 5.9-kilobase fragment of the H2-uptake-complementing cosmid pHU52 [Zuber, M., Harker, A.R., Sultana, M.A. & Evans, H.J. (1986) Proc. Natl. Acad. Sci. USA 83, 7668-7672]. We have now determined that the structural genes for both subunits are present on this fragment. Two open reading frames are present that correspond in size and deduced amino acid sequence to the hydrogenase subunits, except that the small-subunit coding region contains a leader peptide of 46 amino acids. The two genes are separated by a 32-nucleotide intergenic region and likely constitute an operon. Comparison of the deduced amino acid sequences of the B. japonicum genes with those from Desulfovibrio gigas, Desulfovibrio baculatus, and Rhodobacter capsulatus indicates significant sequence identity.
cDNA sequence of rat liver fructose-1,6-bisphosphatase and evidence for down-regulation of its mRNA by insulin.
Authors: el-Maghrabi M R , Pilkis J , Marker A J , Colosia A D , D'Angelo G , Fraser B A , Pilkis S J
Published: May 2006

A coding-length clone of rat liver fructose-1,6-bisphosphatase (EC 3.1.3.11) was isolated by immunological screening of a cDNA library in lambda gt11. Its identity was verified by comparing the deduced amino acid sequence with that obtained by direct sequencing of a complete set of CNBr and proteolytic peptides from the purified protein. The enzyme subunit is composed of 362 amino acids and has N-acetylvaline as the amino-terminal residue. The cDNA, 1255 base pairs (bp) long, consisted of 1086 bp of coding region, 15 bp of 5' untranslated sequence, and 154 bp at the 3' untranslated end. The 3' untranslated sequence contained a polyadenylylation signal (AATAAA) followed after 30 bp by a stretch of 7 adenines at the end of the clone. The deduced amino acid sequence was identical to the primary sequence of the protein and confirmed the alignment of five nonoverlapping peptides. It also confirmed the 27-residue extension, unique to the rat liver subunit, ending with a carboxyl-terminal phenylalanine. RNA blot analyses using the radiolabeled liver cDNA as a probe revealed a single band of fructose-1,6-bisphosphatase mRNA, 1.4 kilobases long, in liver and kidney but not in nongluconeogenic tissues. Fructose-1,6-bisphosphatase mRNA was increased 10-fold in livers from diabetic rats and was reduced to control levels after 24 hr of insulin treatment, suggesting that the changes in enzyme activity observed in diabetes and after insulin treatment are due to alterations in mRNA abundance.
A lamin B receptor in the nuclear envelope.
Authors: Worman H J , Yuan J , Blobel G , Georgatos S D
Published: May 2006

Using a solution binding assay, we show that purified 125I-labeled lamin B binds in a saturable and specific fashion to lamin-depleted avian erythrocyte nuclear membranes with a Kd of approximately 0.2 microM. This binding is significantly greater than the binding of 125I-labeled lamin A and is competitively inhibited by unlabeled ligand. We demonstrate that a 58-kDa integral membrane protein (p58) is a lamin B receptor by virtue of its abundance in the nuclear envelope and association with 125I-labeled lamin B in ligand blotting assays. Specific antibodies raised against p58 recognize one protein in isolated nuclei and partially block 125I-labeled lamin B binding to lamin-depleted nuclear membranes. Cell fractionation and indirect immunofluorescence microscopy show that p58 is located in the periphery of the nucleus. This protein may serve as a membrane attachment site for the nuclear lamina by acting as a specific receptor for lamin B.
cDNA-derived sequence of chicken embryo vinculin.
Authors: Coutu M D , Craig S W
Published: May 2006

We report the complete primary structure of chicken embryo vinculin. The amino acid sequence was derived from the nucleotide sequence of five overlapping cDNA clones isolated from a lambda gt11 phage library. Chicken embryo vinculin contains 1066 amino acids, has a calculated Mr of 116,990, a calculated pI of 5.9, and a hydropathy index of -4.22. A search of the National Biomedical Research Foundation protein sequence data base found no proteins with significant homology to vinculin. A striking feature of the linear sequence is a proline-rich region extending between residues 837 and 879. This region contains 45% proline and 19% aspartic plus glutamic acids; it is also the longest hydrophilic stretch in the molecule. The proline-rich region separates an amino-terminal domain with a calculated pI of 5.4 from a carboxyl-terminal domain with a calculated pI of 9.7. This feature suggests a structural basis for the specific interaction of vinculin with acidic phospholipids and a mechanism for the shuttling of vinculin between cytoplasm and membrane-associated junctional plaque.
Targeted mutation of the Hprt gene in mouse embryonic stem cells.
Authors: Doetschman T , Maeda N , Smithies O
Published: May 2006

The hypoxanthine-guanine phosphoribosyltransferase (Hprt) gene has been mutated in mouse blastocyst-derived embryonic stem cells by site-directed homologous recombination. Embryonic stem cells were electroporated in the presence of a targeting DNA fragment containing two specific features: (i) The targeting DNA contained a promoterless neomycin phosphotransferase (neo) gene that, when located within the endogenous Hprt locus, could be transcribed from the promoter of the target locus. (ii) The targeting fragment had two short regions of homology with the endogenous Hprt gene: one, 132 base pairs long and the other, 1.2 kilobase pairs long. Targeted cells in which the designed homologous recombination event occurred were isolated either by selection with G418 followed by 6-thioguanine or by selection with 6-thioguanine alone. Even though less than 2 kilobases of homology existed between the exogenous and target DNAs, an average of 2.6 embryonic stem cells were successfully targeted for every 10(5) colonies surviving electroporation. Six of the Hprt- cell lines showed homologous recombination. These six lines were further analyzed by nucleotide sequencing a fragment that spans one crossover point after amplification by the polymerase chain reaction. Four lines had the expected sequence, whereas two lines had small deletions abutting the 132-base-pair region of homology.
Immunobiologic differences between normal and leukemic human B-cell precursors.
Authors: Uckun F M , Ledbetter J A
Published: May 2006

The early stages of normal human B-cell differentiation were studied by flow cytometry and cell sorting based on expression of CD10 (CALLA) and CD19 antigens in fetal liver. Both CD10+ CD19+ and CD10+ CD19- precursor populations proliferated in vitro to form B-cell precursor colonies under stimulation from low molecular weight B-cell growth factor (L-BCGF) or recombinant interleukin 3 but did not respond to high molecular weight B-cell growth factor (H-BCGF). The colonies derived from the CD10+ CD19- fraction showed induction of CD19 expression in 10-50% of growing cells, suggesting that CD10 expression precedes CD19 expression in B-cell ontogeny. This hypothesis was corroborated by less-differentiated marker profiles of the progeny of CD10+ CD19- B-cell precursors as compared to CD10+ CD19+ B-cell precursors in BCGF-stimulated cultures and by higher percentages of CD10+CD19- versus CD10-CD19+ B-cell precursors. CD19 crosslinking on normal fetal liver or bone marrow B-cell precursors was associated with an increase in cytoplasmic calcium concentration, but was inhibitory for colony formation. Leukemic B-cell precursors from acute lymphoblastic leukemias (ALLs) differed from normal B-cell precursors in their in vitro proliferative responses, since (i) they responded not only to L-BCGF and rIL-3 but also to H-BCGF and (ii) their proliferation was stimulated rather than inhibited by CD19 crosslinking. A clonogenic leukemic counterpart for the CD10+CD19- normal B-cell precursor population does not exist among malignant cells from B-cell precursor ALL patients, suggesting that the CD19 receptor may be involved in leukemogenesis of human B-cell precursor ALL.
Thymocytes expressing CD8 differentiate into CD4+ cells following intrathymic injection.
Authors: Nikolić-Zugić J , Bevan M J
Published: May 2006

Based on the cell surface expression of CD4 and CD8 molecules, murine thymocytes can be divided into four populations: these include CD4-, CD8- double-negative and CD4+, CD8+ double-positive subpopulations, both of which consist largely of immature cells, and the single positive, CD4+ or CD8+, subsets that contain functional helper or killer cells, respectively. The double-negative subset contains precursors of the other three populations and can reconstitute the thymus following intravenous or intrathymic transfer into irradiated hosts. In an attempt to establish the sequence of CD4 and CD8 expression during intrathymic development, we investigated the differentiation potential of highly purified CD8+ thymocytes by using intravenous or intrathymic adoptive transfer. Unlike the double-negative thymocyte subset, CD8+ cells did not have the ability to home to the thymus following intravenous transfer. However, when CD8+ thymocytes were injected directly into the thymus, they increased in number and gave rise to CD4+, CD8+ double-positive and CD4+ single-positive progeny. Furthermore, the rate of appearance of CD4+ cells from injected CD8+ precursors was faster than from the double-negative subset. Cells expressing a high surface density of CD8 convert to double-positive and CD4+ progeny without increasing in number, whereas CD8+ cells expressing a low surface density of the marker expand greatly and give rise to differentiated progeny. The results suggest that CD8 expression is an intermediate step on the differentiation pathway of mature CD4+ T cells.
Secretion of functional antibody and Fab fragment from yeast cells.
Authors: Horwitz A H , Chang C P , Better M , Hellstrom K E , Robinson R R
Published: May 2006

We have constructed yeast strains that secrete functional mouse-human chimeric antibody and its Fab fragment into the culture medium. For chimeric whole antibody, cDNA copies of the chimeric light-chain and heavy-chain genes of an anti-tumor antibody were inserted into vectors containing the yeast phosphoglycerate kinase promoter, invertase signal sequence, and phosphoglycerate kinase polyadenylylation signal. Simultaneous expression of these genes in yeast resulted in secretion of properly folded and assembled chimeric antibody that bound to target cancer cells. Yeast chimeric antibody exhibited antibody-dependent cellular cytotoxicity activity but not complement-dependent cytotoxicity activity. For production of Fab fragments, a truncated heavy-chain (Fd) gene was created by introducing a stop codon near the codon for the amino acid at which papain digestion occurs. Simultaneous expression of the resulting chimeric Fd and light-chain genes in yeast resulted in secretion of properly folded and assembled Fab fragment that bound to target cancer cells.
Adenosine regulates the Ca2+ sensitivity of mast cell mediator release.
Authors: Lohse M J , Klotz K N , Salzer M J , Schwabe U
Published: May 2006

Mast cells release histamine and other mediators of allergy in response to stimulation of their IgE receptors. This release is generally thought to be mediated by an elevation of cytosolic Ca2+. Recent evidence suggests that there might be factors that modulate the coupling between Ca2+ levels and mediator release. The present report identifies adenosine as one such modulator. Adenosine and several of its metabolically stable analogues were shown to enhance histamine release from rat peritoneal mast cells in response to stimuli such as concanavalin A. Metabolizing endogenous adenosine with adenosine deaminase dampened the response to stimuli, whereas trapping endogenous adenosine inside mast cells with nucleoside-transport inhibitors markedly enhanced stimulated histamine release. The metabolically stable adenosine analogue 5'-(N-ethylcarboxamido)adenosine (NECA) did not affect the initial steps in the sequence from IgE-receptor activation to mediator release, which are generation of inositol trisphosphate and increase of cytosolic Ca2+. However, NECA did enhance the release induced in ATP-permeabilized cells by exogenous Ca2+, but it had no effect on the release induced by phorbol esters. These data suggest that adenosine sensitizes mediator release by a mechanism regulating stimulus-secretion coupling at a step distal to receptor activation and second-messenger generation.
Pituitary-specific expression and glucocorticoid regulation of a proopiomelanocortin fusion gene in transgenic mice.
Authors: Tremblay Y , Tretjakoff I , Peterson A , Antakly T , Zhang C X , Drouin J
Published: May 2006

The product of a single gene encoding proopiomelanocortin (POMC) is differentially processed to produce corticotropin and alpha-melanotropin in anterior and intermediate pituitary cells, respectively. Hormonal control of POMC gene transcription and of corticotropin or alpha-melanotropin release is also tissue-specific; for example, glucocorticoids specifically inhibit anterior but not intermediate pituitary POMC transcription. Outside the pituitary gland, very low levels of POMC mRNAs are present in brain, testes, ovaries, and placenta. We have used transgenic mice to identify POMC 5' flanking sequences that are sufficient for tissue-specific expression and glucocorticoid regulation in anterior and intermediate pituitary cells. Three lines of transgenic mice were established, each carrying 50-75 copies (per cell) of a chimeric rPOMCneo gene constituted of rat POMC promoter sequences and of bacterial neomycin-resistance coding sequence. High levels of rPOMCneo transcripts were detected in pituitaries of mice from all three lineages. In situ hybridization revealed that the ratio of intermediate to anterior pituitary transcripts was similar for the transgene and endogenous POMC mRNA. rPOMCneo transcripts were not detected in any other tissue except at very low levels in the testes in two transgenic lines. Endogenous mouse POMC mRNA increased in response to depletion of plasma glucocorticoids (adrenalectomy) and decreased after glucocorticoid treatment; rPOMCneo transcripts were altered to the same extent by these treatments in all three lines. Intermediate pituitary and testicular rPOMCneo transgene expression was not altered by these treatments. Thus, no more than 769 base pairs of the rat POMC promoter are required for pituitary-specific expression and for specific glucocorticoid inhibition of the POMC gene in the anterior pituitary.
Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4.
Authors: Pinkel D , Landegent J , Collins C , Fuscoe J , Segraves R , Lucas J , Gray J
Published: May 2006

Chromosomes can be specifically stained in metaphase spreads and interphase nuclei by in situ hybridization with entire chromosome-specific DNA libraries. Unlabeled human genomic DNA is used to inhibit the hybridization of sequences in the library that bind to multiple chromosomes. The target chromosome can be made at least 20 times brighter per unit length than the others. Trisomy 21 and translocations involving chromosome 4 can be detected in metaphase spreads and interphase nuclei by using this technique.
Synthesis and expression in Escherichia coli of the gene encoding monocyte-derived neutrophil-activating factor: biological equivalence between natural and recombinant neutrophil-activating factor.
Authors: Lindley I , Aschauer H , Seifert J M , Lam C , Brunowsky W , Kownatzki E , Thelen M , Peveri P , Dewald B , von Tscharner V
Published: May 2006

The neutrophil-activating factor (NAF) purified from the conditioned medium of lipopolysaccharide-stimulated human monocytes was sequenced and found to consist of 72 amino acids: SAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQRVVEKFLKRA ENS. Purified preparations of natural NAF contained, in addition to this main form, minor amounts of three amino-terminal variants with 77 (+AVLPR), 70, and 69 residues. A gene coding for the 72-amino acid NAF was synthesized, cloned, and expressed in Escherichia coli. Western (immunologic) blot analysis of crude bacterial extracts, with an antiserum raised against natural NAF, revealed a single band that comigrated with natural NAF. Recombinant NAF purified to homogeneity had identical amino- and carboxyl-terminal sequences to the 72-amino acid natural NAF. Recombinant NAF was tested on human neutrophils and had the same activity and potency as natural NAF in inducing chemotaxis, rapidly increasing cytosolic free Ca2+, activating the respiratory burst, and releasing specific and azurophilic granular contents.
Transformation of an interleukin 3-dependent hematopoietic cell line by the chronic myelogenous leukemia-specific P210bcr/abl protein.
Authors: Daley G Q , Baltimore D
Published: May 2006

The P210bcr/abl protein is associated with virtually every case of human chronic myelogenous leukemia. Unlike the related P160gag/v-abl oncogene product of Abelson murine leukemia virus, P210bcr/abl does not transform NIH 3T3 fibroblasts. To assess whether P210bcr/abl might transform hematopoietic cell types, retroviral constructs encoding P210bcr/abl were used to infect the bone marrow-derived interleukin 3-dependent Ba/F3 cell line. As for P160gag/v-abl, cell lines expressing P210bcr/abl were growth factor independent and tumorigenic in nude mice. No evidence for autocrine production of interleukin 3 by factor-independent cell lines was found. These experiments establish that P210bcr/abl can transform hematopoietic cell types to tumorigenicity.
Characterization of invasion plasmid antigen genes (ipaBCD) from Shigella flexneri.
Authors: Venkatesan M M , Buysse J M , Kopecko D J
Published: May 2006

The large invasion plasmid of Shigella flexneri M9OT-W was used to generate recombinant plasmids carrying the ipaA, -B, -C, and -D genes, whose products are associated with the entry of the bacteria into colonic epithelial cells. Complete DNA sequences of ipaB, -C, and -D were determined. The proteins predicted (62, 42, and 37 kDa, respectively) from the nucleotide sequences lack a signal-peptide sequence. Hydrophilic segments of the IpaB and IpaC proteins were found to overlap known epitopic domains of these membrane antigens. Analysis of total RNA demonstrated that temperature control of ipa gene expression occurs at the level of transcription. Multiple mRNA bands were detected by using ipa gene fragments as hybridization probes, and a putative transcript map for the ipa genes was constructed. Comparison of this map with the DNA sequence reveals a complex system of ipa gene regulation.
Antiserum raised against residues 159-168 of the guanine nucleotide-binding protein Gi3-alpha reacts with ependymal cells and some neurons in the rat brain containing cholecystokinin- or cholecystokinin- and tyrosine 3-hydroxylase-like immunoreactivities.
Authors: Cortés R , Hökfelt T , Schalling M , Goldstein M , Goldsmith P , Spiegel A , Unson C , Walsh J
Published: May 2006

Antibodies raised against a synthetic deca-peptide corresponding to a specific sequence of Gi3-alpha protein (an inhibitory guanine nucleotide-binding protein) were used to analyze Gi3-alpha-like immunoreactivity in brain sections from colchicine-treated rats by indirect immunofluorescence histochemistry. Gi3-alpha-peptide-positive cell bodies were found in the ventral tegmental area and substantia nigra, and these cells were also cholecystokinin (CCK)- and tyrosine 3-hydroxylase-positive. Gi3-alpha-peptide staining was observed in perikarya in the hippocampus and in fibers in the nucleus accumbens, tuberculum olfactorium, bed nucleus of stria terminalis, and a spino-thalamic tract, where it coexisted with CCK-like immunoreactivity as well. No coexistence with CCK occurred in Gi3-alpha-peptide-positive ependymal cells outlining the aqueduct and ventricles. Preadsorption of Gi3-alpha antibodies with CCK-8 or CCK-33 did not alter Gi3-alpha-peptide staining. The occurrence of Gi3-alpha-peptide-like immunoreactivity in CCK-containing neurons may indicate the presence of Gi3-alpha protein and in CCK/dopamine neurons may indicate an association of this Gi protein with dopamine autoreceptors.
Classification of the European language families by genetic distance.
Authors: Harding R M , Sokal R R
Published: May 2006

Genetic distances among speakers of the European language families were computed by using gene-frequency data for human blood group antigens, enzymes, and proteins of 26 genetic systems. Each system was represented by a different subset of 3369 localities across Europe. By subjecting the matrix of distances to numerical taxonomic procedures, we obtained a grouping of the language families of Europe by their genetic distances as contrasted with their linguistic relationships. The resulting classification largely reflects geographic propinquity rather than linguistic origins. This is evidence for the primary importance of short-range interdemic gene flow in shaping the modern gene pools of Europe. Yet, some language families--i.e., Basque, Finnic (including Lappish), and Semitic (Maltese)--have distant genetic relationships with their geographic neighbors. These results indicate that European gene pools still reflect the remote origins of some ethnic units subsumed by these major linguistic groups.
Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome.
Authors: Rebollo J E , François V , Louarn J M
Published: May 2006

Inversion of many predetermined segments of the Escherichia coli chromosome was attempted by using a system for in vivo selection of genomic rearrangements. Two types of constraints on these inversions were observed: (i) a sensitivity to rich medium when the distance between oriC and the 86- to 91-min region (which carries loci essential for transcription and translation) is increased; (ii) a poor viability or inviability of inversions having at least one endpoint in the one-third of the chromosome around replication terminators (with an exception for some inversions ending between these terminators). Although the first constraint is simply explained by a decreased dosage of the region involved, the second one may result from disruption of two long-range chromosomal organizations. The nondivisible zones thus disclosed coincide remarkably well with the two zones that we have previously described, which are polarized with respect to their replication. It is proposed that the two phenomena result from a sequence-dependent and polarized organization of the terminal region of the chromosome, which defines chromosome replication arms and may participate in nucleoid organization.
An inhibitor of the in vitro elongation reaction of simian virus 40 DNA replication is overcome by proliferating-cell nuclear antigen.
Authors: Lee S H , Ishimi Y , Kenny M K , Bullock P , Dean F B , Hurwitz J
Published: May 2006

The replication of simian virus 40 (SV40) origin-containing DNA has been reconstituted by using SV40 large tumor (T) antigen and cellular proteins purified from HeLa cells. This replication reaction is unaffected by proliferating-cell nuclear antigen (PCNA). In contrast, PCNA has been reported to stimulate SV40 DNA synthesis carried out with crude fractions [Prelich, G., Kostura, M., Marshak, D. R., Mathews, M. B. & Stillman, B. (1987) Nature (London) 326, 471-475]. This difference is caused by the presence of a protein in crude fractions that inhibits the elongation of nascent DNA chains during replication. In the presence of PCNA, crude fractions containing this elongation inhibition factor can extend DNA chains. We describe the partial purification of this inhibitor and show that its addition limited SV40 DNA replication to the synthesis of short chains, an effect reversed by the addition of PCNA. However, the reversal of the inhibition by PCNA in the SV40 system required additional protein fractions distinct from PCNA and the enzymes constituting the purified system. These results suggest that the PCNA-mediated effect on SV40 DNA replication may be indirect. Such an interplay between negative and positive regulatory functions including PCNA may contribute to the control of DNA synthesis characteristic of the eukaryotic cell cycle.
Isolation and characterization of a Xenopus laevis C protein cDNA: structure and expression of a heterogeneous nuclear ribonucleoprotein core protein.
Authors: Preugschat F , Wold B
Published: May 2006

The C proteins are major components of heterogeneous nuclear ribonucleoprotein complexes in nuclei of vertebrate cells. To begin to describe their structure, expression, and function we isolated and determined the DNA sequence of Xenopus laevis C protein cDNA clones. The protein predicted from the DNA sequence has a molecular mass of 30,916 kDa and is very similar to its human counterpart. Although mammalian genomes contain many copies of C protein sequence, the Xenopus genome contains few copies. When C protein RNA was synthesized in vitro and microinjected into stage-VI Xenopus oocytes, newly synthesized C proteins were efficiently localized in the nucleus. In vitro rabbit reticulocyte lysate and in vivo Xenopus oocyte translation systems both produce from a single mRNA two discrete polypeptide species that accumulate in a ratio similar to that of mammalian C1 and C2 proteins in vivo.
Analysis of clustered point mutations in the human ribosomal RNA gene promoter by transient expression in vivo.
Authors: Jones M H , Learned R M , Tjian R
Published: May 2006

We have mapped the cis regulatory elements required in vivo for initiation at the human rRNA promoter by RNA polymerase I. Transient expression in COS-7 cells was used to evaluate the transcription phenotype of clustered base substitution mutations in the human rRNA promoter. The promoter consists of two major elements: a large upstream region, composed of several domains, that lies between nucleotides -234 and -107 relative to the transcription initiation site and affects transcription up to 100-fold and a core element that lies between nucleotides -45 and +20 and affects transcription up to 1000-fold. The upstream region is able to retain partial function when positioned within 100-160 nucleotides of the transcription initiation site, but it cannot stimulate transcription from distances of greater than or equal to 600 nucleotides. In addition, we demonstrate, using mouse-human hybrid rRNA promoters, that the sequences responsible for human species-specific transcription in vivo appear to reside in both the core and upstream elements, and sequences from the mouse rRNA promoter cannot be substituted for them.
Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences.
Authors: Eisenberg S , Civalier C , Tye B K
Published: May 2006

We have isolated a protein from Saccharomyces cerevisiae that binds specifically to a nucleotide sequence associated with the autonomously replicating sequence (ARS) ARS120, located in the telomeric region of a yeast chromosome. "Footprinting" analysis revealed that a 26-base-pair DNA sequence, 5'-CAAGTGCCGTGCATAATGATGTGGGT-3', was protected by this protein from DNase I digestion. A plasmid containing 48 direct tandem repeats of this oligonucleotide was constructed and used to affinity-purify the binding activity. The purified protein, OBF1 (origin binding factor), showed specific binding to ARS120. The 26-base-pair OBF1-protected sequence was sufficient for the recognition and binding of the protein, since the mobility of a DNA fragment containing the synthetic binding site was retarded in agarose gels when incubated with OBF1. By performing competition experiments with a number of different ARSs, we showed that OBF1 binds tightly to some but not all ARSs. Interestingly, OBF1 does not appear to have a discernible affinity for ARS1 or the ARSs associated with mating type loci, HML alpha and HMRa, which are substrates for a DNA-binding activity reported by others. Since OBF1 appears to bind to DNA associated with a number of ARSs, we suggest that this protein may have a function related to ARS activity, perhaps in the initiation of DNA replication at selected ARSs.
Mobility of the human T lymphocyte surface molecules CD3, CD4, and CD8: regulation by a cAMP-dependent pathway.
Authors: Kammer G M , Boehm C A , Rudolph S A , Schultz L A
Published: May 2006

The present study was undertaken to determine whether a cAMP pathway mediates the mobility of CD3, CD4, and CD8 within the membrane. Crosslinking CD3, CD4, and CD8 with monoclonal antibody and anti-antibody induced rapid accumulation of intracellular cAMP, occupancy of cAMP receptors, and was temporally associated with the mobilization and directed movement of these molecules to a pole of the cell. This capping process could be partially inhibited in a dose-dependent manner by treatment of T cells with 2',5'-dideoxyadenosine, a ribose-modified adenosine analogue that binds to the P site of the catalytic subunit of adenylate cyclase and reduces adenylate cyclase activity. Furthermore, inhibition of cAMP-dependent endogenous phosphorylation of 17.5-kDa, 23/25-kDa, and 33.5-kDa bands in intact T cells by N-[2-(methylamino)ethyl]-5-isoquinoline-sulfonamide, a cell-permeable inhibitor of cyclic nucleotide-dependent protein kinase, blocked the capping event. Data support the conclusion that crosslinking of CD3, CD4, and CD8 activates a cAMP-dependent pathway that mediates the mobilization and directed movement of these molecules. cAMP-dependent protein phosphorylation is an integral step leading to the capping process.
Normal polymorphic variations and transcription of the decay accelerating factor gene in paroxysmal nocturnal hemoglobinuria cells.
Authors: Stafford H A , Tykocinski M L , Lublin D M , Holers V M , Rosse W F , Atkinson J P , Medof M E
Published: May 2006

In paroxysmal nocturnal hemoglobinuria (PNH), an acquired hemolytic anemia, deficiency of decay accelerating factor (DAF) renders blood cells susceptible to increased deposition of autologous complement activation fragments (C3b) and complemented-mediated injury. To investigate the mechanism of the DAF defect, DNA and mRNA from normal and PNH leukocytes were compared in blot hybridization assays by using DAF cDNA and oligonucleotide probes. Southern analyses of DNA from normal cells revealed a single gene spanning approximately equal to 35 kilobases of DNA. Six HindIII banding patterns were distinguishable among normal individuals. In family studies, the patterns segregated as three homozygous and three heterozygous genotypes deriving from three haplotypes: A, B, and C with frequencies of 0.47, 0.36, and 0.17, respectively. Oligonucleotide mapping localized the polymorphic HindIII sites to two noncoding regions in the vicinity of exons encoding (i) the protein oligosaccharide-rich domain and (ii) the mRNA 3'-untranslated region. Analyses of DNA from DAF-negative leukocytes of eight PNH patients demonstrated restriction fragment profiles identical to those of normal individuals for all enzymes studied. Three patients had the BC (normals = 3/32), three patients had the AA (normals = 6/32), and two patients had the AC (normals = 8/32) HindIII genotype. Of the three PNH patients exhibiting the BC genotype, family studies of two demonstrated the expected inheritance patterns, and RNA gel blot analyses of two showed mRNA transcripts indistinguishable from those in normal cells. The absence of DAF gene or mRNA alterations in affected PNH cells that lack other glycolipid-anchored proteins as well as DAF argues that the lesion underlying PNH cells resides in the glycolipid-anchor pathway.
Molecular cloning of amyloid cDNA derived from mRNA of the Alzheimer disease brain: coding and noncoding regions of the fetal precursor mRNA are expressed in the cortex.
Authors: Zain S B , Salim M , Chou W G , Sajdel-Sulkowska E M , Majocha R E , Marotta C A
Published: May 2006

To gain insight into factors associated with the excessive accumulation of beta-amyloid in the Alzheimer disease (AD) brain, the present studies were initiated to distinguish between a unique primary structure of the AD-specific amyloid precursor mRNA vis a vis other determinants that may affect amyloid levels. Previous molecular cloning experiments focused on amyloid derived from sources other than AD cases. In the present work, we cloned and characterized amyloid cDNA derived directly from AD brain mRNA. Poly(A)+ RNA from AD cortices was used for the preparation of lambda gt11 recombinant cDNA libraries. An insert of 1564 nucleotides was isolated that included the beta-amyloid domain and corresponded to 75% of the coding region and approximately equal to 70% of the 3'-noncoding region of the fetal precursor amyloid cDNA reported by others. On RNA blots, the AD amyloid mRNA consisted of a doublet of 3.2 and 3.4 kilobases. In control and AD cases, the amyloid mRNA levels were nonuniform and were independent of glial-specific mRNA levels. Based on the sequence analysis data, we conclude that a segment of the amyloid gene is expressed in the AD cortex as a high molecular weight precursor mRNA with major coding and 3'-noncoding regions that are identical to the fetal brain gene product.
Cloning and chromosomal assignment of a human cDNA encoding a T cell- and natural killer cell-specific trypsin-like serine protease.
Authors: Gershenfeld H K , Hershberger R J , Shows T B , Weissman I L
Published: May 2006

A cDNA clone encoding a human T cell- and natural killer cell-specific serine protease was obtained by screening a phage lambda gt10 cDNA library from phytohemagglutinin-stimulated human peripheral blood lymphocytes with the mouse Hanukah factor cDNA clone. In an RNA blot-hybridization analysis, this human Hanukah factor cDNA hybridized with a 1.3-kilobase band in allogeneic-stimulated cytotoxic T cells and the Jurkat cell line, but this transcript was not detectable in normal muscle, liver, tonsil, or thymus. By dot-blot hybridization, this cDNA hybridized with RNA from three cytolytic T-cell clones and three noncytolytic T-cell clones grown in vitro as well as with purified CD16+ natural killer cells and CD3+, CD16- T-cell large granular lymphocytes from peripheral blood lymphocytes (CD = cluster designation). The nucleotide sequence of this cDNA clone encodes a predicted serine protease of 262 amino acids. The predicted protein has a 22-amino acid presegment, a 6-amino acid prosegment, and an active enzyme of 234 amino acids with a calculated unglycosylated molecular weight of 25,820. The active enzyme is 71% and 77% similar to the mouse sequence at the amino acid and DNA level, respectively. The human and mouse sequences conserve the active site residues of serine proteases--the trypsin-specific Asp-189 and all 10 cysteine residues. The gene for the human Hanukah factor serine protease is located on human chromosome 5. We propose that this trypsin-like serine protease may function as a common component necessary for lysis of target cells by cytotoxic T lymphocytes and natural killer cells.
Pumiliotoxin B binds to a site on the voltage-dependent sodium channel that is allosterically coupled to other binding sites.
Authors: Gusovsky F , Rossignol D P , McNeal E T , Daly J W
Published: May 2006

Pumiliotoxin B (PTX-B), an alkaloid that has cardiotonic and myotonic activity, increases sodium influx in guinea pig cerebral cortical synaptoneurosomes. In the presence of scorpion venom (Leiurus) or purified alpha-scorpion toxin, the PTX-B-induced sodium influx is enhanced severalfold. PTX-B alone has no effect on sodium flux in N18 neuroblastoma cells but, in the presence of alpha-scorpion toxin, stimulation of sodium influx by PTX-B reaches levels comparable to that attained with the sodium channel activator veratridine. In neuroblastoma LV9 cells, a variant mutant that lacks sodium channels, neither veratridine nor PTX-B induces sodium fluxes in either the presence or absence of alpha-scorpion toxin. In synaptoneurosomes and in N18 cells, the sodium influx induced by the combination of PTX-B and alpha-scorpion toxin is inhibited by tetrodotoxin and local anesthetics. PTX-B does not interact with two of the known toxin sites on the sodium channel, as evidenced by a lack of effect on binding of [3H]saxitoxin or [3H]batrachotoxinin A benzoate to brain synaptoneurosomes. Synergistic effects on sodium influx with alpha-scorpion toxin, beta-scorpion toxin, and brevetoxin indicate that PTX-B does not interact directly with three other toxin sites on the sodium channel. Thus, PTX-B appears to activate sodium influx by interacting with yet another site on the voltage-dependent sodium channel, a site that is coupled allosterically to sites for alpha-scorpion toxin, beta-scorpion toxin, and brevetoxin.
Sequence-specific binding and photocrosslinking of alpha and beta oligodeoxynucleotides to the major groove of DNA via triple-helix formation.
Authors: Praseuth D , Perrouault L , Le Doan T , Chassignol M , Thuong N , Hélène C
Published: May 2006

A photocrosslinking reagent (p-azidophenacyl) was covalently linked to an octathymidylate synthesized with either the natural (beta) anomer of thymidine or the synthetic (alpha) anomer. The oligothymidylate was further substituted by an acridine derivative to stabilize the hybrid formed with a complementary octadeoxyadenylate sequence via intercalation. A single-stranded 27-mer containing a (dA)8 sequence and a 27-mer duplex containing a (dA.dT)8 sequence were used as targets. Upon UV irradiation, photocrosslinking of the octathymidylate to its target sequence was observed, generating bands that migrated more slowly in denaturing gels. In the 27-mer duplex, both strands were photocrosslinked to the octathymidylate. Upon alkaline treatment of the irradiated samples, cleavage of the 27-mers was observed at specific sites. These reactions were analyzed at different salt concentrations. The location of the cleavage sites allowed us to demonstrate the following. (i) Both alpha and beta oligothymidylates can recognize a DNA double helix containing an oligo(dA).oligo(dT) sequence; the oligothymidylate binds to the major groove of DNA in a parallel orientation with respect to the adenine-containing strand of the DNA double helix. (ii) alpha oligothymidylates form helices with a complementary single-stranded oligodeoxyadenylate; the two strands have a parallel orientation independently of whether or not an intercalating agent is attached to the oligothymidylate. (iii) At low salt concentration, beta oligothymidylates form a double helix with an oligodeoxyadenylate in which, as expected, the two strands are antiparallel; at high salt concentration, a triple helix is formed in which the second oligothymidylate is oriented parallel to the adenine-containing strand. These results show that it is possible to recognize an oligopurine.oligopyrimidine sequence in a DNA double helix via local triple-helix formation and to target photochemical reactions to specific sequences in both double-stranded and single-stranded nucleic acids.
Yeast RNase P: catalytic activity and substrate binding are separate functions.
Authors: Nichols M , Söll D , Willis I
Published: May 2006

During tRNA biosynthesis the 5'-leader sequences in precursor tRNAs are removed by the ribonucleoprotein RNase P, an enzyme whose RNA moiety is required for activity. To clarify some aspects of the enzyme mechanism, we examined substrate binding and product formation with mutant precursor tRNAs. Mutations G-1----A or U-2----C in the Schizosaccharomyces pombe sup3-e tRNASer, which cause mispairing at or near the top of the acceptor stem, prevent the removal of the 5'-leader sequences by Saccharomyces cerevisiae RNase P. Equilibrium binding studies involving specific gel retardation of RNase P-precursor tRNA complexes showed that complexes with wild-type and A-1 and C-2 mutant precursor tRNAs had very similar dissociation constants (average Kd for sup3 = 1.5 +/- 0.2 nM). Thus, the 5'-terminal nucleotides of mature tRNA, on the 3' proximal side of the RNase P cleavage site, affect the enzyme's catalytic function but not substrate binding. The catalytic integrity of the RNA component of RNase P is not essential for binding of tRNA precursors, as demonstrated by gel retardation of micrococcal nuclease-inactivated enzyme. This suggests a possible role for the protein component of the enzyme in substrate binding. Upon restoration of base pairing to the acceptor stem in the A-1 or C-2 mutants, we found that, in addition to a requirement for pairing at these positions, conservation of the wild-type first and second nucleotides of the tRNA was necessary to obtain maximal cleavage by RNase P. This indicates a distinct sequence preference of this enzyme.
Stabilization of type I topoisomerase-DNA covalent complexes by actinomycin D.
Authors: Trask D K , Muller M T
Published: May 2006

The activity of the endogenous DNA topoisomerase type I (EC 5.99.1.2) can be quantified in situ by determining how efficiently the enzyme is trapped in a covalent complex with DNA upon lysis of nuclei with detergents. In this way, we can measure relative levels of topoisomerase binding to DNA at native sites in chromatin. Since the majority of topoisomerase I is localized in the nucleolus at rRNA genes, we have evaluated how low levels of actinomycin D, which terminate transcription of rRNA genes, affect the activity of topoisomerase I. In vivo, as well as in vitro with purified topoisomerase I, we have found that drug treatment extends the half-life of the covalent topoisomerase-DNA complex. Actinomycin D stabilizes the nicked intermediate in the cleavage and resealing reaction but otherwise does not significantly alter the strand-passing ability of topoisomerase I. Sequence-specific cleavages by topoisomerase I were stimulated by actinomycin D at identical sequences recognized by the enzyme in the absence of drug. The localization of topoisomerase I in the nucleolus, coupled with the observation that transcription in this organelle is highly sensitive to actinomycin D and camptothecin treatment, leads us to propose that topoisomerase I contributes to actinomycin D inhibition of transcription.
Transcellular proton current in Achlya bisexualis hyphae: relationship to polarized growth.
Authors: Schreurs W J , Harold F M
Published: May 2006

Growing hyphae of Achlya bisexualis drive an electric current through themselves, such that positive charge flows into the apical region (the anterior 300 micron) and exits distally along the hyphal trunk. They also generate a gradient of extracellular pH, such that the medium surrounding the apex is slightly alkaline whereas that along the hyphal trunk is acid. To explore the genesis of these gradients and their relationship to polarized extension, we examined the effects of changes in the composition of the growth medium. The transcellular electric current was most pronounced in medium rich in amino acids. In leaner medium, containing limited amounts of amino acids or none at all, the current was attenuated or absent. We interpret the results to mean that inward current represents H+/amino acid symport, mediated by porters that are preferentially localized in the apical region. Apical alkalinity may be due to ammonia production. Outward current, and perhaps also the generation of metabolic acid, reflects the distribution of the H+-ATPase, which is excluded from the apex but is abundant along the hyphal trunk. Thanks to the spatial segregation of transport functions, protons characteristically flow into the apical region. However, since hyphae grow apically and at the same rate despite wide variations in current pattern, the flow of electric charge through the hyphae cannot be required to polarize extension or to localize the tip.
Immunoglobulin heavy chain variable region gene evolution: structure and family relationships of two genes and a pseudogene in a teleost fish.
Authors: Wilson M R , Middleton D , Warr G W
Published: May 2006

Nucleotide sequences for two immunoglobulin heavy chain variable region (VH) genes and one pseudogene in the goldfish (Carassius auratus) and the family relationships and distribution of these genes in individual fish are presented. Comparison of the nucleotide and inferred amino acid sequences of goldfish and other vertebrate VH genes indicates that goldfish VH genes show the major VH gene regulatory and structural features (5'-putative promoter region, split hydrophobic leader, three framework and two complementarity-determining regions, and 3'-recombination signals for VH to diversity region joining) and that goldfish VH genes are not more closely related to one another than they are to VH genes of evolutionarily distant vertebrates such as the mammals. Goldfish VH genes appear to exist in distinct families, and individual goldfish can carry from none to apparently greater than 15 genes of a given family. These results suggest that whereas the basic structure of VH genes has been conserved in evolution, there may be substantial variation in the nature and population distribution of VH gene families in the vertebrates.
Consistent chromosome 3p deletion and loss of heterozygosity in renal cell carcinoma.
Authors: Kovacs G , Erlandsson R , Boldog F , Ingvarsson S , Müller-Brechlin R , Klein G , Sümegi J
Published: May 2006

Renal cell carcinoma (RCC) and normal kidney tissues have been examined from 34 patients with sporadic, nonhereditary RCC. Eighteen of the 21 cytogenetically examined tumors (86%) had a detectable anomaly of chromosome arm 3p distal to band 3p11.2-p13, manifested as a deletion, combined with the nonreciprocal translocation of a segment from another chromosome or monosomy 3. Restriction-fragment-length polymorphism analysis showed loss of D1S1 heterozygosity in 16 of the 21 cases (76%). D3S2 heterozygosity was lost in 2 of 11 cases (18%). The variability of the breakpoint between 3p11.2 and 3p13 and the absence of a consistently translocated segment from another chromosome suggests a genetic-loss mechanism, while the activation of a dominant oncogene appears less likely. Together with the previously demonstrated involvement of the 3p14.2 region in a familial case, these findings suggest that RCCs may arise by the deletion of a "recessive cancer gene," as do retinoblastoma and Wilms tumor. The relevant locus must be located on the telomeric side of the D1S1 locus on the short arm of chromosome 3.
Enhancement of synaptic potentials in rabbit CA1 pyramidal neurons following classical conditioning.
Authors: LoTurco J L , Coulter D A , Alkon D L
Published: May 2006

A synaptic potential elicited by high-frequency stimulation of the Schaffer collaterals was enhanced in hippocampal CA1 pyramidal cells from rabbits that were classically conditioned relative to cells from control rabbits. In addition, confirming previous reports, the after-hyperpolarization was reduced in cells from conditioned animals. We suggest that reduced after-hyperpolarization and enhanced synaptic responsiveness in cells from conditioned animals work in concert to contribute to the functioning of hippocampal CA1 pyramidal cells during classical conditioning.