bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of gene expression in single live neurons.
Authors: Eberwine J , Yeh H , Miyashiro K , Cao Y , Nair S , Finnell R , Zettel M , Coleman P
Published: May 2006

We present here a method for broadly characterizing single cells at the molecular level beyond the more common morphological and transmitter/receptor classifications. The RNA from defined single cells is amplified by microinjecting primer, nucleotides, and enzyme into acutely dissociated cells from a defined region of rat brain. Further processing yields amplified antisense RNA. A second round of amplification results in greater than 10(6)-fold amplification of the original starting material, which is adequate for analysis--e.g., use as a probe, making of cDNA libraries, etc. We demonstrate this method by constructing expression profiles of single live cells from rat hippocampus. This profiling suggests that cells that appear to be morphologically similar may show marked differences in patterns of expression. In addition, we characterize several mRNAs from a single cell, some of which were previously undescribed, perhaps due to "rarity" when averaged over many cell types. Electrophysiological analysis coupled with molecular biology within the same cell will facilitate a better understanding of how changes at the molecular level are manifested in functional properties. This approach should be applicable to a wide variety of studies, including development, mutant models, aging, and neurodegenerative disease.
Expression, regulation, and chromosomal localization of the Max gene.
Authors: Wagner A J , Le Beau M M , Diaz M O , Hay N
Published: May 2006

The Max gene encodes a protein that interacts specifically with the Myc protein to form a heterodimer with high affinity for the specific cognate DNA binding site of Myc. Here we examine the expression of Max RNA in comparison to Myc RNA during cell growth and differentiation. Two species of RNA, a major 2.0- and a minor 1.7-kilobase species, hybridized specifically to a Max cDNA probe in all human and murine cell lines that were tested. Unlike Myc, the steady-state level of Max RNA is not significantly modulated with respect to proliferation or differentiation. Max RNA is expressed in quiescent BALB/c 3T3 cells and is modestly increased 3 h after addition of serum to the quiescent cells. In contrast to Myc RNA, Max RNA does not decline immediately upon induction of differentiation of HL60 cells by dimethyl sulfoxide, and only a modest decrease of Max RNA was observed 72 h after induction of differentiation. Unlike Myc RNA, Max RNA is relatively stable with a half-life of greater than 3 h and, therefore, does not exhibit the characteristic short half-life of RNAs encoded by most immediate early genes. The human Max gene was localized to chromosome 14, band q23. With respect to the recurring abnormalities in human tumors, this region of chromosome 14 is involved in deletions in B-cell chronic lymphocytic leukemia and malignant lymphomas and in the 12;14 translocation in uterine leiomyomas.
Targeted cleavage of mRNA in vitro by RNase P from Escherichia coli.
Authors: Li Y , Guerrier-Takada C , Altman S
Published: May 2006

External guide sequences (EGSs) complementary to mRNAs that encode beta-galactosidase from Escherichia coli and nuclease A from Staphylococcus aureus can target these RNAs for cleavage in vitro by RNase P from E. coli. Specific cleavage occurs at locations predicted by the nucleotide sequences of the EGSs. EGSs with regions complementary to the mRNAs that are as short as 13 nucleotides function efficiently and turn over slowly during incubation with the target substrate and the enzyme. EGSs composed of deoxyribonucleotides as well as those composed of ribonucleotides are effective, but cleavage of the targeted substrate with DNA as an EGS is about 10-fold less efficient than that with RNA as an EGS. An RNA EGS inhibited the formation of beta-galactosidase activity in a crude extract (S30) of E. coli that was capable of catalyzing coupled transcription-translation reactions.
GLUT4 facilitates insulin stimulation and cAMP-mediated inhibition of glucose transport.
Authors: Lawrence J C , Piper R C , Robinson L J , James D E
Published: May 2006

The glucose transporter isoform GLUT4 is found only in cells that exhibit insulin-sensitive glucose transport. To investigate the function of this transporter, L6 myoblasts were stably transfected with GLUT4 cDNA. GLUT4 underwent insulin-dependent movement to the cell surface in myoblasts overexpressing the transporter. One cell line (243-6) expressed sufficient levels of the GLUT4 protein to study insulin-dependent glucose transport. Unlike wild-type L6 cells, 243-6 myoblasts exhibited two features that are characteristic of differentiated muscle fibers and adipocytes in vivo: a large insulin-stimulated component of glucose transport and inhibition of this stimulated component by cAMP. Relative to normal L6 cells, 243-6 cells responded to insulin or insulin-like growth factor 1 with a 5-fold larger increase in 2-deoxy[3H]glucose uptake. N6,O2'-Dibutyryladenosine 3',5'-cyclic monophosphate (Bt2cAMP) did not inhibit transport in normal L6 myoblasts, which express only GLUT1, but inhibited IGF-1/insulin-stimulated transport by 50% in 243-6 cells. The effect of cAMP was investigated further by using Chinese hamster ovary cells transiently expressing GLUT1 and GLUT4. Bt2cAMP inhibited glucose transport only in Chinese hamster ovary cells expressing GLUT4. These results indicate that cAMP-mediated inhibition of glucose transport is dependent on expression of the GLUT4 isozyme.
Alternative splicing of HLA-G transcripts yields proteins with primary structures resembling both class I and class II antigens.
Authors: Ishitani A , Geraghty D E
Published: May 2006

We have investigated HLA-G mRNA expression in cells and tissues expressing the gene. This analysis has demonstrated that the HLA-G primary transcript is alternatively spliced to yield at least three distinct mature mRNAs. Sequencing of the transcripts has shown that the largest mRNA is essentially that previously characterized, encoding a leader sequence, three external domains, a transmembrane region, and a cytoplasmic sequence. Of the two smaller messages, a 900-base mRNA does not include exon 3, resulting in a predicted protein sequence with the alpha 1 and alpha 3 external domains joined. The smallest mRNA results from splicing out exons 3 and 4, connecting the alpha domain directly to the transmembrane sequence. Alternative splicing of HLA-G mRNA was found in placental tissues and in eye tissue as well as in HLA-G-transfected cell lines. In term placental tissue the smallest mRNA appeared to be more abundant than the full-length form, while in a cell line derived from an earlier developmental stage the larger form predominated. Immunoprecipitation of [35S]methionine-labeled cell lysates showed that three different HLA-G proteins were present in transfected cells, with sizes corresponding to those predicted from the three alternative mRNA sequences. These findings are discussed in terms of potential functions of the alternative HLA-G proteins.
Preferential hydroxylation by the chemical nuclease meso-tetrakis-(4-N-methylpyridiniumyl)porphyrinatomanganeseIII pentaacetate/KHSO5 at the 5' carbon of deoxyriboses on both 3' sides of three contiguous A.T base pairs in short double-stranded oligonucleotides.
Authors: Pitié M , Pratviel G , Bernadou J , Meunier B
Published: May 2006

Selected double-stranded oligodeoxyribonucleotides have been used to probe, at the molecular level, DNA chain breakages induced by the chemical nuclease mesotetrakis(4-N- methylpyridiniumyl)porphyrinatomanganeseIII pentaacetate/KHSO5. The results show that cleavage selectively occurs on the two 3' sides of three contiguous A.T base pairs (an A.T triplet). Hydroxylation at 5' carbon of the deoxyribose targets represents the initial damage on the sugar-phosphodiester backbone and leaves a 3' phosphate and a 5' aldehyde at the ends. The fragments were separated by HPLC and unambiguously identified through chemical and biochemical reactions and/or sequencing after enzymatic conversion to mononucleosides. Also studied was the degradation of a 22-nucleotide DNA molecule containing two A.T triplets. Gel electrophoresis analyses on the corresponding 5'-32P-end-labeled substrate supported the above cleavage specificity and mechanism.
DNA systematics and evolution of the artiodactyl family Bovidae.
Authors: Allard M W , Miyamoto M M , Jarecki L , Kraus F , Tennant M R
Published: May 2006

Nine additional sequences from representatives of different tribes of the family Bovidae were combined with six published artiodactyl sequences to provide orthologous mtDNA for investigation of bovid phylogeny and evolution. Each species was represented by a homologous 2.7-kilobase-pair stretch of mtDNA for the complete 12S and 16S rRNA genes and three adjacent tRNA genes. These data, when compared to other results, provided evidence for a monophyletic Bovidae and for two clades within the family: one including the tribes Boselaphini, Bovini, and Tragelaphini and another for an Antilopini/Neotragini grouping. All other intrafamilial relationships were only weakly supported. These sequence comparisons suggest that most bovid tribes originated early in the Miocene with all extant lineages present by approximately 16-17 million years ago. Thus, bovid tribes provide an example of rapid cladogenesis, following the origin of families in the infraorder Pecora.
Enzymatic defect in "X-linked" sideroblastic anemia: molecular evidence for erythroid delta-aminolevulinate synthase deficiency.
Authors: Cotter P D , Baumann M , Bishop D F
Published: May 2006

Recently, the human gene encoding erythroid-specific delta-aminolevulinate synthase was localized to the chromosomal region Xp21-Xq21, identifying this gene as the logical candidate for the enzymatic defect causing "X-linked" sideroblastic anemia. To investigate this hypothesis, the 11 exonic coding regions of the delta-aminolevulinate synthase gene were amplified and sequenced from a 30-year-old Chinese male with a pyridoxine-responsive form of X-linked sideroblastic anemia. A single T----A transition was found in codon 471 in a highly conserved region of exon 9, resulting in an Ile----Asn substitution. This mutation interrupted contiguous hydrophobic residues and was predicted to transform a region of beta-sheet structure to a random-coil structure. Prokaryotic expression of the normal and mutant cDNAs revealed that the mutant construct expressed low levels of enzymatic activity that required higher concentrations of pyridoxal 5'-phosphate to achieve maximal activation than did the normal enzyme. The amino acid substitution occurred in the exon containing the putative pyridoxal 5'-phosphate binding site and may account for the reduced ability of the cofactor to catalyze the formation of delta-aminolevulinic acid.
A genetic system for studying the activity of a proteolytic enzyme.
Authors: Dasmahapatra B , DiDomenico B , Dwyer S , Ma J , Sadowski I , Schwartz J
Published: May 2006

We describe a genetic system for monitoring the activity of a specific proteolytic enzyme by taking advantage of the properties of the yeast transcriptional activator GAL4. The GAL4 protein contains two separable and functionally essential domains: the amino-terminal DNA binding domain and the carboxyl-terminal transcriptional activating domain. We constructed two hybrid proteins by inserting between the DNA binding domain and the activation domain of GAL4 either (i) a self-cleaving protease (3C protease of a picornavirus, coxsackievirus B3) or (ii) a mutant form of the protease that is unable to cleave. We show that, although the hybrid protein containing the mutant protease activates transcription of GAL1-lacZ reporter gene, the hybrid protein bearing the wild-type protease is proteolytically cleaved and fails to activate transcription. Our approach to monitor the proteolytic activity could be used to develop simple genetic systems to study other proteases.
Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein.
Authors: Babitzke P , Yanofsky C
Published: May 2006

We have reconstituted Bacillus subtilis trp attenuation in vitro. Purification of the mtrB gene product (TRAP) to near homogeneity allowed us to demonstrate that addition of this protein plus L-tryptophan to template, RNA polymerase, and nucleoside triphosphates caused transcription termination in the trpEDCFBA leader region. TRAP acts by binding to the nascent transcript and preventing formation of an RNA antiterminator structure, thereby allowing terminator formation and transcription termination. Oligonucleotides complementary to segments of the antiterminator were used to demonstrate that formation of this RNA hairpin was responsible for transcription read-through. TRAP was found to be a 60-kDa multimeric protein composed of identical 6- to 8-kDa subunits, and its elution profile on a chromatographic column did not change in the presence of tryptophan.
Serologic response to the Borrelia burgdorferi flagellin demonstrates an epitope common to a neuroblastoma cell line.
Authors: Fikrig E , Berland R , Chen M , Williams S , Sigal L H , Flavell R A
Published: May 2006

Antibodies in sera of 7 patients with neurologic manifestations of Lyme borreliosis and a monoclonal antibody (mAb H9724) to the flagellin of Borrelia burgdorferi have been shown to bind neural tissue. To identify the antibody binding site common to the B. burgdorferi flagellin and the neural tissue, we made recombinant fusion proteins expressing epitopes of flagellin. Antibodies in patients' sera and mAb H9724 bound within an 18-amino acid epitope (residues 208-225) in the central region of flagellin, whereas two other mAbs bound to epitopes mapping elsewhere in the protein. Antibodies in patients sera and mAb H9724 also bound to a human neuroblastoma cell line. Absorption of patients sera with a peptide, EGVQQEGAQQPA, corresponding to amino acids 213-224 of flagellin, inhibited binding to the neuroblastoma cell line. The data suggest that the immune response to a specific B-cell epitope within flagellin, shared by a human neuroblastoma cell line, may be involved in the pathogenesis of neuroborreliosis.
Reversible loss of dendritic spines and altered excitability after chronic epilepsy in hippocampal slice cultures.
Authors: Müller M , Gähwiler B H , Rietschin L , Thompson S M
Published: May 2006

The morphological and functional consequences of epileptic activity were investigated by applying the convulsants bicuculline and/or picrotoxin to mature rat hippocampal slice cultures. After 3 days, some cells in all hippocampal subfields showed signs of degeneration, including swollen somata, vacuolation, and dendritic deformities, whereas others displayed only a massive reduction in the number of their dendritic spines. Intracellular recordings from CA3 pyramidal cells revealed a decrease in the amplitude of evoked excitatory synaptic potentials. gamma-Aminobutyric acid-releasing interneurons and inhibitory synaptic potentials were unaffected. Seven days after withdrawal of convulsants, remaining cells possessed a normal number of dendritic spines, thus demonstrating a considerable capacity for recovery. The pathological changes induced by convulsants are similar to those found in the hippocampi of human epileptics, suggesting that they are a consequence, rather than a cause, of epilepsy.
Characterization of a G-protein-regulated outward K+ current in mesophyll cells of vicia faba L.
Authors: Li W , Assmann S M
Published: May 2006

Whole-cell voltage-dependent currents in isolated mesophyll protoplasts of Vicia faba were investigated by patch-clamp techniques. With 104 mM K+ in the cytosol and 13 mM K+ in the external solution, depolarization of the plasma membrane from -47 mV to potentials between -15 and +85 mV activated a voltage- and time-dependent outward current (Iout). The average magnitude of Iout at +85 mV was 28.5 +/- 3.3 pA.pF-1. No inward voltage-dependent current was observed upon hyperpolarization of the plasma membrane from -55 mV to potentials as negative as -175 mV. Time-activated outward current was blocked by Ba2+ (1 mM BaCl2) and was not observed when K+ was eliminated from the external and internal solutions, indicating that this outward current was carried primarily by K+ ions. The voltage dependency of outward K+ current revealed a possible mechanism for K+ efflux from mesophyll cells. A GDP analogue guanosine 5'-[beta-thio]diphosphate (500 microM) significantly enhanced outward K+ current. The outward K+ current was inhibited by the GTP analogue guanosine 5'-[gamma-thio]triphosphate (500 microM) and by an increase in cytoplasmic free Ca2+ concentrations. Cholera toxin, which ADP-ribosylates guanine nucleotide-binding regulatory proteins, also inhibited outward K+ current. These findings illustrate the presence in mesophyll cells of outward-rectifying K+ channels that are regulated by GTP-binding proteins and calcium.
Glutathione ester delays the onset of scurvy in ascorbate-deficient guinea pigs.
Authors: Mårtensson J , Han J , Griffith O W , Meister A
Published: May 2006

Previous studies showed that administration of ascorbate to glutathione (GSH)-deficient newborn rats and guinea pigs prevented toxicity and mortality and led to increased tissue and mitochondrial GSH levels; ascorbate thus spares GSH. In the present work, we tried to answer the converse question: Does administration of GSH spare ascorbate? Because administered GSH is not well transported into most cells, we gave GSH monoethyl ester (which is readily transported and converted into GSH intracellularly) to guinea pigs fed an ascorbate-deficient diet. We found that treatment with GSH ester significantly delays appearance of the signs of scurvy and that this treatment spares ascorbate; thus, the decrease of tissue levels of ascorbate was delayed. The findings support the conclusions that (i) GSH is essential for the physiological function of ascorbate because it is required in vivo for reduction of dehydroascorbate and (ii) there is metabolic redundancy and overlap of the functions of these antioxidants. The sparing effect of GSH in scurvy may be mediated through an increase in the reduction of dehydroascorbate (which would otherwise be degraded) and to antioxidant effects of GSH that are also produced by ascorbate. Other studies indicate that GSH deficiency in adult mice stimulates ascorbate synthesis in liver. During this work we found that administration of GSH itself is highly toxic to ascorbate-deficient guinea pigs when given in divided i.p. doses totaling 3.75 mmol/kg daily.
Plasmacytoid differentiation of Epstein-Barr virus-transformed B cells in vivo is associated with reduced expression of viral latent genes.
Authors: Rochford R , Hobbs M V , Garnier J L , Cooper N R , Cannon M J
Published: May 2006

The Epstein-Barr virus (EBV)-associated B-cell lymphoproliferative disorders that arise in immunosuppressed individuals are considered to resemble EBV-transformed in vitro lymphoblastoid cell lines (LCLs) with a mature activated B-cell phenotype. In this study of human lymphoproliferative disorders in the severe combined immunodeficiency mouse model, however, we demonstrate that EBV-infected tumor cells are not LCL-like but are predominantly plasmacytoid and that this phenotype correlates with reduced expression of EBV latent genes. B-cell tumors developed within 3-6 weeks after injection of LCLs into severe combined immunodeficiency mice. The tumors and the injected LCLs were analyzed by flow cytofluorometry for B-cell differentiation and activation markers and by ribonuclease protection assay for cellular and viral gene expression. No differences in the expression of CD19 and CD21 were observed. However, a decrease in CD23, CD11a (lymphocyte function-associated antigen LFA-1), and CD58 (LFA-3) expression and an increase in CD38 (a plasma-cell-associated antigen), CD54 (intracellular adhesion molecule ICAM-1), and HLA class I in the tumor cells relative to the LCLs was observed. Two-color flow cytofluorometric analysis showed that the predominant population (> 80%) in LCLs was CD23hi/CD38lo and that the major population in LCL-derived tumors was CD23lo/CD38hi. Cell cycle analysis showed that, in contrast to actively cycling LCLs, the majority of tumor cells had exited the cell cycle and were restricted to G0/G1 phase. Finally, and most important, a reduction in mRNA for the EBV latent genes EBV nuclear antigen 2 (EBNA2) and latent membrane protein (LMP1) was observed in the tumors.
Casimir light: photon pairs.
Authors: Schwinger J
Published: May 2006

Expressions are developed for weak single pair emission probability and strong emission average number of pairs. The water transparency cutoff is closely realized, showing that the fundamental time scale is even shorter.
Genes on chromosomes 4, 9, and 19 involved in 11q23 abnormalities in acute leukemia share sequence homology and/or common motifs.
Authors: Nakamura T , Alder H , Gu Y , Prasad R , Canaani O , Kamada N , Gale R P , Lange B , Crist W M , Nowell P C
Published: May 2006

Chromosome translocations involving band 11q23 are associated with human acute leukemias. These translocations fuse the ALL-1 gene, homolog of Drosophila trithorax and located at chromosome band 11q23, to genes from a variety of chromosomes. We cloned and sequenced cDNAs derived from transcripts of the AF-4 and AF-9 genes involved in the most common chromosome abnormalities, t(4:11)(q21:q23) and t(9:11)(p22:q23), respectively. Sequence analysis indicates high homology between the AF-9 gene protein product and the protein encoded by the ENL gene fused to ALL-1 in (11:19) chromosome translocations. AF-4, AF-9, and ENL proteins contain nuclear targeting sequences as well as serine-rich and proline-rich regions. Stretches abundant in basic amino acids are also present in the three proteins. These results suggest that the different proteins fused to ALL-1 polypeptide(s) provide similar functional domains.
Synthetic peptides based on motifs present in human band 3 protein inhibit cytoadherence/sequestration of the malaria parasite Plasmodium falciparum.
Authors: Crandall I , Collins W E , Gysin J , Sherman I W
Published: May 2006

Synthetic peptides patterned on the amino acid sequences found in two exofacial regions of band 3 protein (residues 824-829 of loop 7 and residues 547-553 of loop 3) blocked, in a dose-dependent fashion, the in vitro adherence of Plasmodium falciparum-infected erythrocytes to C32 amelanotic melanoma cells. Intravenous infusion of these synthetic peptides into Aotus and Saimiri monkeys infected with sequestering isolates of P. falciparum resulted in the appearance of mature forms of the parasite in the peripheral circulation. The finding that the peptides were effective as adhesion blockers in the micromolar range suggests that cerebral malaria could be managed through antiadhesion therapy.
Feedback inhibition of fully unadenylylated glutamine synthetase from Salmonella typhimurium by glycine, alanine, and serine.
Authors: Liaw S H , Pan C , Eisenberg D
Published: May 2006

Bacterial glutamine synthetase (GS; EC 6.3.1.2) was previously shown to be inhibited by nine end products of glutamine metabolism. Here we present four crystal structures of GS, complexed with the substrate Glu and with each of three feedback inhibitors. The GS of the present study is from Salmonella typhimurium, with Mn2+ ions bound, and is fully unadenylylated. From Fourier difference maps, we find that L-serine, L-alanine, and glycine bind at the site of the substrate L-glutamate. In our model, these four amino acids bind with the atoms they share in common (the "main chain" +NH3-CH-COO-) in the same positions. Thus on the basis of our x-ray work, glycine, alanine, and serine appear to inhibit GS-Mn by competing with the substrate glutamate for the active site.
Chaos and the evolution of cooperation.
Authors: Nowak M , Sigmund K
Published: May 2006

The "iterated prisoner's dilemma" is the most widely used model for the evolution of cooperation in biological societies. Here we show that a heterogeneous population consisting of simple strategies, whose behavior is totally specified by the outcome of the previous round, can lead to persistent periodic or highly irregular (chaotic) oscillations in the frequencies of the strategies and the overall level of cooperation. The levels of cooperation jump up and down in an apparently unpredictable fashion. Small recurrent and simultaneous invasion attempts (caused by mutation) can change the evolutionary dynamics from converging to an evolutionarily stable strategy to periodic oscillations and chaos. Evolution can be twisted away from defection, toward cooperation. Adding "generous tit-for-tat" greatly increases the overall level of cooperation and can lead to long periods of steady cooperation. Since May's paper [May, R. M. (1976) Nature (London) 261, 459-467], "simple mathematical models with very complicated dynamics" have been found in many biological applications, but here we provide an example of a biologically relevant evolutionary game whose dynamics display deterministic chaos. The simulations bear some resemblance to the irregular cycles displayed by the frequencies of host genotypes and specialized parasites in evolutionary "arms races" [Hamilton, W. D., Axelrod, R. & Tanese, R. (1990) Proc. Natl. Acad. Sci. USA 87, 3566-3573; Seger, J. (1988) Philos. Trans. R. Soc. London B 319, 541-555].
Release of amyloid beta-protein precursor derivatives by electrical depolarization of rat hippocampal slices.
Authors: Nitsch R M , Farber S A , Growdon J H , Wurtman R J
Published: May 2006

Proteolytic processing of the beta-amyloid protein precursor (APP) is regulated by cell-surface receptors. To determine whether neurotransmitter release in response to neuronal activation regulates APP processing in brain, we electrically depolarized superfused rat hippocampal slices and measured soluble APP derivatives released into the superfusate. Electrical depolarization caused a rapid increase in the release of both neurotransmitters and amino-terminal APP cleavage products. These derivatives lacked the APP carboxyl terminus and were similar to those found in both cell culture media and human cerebrospinal fluid. Superfusate proteins including lactate dehydrogenase were not changed by electrical depolarization. The release of amino-terminal APP derivatives increased with increasing stimulation frequencies from 0 to 30 Hz. The increased release was inhibited by the sodium-channel antagonist tetrodotoxin, suggesting that action-potential formation mediates the release of large amino-terminal APP derivatives. These results suggest that neuronal activity regulates APP processing in the mammalian brain.
Identification of the gene associated with the recurring chromosomal translocations t(3;14)(q27;q32) and t(3;22)(q27;q11) in B-cell lymphomas.
Authors: Baron B W , Nucifora G , McCabe N , Espinosa R , Le Beau M M , McKeithan T W
Published: May 2006

Chromosomal translocations involving chromosome 3, band q27, are among the most common rearrangements in B-cell non-Hodgkin lymphoma. From a bacteriophage lambda library prepared from a lymphoma characterized by a t(3;14)(q27;q32), genomic clones were isolated using a probe from the immunoglobulin heavy chain locus (IGH) joining region. In addition to clones containing an apparently normal IGH rearrangement, others were found to contain one of the translocation breakpoint junctions. Normal chromosome 3 sequences and the reciprocal breakpoint junction were subsequently isolated. DNA probes on each side of the chromosome 3 breakpoint hybridized at high stringency to the DNA of various mammalian species, demonstrating evolutionary conservation. One such probe from the presumptive der(3) chromosome detected an 11-kilobase transcript when hybridized to RNA of B- and T-cell lines. A probe made from partial cDNA clones isolated from a T-cell line hybridized with genomic DNA from both sides of the chromosome 3 breakpoint, indicating that the t(3;14) is associated with a break within the gene on chromosome 3. In situ chromosomal hybridization revealed that the same gene is involved in the t(3;22)(q27;q11). Preliminary nucleotide sequencing shows no identity of the cDNA to gene sequences in available data banks. We propose the name BCL6 (B-cell lymphoma 6) for this gene, since it is likely to play a role in the pathogenesis of certain B-cell lymphomas.
Mapping of residues forming the voltage sensor of the voltage-dependent anion-selective channel.
Authors: Thomas L , Blachly-Dyson E , Colombini M , Forte M
Published: May 2006

Voltage-gated ion-channel proteins contain "voltage-sensing" domains that drive the conformational transitions between open and closed states in response to changes in transmembrane voltage. We have used site-directed mutagenesis to identify residues affecting the voltage sensitivity of a mitochondrial channel, the voltage-dependent anion-selective channel (VDAC). Although charge changes at many sites had no effect, at other sites substitutions that increased positive charge also increased the steepness of voltage dependence and substitutions that decreased positive charge decreased voltage dependence by an appropriate amount. In contrast to the plasma membrane K+ and Na+ channels, these residues are distributed over large parts of the VDAC protein. These results have been used to define the conformational transitions that accompany voltage gating of an ion channel. This gating mechanism requires the movement of large portions of the VDAC protein through the membrane.
p53 mutations increase resistance to ionizing radiation.
Authors: Lee J M , Bernstein A
Published: May 2006

Mouse and human tumors of diverse origin frequently have somatically acquired mutations or rearrangements of the p53 gene, or they have lost one or both copies of the gene. Although wild-type p53 protein is believed to function as a tumor-suppressor gene, it is as yet unclear how p53 mutations lead to neoplastic development. Wild-type p53 has been postulated to play a role in DNA repair, suggesting that expression of mutant forms of p53 might alter cellular resistance to the DNA damage caused by gamma radiation. Moreover, p53 is thought to function as a cell cycle checkpoint after irradiation, also suggesting that mutant p53 might change the cellular proliferative response to radiation. We have used transgenic mice expressing one of two mutant alleles of p53 to test this prediction. Our results show that expression of both mutant variants of the mouse p53 gene significantly increases the cellular resistance of a variety of hematopoietic cell lineages to gamma radiation. These observations provide direct evidence that p53 mutations affect the cellular response to DNA damage, either by increasing DNA repair processes or, possibly, by increasing cellular tolerance to DNA damage. The association of p53 mutations with increased radioresistance suggests possible mechanisms through which alterations in the p53 gene might lead to oncogenic transformation.
Serum "big insulin-like growth factor II" from patients with tumor hypoglycemia lacks normal E-domain O-linked glycosylation, a possible determinant of normal propeptide processing.
Authors: Daughaday W H , Trivedi B , Baxter R C
Published: May 2006

The insulin-like growth factor II (IGF-II) gene is overexpressed in many mesenchymal tumors and can lead to non-islet-cell tumor hypoglycemia (NICTH). ProIGF-II consists of the 67 aa of IGF-II with a carboxyl 89-aa extension, the E domain. A derivative of proIGF-II containing only the first 21 aa of the E domain [proIGF-II-(E1-21)] has been isolated by others from normal serum and has O-linked glycosylation. We found that the "big IGF-II" of normal serum, as detected by an RIA directed against residues 1-21 of the E domain of proIGF-II, was reduced in size by treatment with neuraminidase and O-glycosidase. The big IGF-II, which is greatly increased in NICTH sera, was unaffected by neuraminidase and O-glycosidase treatment. We have also shown that big IGF-II from normal serum is retained by jacalin lectin columns and that big IGF-II from NICTH serum was not retained, indicating that it lacked O-glycosylation. Normal O-linked glycosylation may be required for proper peptidase processing of proIGF-II. The lack of normal O-linked glycosylation by tumors may explain the predominance of big IGF-II in NICTH sera. In normal serum, most of the IGF-II is present in a 150-kDa ternary complex with IGF-II binding protein (IGFBP) 3 and alpha subunit. In NICTH serum, however, the complexes carrying big IGF-II are < 50 kDa. We investigated whether big IGF-II of NICTH was responsible for this abnormality. Tumor big IGF-II and IGF-II were equally effective in forming the 150-kDa complex with purified IGFBP-3 and 125I-labeled alpha subunit. Both 125I-labeled IGF-II and 125I-labeled proIGF-II-(E1-21), when incubated with normal serum, formed the 150-kDa complex as detected by Superose 12 exclusion chromatography. We conclude that the nonglycosylated big IGF-II of NICTH serum can form normal complexes with serum IGFBPs. The defective binding in NICTH is attributable to defective IGFBP-3 binding.
A gene in the chromosomal region 3p21 with greatly reduced expression in lung cancer is similar to the gene for ubiquitin-activating enzyme.
Authors: Kok K , Hofstra R , Pilz A , van den Berg A , Terpstra P , Buys C H , Carritt B
Published: May 2006

The chromosomal region 3p21 is thought to be the site of a lung tumor suppressor gene. We recently cloned a gene from this region that has greatly reduced expression in almost all lung tumor cell lines examined, in spite of being widely expressed in a variety of other tumor and nontumor cell types. We report here the sequence of this gene and show that it has significant homology to the genes encoding the ubiquitin-activating enzymes of three species, including humans. This suggests it is a second, autosomal member of this gene family in humans and may play a role in the ubiquitin conjugation pathway, which is of central importance in all eukaryotes.
Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1.
Authors: Lee J S , Galvin K M , Shi Y
Published: May 2006

Two promoter elements are important for basal-level transcription, the TATA motif typically located 30 nucleotides upstream of the transcription initiation site and the initiator (Inr) element encompassing the start site. The mechanism of how Inr elements work is poorly understood, partly because very few proteins that bind to Inr elements have been identified and isolated. The recently cloned YY1 is such an Inr-binding protein. YY1 is able to direct transcription upon binding to its recognition sequence in vitro. The ability of YY1 to initiate transcription is augmented by the presence of a TATA motif or binding sites for transcription factor Sp1. To study the mechanism underlying the apparent functional cooperation between YY1 and Sp1, we explored the possibility of protein-protein interactions between these two transcription factors. We found that YY1 and Sp1 can form a physical complex. In addition, we identified domains within YY1 and Sp1 that mediate their interactions with each other. The physical interaction between YY1 and Sp1 may thus form the basis for the functional interplay observed previously.
Expansion of the Hox gene family and the evolution of chordates.
Authors: Pendleton J W , Nagai B K , Murtha M T , Ruddle F H
Published: May 2006

Homeobox genes encode DNA-binding transcription regulators that participate in the formation of embryonic pattern or contribute to cell-type specificity during metazoan development. Homeobox genes that regulate axial patterning and segmental identity (Hox/HOM genes) share a conserved clustered genomic organization. Mammals have four clusters that have likely arisen from the duplication of a single ancestral cluster. The number of Hox-type genes in other deuterostomes was estimated by using a polymerase chain reaction sampling method. Increased Hox gene complements are associated with the appearance of chordate and vertebrate characters. Our data suggest the presence of one Hox cluster in the acorn worm, a hemichordate; two Hox clusters in amphioxus, a cephalochordate; and three in the lamprey, a primitive vertebrate.
Preferential and asymmetric interaction of linker histones with 5S DNA in the nucleosome.
Authors: Hayes J J , Wolffe A P
Published: May 2006

We establish that linker histones H1 and H5 bind preferentially to a Xenopus borealis somatic 5S RNA gene associated with an octamer of core histones rather than to naked 5S DNA. This preferential binding requires free linker DNA to either side of the nucleosome core. Incorporation of a single linker histone molecule into the nucleosome protects an additional 20 bp of linker DNA from micrococcal nuclease digestion. This additional DNA is asymmetrically distributed with respect to the nucleosome core. Incorporation of linker histones causes no change to the cleavage of DNA in the nucleosome by hydroxyl radical or DNase I.
Differentiation and characterization of B-cell precursors detected in the yolk sac and embryo body of embryos beginning at the 10- to 12-somite stage.
Authors: Cumano A , Furlonger C , Paige C J
Published: May 2006

The embryonic sites in which progenitors of the hematopoietic lineages first emerge are ideal regions to characterize both the cells and environment needed to initiate blood cell development. For a number of years both the murine yolk sac and embryo have been recognized to contain progenitors of B lymphocytes. However, clonal, quantitative in vitro assays, which allow precise observation of precursors and their progeny, have been lacking. Moreover, the site of origin of the initial events remains controversial. In this report we document the presence of B-cell progenitors in yolk sac and embryonic tissue obtained from mouse fetuses beginning at the 10-somite stage, day 8.5. We determine the frequency, cell-surface phenotype, and growth properties of these progenitors. We show that these cells can differentiate into immunoglobulin-secreting cells and that the progeny derived from single progenitors are diverse with respect to immunoglobulin heavy-chain allotype expression, diversity-joining region use, and heavy-chain variable-region utilization.
A Jun-binding protein related to a putative tumor suppressor.
Authors: Monteclaro F S , Vogt P K
Published: May 2006

A lambda gt11 cDNA library of chicken embryo fibroblasts was screened with biotinylated Jun protein to identify Jun-binding clones. Eight such clones were isolated; one contains a gene referred to as jif-1 that is homologous to the putative tumor suppressor gene QM. jif-1 codes for a protein of 25 kDa that binds to the leucine zipper of viral and cellular Jun. The Jif-1 protein also binds to itself. Jif-1 does not contain a leucine zipper, and it does not bind to the 12-O-tetradecanoylphorbol 13-acetate response element DNA sequence. Complex formation of Jif-1 with Jun inhibits DNA binding and reduces transactivation by Jun. Addition of Fos protein to Jun-Jif-1 complexes restores DNA-binding activity. These observations suggest that Jif-1 is a negative regulator of Jun.
Corticotropin-releasing factor mRNA in rat thymus and spleen.
Authors: Aird F , Clevenger C V , Prystowsky M B , Redei E
Published: May 2006

Corticotropin-releasing factor (CRF) initiates stress-induced immunosuppression via the hypothalamic-pituitary-adrenal axis. CRF has also been shown to have direct stimulatory and suppressive effects on immune cells. We have previously detected immunoreactive and bioactive CRF in the rat spleen and thymus. To determine if CRF is synthesized in these tissues, we analyzed rat spleen and thymus for the presence of CRF mRNA. RNA was reverse transcribed, and the resulting cDNA was amplified by the polymerase chain reaction with CRF gene-specific oligonucleotide primers. After Southern blotting and hybridization with an internal CRF gene probe, a product of the expected size was detected in the spleen, thymus, and hypothalamus (positive control) but not in liver or kidney (negative controls), indicating that CRF is synthesized in the spleen and thymus. Furthermore, CRF could be secreted from splenic and thymic adherent cells in culture. Secretion increased severalfold in response to nordihydroguaiaretic acid (NDGA), a lipoxygenase pathway inhibitor, whereas interleukin 1 had no effect, suggesting that regulation of CRF secretion may differ from that in the hypothalamus. CRF mRNA was detected in NDGA-stimulated thymic adherent cells and in both control and NDGA-stimulated splenic nonadherent cells. The finding that CRF is synthesized in the spleen and thymus suggests that locally synthesized "immune" CRF, acting as an autocrine or paracrine cytokine, may have direct regulatory effects on immune function.
Mutations in the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2 alpha) that overcome the inhibitory effect of eIF-2 alpha phosphorylation on translation initiation.
Authors: Vazquez de Aldana C R , Dever T E , Hinnebusch A G
Published: May 2006

Phosphorylation of eIF-2 alpha in Saccharomyces cerevisiae by the protein kinase GCN2 leads to inhibition of general translation initiation and a specific increase in translation of GCN4 mRNA. We isolated mutations in the eIF-2 alpha structural gene that do not affect the growth rate of wild-type yeast but which suppress the toxic effects of eIF-2 alpha hyperphosphorylation catalyzed by mutationally activated forms of GCN2. These eIF-2 alpha mutations also impair translational derepression of GCN4 in strains expressing wild-type GCN2 protein. All four mutations alter single amino acids within 40 residues of the phosphorylation site in eIF-2 alpha; however, three alleles do not decrease the level of eIF-2 alpha phosphorylation. We propose that these mutations alter the interaction between eIF-2 and its recycling factor eukaryotic translation initiation factor 2B (eIF-2B) in a way that diminishes the inhibitory effect of phosphorylated eIF-2 on the essential function of eIF-2B in translation initiation. These mutations may identify a region in eIF-2 alpha that participates directly in a physical interaction with the GCN3 subunit of eIF-2B.
Casimir light: pieces of the action.
Authors: Schwinger J
Published: May 2006

More realistic dynamics for the collapsing dielectric fluid are introduced in stages by adding contributions to the Lagrangian that forms the action. The elements are kinetic energy, Casimir potential energy, air pressure potential energy, and electromagnetic coupling to the moving dielectric. There are successful tests of partial collapse time and of minimum radius.
The Ets1 transcription factor is widely expressed during murine embryo development and is associated with mesodermal cells involved in morphogenetic processes such as organ formation.
Authors: Kola I , Brookes S , Green A R , Garber R , Tymms M , Papas T S , Seth A
Published: May 2006

The Ets family of genes encodes a class of transcription factors. Ets1 is predominantly expressed in the lymphoid organs of neonatal and adult mice, whereas Ets2 is expressed in every organ examined. In this study, we investigate the expression of Ets1 and Ets2 during murine embryonic development. Our data show that Ets1 expression increases in embryos after implantation and during organogenesis such that it is expressed in all the organs of day-15 embryos studied. In later fetal stages, Ets1 expression is predominant in the lymphoid tissues, brain, and organs that are undergoing branching morphogenesis (e.g., lung) but is dramatically reduced in other organs such as the stomach and intestine. In neonatal development, Ets1 is expressed only in the lymphoid organs and brain. In situ hybridization analysis demonstrates that expression of Ets1 occurs in mesenchymal cells of developing organs, in the nervous system, and in forming bone. Furthermore, expression of Ets1 is upregulated in P19 cells induced to differentiate into mesoderm-like cells. Ets2, on the other hand, is expressed in differentiated and undifferentiated P19 and F9 cells and in all organs of embryonic, neonatal, and adult mice studied. These data suggest that Ets1 plays an important role in mesodermal cells associated with morphogenetic processes such as organ formation and tissue modeling, whereas Ets2 plays a more fundamental role in cells.
Identification of small GTP-binding rab proteins in human platelets: thrombin-induced phosphorylation of rab3B, rab6, and rab8 proteins.
Authors: Karniguian A , Zahraoui A , Tavitian A
Published: May 2006

The activation of platelets by specific agonists is a tightly regulated mechanism that leads to the secretion of the dense- and alpha-granule contents. Platelets have been shown to possess small GTP-binding proteins thought to be involved in central biological processes; however, no rab proteins, which may regulate the exocytic process at different stages, have been reported. This study has shown that rab1, rab3B, rab4, rab6, and rab8 proteins, but not rab3A protein, were present in platelets and in endothelial cells. To probe their functional significance in platelets, rab3B, rab6, and rab8 proteins were further characterized with regard to their intracellular localization and their phosphorylation properties. Whereas rab3B protein was found to be mainly cytosolic, rab6 and rab8 proteins were preferentially targeted to the plasma membrane and to the alpha granules. The activation of platelets by thrombin, a potent inducer of secretion, resulted in the phosphorylation of rab3B, rab6, and rab8 proteins, whereas no phosphorylation was observed in the presence of prostaglandin E1, which stimulates cAMP-dependent protein kinase and inhibits the secretion process. These findings provide evidence that members of the subfamily of rab proteins, rab6 and rab8, are localized in platelets to one type of specific secretory vesicle, the alpha granule, and would suggest their possible implication in the secretion process through phosphorylation mechanisms.
Antisense oligodeoxynucleotides to the blk tyrosine kinase prevent anti-mu-chain-mediated growth inhibition and apoptosis in a B-cell lymphoma.
Authors: Yao X R , Scott D W
Published: May 2006

Crosslinking of membrane immunoglobulin (mIg) receptors by anti-Ig causes growth inhibition and subsequent cell death due to apoptosis in a murine B-cell lymphoma model. The earliest signal transduction via mIg has recently been shown to be dependent on the activation of one or more protein tyrosine kinases (PTKs). In this study, we utilized the CH31 lymphoma, which is extremely sensitive to growth inhibition by anti-Ig, to examine the role of PTKs in cell cycle arrest. This cell line expresses multiple PTKs, whose activities are stimulated by crosslinking mIg. To determine whether PTK activity is essential for the inhibition of cell growth, we exposed CH31 cells to antisense oligodeoxynucleotides for the blk PTK prior to the growth inhibition assay. We found that exposure of CH31 cells to blk antisense effectively prevented anti-mu-chain-mediated growth inhibition and subsequent apoptosis. Corresponding blk sense or antisense oligonucleotides for other PTKs had no protective effect against anti-mu. Moreover, antisense blk oligonucleotides had no effect on transforming growth factor beta-mediated growth arrest and apoptosis. Further experiments showed significantly reduced endogenous p55blk in blk antisense-treated cells. In addition, anti-mu stimulation of antisense-treated cells failed to induce any detectable increase in kinase activity of p55blk, a result suggesting the uncoupling of blk proteins from normal signal pathways that are essential for growth inhibition. These results implicate a role of blk kinase in anti-mu-mediated pathway to cell cycle arrest.