bluuebunny/crossref_metadata_2025 huggingface dataset:
Importance of bound divalent cations to the tyrosine deprotonation during the photocycle of bacteriorhodopsin
Authors: Dupuis Paul , Corcoran Timothy C. , El-Sayed M. A.
Published: May 2006

The transient absorption changes occurring at 297 nm during the photocycles of the deionized and acidified bacteriorhodopsins (blue membranes) were studied. As opposed to what happens during the photocycle of the purple membrane, for the blue membranes only the fast absorption increase corresponding to
trans-cis
isomerization of the retinal chromophore is present; the slow rise attributed to the tyrosine deprotonation is not observed. The addition of different salts to the deionized membrane restores the original color and causes a tyrosine deprotonation during the photocycle. This suggests that the presence of cations is required for the deprotonation of tyrosine as it is for the deprotonation of the retinylidene Schiff base. These results are discussed in terms of the recently proposed cation model for the observed deprotonation processes in the photocycle of bacteriorhodopsin.
Assignment of the human gene for the glucocorticoid receptor to chromosome 5.
Authors: Gehring U , Segnitz B , Foellmer B , Francke U
Published: May 2006

Human lymphoblastic leukemia cells of line CEM-C7 are glucocroticoid-sensitive and contain glucocorticoid receptors of wild-type characteristics. EL4 mouse lymphoma cells are resistant to lysis by glucocorticoids due to mutant receptors that exhibit abnormal DNA binding. Hybrids between the two cell lines were prepared and analyzed with respect to glucocorticoid responsiveness and to receptor types by DNA-cellulose chromatrography. Sensitive hybrid cell clones contained the CEM-C7-specific receptor in addition to the EL4 type of receptor. Several sensitive hybrid cell clones were used for selection of resistant segregants by growth in the presence of high concentrations of glucocorticoid. These segregants had lost the wild-type CEM-C7 receptor, while the EL4-specific receptor was retained. To identify the human chromosome that was lost concordantly with the CEM-C7 receptor the chromosomes of hybrid cells were studied by alkaline Giemsa (G-11) staining and trypsin/Giemsa banding. All hybrids contained human chromosomes in addition to one to two sets of EL4 chromosomes. Human chromosome 5 was present in all hybrid cell clones that expressed the CEM-C7 receptor and it was absent from those that did not. This absolute correlation was not observed for any other human chromosome. We conclude that the human gene for the glucocorticoid receptor is located on chromosome 5.
Reduced in vivo mutagenesis by mutant herpes simplex DNA polymerase involves improved nucleotide selection.
Authors: Hall J D , Furman P A , St Clair M H , Knopf C W
Published: May 2006

We present evidence that mutation frequencies in a mammalian system can vary according to the replication fidelity of the DNA polymerase. We demonstrated previously that several derivatives of herpes simplex virus type 1 that encode polymerases resistant to various antiviral drugs (e.g., nucleotide analogues) also produce reduced numbers of spontaneous mutants. Here we show that the DNA polymerase from one antimutator virus exhibits enhanced replication fidelity. First, the antimutator virus showed a reduced response to known mutagens that promote base mispairing during DNA replication (N-methyl-N'-nitro-N-nitrosoguanidine, 5-bromo-deoxyuridine). Second, purified DNA polymerase from the antimutator produced fewer replication errors in vitro, based on incorporation of mispaired nucleotides or analogues with abnormal sugar rings. We have investigated possible mechanisms for the enhanced fidelity of the antimutator polymerase. We show that the mutant enzyme has altered interactions with nucleoside triphosphates, as indicated by its resistance to nucleotide analogues and elevated Km values for normal nucleoside triphosphates. We present evidence against increased proofreading by an associated 3',5' exonuclease (as seen for T4 bacteriophage antimutator polymerases), based on nuclease levels in the mutant polymerase. We propose that reduced affinity of the polymerase for nucleoside triphosphates accounts for the antimutator phenotype by accentuating differences in base-pair stability, thus facilitating selection of correct nucleotides.
Stimulation of in vitro human skin collagenase expression by platelet-derived growth factor.
Authors: Bauer E A , Cooper T W , Huang J S , Altman J , Deuel T F
Published: May 2006

Platelet-derived growth factor (PDGF) is both chemoattractant and mitogenic for stromal cells. Here, we examined the effects of PDGF on collagenase expression by normal human skin fibroblasts. Culturing cells for 24 hr in the presence of PDGF at 0-180 ng/ml resulted in a dose-dependent, saturable increase in collagenase activity in the culture medium that was paralleled by equal increases in immunoreactive collagenase protein, suggesting enhanced synthesis of a catalytically unaltered enzyme. The specificity of this effect was demonstrated by comparing the collagenase-stimulatory effect with that on total protein synthesis and DNA synthesis. Under in vitro conditions that produced a 2.5-fold increase in collagenase synthesis, there was an approximately equal to 20% increase in total protein synthesis and no change in DNA synthesis. In addition, platelet factor 4, another platelet-derived protein, caused a less than 20% increase in collagenase expression. In time-course studies, stimulation of collagenase synthesis was first observed 8-10 hr after exposure to the growth factor. Conversely, when cells were primed with PDGF for approximately equal to 24 hr and the stimulator was then removed, an increased rate of synthesis was seen for an additional approximately equal to 6 hr, after which the rate reverted to control levels. Since the kinetic data suggested a possible pretranslational effect, fibroblasts cultured with PDGF were used to prepare mRNA. In cell-free translation, total protein synthesis was essentially unaltered; however, the growth factor caused a greater than 2-fold increase in translatable collagenase mRNA. The data suggest that PDGF specifically modulates collagenase synthesis, possibly through a series of events that lead to increased transcription or preferential translation of collagenase mRNA.
In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction.
Authors: Berrios M , Osheroff N , Fisher P A
Published: May 2006

DNA topoisomerase II has been immunochemically identified on protein blots as a major polypeptide component of the Drosophila nuclear matrix-pore complex-lamina fraction. Indirect immunofluorescence analyses of larval cryosections have confirmed the nuclear localization of topoisomerase II in situ. Although apparently excluded from the nucleolus, the topoisomerase protein is otherwise distributed throughout the interior of interphase nuclei. Similar immunocytochemical studies performed with permeabilized whole giant cells from third-instar larval salivary glands have shown topoisomerase II to be largely restricted to the polytene chromosomes. Upon nuclear disassembly during mitosis, the topoisomerase polypeptide appears to redistribute diffusely throughout the cell. Faint immunofluorescent staining of mitotic chromosomes is also observed.
Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues.
Authors: Gojobori T , Yokoyama S
Published: May 2006

A method is proposed for computing the rates of nucleotide substitution for an oncogene of a retrovirus (v-onc), its cellular homologue (c-onc), and the retrovirus genome simultaneously. The method has been applied to DNA sequences of the v-mos gene of Moloney murine sarcoma virus (Mo-MuSV) and the c-mos and gag genes of Mo-MuSV and Moloney murine leukemia virus (Mo-MuLV). The rates of nucleotide substitution for c-mos, the gag gene, and v-mos are estimated to be 1.71 X 10(-9), 6.3 X 10(-4), and 1.31 X 10(-3) per site per year, respectively. The rate of evolution of c-mos is comparable to that of many functional genes in DNA genomes, suggesting some important biological function played by cellular oncogenes. The rates of nucleotide substitution in the v-mos and gag genes are very high and are similar to those of RNA viral genes such as the hemagglutinin and neuraminidase genes in the influenza A virus. Thus, oncogenes seem to exemplify a general feature of genome evolution: the rate of evolution of RNA genomes can be more than a million times greater than that of DNA genomes because of a high mutation rate in the RNA genome.
Two-codon insertion mutagenesis of plasmid genes by using single-stranded hexameric oligonucleotides.
Authors: Barany F
Published: May 2006

An efficient method for introducing two codons into a cloned gene has been applied to studying functional regions of the pBR322-encoded tetracycline-resistance gene and beta-lactamase (ampicillin-resistance) gene. Single-stranded hexameric linkers are inserted into a preexisting cohesive end restriction site to create a new (six-base recognition) restriction site. Insertion mutations are enriched by using biochemical selection or are selected by using a kanamycin-resistance cassette (biological selection). Phenotypes of insertion mutations isolated in the tetracycline-resistance gene support the hypothesis that it is comprised of two domains connected by a central hinge. Mutations in the beta-lactamase gene are temperature sensitive and demonstrate altered sensitivity to various beta-lactams and inhibitors.
Sequence and expression of the rat prodynorphin gene.
Authors: Civelli O , Douglass J , Goldstein A , Herbert E
Published: May 2006

We report here the isolation of a lambda genomic clone that contains the nucleotide sequence coding for the main exon of the rat prodynorphin (proenkephalin B) gene. This exon codes for the majority of the translated region of prodynorphin mRNA including the opioid peptides alpha-neo-endorphin, dynorphin A, and dynorphin B. The entire 3' untranslated region is also contained on the lambda clone. Nucleotide sequence comparison with the main exon of the human prodynorphin gene reveals both structural and sequence homology. RNA blot analysis reveals that prodynorphin transcripts can be seen in numerous regions of the rat brain and in the adrenal gland, spinal cord, testis, and anterior pituitary.
ATP is essential for protein translocation into Escherichia coli membrane vesicles.
Authors: Chen L , Tai P C
Published: May 2006

The energy requirement for translocation of alkaline phosphatase and the outer membrane protein OmpA into Escherichia coli membrane vesicles was studied under conditions that permit posttranslational translocation and, hence, prior removal of various components necessary for protein synthesis. Translocation could be supported by an ATP-generating system or, less well, by the protonmotive force generated by D-lactate oxidation; the latter might act by generating ATP from residual bound nucleotides. However, when protonmotive force inhibitors were used or when ATP was further depleted by E. coli glycerol kinase, D-lactate no longer supported the translocation. Furthermore, ATP could still support protein translocation in the presence of proton uncouplers or with membranes defective in the F1 fraction of the H+-ATPase. We conclude that ATP is required for protein translocation in this posttranslational system (and probably also in cotranslational translocation); the protonmotive force may contribute but does not appear to be essential.
Arterial smooth muscle cells in primary culture produce a platelet-derived growth factor-like protein.
Authors: Nilsson J , Sjölund M , Palmberg L , Thyberg J , Heldin C H
Published: May 2006

Adult rat arterial smooth muscle cells (SMC) in primary culture modulate from contractile to synthetic phenotype. This process includes partial loss of myofilaments and formation of an extensive rough endoplasmic reticulum and a large Golgi complex. It gives the cells the ability to initiate DNA synthesis and actively proliferate when stimulated with serum or isolated growth factors. After a few divisions, growth becomes partly independent of exogenous mitogens and does not cease until multiple cell layers have been formed. Here, it is demonstrated that serum-free conditioned medium from primary cultures of adult rat arterial SMC contains a factor that initiates DNA synthesis in growth-arrested secondary cultures of SMC. The mitogenic activity was neutralized by antibodies to platelet-derived growth factor (PDGF), and no mitogenic activity occurred in conditioned medium from cultures pretreated with actinomycin D, excluding release into the medium of PDGF adsorbed to the plastic vessels during the initial culture in serum-containing medium. Exposure of human fibroblasts to samples of the conditioned medium at 4 degrees C inhibited subsequent binding of 125I-labeled PDGF. It was further shown that the SMC of the primary cultures were able to initiate DNA synthesis in a chemically defined medium lacking PDGF and other growth factors. During the early, most active, and partly autonomous growth phase, the SMC had a low binding capacity for 125I-labeled PDGF and responded but little to stimulation with exogenous PDGF. Later on, with increasing cell density and decreasing growth rate, the ability to bind and respond to exogenous PDGF increased. Taken together, the observations suggest that modulation of SMC from contractile to synthetic phenotype is accompanied by production of a PDGF-like protein and autocrine or possibly by mitogen-independent initiation of DNA synthesis. Functionally, this may be important during wound healing and in the development of atherosclerotic lesions.
Cell-cycle-specific genes differentially expressed in human leukemias.
Authors: Calabretta B , Kaczmarek L , Mars W , Ochoa D , Gibson C W , Hirschhorn R R , Baserga R
Published: May 2006

Three cDNA clones isolated from Syrian hamster cells (p4F1, p2F1, and p2A9) contain sequences that are preferentially expressed in the G1 phase of the cell cycle. The expression of these sequences was investigated in human peripheral blood cells from normal individuals and from patients with leukemia. The expression of p4F1 and p2F1 is clearly dependent on the cell cycle in peripheral blood mononuclear cells stimulated to proliferate with phytohemagglutinin; the p2A9 sequences cannot be clearly detected in human lymphocytes but are expressed in a cell-cycle-dependent manner in human diploid fibroblasts (WI-38). These genes also show different levels of expression in lymphoid and myeloid leukemias. The highest level of expression for p2A9 is found in patients with chronic myelogenous leukemia, and the lowest in patients with chronic lymphocytic leukemia. For p2F1 and p4F1, the highest levels of expression are found in chronic and acute myelogenous leukemia. At least two other cell-cycle genes are not expressed at detectable levels in human leukemias. These findings suggest that the activation of cell-division-cycle genes might contribute, like cellular oncogenes, to the phenotype of human malignancies and that, perhaps, new oncogenes could be found by identifying and isolating genes whose expression is dependent on the cell cycle.
Human cytotoxic T-lymphocyte recognition of an HLA-A3 gene product expressed on murine L cells: the only human gene product required on the target cells for lysis is the class I heavy chain.
Authors: Cowan E P , Coligan J E , Biddison W E
Published: May 2006

To dissect the molecular basis for T-cell recognition of class I major histocompatibility complex antigens, we have examined the ability of human cytotoxic T lymphocytes (CTL) to recognize murine L cells transformed with a human class I gene. Three transformed L-cell lines were generated that expressed the human HLA-A3 gene from donor E1 at levels comparable to those of the endogenous L-cell H-2Kk molecules. CTL were generated in secondary and tertiary mixed lymphocyte culture against the HLA-A3 subtype of donor E1 by culturing irradiated E1 peripheral blood lymphocytes with the peripheral blood lymphocytes of responder donor M3 (M3 shares all defined class I antigens with E1 but expresses a different HLA-A3 subtype). Each of the HLA-A3-transformed L cells was lysed by M3 anti-E1 CTL in a short-term 51Cr release assay and this recognition was blocked by a monoclonal anti-HLA-A3 antibody. Antibodies specific for the human T8 and LFA-1 molecules on the CTL effectors (but absent from the transformed targets) also blocked lysis of each of the HLA-A3 transformed L-cell targets. Antibodies to other T-cell molecules failed to block lysis. The present results demonstrate that human CTL can recognize human class I molecules on targets that do not express any other human gene product and further suggest that effector T-cell molecules T8 and LFA-1 are functionally involved in this recognition process.
Regulation of T-cell receptor gene expression in human T-cell development.
Authors: Collins M K , Tanigawa G , Kissonerghis A M , Ritter M , Price K M , Tonegawa S , Owen M J
Published: May 2006

A cDNA clone encoding the alpha chain of the human T-cell antigen receptor was isolated by screening a library from the human T-cell line Jurkat with a mouse alpha-chain cDNA clone. This human alpha-chain clone, together with a human antigen receptor beta-chain cDNA clone, was used to determine the stage of T-cell development at which antigen receptor mRNAs first appear. Blot-hybridization analysis of mRNA isolated from a panel of human thymic tumor lines clearly demonstrated that beta-chain transcripts could be detected in all T-lineage cells. However, alpha-chain transcripts were only found in the most phenotypically mature lines, which express the antigen receptor-associated molecule T3. Furthermore, beta-chain transcripts were abundant in RNA prepared from purified T3-negative thymocytes, whereas alpha-chain transcripts were virtually absent. From these results we conclude that alpha-chain expression occurs later in thymic ontogeny than that of the beta chain and propose that it controls surface expression of the antigen receptor-T3 complex.
Alpha and beta human transforming growth factors stimulate prostaglandin production and bone resorption in cultured mouse calvaria.
Authors: Tashjian A H , Voelkel E F , Lazzaro M , Singer F R , Roberts A B , Derynck R , Winkler M E , Levine L
Published: May 2006

Human alpha and beta transforming growth factors (TGF-alpha and TGF-beta) stimulated the production of prostaglandin E2 (PGE2) and bone resorption in neonatal mouse calvaria in organ culture. Significant stimulation of bone resorption by TGF-alpha was observed with a concentration of 0.2 ng/ml (35 pM) and by TGF-beta with 0.2 ng/ml (8.0 pM). Enhanced production of PGE2 and bone resorption stimulated by either TGF-alpha or TGF-beta were both inhibited by indomethacin. We conclude that TGF-alpha and TGF-beta are potent and powerful stimulators of the resorption of mouse bone by a mechanism that involves the enhanced local production of PGE2.
ATP-dependent bioluminescence in the firefly squid,
Watasenia scintillans
Authors: Tsuji Frederick I.
Published: May 2006

The Japanese firefly squid,
Watasenia scintillans
, emits intense flashes of light from three tiny luminous organs that are located at the tip of each of a pair of ventral arms. Light is also produced from hundreds of other minute organs that are scattered over the body. The luminescence is due to an ATP-dependent reaction, with an optimal pH of 8.80. The decay of light intensity follows first-order kinetics and the decay constant is independent of initial ATP concentration. The light emission also requires MgCl
2
, a soluble component, and an insoluble component that is membrane bound. Squids represent a major group of organisms unrelated to fireflies in which ATP is required for bioluminescence.
Homology requirements for recombination in Escherichia coli.
Authors: Watt V M , Ingles C J , Urdea M S , Rutter W J
Published: May 2006

The DNA sequence homology required for recombination in Escherichia coli has been determined by measuring the recombination frequency between insulin DNA in a miniplasmid pi VX and a homologous sequence in a bacteriophage lambda vector. A minimum of approximately equal to 20 base pairs in a completely homologous segment is required for significant recombination. There is an exponential increase in the frequency of recombination when the length of homologous DNA is increased from 20 base pairs to 74 base pairs and an apparently linear increase with longer DNA segments. Mismatches within a homologous segment can dramatically decrease the frequency of recombination. Thus, the process of recombination is sensitive to the length of precisely base-paired segments between recombining homologues.
Deletions within a defective suppressor-mutator element in maize affect the frequency and developmental timing of its excision from the bronze locus.
Authors: Schiefelbein J W , Raboy V , Fedoroff N V , Nelson O E
Published: May 2006

Six independent derivatives of the bz-m13 allele, which contains a 2.2-kilobase-pair defective Suppressor-mutator (dSpm) insertion at the bronze (bz) locus, have been isolated and analyzed. The derivatives were selected for alterations in the frequency and timing of somatic reversion; such derivatives have previously been analyzed genetically and designated "changes in state" by McClintock [McClintock, B. (1955) Carnegie Inst. Washington, Yearb. 54, 245-255]. All of the derivatives analyzed in the present study revert substantially later in development than the original insertion mutation and some show a very low frequency of reversion as well. All of the derivatives contain insertions at the same site as the parent bz-m13 allele. Deletions of 400-1300 base pairs were found in the dSpm elements in four of the six derivatives; the remaining derivatives could not be distinguished structurally from the original mutant allele. The results suggest that changes in the frequency and developmental timing of excision are attributable to alterations in the dSpm element. Furthermore, these data suggest that DNA sequences near the ends of the element are important for responding to the two transacting functions supplied by the transposition-competent Suppressor-mutator (Spm) element.
Peroxide-producing potential of tissues: inverse correlation with longevity of mammalian species.
Authors: Cutler R G
Published: May 2006

Peroxidation reactions may cause many of the dysfunctions associated with aging. Accordingly, the 30-fold differences in aging rate among the mammalian species could be determined in part by peroxidation defense processes. This possibility was tested by measuring the spontaneous autoxidation of aerobically incubated brain and kidney tissue homogenates of 24 different mammalian species as a function of their maximum lifespan potential. Results show a statistically significant inverse correlation between both the rate of autoxidation and the amount of peroxidizable substrate with maximum lifespan potential. Kinetic analysis of the data indicates that the amount of peroxidizable substrate was the major factor determining the rate of autoxidation. For human tissues, antioxidants also appear to contribute to their unusually low sensitivity to peroxidation. These results support the hypothesis that aging may be caused in part by oxygen radicals initiating peroxidation reactions and that peroxidation defense processes are involved in governing the longevity of mammalian species.
Solubilization of a vectorial transmembrane receptor in functional form: aspartate receptor of chemotaxis.
Authors: Bogonez E , Koshland D E
Published: May 2006

The aspartate receptor, an integral membrane protein in the bacterial chemosensory system, has been solubilized in functional form by a combination of detergent, phospholipid, and glycerol. The conformation of the solubilized receptor is the same as that of the protein in vivo, as indicated by aspartate binding, rates of methyl esterification, and quantitative correlation of stimulus with this covalent modification. Studying the functional solubilized receptor in a homogeneous solution avoids many difficulties associated with an in vivo or a vesicle-reconstituted receptor. The technique of adding lipids, detergent, and glycerol to solubilize the protein in active form appears to be generally applicable.
Cloning and sequence analysis of cDNA for human cathepsin D.
Authors: Faust P L , Kornfeld S , Chirgwin J M
Published: May 2006

An 1110-base-pair cDNA clone for human cathepsin D was obtained by screening a lambda gt10 human hepatoma G2 cDNA library with a human renin exon 3 genomic fragment. Poly(A)+ RNA blot analysis with this cathepsin D clone demonstrated a message length of about 2.2 kilobases. The partial clone was used to screen a size-selected human kidney cDNA library, from which two cathepsin D recombinant plasmids with inserts of about 2200 and 2150 base pairs were obtained. The nucleotide sequences of these clones and of the lambda gt10 clone were determined. The amino acid sequence predicted from the cDNA sequence shows that human cathepsin D consists of 412 amino acids with 20 and 44 amino acids in a pre- and a prosegment, respectively. The mature protein region shows 87% amino acid identity with porcine cathepsin D but differs in having nine additional amino acids. Two of these are at the COOH terminus; the other seven are positioned between the previously determined junction for the light and heavy chains of porcine cathepsin D. A high degree of sequence homology was observed between human cathepsin D and other aspartyl proteases, suggesting a conservation of three-dimensional structure in this family of proteins.
Involvement of helicase II (uvrD gene product) and DNA polymerase I in excision mediated by the uvrABC protein complex.
Authors: Caron P R , Kushner S R , Grossman L
Published: May 2006

The bimodal-incision nature of the reaction of UV-irradiated DNA catalyzed by the Escherichia coli uvrABC protein complex potentially leads to excision of a 12- to 13-nucleotide-long damaged fragment. However, the oligonucleotide fragment containing the UV-induced pyrimidine dimer is not released under nondenaturing in vitro reaction conditions. Also, the uvrABC proteins are stably bound to the incised DNA and do not turn over after the incision event. In this communication it is shown that release of the damaged fragment from the parental uvrABC-incised DNA is dependent upon either chelating conditions or the simultaneous addition of the uvrD gene product (helicase II) and the polA gene product (DNA polymerase I) when polymerization of deoxynucleoside triphosphate substrates is concomitantly catalyzed. The product of this multiprotein-catalyzed series of reactions serves as a substrate for polynucleotide ligase, resulting in the restoration of the integrity of the strands of DNA. The addition of the uvrD protein to the incised DNA-uvrABC complex also results in turnover of the uvrC protein. It is suggested that the repair processes of incision, excision, resynthesis, and ligation are coordinately catalyzed by a complex of proteins in a "repairosome" configuration.
Removal of a 67-base-pair sequence in the noncoding region of protooncogene fos converts it to a transforming gene.
Authors: Meijlink F , Curran T , Miller A D , Verma I M
Published: May 2006

Transformation of fibroblasts by protooncogene fos (c-fos) requires the linkage of viral long terminal repeat (LTR) sequences and interruption of 3'-noncoding sequences. We have identified an A + T-rich stretch of 67 nucleotides, located 627-693 base pairs downstream from the coding domain and 123-189 base pairs upstream from the putative poly(A) addition site, removal of which confers transforming activity to the c-fos gene. A novel regulation of the expression of the c-fos gene is proposed, which may be functional in vivo to prevent the gene from becoming an oncogene.
The cytoplasmic matrix: its volume and surface area and the diffusion of molecules through it.
Authors: Gershon N D , Porter K R , Trus B L
Published: May 2006

In this work we look into the problem of why proteins, unlike small molecules, diffuse in the cytoplasm much more slowly than in aqueous solutions. In order to examine whether the cytoplasmic matrix could, by simple obstruction, retard protein diffusion to such an extent, we developed a method to measure semiquantitatively the fractional volume occupied by the cytoplasmic matrix (which includes the microfilaments, intermediate filaments, microtubules, and the microtrabeculae of the cytoplasmic matrix). This method yielded values in the range of only 16-21%. Thus, a more elaborate model is suggested in which the diffusing proteins bind and dissociate constantly from the surfaces in the cytoplasmic matrix. From this model, the diffusion coefficients and the measured values of the fractional volumes, we calculated the corresponding binding constants. These values indicate that most of the diffusing proteins are bound to the matrix at any given time, in spite of the possibility that they may bind and dissociate very rapidly. In addition, from our measurements, we estimate the surface area of structures within the cytoplasmic matrix to be in the range of 69,000-91,000 micron 2 per cell.
Presence of retrovirus reverse transcriptase-related gene sequences in avian cells lacking endogenous avian leukosis viruses.
Authors: Dunwiddie C , Faras A J
Published: May 2006

Using a molecularly cloned viral DNA probe representing the entire avian sarcoma virus (ASV) reverse transcriptase (pol) gene, we have detected related sequences in DNA preparations from two avain species, ev- chickens and Japanese quail, previously demonstrated to lack all endogenous avain leukosis viruses. Nucleotide sequence homology was detected only when hybridization conditions, which allowed the formation of stable duplexes with as much as 30% base mismatch, were used. No sequence homology could be detected when stringent hybridization conditions were used. Nucleotide sequence analysis of a clone representing the major pol-specific EcoRI restriction fragment from ev- chicken embryo fibroblasts revealed DNA homology as high as 72% and implied amino acid homology as high as 82% when compared to the sequence of the ASV strain Prague C pol gene. These data reveal the presence of retroviral pol gene sequences in avian cell lines that lack endogenous retrovirus sequences, suggesting that a reverse transcriptase-related gene exists in these cells as either part of a more distantly evolved retrovirus or a cellular gene.
T-DNA border sequences required for crown gall tumorigenesis.
Authors: Peralta E G , Ream L W
Published: May 2006

Similar 23-base-pair (bp) direct repeats occur at the ends of two adjacent but noncontiguous T-DNAs, TL and TR (left and right T-DNA), in the tumor-inducing plasmid pTiA6NC. Thus, three border repeats lie right and one lies left of TL, which carries the genes needed for tumor maintenance. To determine whether T-DNA transfer and integration (subsequently called T-DNA transmission) require sequences in addition to the 23-bp border repeat, we constructed a deletion removing the three potential TL right borders (the TL right border and both TR borders). Since this deletion severely attenuated virulence, we reintroduced restriction fragments containing the TL right border repeat at a new location to the right of TL and tested their ability to restore virulence. Fragments that carried the border repeat flanked by at least 67 bp of wild-type Ti plasmid sequences on the left and 1035 bp on the right restored virulence completely. Smaller fragments restored virulence significantly but not fully, even though the border repeat remained intact. Therefore, T-region sequences flanking the border repeat in the fully active fragments stimulated T-DNA integration. Fragments that restored virulence fully when inserted in the wild-type orientation stimulated virulence only slightly in the opposite orientation. Thus, the right border sequence promotes T-DNA transfer and integration best in one direction.
Identification of a unique tumor-specific antigen as a novel class I major histocompatibility molecule.
Authors: Philipps C , McMillan M , Flood P M , Murphy D B , Forman J , Lancki D , Womack J E , Goodenow R S , Schreiber H
Published: May 2006

Cancers induced by physical or chemical carcinogens express tumor-specific antigens that are uniquely specific for any given tumor; therefore, there is a seemingly endless variety of these unique antigens. We have studied a UV-induced fibrosarcoma, designated 1591, to elucidate the obscure molecular nature and genetic origins of unique tumor-specific antigens. A monoclonal antibody raised against syngeneic 1591 tumor cells has unique tumor specificity. This tumor-specific monoclonal antibody precipitated from the tumor a 45-kDa molecule associated with a 12-kDa molecule having the pI of beta2-microglobulin. This and other evidence indicated that the 1591 tumor expresses a novel class I molecule. A 1591 variant selected for the absence of binding to the monoclonal antibody lacked the novel class I MHC molecule as well as reactivity with cytotoxic T lymphocytes specific for the 1591 tumor. Furthermore, tumor cells bearing the antigen are rejected while variants that have lost the antigen grow progressively. Fourteen of 14 host-selected progressor tumor variants lost reactivity with the monoclonal antibody and provided further evidence that this novel class I molecule is a transplantation antigen on the parental 1591 tumor required for immune rejection. The identification of a unique tumor-specific antigen as a novel class I major histocompatibility complex gene product allows us to search for the possible genetic mechanisms involved and to explore further the role such molecules play in tumor immunity and malignancy.
A role for suppressor T cells in induction of self-tolerance.
Authors: Gibson J , Basten A , Walker K Z , Loblay R H
Published: May 2006

The potential role of suppressor T cells (Ts) in the induction of self-tolerance was investigated by eliminating I-J+ cells during ontogeny (I-J antigens are encoded by the I-J subregion of the murine major histocompatibility complex). To achieve this, F1 mice were exposed to anti-I-J antibodies via the transplacental route by mating B10.A(3R) females, preimmunized with B10.A(5R) cells, with CBA males. At 6 weeks of age, the offspring were injected with rat erythrocytes (RRBC) to induce erythrocyte autoantibodies. By comparison with age-matched controls, Ts-depleted mice produced significantly higher titers of autoantibody, whereas there was no difference in the antibody response of the two groups to the foreign determinants on the RRBC. The selective increase in autoantibody production was mirrored at the clonal level by the appearance of self-reactive B-cell hybridomas after fusion of RRBC-immune spleen cells with the NS-1 cell line. On the other hand, when helper cell function of RRBC-primed cells was measured in a T-cell proliferative assay, Ts depletion in utero resulted in enhanced T-cell activity to nonself (RRBC) but not to self (mouse erythrocyte) determinants. Thus, helper T cells recognizing nonself determinants on RRBC appeared to be responsible for activating self-specific B cells, presumably through linked recognition of different epitopes on mouse erythrocytes. Taken together, these findings indicate that elimination of I-J+ cells during ontogeny can lead to the appearance and activation of "forbidden" B-cell clones and points to a central role for Ts in induction as well as maintenance of self-tolerance.
Monoclonal antibodies specific for p24, the major core protein of human T-cell leukemia virus type III.
Authors: di Marzo Veronese F , Sarngadharan M G , Rahman R , Markham P D , Popovic M , Bodner A J , Gallo R C
Published: May 2006

Four mouse hybridomas secreting monoclonal antibodies specific for p24, the major core antigen of the human T-cell leukemia virus type III (HTLV-III), have been developed, and their specificities have been partially characterized. These antibodies specifically recognized p24 of HTLV-III in extracts of HTLV-III and in HTLV-III-producing cells. No epitopes cross-reactive with HTLV-I and -II were detected with these antibodies. These hybridomas will be extremely valuable reagents in identifying expression of HTLV-III in infected cultures and in cells or tissues from patients with suspected immunodeficiency syndrome.
Nanomolar concentrations of Bowman-Birk soybean protease inhibitor suppress x-ray-induced transformation in vitro.
Authors: Yavelow J , Collins M , Birk Y , Troll W , Kennedy A R
Published: May 2006

Experiments reported here indicate a crude soybean extract, if defatted with acetone, effectively blocks cell transformation in vitro. An active component of this crude extract is the Bowman-Birk trypsin and chymotrypsin inhibitor. The chymotrypsin-inhibitory region of the Bowman-Birk inhibitor is responsible for suppressing in vitro transformation. Another low molecular weight soybean trypsin inhibitor does not significantly suppress transformation. The Bowman-Birk inhibitor (i) has an irreversible effect on the transformation process, (ii) can suppress radiation-induced transformation even when added to cultures many days after the carcinogen exposure, and (iii) is effective in its ability to suppress transformation when present in the medium at a concentration as low as 0.125 nM.
Microtubule-associated protein 1B: identification of a major component of the neuronal cytoskeleton.
Authors: Bloom G S , Luca F C , Vallee R B
Published: May 2006

The major nontubulin proteins in purified brain microtubules are high molecular weight species traditionally classified into two groups known as microtubule-associated proteins 1 and 2 (MAP 1 and MAP 2). In an earlier study, we found that MAP 1 consisted of a complex of polypeptides and we characterized the highest molecular weight species--MAP 1A--with the use of a monoclonal antibody. In the current report, we describe four monoclonal antibodies raised against electrophoretically purified MAP 1B. All of the antibodies reacted exclusively with this protein. Together with peptide mapping, these results indicated that MAP 1B was structurally distinct from the other MAPs. Another distinctive property of MAP 1B was that most of it remained soluble during microtubule polymerization, resulting in an extreme underestimate of its abundance in the brain. Immunofluorescence microscopy of rat brain sections and cultured rat brain cells indicated that compared to MAP 1A and MAP 2, MAP 1B was particularly prominent in axonal as well as dendritic processes. Together, these data indicate that MAP 1B is a major, previously undescribed component of the neuronal cytoskeleton.
Activation regions in a yeast transposon have homology to mating type control sequences and to mammalian enhancers.
Authors: Errede B , Company M , Ferchak J D , Hutchison C A , Yarnell W S
Published: May 2006

The DNA sequence of the Ty1 activating region from the CYC7-H2 mutant of Saccharomyces cerevisiae is presented. Analysis of the data revealed the presence of four simian virus 40-type enhancer core sequences. Two of the Ty1 enhancer cores are contiguous with sequences also homologous to the diploid control site at MAT alpha. We postulate that these two Ty1 regions of approximately equal to 30 base pairs are regulatory blocks, and we have analyzed deletions to ascertain whether they are necessary for effects of Ty1 on adjacent gene expression. We found that activation is lost when a restriction fragment encompassing both postulated regulatory blocks is deleted. Deletion of restriction fragments that remove only one of the two regulatory blocks has little or no effect on Ty1 activating ability in haploid yeast cells or on repression of this function in diploid yeast cells. Because the most significant internal homologies in the restriction fragments analyzed are the putative regulatory blocks, these observations suggest that enhancer-like sequences are involved in cell-type control of Ty1 effects on gene expression.
T-cell activation by peptide antigen: effect of peptide sequence and method of antigen presentation.
Authors: Watts T H , Gariépy J , Schoolnik G K , McConnell H M
Published: May 2006

A series of synthetic peptide analogues of a determinant recognized by the ovalbumin-specific, I-Ad-restricted, T-cell hybridoma 3DO-54.8 were synthesized. The resulting peptides were tested for activation of 3DO-54.8 cells by using glutaraldehyde-fixed cells as well as reconstituted membranes as antigen-presenting surfaces. The results show that the minimum epitope for activation of this T cell is between 7 and 11 amino acids in length. This region includes two important histidine residues. The order of preference of the various peptide analogues was the same regardless of the method of antigen presentation. However, the amount of peptide required for T-cell activation was considerably higher when reconstituted membranes, rather than fixed cells, were used as antigen-presenting surfaces.
Molecular characterization of novel H-2 class I molecules expressed by a C3H UV-induced fibrosarcoma.
Authors: McMillan M , Lewis K D , Rovner D M
Published: May 2006

Two novel class I-like molecules expressed on tumor 1591, a C3H UV-induced fibrosarcoma, are biochemically characterized using two-dimensional gel electrophoresis, a cross-blocking RIA, and tryptic peptide mapping. One novel molecule that reacts with CP28, a syngeneic tumor-specific monoclonal antibody, appears mosaic because it possesses characteristics of both Kk and Dk class I molecules. The second molecule is closely related but not identical to the bona fide Ld molecule expressed on BALB/c spleen. Thus 1591 expresses at least two novel class I molecules and is vigorously rejected by normal C3H mice, while a variant tumor derived from 1591, termed AS7, does not express these two class I molecules although it still expresses Kk and Dk. The significance of these observations to the immunobiology and genetics of the UV-induced fibrosarcoma system is discussed. Speculations on the role that the major histocompatibility complex may play in the immunosurveillance of neoplasms are also presented.
High prevalence of antibodies to acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) in AIDS and related conditions but not in other disease states.
Authors: Kaminsky L S , McHugh T , Stites D , Volberding P , Henle G , Henle W , Levy J A
Published: May 2006

A rapid, sensitive indirect immunofluorescence assay has been developed for detection of antibodies to the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV). The human T-cell line HUT-78 was chronically infected with ARV-2 and used to detect antibodies to virus-specific cytoplasmic antigens. Because the helper T-cell marker Leu-3 is substantially reduced in this cell line after ARV infection, it appears to be an important receptor for virus infection. Nearly all patients with AIDS and most cases with related conditions showed antibodies against ARV. Some healthy individuals in risk groups for developing AIDS also had antibodies to the agent. In contrast, no antibodies to the virus were found in any individuals outside the risk groups for developing AIDS or with diseases other than those associated with AIDS. The titers of antibodies to ARV and to Epstein-Barr virus varied independently from each other. The level of anti-ARV antibodies in a patient's serum was found to reflect the severity of the disease; it was lower in individuals with more severe manifestations. Taken together, these data support the role of ARV in AIDS and its related disorders.
Effect of side chain-backbone electrostatic interactions on the stability of alpha-helices.
Authors: Scheraga H A
Published: May 2006

An apparent discrepancy between the observed stability of the C-peptide alpha-helix of ribonuclease A and that computed from the Zimm-Bragg parameters sigma and s (obtained by the host-guest technique) is resolved. Side chain-backbone ion-dipole interactions play a role in both systems. However, they are averaged out in the random copolymers used to determine sigma and s for charged residues such as glutamic acid but not in the specific-sequence copolymer, namely, the C-peptide, where they contribute significantly to the helix stability. In considering a specific-sequence alpha-helix, its intrinsic stabilizing free energy (expressed in terms of sigma and s) must be augmented by position-dependent stabilizing long-range electrostatic interactions.
Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression.
Authors: Reddy P , Peterkofsky A , McKenney K
Published: May 2006

Roy et al. [Roy, A., Haziza, C. & Danchin, A. (1983) EMBO J. 2, 791-797] established that translation of Escherichia coli adenylate cyclase initiates at a UUG codon, and they suggested this might decrease the efficiency of translation. We investigated the effect of varying the initiation codon on the expression of the adenylate cyclase (cya) gene. Using oligonucleotide-directed mutagenesis, we changed the UUG initiation codon to GUG and the more common initiator AUG and assayed for cya gene expression in a number of ways. First, the GUG initiation codon, in place of UUG, doubled cya expression when cya was expressed from the dual cya P1/P2 promoters. The corresponding AUG codon construct was nonviable. Second, when the cya gene was placed under the transcriptional control of the thermoinducible phage lambda PL promoter, the relative amounts of cya gene product were 1:2:6 for the UUG, GUG, and AUG initiation codons, respectively. Finally, the cya P2 promoter, Shine-Dalgarno sequence, and the DNA corresponding to the first 86 codons of cya were fused to DNA encoding the E. coli galactokinase gene beginning at the second codon. The relative amounts of the fusion polypeptides, which had galactokinase activity, were 1:2:3 for the UUG, GUG, and AUG initiation codons, respectively. These results demonstrate that the cya UUG initiation codon limits cya expression at the level of translation.
Gene-culture coevolution: models for the evolution of altruism with cultural transmission.
Authors: Feldman M W , Cavalli-Sforza L L , Peck J R
Published: May 2006

Models of sexual haploids under kin selection are constructed. The trait of altruism is transmitted vertically from parent to child, but not in a strictly genetic manner. Two systems of altruism are considered: parent-to-offspring and sib-to-sib. In the former case it is shown that even when Hamilton's conditions for the success of genetically determined altruism are met, genes that increase the transmission of altruism may not invade the population. With sib-to-sib altruism, such genes will always increase initially.
A mutation in the beta-globin gene detected in the progeny of a female mouse treated with ethylnitrosourea.
Authors: Lewis S E , Johnson F M , Skow L C , Popp D , Barnett L B , Popp R A
Published: May 2006

A mouse with a variant hemoglobin was discovered during electrophoretic screening of (C57BL/6J X DBA/2J)F1 progeny of females treated with ethylnitrosourea. The variant trait was transmitted as a simple Mendelian alternate at the Hbb locus in all crosses except those involving the original carrier of the mutation. The proband mouse which received the mutation directly from the mutagen-treated parent was a germinal mosaic for the mutant and normal Hbbs alleles. The mutant allele was designated Hbbs2. The mutant haplotype specifies both an electrophoretically fast hemoglobin band and a hemoglobin band in the normal beta single hemoglobin position. Thus, the mutation has altered one of the tandemly duplicated genes at the Hbbs locus. A comparison of the relative concentrations of the two hemoglobins in Hbbs2 mice demonstrates preferential expression of the mutant gene, possibly analogous to the enhanced expression of Hbbdmaj in the Hbbd haplotype. Analysis of the amino acid sequence of the variant beta-globin revealed that the valine at position 60 was changed to glutamic acid. The simplest mutation mechanism for such an alteration is an A X T----T X A transversion.