bluuebunny/crossref_metadata_2025 huggingface dataset:
Calorie restriction suppresses subgenomic mink cytopathic focus-forming murine leukemia virus transcription and frequency of genomic expression while impairing lymphoma formation.
Authors: Shields B A , Engelman R W , Fukaura Y , Good R A , Day N K
Published: May 2006

Calorie restriction suppresses mammary proviral mRNA expression and protooncogene activation in breast tumor-prone C3H/Ou mice while inhibiting tumor formation. To determine whether the beneficial effects of chronic energy-intake restriction (CEIR) can be extended to an organ site of retrovirus-induced tumorigenesis where the dynamics of growth and sexual maturity are not paramount as they are in breast tissue, calorie restriction of 40% was imposed on thymic lymphoma-prone AKR mice when 4 weeks old. Recombination between various murine leukemia virus (MuLV) mRNAs, resulting in the generation of an 8.4-kilobase genomic-length transcript with mink cytopathic focus-forming (MCF) characteristics, is considered the proximal retroviral event in AKR lymphomagenesis. Thymic expression of subgenomic MCF MuLV mRNA was uniformly suppressed among 6- and 8-week-old CEIR mice (P less than 0.02). This suppression of MuLV transcription preceded a 25% reduction in the appearance of genomic-length MCF transcripts among CEIR mice and a 28% reduction in cumulative lymphoma mortality. The latency to median tumor incidence was extended greater than 3 months by calorie restriction, and median lifespan was extended approximately 50%. Survival curves for the full-fed and CEIR dietary cohorts were found to be significantly different (P less than 0.0001), with full-fed mice experiencing a 3 times greater risk of lymphoma mortality. These findings extend the known range of pathologic states influenced by CEIR in inbred mice and show that retroviral mechanisms involved in generation of lymphoid malignancy can be significantly impaired by calorie restriction.
Identification of a 170-kDa protein associated with the vacuolar Na+/H+ antiport of Beta vulgaris.
Authors: Barkla B J , Blumwald E
Published: May 2006

The effect of the addition of amiloride to the growth medium was tested on the Na+/H+ antiport activity of tonoplast vesicles isolated from sugar beet (beta vulgaris L.) cell suspensions. Cells grown in the presence of NaCl and amiloride displayed an increased antiport activity. Analysis of the kinetic data showed that while the affinity of the antiport for Na+ ions did not change, the maximal velocity of the Na+/H+ exchange increased markedly. These results suggest the addition of more antiport molecules to the tonoplast and/or an increase in the turnover rate of the Na+/H+ exchange. The increase in activity of the antiport by the presence of amiloride was correlated with the enhanced synthesis of a tonoplast 170-kDa polypeptide. The increased synthesis of this polypeptide was detected not only upon exposure of the cells to amiloride but also when the cells were exposed to high NaCl concentrations. Polyclonal antibodies against the 170-kDa polypeptide almost completely inhibited the antiport activity. These results suggest the association of the 170-kDa polypeptide with the vacuolar Na+/H+ antiport.
Dose-dependent differences in the profile of mutations induced by an ultimate carcinogen from benzo[a]pyrene.
Authors: Wei S J , Chang R L , Wong C Q , Bhachech N , Cui X X , Hennig E , Yagi H , Sayer J M , Jerina D M , Preston B D
Published: May 2006

Mutations in the coding region of the hypoxanthine (guanine) phosphoribosyltransferase (HPRT) gene of Chinese hamster V-79 cells were examined after exposure of the cells to a high cytotoxic dose (0.48 microM; 35% survival) and a low noncytotoxic dose (0.04 microM; 100% survival) of the ultimate carcinogen (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-BPDE]. Independent 8-azaguanine-resistant colonies were isolated and cDNAs were prepared by reverse transcription. The coding region of the cDNA of the HPRT gene was amplified by the polymerase chain reaction and sequenced. An examination of the DNA base sequence changes induced by different doses of (+)-BPDE demonstrated that the high dose of (+)-BPDE caused base substitution mutations almost exclusively at G.C base pairs whereas the low dose of (+)-BPDE caused mutations at both G.C and A.T base pairs. Thus, use of a low dose of (+)-BPDE allowed the detection of mutations (at A.T base pairs) that were not readily observed with a high dose of (+)-BPDE. The data also suggest that the low dose of (+)-BPDE may have caused a different profile of base substitutions at G.C base pairs and exon deletions than the high dose. The results indicate dose-dependent differences in the profile of mutations for an ultimate carcinogen.
Evolution of human immunodeficiency virus type 1 nucleotide sequence diversity among close contacts.
Authors: Burger H , Weiser B , Flaherty K , Gulla J , Nguyen P N , Gibbs R A
Published: May 2006

The degree of change in the nucleotide sequence of human immunodeficiency virus type 1 (HIV-1) that occurs when it is transmitted sexually from one individual to another or vertically from mother to child is unknown. Previous studies have shown that most cultured HIV-1 isolates from the same individuals differed in the entire envelope gene nucleotide sequence by up to 2%, although most isolates from unrelated individuals differed by 6-22%. To examine diversity among HIV-1 isolates from close contacts, we determined the nucleotide sequences of viruses from a family with a known epidemiologic profile, in which a woman transmitted HIV-1 heterosexually to her partner and vertically to her daughter. Direct DNA sequence analysis of primary HIV-1 isolates amplified by PCR was used to distinguish the major and minor viral sequences, termed quasispecies, to rapidly determine the predominant sequences and their phylogenetic relationships. The nucleotide sequence diversity of a major portion of the HIV-1 envelope gene was 3.7% between isolates from the woman and her heterosexual partner and 8.5% between isolates from this woman and her daughter, who had been infected for a longer period than the partner. The configuration of the phylogenetic tree demonstrated that the daughter's predominant isolate evolved from a progenitor of her mother's current strain. This study provides evidence of a continuous spectrum of sequence diversity between any two isolates ranging from those derived from the same person to those from close contacts and, ultimately, those from unrelated individuals. These data and methods can be applied to epidemiologic investigations of possible HIV-1 transmission between health care workers and their patients.
Penetration of hard substrates by a fungus employing enormous turgor pressures.
Authors: Howard R J , Ferrari M A , Roach D H , Money N P
Published: May 2006

Many fungal pathogens penetrate plant leaves from a specialized cell called an appressorium. The rice blast pathogen Magnaporthe grisea can also penetrate synthetic surfaces such as poly(vinyl chloride). Previous experiments have suggested that penetration requires an elevated appressorial turgor pressure. In the present report we have used nonbiodegradable Mylar membranes, exhibiting a range of surface hardness, to test the proposition that penetration is driven by turgor. Reducing appressorial turgor by osmotic stress inhibited penetration of these membranes. The size of the turgor deficit required to inhibit penetration was a function of the surface hardness. Penetration of the hardest membranes was inhibited by small decreases in appressorial turgor, while penetration of the softer membranes was sensitive only to large decreases in turgor. Similarly, penetration of the host surface was inhibited in a manner comparable to penetration of the hardest Mylar membranes. Indirect measurements of turgor, obtained through osmotically induced collapse of appressoria, indicated that the infection apparatus can generate turgor pressures in excess of 8.0 MPa (80 bars). We conclude that penetration of synthetic membranes, and host epidermal cells, is accomplished by application of the physical force derived from appressorial turgor.
Characterization of the promoter of the human gene encoding the high-affinity IgG receptor: transcriptional induction by gamma-interferon is mediated through common DNA response elements.
Authors: Pearse R N , Feinman R , Ravetch J V
Published: May 2006

Expression of the high-affinity receptor for IgG (Fc gamma RI) is restricted to cells of myeloid lineage and is induced by gamma-interferon (IFN-gamma) but not by IFN-alpha/beta. The organization of the human Fc gamma RI gene has been determined and the DNA elements governing its cell type-restricted transcription and IFN-gamma induction are reported here. A 39-nucleotide sequence (IFN-gamma response region, or GRR) is defined that is both necessary and sufficient for IFN-gamma inducibility. Sequence analysis of the GRR reveals the presence of promoter elements initially defined for the major histocompatibility complex class II genes: i.e., X, H, and gamma-IRE sequences. Comparison of a number of genes whose expression is induced selectively by IFN-gamma indicates that the presence of these elements is a general feature of IFN-gamma-responsive genes. Our studies suggest that the combination of X, H, and gamma-IRE elements is a common motif in the pathway of transcriptional induction by this lymphokine.
The E-cadherin promoter: functional analysis of a G.C-rich region and an epithelial cell-specific palindromic regulatory element.
Authors: Behrens J , Löwrick O , Klein-Hitpass L , Birchmeier W
Published: May 2006

The cell-cell adhesion molecule E-cadherin is specifically expressed in epithelia and is involved in the maintenance of the epithelial phenotype. Expression of E-cadherin is downregulated in many poorly differentiated carcinomas, which leads to higher motility and invasiveness of the cells. To examine the mechanisms that regulate tissue-specific expression, we have characterized the promoter of the E-cadherin gene. We found that an upstream fragment (positions -178 to +92) mediates strong expression of a chloramphenicol acetyltransferase reporter gene in epithelial cells (i.e., 60% of the level obtained with simian virus 40 promoter/enhancer constructs), whereas in nonepithelial cells this promoter was either inactive or much less active. By DNase I footprinting and gel retardation analysis as well as through functional dissection of the regulatory sequences, we identified two regions that contribute to tissue-specific activity of the promoter: (i) a G-C-rich region between -25 and -58 that generates basic epithelial promoter activity, most likely in combination with an "initiator" element present at the single transcription start site of the gene, and (ii) a palindromic sequence between -75 and -86 (named E-pal) that potentiates the activity of the proximal E-cadherin promoter and confers epithelial cell-specific activity on a simian virus 40 promoter. The E-pal sequence is homologous to cis regulatory elements active in keratin gene promoters and competes with these elements for nuclear factor binding. Interestingly, the activity of the E-cadherin promoter was reduced in dedifferentiated breast carcinoma cells, indicating that the identified elements are subject to negative regulation during tumor progression.
A gene expression screen.
Authors: Wang Z , Brown D D
Published: May 2006

A gene expression screen identifies mRNAs that differ in abundance between two mRNA mixtures by a subtractive hybridization method. The two mRNA populations are converted to double-stranded cDNAs, fragmented, and ligated to linkers for polymerase chain reaction (PCR) amplification. The multiple cDNA fragments isolated from any given gene can be treated as alleles in a genetic screen. Probability analysis of the frequency with which multiple alleles are found provides an estimation of the total number of up- and down-regulated genes. We have applied this method to genes that are differentially expressed in amphibian tadpole tail tissue in the first 24 hr after thyroid hormone treatment, which ultimately induces tail resorption. We estimate that there are about 30 up-regulated genes; 16 have been isolated.
Multiple forms of maturation-promoting factor in unfertilized Xenopus eggs.
Authors: Kuang J , Penkala J E , Ashorn C L , Wright D A , Saunders G F , Rao P N
Published: May 2006

Maturation-promoting factor (MPF), which is functionally defined by its ability to induce frog oocyte maturation independent of protein synthesis, is hypothesized to be the mitotic inducer in eukaryotic cells. Previous studies have demonstrated that the cdc2 protein kinase complex (p34cdc2-cyclin) meets the criteria for MPF. In the present study, we show that MPF activity in extracts of unfertilized Xenopus eggs can be resolved into three fractions by Q-Sepharose chromatography. Of the total MPF activity recovered, approximately 20% was in the flow-through fraction that was accounted for by the cdc2 kinase complex, approximately 40% was in the 0.2 M NaCl eluate, and the remaining approximately 40% was in the 0.5 M NaCl eluate. Neither eluate contained cdc2 kinase, but each could activate cdc2 kinase upon microinjection into Xenopus oocytes. The MPF activity in the two eluates, but not in the flow-through fraction, could be depleted by the mitosis-specific monoclonal antibody MPM-2. This antibody has been shown to inhibit Xenopus oocyte maturation and deplete MPF activity from mature oocyte extract but does not recognize the cdc2 kinase complex. The three MPFs differed in apparent molecular size, H1 kinase activity, and stability at 4 degrees C. We propose that MPF activity in unfertilized Xenopus eggs resides in at least three different molecular species, the combined activities of which may be required for autoamplification of MPF.
Specific initiation by RNA polymerase I in a whole-cell extract from yeast.
Authors: Schultz M C , Choe S Y , Reeder R H
Published: May 2006

A protocol is described for making a soluble whole-cell extract from yeast (Saccharomyces cerevisiae) that supports active and specific transcription initiation by RNA polymerases I, II, and III. Specific initiation by polymerase I decreases in high-density cultures, paralleling the decrease in abundance of the endogenous 35S rRNA precursor. This extract should be useful for studying the molecular mechanisms that regulate rRNA transcription in yeast.
Comparison of long and short forms of the prolactin receptor on prolactin-induced milk protein gene transcription.
Authors: Lesueur L , Edery M , Ali S , Paly J , Kelly P A , Djiane J
Published: May 2006

The biological activities of long and short forms of the prolactin receptor have been compared. These two receptors expressed in mammalian cells were shown to bind prolactin with equal high affinity. The ability of these different forms to transduce the hormonal message was estimated by their capacity to stimulate transcription by using the promoter of a milk protein gene fused to the chloramphenicol acetyltransferase (CAT) coding sequence. Experiments were performed in serum-free conditions to avoid the effect of lactogenic factors present in serum. An approximately 17-fold induction of CAT activity was obtained in the presence of prolactin when the long form of the prolactin receptor was expressed, whereas no induction was observed when the short form was expressed. The present results clearly establish that only the long form of the prolactin receptor is involved in milk protein gene transcription.
Cyclic AMP mediates the direct antiproliferative action of mismatched double-stranded RNA.
Authors: Hubbell H R , Boyer J E , Roane P , Burch R M
Published: May 2006

Previous experiments have demonstrated that double-stranded RNAs (dsRNAs) can exert an antiproliferative effect on human tumor cells, independent of interferon (IFN) induction. However, the mechanism by which dsRNAs inhibit tumor growth has not been elucidated. As a first step in determining the molecular events responsible for growth arrest, we have explored the role of signal transduction through the cAMP system in the antiproliferative effect of the mismatched dsRNA, r(I)n.r(C12,U)n (Ampligen). These studies utilized the human glioma cell line A1235, which does not produce detectable levels of IFN-alpha, -beta, or -gamma in response to mismatched dsRNA treatment. Treatment of A1235 cells with mismatched dsRNA in combination with either 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H-7), which inhibits cAMP-dependent protein kinase and protein kinase C, or N-(2-guanidinoethyl)-5-isoquinolinesulfonamide (HA1004), which preferentially inhibits the cAMP-dependent protein kinase, yielded an antagonism of the mismatched dsRNA-induced antiproliferative effect. Measurement of adenylate cyclase activation showed a dose-dependent increase in activity at antiproliferative mismatched dsRNA concentrations, but not at lower, nonantiproliferative doses. This increase in activity was rapid, seen as early as 30 sec after initiation of treatment, and it was sustained at peak levels for 1-2 hr. Analysis of the intracellular cAMP concentration gave similar kinetics of induction. Exposure of cells to the stable cAMP analogue dibutyryl cAMP yielded dose-dependent inhibition of cell growth. The cAMP phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine also inhibited proliferation. In contrast, neither H-7 nor HA1004 had an effect on growth inhibition induced by human natural IFN-alpha treatment. In addition, antiproliferative doses of IFN-alpha did not increase cAMP concentrations. These results indicate that the cAMP system is utilized by mismatched dsRNA as an early signal transduction mechanism for growth control. Furthermore, the antiproliferative effects induced by mismatched dsRNA and IFN can occur by different mechanisms of action.
The use of sarkosyl in generating soluble protein after bacterial expression.
Authors: Frankel S , Sohn R , Leinwand L
Published: May 2006

Actin, like many other proteins, is highly insoluble after expression in Escherichia coli. In order to understand the origin of insoluble aggregates, we asked whether morphological inclusions were always correlated with insolubility. The strain expressing actin was compared to one that expresses part of the myosin tail; the latter strain yields soluble protein after various cell lysis or disruption procedures. Morphological inclusions were observed in both strains, indicating there is no obligate relationship between solubility and inclusions. Studies presented here suggest that extreme insolubility results from coaggregation of the actin with bacterial outer membrane components upon bacterial lysis. The properties of the outer membrane have been exploited in the development of nondenaturing procedures that yield soluble actin. One procedure involves the disruption of coaggregates with sarkosyl detergent (N-laurylsarcosine); another prevents the formation of coaggregates by lysing in the presence of sarkosyl. These methods may be useful for other proteins that become insoluble after bacterial expression.
Cocaine induces striatal c-fos-immunoreactive proteins via dopaminergic D1 receptors.
Authors: Young S T , Porrino L J , Iadarola M J
Published: May 2006

The protooncogene c-fos produces a phosphoprotein, Fos, which regulates gene transcription processes. In neuronal systems, Fos has been proposed to couple synaptic transmission to changes in gene expression by acting in the cell nucleus in concert with other proteins to form complexes in the promoter regions of target genes. We report here that the acute administration of a single dose of the indirect-acting dopaminergic agonist cocaine increases multiple Fos proteins in rat caudate nucleus. The increase is dose-dependent and is apparent immunocytochemically at 1 hr, maximal at 2 hr, and absent 48 hr after treatment. The increase seen immunocytochemically is composed of several molecular weight species as assessed by Western blotting of proteins from isolated striatal cell nuclei. Administration of the specific dopaminergic receptor antagonists sulpiride and SCH-23390 prior to cocaine support a significant role for D1 but not for D2 receptors in mediating this effect. These data indicate that D1 dopamine receptors are linked to a cellular immediate-early gene system(s) and suggest an action of cocaine at one or more levels of gene expression via modulation of transcriptional processes in activated cells.
Influence of chromosomal integration on glucocorticoid-regulated transcription of growth-stimulating papillomavirus genes E6 and E7 in cervical carcinoma cells.
Authors: von Knebel Doeberitz M , Bauknecht T , Bartsch D , zur Hausen H
Published: May 2006

In most cervical carcinoma cells the E6 and E7 genes of specific human papillomaviruses are transcribed from viral sequences integrated into host cell chromosomes. Glucocorticoids activate the promoter elements of various human papillomaviruses in transient-expression assays. We have analyzed the effect of dexamethasone on the transcription rate of human papillomavirus 18 E6 and E7 genes integrated at different chromosomal sites in four cervical cancer cell lines. Dexamethasone led to an increase in the transcription rate of the integrated E6-E7 sequences in C4-1 and C4-2 cells but led to a decrease in SW 756 cells and did not affect the transcription rate in HeLa cells. However, when the viral promoter elements derived from HeLa or SW 756 cells, in which dexamethasone does not activate transcription of the integrated E6-E7 sequences, were tested in transient-expression assays within the same cell lines, dexamethasone consistently activated the viral promoter. It thus appears that dominant regulatory mechanisms presumably depending on the chromosomal integration site are able to override the response of the viral promoter to steroid hormones. The growth rate of all dexamethasone-treated cell lines correlated consistently with the expression of the papillomavirus E6 and E7 genes, supporting their role in the maintenance of the proliferative phenotype of cervical carcinoma cells. Since human papillomaviruses are integrated into the host cell genome at variable, presumably randomly selected chromosomal loci, regulatory mechanisms that influence viral gene expression, and hence cell growth, may differ among cancers of independent clonal origin.
Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12.
Authors: Lundrigan M D , Köster W , Kadner R J
Published: May 2006

The Escherichia coli btuB gene product is an outer membrane protein required for the active transport of vitamin B12 and other cobalamins. Synthesis of BtuB is repressed when cells are grown in the presence of cobalamins. Mapping of the 5' end of the btuB transcript revealed that a 240-nucleotide transcribed leader precedes the coding sequence. Point mutations causing increased expression under repressing conditions were isolated by use of a btuB-lacZ gene fusion. Mutations at many sites within the leader region affected btuB-lacZ regulation, whereas some base changes upstream of the start of transcription affected the absolute level of expression but not its repressibility. Analysis of btuB-phoA gene fusions and btuB-lacZ operon and gene fusions of various lengths showed that sequences within the btuB coding region (between nucleotides +250 and +350) had to be present for proper expression and transcriptional regulation. Sequences within the leader region (up to +250) conferred regulation of translational fusions. These results indicate that btuB expression is controlled at both the transcriptional and translational levels and that different but possibly overlapping sequences in the transcribed region, including the coding region for the transport protein itself, mediate these two modes of regulation.
In vitro apolipoprotein B mRNA editing: identification of a 27S editing complex.
Authors: Smith H C , Kuo S R , Backus J W , Harris S G , Sparks C E , Sparks J D
Published: May 2006

Specific apolipoprotein B (apoB) mRNA editing can be performed in vitro on apoB RNA substrates. Native gels and glycerol gradient sedimentation have been used to determine the physical properties of the in vitro editing activity in rat liver cytosolic S100 extracts. ApoB RNA substrates were progressively assembled as 27S complexes for 3 hr with similar kinetics as seen for the accumulation of edited RNA. Assembly was not observed on RNAs from apoB deletion constructs that did not support editing. The 27S complex contained both edited and unedited RNA sequences. Inhibition of 27S complex assembly by vanadyl-ribonucleoside complexes was accompanied by inhibition of editing. Based on these data, we propose that the 27S complex is the in vitro "editosome," A "mooring sequence" model for RNA recognition and editosome assembly has been proposed involving RNA sequences flanking the edited nucleotide.
Microglial progenitors with a high proliferative potential in the embryonic and adult mouse brain.
Authors: Alliot F , Lecain E , Grima B , Pessac B
Published: May 2006

Single cell suspensions, prepared from brain stem, cerebellum, and forebrain parenchyma of embryonic and adult mice, were plated on monolayers of an astroglial cell line derived from a spontaneously immortalized mouse cerebellar culture, the D19 clone. A few of the brain cells adhering to the D19 monolayers were immunoreactive to the Mac-1 antibody, which labels all cells of the monocytic and granulocytic lineages. The Mac-1-positive cells proliferated vigorously and later most of them acquired the F4/80 epitope specific for macrophages and microglia cells. Studies in clonal conditions allowed development of large colonies of about 2 x 10(5) cells that expressed typical microglia markers. Bone marrow Mac-1-positive cells cocultured on D19 monolayers were also induced to proliferate, whereas peritoneal macrophages were not. D19 astrocytes express macrophage colony-stimulating factor (CSF-1) activity at a high level, and their conditioned media induced the proliferation of brain and bone marrow Mac-1-positive cells. A specific anti-CSF-1 antiserum completely blocked bone marrow macrophage progenitor proliferation and significantly reduced the multiplication of microglial precursors induced by the D19-conditioned medium. These data indicate that the embryonic and adult mouse brain parenchyma contains potential progenitors for microglial cells.
Characterization of the terminal regions of hepatitis C viral RNA: identification of conserved sequences in the 5' untranslated region and poly(A) tails at the 3' end.
Authors: Han J H , Shyamala V , Richman K H , Brauer M J , Irvine B , Urdea M S , Tekamp-Olson P , Kuo G , Choo Q L , Houghton M
Published: May 2006

We have determined the nucleotide sequence at the extreme 5' and 3' termini of the hepatitis C virus (HCV) genome. Our analyses of these sequences show (i) the nucleotide sequence in the 5' untranslated region is highly conserved among HCV isolates of widely varying geographical origin, (ii) within this region, there are blocks of nucleotide sequence homology with pestiviruses but not with other viruses, (iii) the relative position of short open reading frames present in the same region of the HCV genome is similar to that of the pestiviral genome, (iv) RNAs truncated at the 5' and 3' ends are found, but the origin and functions of these RNAs are unknown, and (v) poly(A) tails appear to be present on 3' subgenomic RNAs. These data differentiate HCV from the flaviviruses and indicate a closer evolutionary relationship of HCV with the pestiviruses. However, HCV also appears to be substantially different from other known pestiviruses. These data are consistent with the assignment of HCV to a separate viral genus.
Lambda YES: a multifunctional cDNA expression vector for the isolation of genes by complementation of yeast and Escherichia coli mutations.
Authors: Elledge S J , Mulligan J T , Ramer S W , Spottswood M , Davis R W
Published: May 2006

This work describes a multifunctional phage lambda expression vector system, lambda YES, designed to facilitate gene isolation from eukaryotes by complementation of Escherichia coli and Saccharomyces cerevisiae mutations. lambda YES vectors have a selection for cDNA inserts using an oligo adaptor strategy and are capable of expressing genes in both E. coli and S. cerevisiae. They also allow conversion from phage lambda to plasmid clones by using the cre-lox site-specific recombination system, referred to here as automatic subcloning. A simple method has been developed for the conversion of any plasmid into a phage lambda cDNA cloning vector with automatic subcloning capability. cDNA libraries constructed in these vectors were used to isolate genes from humans and Arabidopsis thaliana by complementation of yeast and bacterial mutations, respectively.
Comparison of cloned genes provides evidence for intergenomic exchange of DNA in the evolution of a tobacco glucan endo-1,3-beta-glucosidase gene family.
Authors: Sperisen C , Ryals J , Meins F
Published: May 2006

Two genes for prepro glucan endo-1,3-beta-glucosidase (1,3-beta-glucanase; 1,3-beta-D-glucan glucanohydrolase, EC 3.2.1.39) of tobacco were cloned and their sequences were compared with cDNA clones. Southern analysis indicates that the genomic clones represent genes derived from ancestral parents of tobacco similar to the present day species Nicotiana sylvestris and Nicotiana tomentosiformis, whereas the genes represented by two of the cDNA clones appear to be unique to tobacco. The coding sequences of the genomic clones and cDNA clones differed at less than 2.2% of the positions, indicating that the tobacco 1,3-beta-glucanase gene family is highly conserved. Alternating blocks of sequence in the cDNA clones were identical to the coding sequence of the two genomic clones. These results and an analysis of evolutionary distances for nucleotide substitution are consistent with the hypothesis that the evolution of the tobacco 1,3-beta-glucanase gene family has involved exchange of DNA between members of the tomentosiformis and sylvestris subgenomes by recombination or gene conversion.
Mutational analysis of yeast vacuolar H(+)-ATPase.
Authors: Noumi T , Beltrán C , Nelson H , Nelson N
Published: May 2006

Yeast mutants in which genes encoding subunits of the vacuolar H(+)-ATPase were interrupted were assayed for their vacuolar ATPase and proton-uptake activities. The vacuoles from the mutants lacking subunits A (72 kDa), B (57 kDa), or c (proteolipid, 16 kDa) were completely inactive in these reactions. Immunological studies revealed that in the absence of each one of those subunits the catalytic sector was not assembled. Labeling with N,N'-[14C]dicyclohexylcarbodiimide showed the presence of the proteolipid in vacuoles of mutants in which genes encoding subunits of the catalytic sectors were interrupted. No labeling was detected in the mutant in which the gene encoding the proteolipid was interrupted. We conclude that of all the ATPase subunits only the proteolipid is assembled independently and it serves as a template for the assembly of the other subunits. Site-specific mutations were generated in the gene encoding the proteolipid. All of the drastic changes and replacements gave inactive proteins. About half of the single amino acid replacements gave active proteins. Replacing glutamic acid-137 by any of several amino acids, except for aspartic acid, abolished the activity of the enzyme. Other amino acids that may function in proton conductance were changed. It was found that glycine residues may replace amino acids with exchangeable protons.
Differentiation of HL-60 leukemia by type I regulatory subunit antisense oligodeoxynucleotide of cAMP-dependent protein kinase.
Authors: Tortora G , Yokozaki H , Pepe S , Clair T , Cho-Chung Y S
Published: May 2006

A marked decrease in the type I cAMP-dependent protein kinase regulatory subunit (RI alpha) and an increase in the type II protein kinase regulatory subunit (RII beta) correlate with growth inhibition and differentiation induced in a variety of types of human cancer cells, in vitro and in vivo, by site-selective cAMP analogs. To directly determine whether RI alpha is a growth-inducing protein essential for neoplastic cell growth, human HL-60 promyelocytic leukemia cells were exposed to 21-mer RI alpha antisense oligodeoxynucleotide, and the effects on cell replication and differentiation were examined. The RI alpha antisense oligomer brought about growth inhibition and monocytic differentiation, bypassing the effects of an exogenous cAMP analog. These effects of RI alpha antisense oligodeoxynucleotide correlated with a decrease in RI alpha receptor and an increase in RII beta receptor level. The growth inhibition and differentiation were abolished, however, when these cells were exposed simultaneously to both RI alpha and RII beta antisense oligodeoxynucleotides. The RII beta antisense oligodeoxynucleotide alone has been previously shown to specifically block the differentiation inducible by cAMP analogs. These results provide direct evidence that RI alpha cAMP receptor plays a critical role in neoplastic cell growth and that cAMP receptor isoforms display specific roles in cAMP regulation of cell growth and differentiation.
Tyrosine phosphatase CD45 is required for T-cell antigen receptor and CD2-mediated activation of a protein tyrosine kinase and interleukin 2 production.
Authors: Koretzky G A , Picus J , Schultz T , Weiss A
Published: May 2006

CD45, a hematopoietic cell-specific surface antigen, has recently been shown to be a protein tyrosine phosphatase. Expression of CD45 is essential for the T-cell antigen receptor to couple with the phosphatidylinositol second messenger pathway and for antigen-mediated proliferation of T lymphocytes. In this report we describe a CD45-deficient mutant of the human T-cell leukemia line Jurkat. CD45 expression is required for the activation of a T-cell receptor-associated tyrosine kinase as well as the phosphatidylinositol pathway. Additionally, stimulation of T lymphocytes by way of the accessory molecule CD2 requires the expression of CD45. The mutation in the CD45-deficient cell specifically impairs signal transduction by the T-cell receptor and CD2 because activation events by way of another accessory molecule, CD28, are unimpaired.
Design, synthesis, and functional expression of a gene for charybdotoxin, a peptide blocker of K+ channels.
Authors: Park C S , Hausdorff S F , Miller C
Published: May 2006

A gene encoding charybdotoxin (CTX), a K+ channel blocker from scorpion venom, was designed, synthesized, and expressed as a cleavable fusion protein in Escherichia coli. A sequence-specific protease, factor Xa, was used to cleave the fusion protein and thus release the toxin peptide. The recombinant toxin was purified, oxidized to form disulfide bonds, and treated to form N-terminal pyroglutamate. Recombinant CTX is identical to the native venom CTX with respect to high-performance liquid chromatography mobility, amino acid composition, and N-terminal modification. With single Ca2(+)-activated K+ channels as an assay system, recombinant CTX shows blocking and dissociation kinetics identical to the native venom toxin. The synthetic gene and high-level expression of functionally active CTX make it possible to study the fundamental mechanism of the toxin-ion channel interaction.
Dendritic location of neural BC1 RNA.
Authors: Tiedge H , Fremeau R T , Weinstock P H , Arancio O , Brosius J
Published: May 2006

In nerve cells, a specialized protein synthetic machinery is thought to operate in local compartments of dendrites, in particular beneath synaptic junctions, and thereby to facilitate swift adjustments of the postsynaptic protein repertoire in situ. This notion has been supported by the identification of polyribosomes and selected mRNAs in those compartments. In this study, we report the discovery of a specific RNA polymerase III transcript in dendrites. This RNA, a noncoding, 152-nucleotide-long, single-gene transcript known as BC1 RNA, is expressed almost exclusively in the nervous system. In adult rats as well as in immature rats in late developmental stages, BC1 RNA has been located in the dendrites and somata of a subset of neurons in the central and peripheral nervous system. The colocalization of BC1 RNA with dendritic mRNAs and polyribosomes may indicate a role--possibly within the functional unit of a high molecular mass ribonucleoprotein particle--in specific pre- or posttranslational processes in postsynaptic compartments of neurons.
A second maternally expressed Drosophila gene encodes a putative RNA helicase of the "DEAD box" family.
Authors: de Valoir T , Tucker M A , Belikoff E J , Camp L A , Bolduc C , Beckingham K
Published: May 2006

Recently, a family of proteins containing the conserved motif Asp-Glu-Ala-Asp, the "DEAD box" proteins, has been identified. This family is typified by the eukaryotic translation initiation factor eIF4A, and its members are believed to share the functional property of ATP-dependent RNA unwinding. One of the previously identified members of this family (vasa) is the product of a maternally expressed gene from Drosophila melanogaster that is known to play a role in the formation of the embryonic body plan. We report here the isolation of a Drosophila gene that has an mRNA expression pattern somewhat similar to that of vasa and also encodes a DEAD box protein. We have termed this gene ME31B to reflect its maternal (ovarian germ-line) expression and its location within the 31B chromosome region. Comparisons with the other members of this family reveal that although ME31B is most like the protein Tif1/Tif2, which probably represents the Saccharomyces cerevisiae version of eIF4A, it is unlikely that ME31B represents the Drosophila eIF4A protein per se. A search for mutations in the ME31B gene has established that the P element which causes the female-sterile mutation flipper lies in the 3' flank of the ME31B gene.
Different mRNAs code for dopa decarboxylase in tissues of neuronal and nonneuronal origin.
Authors: Krieger M , Coge F , Gros F , Thibault J
Published: May 2006

A cDNA clone for dopa decarboxylase (EC 4.1.1.28) has been isolated from a rat pheochromocytoma cDNA library and the cDNA sequence has been determined. It corresponds to an mRNA of 2094 nucleotides. The length of the mRNA was measured by primer-extension of rat pheochromocytoma RNA and the 5' end of the sequence of the mRNA was confirmed by the PCR. A probe spanning the translation initiation site of the mRNA was used to hybridize with mRNAs from various organs of the rat. S1 nuclease digestion of the mRNAs annealed with this probe revealed two classes of mRNAs. The comparison of the cDNA sequence and published sequences for rat liver, human pheochromocytoma, and Drosophila dopa decarboxylase supported the conclusion that two mRNAs are produced: one is specific for tissue of neuronal origin and the other is specific for tissues of nonneuronal (mesodermal or endodermal) origin. The neuronal mRNA contains a 5' untranslated sequence that is highly conserved between human and rat pheochromocytoma including a GA stretch. The coding sequence and the 3' untranslated sequence of mRNAs from rat liver and pheochromocytoma are identical. The rat mRNA differs only in the 5' untranslated region. Thus a unique gene codes for dopa decarboxylase and this gene gives rise to at least two transcripts presumably in response to different signals during development.
Fibroblast growth factor-mediated proliferation of central nervous system precursors depends on endogenous production of insulin-like growth factor I.
Authors: Drago J , Murphy M , Carroll S M , Harvey R P , Bartlett P F
Published: May 2006

Fibroblast growth factor stimulates proliferation and subsequent differentiation of precursor cells isolated from the neuroepithelium of embryonic day 10 mice in vitro. Here we show that fibroblast growth factor-induced proliferation is dependent on the presence of insulin-like growth factors (IGFs) and that IGF-I is endogenously produced by the neuroepithelial cells. Blocking of endogenous IGF-I activity with anti-IGF-I antibodies results in complete inhibition of fibroblast growth factor-mediated proliferation and in cell death. IGF-I alone acts as a survival agent. These observations correlate with the detection of transcripts for IGF-I and basic fibroblast growth factor in freshly isolated neuroepithelium and are consistent with an autocrine action of these factors in early brain development in vivo.
Approximate entropy as a measure of system complexity.
Authors: Pincus S M
Published: May 2006

Techniques to determine changing system complexity from data are evaluated. Convergence of a frequently used correlation dimension algorithm to a finite value does not necessarily imply an underlying deterministic model or chaos. Analysis of a recently developed family of formulas and statistics, approximate entropy (ApEn), suggests that ApEn can classify complex systems, given at least 1000 data values in diverse settings that include both deterministic chaotic and stochastic processes. The capability to discern changing complexity from such a relatively small amount of data holds promise for applications of ApEn in a variety of contexts.
Sodium pump isozymes are differentially expressed in electrically dissimilar regions of colonic circular smooth muscle.
Authors: Burke E P , Sanders K M , Horowitz B
Published: May 2006

Molecular analyses of Na,K-ATPase abundance and alpha-subunit isoform distribution were performed to determine whether pump expression varies at different points through the thickness of the circular layer of colonic smooth muscle. The mRNA and polypeptides of Na,K-ATPase alpha 1 and beta subunits were twice as abundant in the submucosal region of the circular layer, which has previously been shown to generate large pump potentials. Sodium pump activity directly correlated with the relative abundance of the alpha 1 polypeptide. These data show that sodium pump expression varies in electrically dissimilar regions of the circular layer.
Error bounds for the fundamental and secondary theorems of natural selection.
Authors: Nagylaki T
Published: May 2006

Error bounds are derived for the approximation delta Z approximately C/W, where delta Z, C, and W denote the rate of change of the mean of a character under selection, the genic (or additive genetic) covariance of the character and fitness (i.e., the covariance of the average effect on the character and the average excess for fitness of every allele that affects the character), and the mean fitness, respectively. Generations are discrete and nonoverlapping; the monoecious population mates at random. The character is determined by arbitrarily many multiallelic loci without epistasis; the linkage map is also arbitrary. The genotypic values of the character are constant. Rounds on the absolute error in the above approximation are deduced for an arbitrary character, and these are converted to bounds on the relative error when the character is fitness itself. In that case, C is the genic variance in fitness, and the relative error cannot exceed one half the greatest genotypic selection coefficient.
Expression of a mitogen-responsive gene encoding prostaglandin synthase is regulated by mRNA splicing.
Authors: Xie W L , Chipman J G , Robertson D L , Erikson R L , Simmons D L
Published: May 2006

Rous sarcoma virus was shown to induce in chicken embryo fibroblasts (CEF) a 4.1-kilobase mRNA (designated CEF-147) encoding a 603-amino acid protein. Analysis of the protein sequence showed that it shared 59% amino acid identity with sheep prostaglandin G/H synthase, the enzyme that catalyzes the rate-limiting steps in the production of prostaglandins. Significant differences, at both the protein and mRNA levels, existed between the src oncogene product-inducible prostaglandin synthase and the protein isolated and cloned from sheep seminal vesicle, suggesting that the src-inducible prostaglandin synthase may be a new form of the enzyme. A distinguishing feature of src-inducible prostaglandin synthase mRNA is its low abundance in nonproliferating chicken embryo fibroblasts and its relatively high abundance in src-transformed cells. Additionally, the majority of the src-inducible prostaglandin synthase RNA present in nonproliferating cells was found to be nonfunctional because of the presence of an unspliced intron that separated the signal peptide from the remainder of the protein. Upon mitogenic stimulation, this intron was removed, resulting in the induction of fully-spliced CEF-147 mRNA.
Effects of pH and polysaccharides on peptide binding to class II major histocompatibility complex molecules.
Authors: Harding C V , Roof R W , Allen P M , Unanue E R
Published: May 2006

The binding of immunogenic peptides to class II major histocompatibility molecules was examined at various pH values. We studied binding of peptides containing residues 52-61 from hen egg lysozyme (HEL) to I-Ak on fixed peritoneal macrophages or to solubilized affinity-purified I-Ak. Optimum binding occurred at pH 5.5-6.0 with accelerated kinetics relative to pH 7.4; equilibrium binding was also higher at pH 5.5-6.0 than at 7.4. Similar enhancement at pH 5-6 was observed for the binding of hemoglobin-(64-76) to I-Ek and of ribonuclease-(41-61) to I-Ak. In contrast, the binding of HEL-(34-45) to I-Ak was minimally enhanced at acid pH. Dissociation of cell-associated or purified peptide-I-Ak complexes was minimal between pH 5.5 and 7.4, with increased dissociation only at or below pH 4.0 [HEL-(46-61)] or pH 5.0 [HEL-(34-45)]. Thus, optimum peptide binding occurs at pH values similar to the endosomal environment, where the complexes appear to be formed during antigen processing. In addition, we examined the effect of a number of polysaccharides on the binding of peptide to I-Ak. None of these competed with the HEL peptide 125I-labeled YE52-61 for binding to I-Ak. [3H]Dextran also failed to bind purified I-Ak. Polysaccharides do not appear to bind to class II major histocompatibility complex molecules, which explains the T-cell independence of polysaccharide antigens.
Analysis of affinity and structural selectivity in the binding of proteins to glycosaminoglycans: development of a sensitive electrophoretic approach.
Authors: Lee M K , Lander A D
Published: May 2006

Members of several families of cell surface and secreted proteins bind glycosaminoglycans (GAGs), the structurally heterogeneous polysaccharides found on proteoglycans. To understand the physiological significance of the interactions of proteins with GAGs, it is critical that relationships between GAG structure and binding be analyzed. It is particularly important that interactions depending on common structural features of GAGs (e.g., size, charge density, and disaccharide repeat unit) be distinguished from those mediated by specific sequences of carbohydrate modification. Gathering the information needed to make such distinctions has so far been difficult, however, partly because structurally homogeneous samples of GAGs are lacking but also because of technical difficulties associated with performing and interpreting assays of protein-GAG binding. We describe an electrophoretic method useful for both measuring affinity and evaluating structural selectivity in protein-GAG binding. Data are presented on the binding of the GAG heparin to the protease inhibitor antithrombin III, the acidic and basic fibroblast growth factors, and the extracellular matrix protein fibronectin. Results obtained with fibronectin are consistent with a model in which high-affinity binding (Kd approximately 34 nM) is mediated through the recognition of specific carbohydrate sequences.