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At least 559 records · Page 31Linked to original sources
PubMed1994

Expression of functional influenza virus A polymerase proteins and template from cloned cDNAS in recombinant vaccinia virus infected cells.

cDNAs containing the coding sequences of influenza type A virus polymerase proteins (PB1, PB2 and PA) and nucleoprotein (NP) have been expressed in mammalian cells by T7 polymerase provided by a recombinant vaccinia virus. The resulting proteins are able to form a complex that can copy a negative sense influenza-like RNA, transcribed from input DNA by the T7 polymerase, into a positive sense RNA that is translated into active chloramphenicol acetyltransferase (CAT). In this system there is no requirement for helper virus or purified viral core proteins, thus it will allow manipulation of all proteins as well as template for studies of replication in influenza virus.

Animals↗
PubMed2000

Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve.

The Z curve is a three-dimensional space curve constituting the unique representation of a given DNA sequence in the sense that each can be uniquely reconstructed from the other. Based on the Z curve, a new protein coding gene-finding algorithm specific for the yeast genome at better than 95% accuracy has been proposed. Six cross-validation tests were performed to confirm the above accuracy. Using the new algorithm, the number of protein coding genes in the yeast genome is re-estimated. The estimate is based on the assumption that the unknown genes have similar statistical properties to the known genes. It is found that the number of protein coding genes in the 16 yeast chromosomes is </=5645, significantly smaller than the 5800-6000 which is widely accepted, and much larger than the 4800 estimated by another group recently. The mitochondrial genes were not included into the above estimate. A codingness index called the YZ score (YZ OE [0,1]) is proposed to recognize protein coding genes in the yeast genome. Among the ORFs annotated in the MIPS (Munich Information Centre for Protein Sequences) database, those recognized as non-coding by the present algorithm are listed in this paper in detail. The criterion for a coding or non-coding ORF is simply decided by YZ > 0.5 or YZ < 0.5, respectively. The YZ scores for all the ORFs annotated in the MIPS database have been calculated and are available on request by sending e-mail to the corresponding author.

Algorithms↗
PubMed1997

Keratin 8 and 18 expression in mesenchymal progenitor cells of regenerating limbs is associated with cell proliferation and differentiation.

Keratins are considered markers of epithelial differentiation. In lower vertebrates, however, immunoreactivity for keratin 8 and 18 has been reported in nonepithelial cells, particularly in mesenchymal progenitor cells of regenerating complex body structures. To confirm that such reactivity does indeed reflect keratin expression and to investigate their possible role in regeneration, we have isolated clones coding for the newt homologues of keratin 8 and 18 (NvK8 and NvK18, respectively) and studied their distribution and changes in their expression following experimental manipulations. Analysis of NvK8 and NvK18 transcripts confirms that K8 and K18 are expressed in the blastemal cells of regenerating newt limbs and that their expression is first observed 3-5 days after amputation, when the blastemal cells start to proliferate under the influence of the nerve, whose presence is essential for regeneration to proceed. In contrast, no induction of these keratins is observed following amputation of a larval limb at a stage when organogenesis is proceeding in a nerve-independent manner. To establish whether there is a causal relationship between keratin expression and cell proliferation in the adult limb blastema, we have investigated whether their expression is nerve-dependent and whether suppression of their expression in cultured blastemal cells affects cell division and differentiation. Analysis of keratins in denervated limbs demonstrates that the nerve is not necessary to induce their expression. However, treatment of cultured blastemal cells with K8 and K18 anti-sense oligonucleotides significantly decreases DNA synthesis and induces changes in cell morphology, suggesting that expression of these keratins during regeneration may be necessary for the maintenance of the undifferentiated and proliferative state of blastemal cells.

Amino Acid Sequence↗
PubMed2002

Negative regulation of monocyte chemoattractant protein-1 gene expression by a mouse estrogen-enhanced transcript.

A novel gene containing two typical estrogen responsive elements (ERE) was cloned from MTEC1 cells, a mouse thymus epithelial cell line that produces constitutively many chemokines. This gene is a homologue of the rat estrogen-enhanced transcript (EET) gene, and is called the mEET gene. mEET protein is expressed in cytoplasm. Addition of 17 beta-estradiol (E2) to the MTEC1 cell cultures enhanced mEET mRNA expression and, meanwhile, significantly inhibited monocyte chemoattractant protein-1 (MCP-1) production. To analyze the functional links between the expression of mEET and of MCP-1, we transfected MTEC1 cells with ERE-deleted antisense- or sense-mEET complementary (c)DNA construct and activated the transfected mEET cDNA in stable MTEC1 transfectants with doxycycline (Dox). Dox-induced activation of the mEET gene profoundly inhibited MCP-1 expression at both mRNA and protein levels and alleviated its chemotactic activity. Conversely, inactivation of the mEET gene substantially augmented MCP-1 expression. Activation of the mEET gene markedly attenuated activity of nuclear NF-kappaB. In summary, we have first demonstrated that estrogen-imposed inhibition of MCP-1 expression occurs through the activation of the mEET gene, its product suppresses nuclear NF-kappaB and negatively regulates MCP-1 gene activation.

Amino Acid Sequence↗
PubMed2003

Bioinformatic principles underlying the information content of transcription factor binding sites.

Empirically, it has been observed in several cases that the information content of transcription factor binding site sequences (R(sequence)) approximately equals the information content of binding site positions (R(frequency)). A general framework for formal models of transcription factors and binding sites is developed to address this issue. Measures for information content in transcription factor binding sites are revisited and theoretic analyses are compared on this basis. These analyses do not lead to consistent results. A comparative review reveals that these inconsistent approaches do not include a transcription factor state space. Therefore, a state space for mathematically representing transcription factors with respect to their binding site recognition properties is introduced into the modelling framework. Analysis of the resulting comprehensive model shows that the structure of genome state space favours equality of R(sequence) and R(frequency) indeed, but the relation between the two information quantities also depends on the structure of the transcription factor state space. This might lead to significant deviations between R(sequence) and R(frequency). However, further investigation and biological arguments show that the effects of the structure of the transcription factor state space on the relation of R(sequence) and R(frequency) are strongly limited for systems which are autonomous in the sense that all DNA-binding proteins operating on the genome are encoded in the genome itself. This provides a theoretical explanation for the empirically observed equality.

Animals↗
PubMed1996

The mutation rate of human immunodeficiency virus type 1 is influenced by the vpr gene.

A system has been designed to study the in vivo forward rate of mutation of human immunodeficiency virus type 1 (HIV-1) during one round of replication. A HIV-1 shuttle vector was used that contained the lacZ alpha peptide gene as a reporter for mutations. The forward mutation rate of HIV-1 was found to be 3 x 10(-5) mutations per target base pair per cycle, or about 20-fold lower than the error rates reported for purified HIV-1 reverse transcriptase with sense-strand RNA and DNA templates of the lacZ alpha peptide gene in a cell-free system. To test the hypothesis that the vpr gene product might, at least in part, account for the lower mutation rate observed in vivo, a HIV-1 vector was replicated to determine if the mutation rate was higher in the absence of the wild-type vpr gene product. A vpr- shuttle vector had an overall mutation rate as much as 4-fold higher than that of the parental vector. A shuttle vector with an amino acid substitution in Vpr that prevents efficient incorporation of Vpr into virus particles was found to have a mutation frequency similar to that of the vpr- vector, and was interpreted to indicate a requirement for Vpr incorporation into the virus particle in order to observe the influence of vpr on the mutation rate. Replication of a vpr- shuttle vector in the presence of a wild-type vpr expression plasmid led to a mutation frequency similar to that of the parental vector, suggesting that the vpr mutation could be complemented in trans. Immunoprecipitation analysis indicated that Vpr virion incorporation coincided with the influence of vpr on the mutation rate.

Animals↗
PubMed1994

The FNR family of transcriptional regulators.

Homologues of the transcriptional regulator FNR from Escherichia coli have been identified in a variety of taxonomically diverse bacterial species. Despite being structurally very similar, members of the FNR family have disparate regulatory roles. Those from Shewanella putrefaciens, Pseudomonas aeruginosa, Pseudomonas stutzeri and Rhodopseudomonas palustris are functionally similar to FNR in that they regulate anaerobic respiration or carbon metabolism. Four rhizobial proteins (from Rhizobium meliloti, R. leguminosarum, B. japonicum and Azorhizobium caulinodans) are involved in the regulation of nitrogen fixation; a fifth (from Rhizobium strain IC3342) has unknown function. Two proteins from mammalian pathogens (Actinobacillus pleuropneumoniae and Bordetella pertussis) may be involved in the regulation of toxin expression. The FNR protein of Vibrio fischeri regulates bioluminescence, and the function of the one known FNR homologue from a Gram-positive organism (Lactobacillus casei) remains to be elucidated. Some members of this family, like FNR itself, appear to function as sensors of oxygen availability, whereas others do not. The ability to sense and respond to oxygen limitation may be correlated with the presence of cysteine residues which, in the case of FNR, are thought to be involved in oxygen or redox sensing. The mechanism of DNA sequence recognition is probably conserved, or very similar, throughout this family. In a number of other Gram-negative species, there is good indirect evidence for the existence of FNR analogues; these include Alcaligenes eutrophus, A. denitrificans, A. faecalis, Paracoccus denitrificans and a number of Pseudomonas species.

Amino Acid Sequence↗
PubMed1994

A rapid method for detection and identification of flaviviruses by polymerase chain reaction and nucleic acid hybridization.

A polymerase chain reaction (PCR) technique was developed and evaluated for the detection of flaviviruses. A set of sense and antisense oligomeric DNA primers were constructed from nucleotide sequences of the conserved region of the genome of several different flaviviruses. Virus specific complementary DNA (cDNA) was prepared by reverse transcription of total RNA extracted from infected cell cultures. Amplified cDNA was identified by nucleic acid hybridization with specific oligomeric internal probes. Various conditions, such as number of cycles and annealing temperature were examined to optimize the detection of viral RNAs from infected cell cultures. Slot blot hybridization with a radioactive probe was used to evaluate the sensitivity of PCR amplification. The PCR amplified RNA sequences of dengue 2 (DEN-2), West Nile (WN), St. Louis encephalitis (SLE) and Kunjin (KUN) virus and detected 0.1 to 1 pg of viral RNA. Japanese encephalitis (JE), Yellow Fever virus (YF), DEN-1, 3, and 4 viruses were not amplified. The more frequent occurrence of mismatches in the 3' primer binding site may explain the failure to amplify cDNA of these viruses.

Aedes↗
PubMed2005

Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray.

In this study, we constructed a 22k wheat oligo-DNA microarray. A total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multistep selection of the sense strand, 21,939 60-mer oligo-DNA probes were selected for attachment on the microarray slide. This 22k oligo-DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than 2-fold in response to salt. These included genes known to mediate response to salt, as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo-DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.

Expressed Sequence Tags↗
PubMed2004

Nucleotide binding to DNA gyrase causes loss of DNA wrap.

DNA gyrase negatively supercoils DNA in a reaction coupled to the binding and hydrolysis of ATP. Limited supercoiling can be achieved in the presence of the non-hydrolysable ATP analogue, 5'-adenylyl beta,gamma-imidodiphosphate (ADPNP). In order to negatively supercoil DNA, gyrase must wrap a length of DNA around itself in a positive sense. In previous work, the effect of ADPNP on the gyrase-DNA interaction has been assessed but has produced conflicting results; the aim of this work was to resolve this conflict. We have probed the wrapping of DNA around gyrase in the presence and in the absence of ADPNP using direct observation by atomic force microscopy (AFM). We confirm that gyrase indeed generates a significant curvature in DNA in the absence of nucleotide and we show that the addition of ADPNP leads to a complete loss of wrap. These results have been corroborated using a DNA relaxation assay involving topoisomerase I. We have re-analysed previous hydroxyl-radical footprinting and crystallography data, and highlight the fact that the gyrase-DNA complex is surprisingly asymmetric in the absence of nucleotide but is symmetric in the presence of ADPNP. We suggest a revised model for the conformation of DNA bound to the enzyme that is fully consistent with these AFM data, in which a closed loop of DNA is stabilised by the enzyme in the absence of ADPNP and is lost in the presence of nucleotide.

Adenosine Triphosphate↗
PubMed1998

Metastasis of human colon cancer is altered by modifying expression of the beta-galactoside-binding protein galectin 3.

BACKGROUND & AIMS: Galectin 3 is a beta-galactoside-binding protein whose expression has been correlated with advanced tumor stage in the colon, but direct evidence for a role in metastasis is lacking. The current study was designed to more directly establish the role of galectin 3 in colon cancer metastasis. METHODS: Galectin 3 levels were manipulated in human colon cancer cells using eukaryotic expression constructs designed to express the complete galectin 3 complementary DNA in either the sense or antisense orientation. Liver colonization was assessed in athymic mice after splenic-portal inoculation or after spontaneous metastasis during cecal growth. RESULTS: Introduction of galectin 3 antisense into metastatic colon cancer cells (LSLiM6, HM7) resulted in a significant reduction in galectin 3-specific messenger RNA and total and cell surface galectin 3 protein. Conversely, stable integration of galectin 3 in the sense orientation resulted in an increase in cellular and cell surface galectin 3 in cells of low metastatic potential (LS174T). Reduction in galectin 3 levels was associated with a marked decrease in liver colonization and spontaneous metastasis by LSLiM6 and HM7 cells, whereas up-regulation of galectin 3 resulted in increased metastasis by LS174T cells. CONCLUSIONS: This study provides direct evidence that galectin 3 plays an important role in colon cancer metastasis.

Adenocarcinoma↗
PubMed1981

Anthramycin binding to deoxyribonucleic acid-mitomycin C complexes. Evidence for drug-induced deoxyribonucleic acid conformational change and cooperativity in mitomycin C binding.

Anthramycin and mitomycin C (MC) are two DNA reactive drugs, which bind covalently to GC pairs producing different effects on DNA: anthramycin stiffening and MC distorsion. This paper describes experiments in which we have used anthramycin as a probe to sense quantitatively the effects on DNA of MC binding. Saturation binding experiments show that both anthramycin and MC partially inhibit the binding of the other drug to DNA (maximum inhibition by MC and anthramycin, 22.4% and 19.7%, respectively) but by a mechanism other than direct site exclusion. This suggests that MC binds in the major groove of DNA, since anthramycin is known to bind in the minor groove. An abrupt reduction in the binding of anthramycin to DNA-MC complexes occurs between MC binding ratios of 0.030 and 0.035, which parallels and probably results from sudden intensification of a MC-induced DNA conformational change occurring between these binding ratios. Dialysis measurements indicate that anthramycin is very possibly binding at sites distant from MC sites and suggest a clustering of closely bound MC chromophores resulting from possible cooperative binding. S1 nuclease digest experiments demonstrate an initial enhancement of nuclease activity in DNA-MC complexes, the magnitude of which correlates well with the reduction of anthramycin binding, relative to the degree of MC binding. The enhanced nuclease activity in these complexes indicates regions of exposed DNA or helix base distortion which is related to or is the result of conformational change.

Animals↗
PubMed2003

p53's believe it or not: lessons on transcription-independent death.

The requirement for an intact p53 signaling pathway to sense tumor-promoting DNA damage is evident from over 20 years of molecular, cellular, and whole animal studies. Without a doubt, p53's major contribution in maintaining the genomic integrity of multicellular organisms is through transcriptional regulation of genes required for cell cycle arrest, DNA repair, and apoptosis. Nonetheless, evidence is mounting that p53 has an extranuclear role in the cytoplasm to induce apoptosis, perhaps coupled to its transcriptional effects, or conceivably at instances when transcription is not optimal or possible. This phenomenon, transcription-independent p53-induced apoptosis (TIPA), has been described for almost 10 years, yet little is known about mechanisms by which p53 can directly engage the apoptotic cascade in the absence of transcription. Here we will explore what is currently known about TIPA learned from various p53 mutants and truncations, along with discussing several proposed mechanisms.

Animals↗
PubMed2004

Human hRad1 but not hRad9 protects hHus1 from ubiquitin-proteasomal degradation.

Three of the Rad family proteins, Rad9, Rad1, and Hus1, can interact with each other and form a heterotrimeric complex that is thought to play a role in the sensing step of the DNA integrity checkpoint pathways, but the nature of the Rad9-Rad1-Hus1 complex assembly remains enigmatic. Here, we demonstrate that the human hRad1 protein plays a significant role as molecular chaperone in the process of the hRad9-hRad1-hHus1 heterotrimeric complex formation. In contrast to hRad1, hHus1 is an unstable protein that is actively degraded via the ubiquitin-proteasome pathway. We show that treating cells with proteasome-specific inhibitors stabilizes hHus1 expression. Moreover, hRad1 can associate with hHus1 in the absence of hRad9 and protect hHus1 from ubiquitination and degradation in the cytoplasm. Importantly, genotoxic stress induces hRad1 expression and stabilizes the hHus1 protein. Taken together, these findings suggest a novel role of hRad1 as a potential intrinsic chaperone in the stabilization of hHus1 for the hRad9-hRad1-hHus1 checkpoint complex formation.

Cell Cycle↗
PubMed2026

Symmetric and near-symmetric cyanine probes for G-quadruplexes: molecular recognition, signal transduction, and biological applications.

G-quadruplexes (G4s) are dynamic noncanonical nucleic-acid structures involved in genome maintenance, transcription, RNA metabolism, and mitochondrial function, and are implicated in disease-associated processes. Symmetric and near-symmetric cyanines are versatile platforms for G4 recognition because their polymethine length, terminal heterocycles, charge distribution, conformational freedom, and supramolecular organization can be systematically tuned within related scaffolds. This review discusses how these structural features control G4 recognition and optical signal transduction through terminal G-tetrad stacking, loop and groove contacts, restriction of molecular motion, and aggregate reorganization. We first summarize in vitro recognition, structural discrimination, and G4-mediated sensing, and then discuss DNA and RNA G4 imaging, G4-associated biological processes, and emerging in vivo applications. Particular attention is given to several distinctions that are essential for interpreting probe performance: binding affinity versus fluorescence activation, topology preference versus DNA/RNA selectivity, organelle accumulation versus molecular targeting, and imaging contrast versus biological validation. Overall, molecular symmetry is considered a tunable design variable rather than a direct predictor of performance. Future studies should emphasize matched structural series, reversible and minimally perturbing probes, optical readouts that are less dependent on probe concentration, clear separation of DNA and RNA contributions, and standardized validation across solution, cellular, and whole-organism studies.

Journal Article↗
PubMed1999

Role of tissue factor expression on tumour cell invasion and growth of experimental pancreatic adenocarcinoma.

BACKGROUND: Tissue factor (TF), the physiological procoagulant, is expressed in pancreatic tissue as a result of malignant transformation. The aim of this investigation was to assess its role in pancreatic tumour cell invasion and primary tumour growth. METHODS: The full-length TF gene (1360 base pairs) was cloned into the plasmid DNA vector pcDNA3 in sense and antisense orientations, and these vectors were used to transfect the MIA PaCa-2 human pancreatic adenocarcinoma cell line. TF gene expression was characterized by Northern blot analysis, total cellular antigenic content by enzyme-linked immunosorbent assay and cell surface procoagulant activity by enzymatic assay. Invasion of tumour cells in vitro was determined by a standard Matrigel assay, and primary tumour growth was measured in immunodeficient mice. RESULTS: Overexpression of the TF gene, confirmed by an increased signal on Northern blotting, was associated with increases in both total antigenic content for TF (P = 0.001) and cell surface procoagulant activity (P = 0.008) in sense cells compared with wild-type cells. Likewise, both in vitro tumour cell invasion (P = 0.001) and primary tumour growth (P = 0.007) were increased in sense transfectants. CONCLUSION: Expression of TF enhances in vitro invasion and primary tumour growth of MIA PaCa-2 cells, suggesting that this procoagulant molecule might have a role in pancreatic tumour biology. Presented in part to the 83rd meeting of the Surgical Research Society, Oxford, UK, January 1996 and awarded the David Patey Prize, and in part to the 1997 Annual Meeting of the Association of Surgeons of Great Britain and Ireland, Bournemouth, UK, April 1997.

Adenocarcinoma↗
PubMed2004

Regulation of ultraviolet light-induced gene expression by gene size.

UV light induces the expression of a wide variety of genes. At present, it is unclear how cells sense the extent of DNA damage and alter the expression of UV-induced genes appropriately. UV light induces DNA damage that blocks transcription, and the probability that a gene sustains transcription-blocking DNA damage is proportional to locus size and dose of UV light. Using colon carcinoma cells that express a temperature-sensitive variant of p53 and undergo p53-dependent apoptosis after UV irradiation, we found that the number of p53-induced genes identified by oligonucleotide microarray analysis decreased in a UV dose-dependent manner. This was associated with a statistically significant shift in the spectrum of p53-induced genes toward compact genes with fewer and smaller introns. Genes encoding proapoptotic proteins involved in the initiation of the mitochondrial apoptotic cascade were prominent among the compact p53 target genes, whereas genes encoding negative regulators of p53 and the mitochondrial apoptotic pathway were significantly larger. We propose that the shift in spectrum of UV-responsive gene expression caused by passive effects of UV lesions on transcription acts as a molecular dosimeter, ensuring the elimination of cells sustaining irreparable transcription-blocking DNA damage.

Base Sequence↗
PubMed2002

Electronic detection of DNA by its intrinsic molecular charge.

We report the selective and real-time detection of label-free DNA using an electronic readout. Microfabricated silicon field-effect sensors were used to directly monitor the increase in surface charge when DNA hybridizes on the sensor surface. The electrostatic immobilization of probe DNA on a positively charged poly-l-lysine layer allows hybridization at low ionic strength where field-effect sensing is most sensitive. Nanomolar DNA concentrations can be detected within minutes, and a single base mismatch within 12-mer oligonucleotides can be distinguished by using a differential detection technique with two sensors in parallel. The sensors were fabricated by standard silicon microtechnology and show promise for future electronic DNA arrays and rapid characterization of nucleic acid samples. This approach demonstrates the most direct and simple translation of genetic information to microelectronics.

Buffers↗