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PubMed1994

CD44 mediates human glioma cell adhesion and invasion in vitro.

Human gliomas are characterized by their invasion of normal brain structures irrespective of their grade of malignancy. Factors involved in the control of this invasive behavior are poorly documented. Human gliomas have also been found to express CD44 adhesion molecules. Expression of splice variants of CD44 has been correlated to metastasis in nonglial solid tumors. In this study, 8-microns porosity polycarbonate filters incorporated in modified Boyden chambers and coated with the extracellular matrix composite Matrigel were used to investigate the role of CD44 in invasion of eight human glioma cell lines in vitro. Invasion of Matrigel was found to be inhibited to different extents by a CD44 monoclonal antibody. Moreover, this invasion was highly inhibited in two cell lines and completely arrested in five other glioma cell lines by a CD44-specific antisense oligonucleotide which inhibited CD44 expression. In addition, adhesion of glioma cells to fibronectin, laminin, vitronectin, and collagen I was inhibited by the CD44 monoclonal antibody. These results strongly suggest that CD44 is involved in human glioma cell invasion in vitro, probably through its role in cell interactions with extracellular matrix proteins. Interference with glioma invasion, by targeting CD44 expression, may be envisaged in animal models.

Base Sequence↗
PubMed1998

Maximum A posteriori classification of DNA structure from sequence information.

We introduce an algorithm, LLLAMA, which combines simple pattern recognizers into a general method for estimating the entropy of a sequence. Each pattern recognizer exploits a partial match between subsequences to build a model of the sequence. Since the primary features of interest in biological sequence domains are subsequences with small variations in exact composition, LLLAMA is particularly suited to such domains. We describe two methods, LLLAMA-length and LLLAMA-alone, which use this entropy estimate to perform maximum a posteriori classification. We apply these methods to several problems in three-dimensional structure classification of short DNA sequences. The results include a surprisingly low 3.6% error rate in predicting helical conformation of oligonucleotides. We compare our results to those obtained using more traditional methods for automated generation of classifiers.

Algorithms↗
PubMed1985

Effect of terminal base pairs on the CD spectra of oligodeoxynucleotide duplexes.

Oligodeoxynucleotide duplexes having terminal C:G base pairs and recognition sequences for restriction endonucleases Bgl II and Sau 3Al were synthesized by the solid or liquid phase phosphotriester approach. Among them, the self-complementary oligonucleotides with C or CC at the 5'-end and G or GG at the 3'-end exhibited unusual CD spectra in contrast to those of the usual B-DNA type CD spectra of the oligonucleotide with G or GG at the 5'-end. The spectra are different to those of the Z-DNA, and regarded to the terminal base effect of the C:G pairs.

Base Composition↗
PubMed1991

Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch.

Four-arm DNA branched junctions are stable analogues of Holliday recombinational intermediates. A number of four-arm DNA junctions synthesized from oligonucleotides have now been studied. Gel mobility or chemical footprinting experiments on several immobile four-arm junctions indicate that in the presence of Mg2+, they assume a preferred conformation consisting of two helical domains, each formed by stacking a particular pair of arms on each other. We show here that a junction we designate as J1c that has the same chemical composition as one we have previously studied in detail, J1, but is formed from the four strands complementary to those of the latter, exhibits the reverse stacking preference. The pattern of self-protection of the strands of J1c exposed to Fe(II).EDTA-induced scission reveals that twofold symmetry is preserved, but the opposite pair of strands preferentially cross over. Moreover, the Fe(II).EDTA scission profiles of J1c indicate that this junction exhibits a weaker bias as to which strands cross over than is observed in J1. The preference for the dominant species in J1 is 1.3 times greater than in J1c at 4 degrees C and in the presence of 10 mM Mg2+, based on chemical reactivity data. This is confirmed by a cleavage experiment using the resolvase enzyme, endonuclease I, from bacteriophage T7. This difference could reflect either sequence-dependent differences in the equilibrium among isomers, or in the structure of these junctions. Chemical footprinting experiments using the probes MPE.Fe(II) and (OP)2Cu(I) show that the high-affinity ligand binding site in immobile junctions is determined by junction geometry.

Base Sequence↗
PubMed2002

Spicule matrix protein LSM34 is essential for biomineralization of the sea urchin spicule.

Biomineralized skeletal structures are composite materials containing mineral and matrix protein(s). The cell biological mechanisms that underlie the formation, secretion, and organization of the biomineralized materials are not well understood. Although the matrix proteins influence physical properties of the structures, little is known of the role of these matrix proteins in the actual formation of the biomineralized structure. We present here results using an antisense oligonucleotide directed against a spicule matrix protein, LSM34, present in spicules of embryos of Lytechinus pictus. After injection of anti-LSM34 into the blastocoel of a sea urchin embryo, LSM34 protein in the primary mesenchyme cells decreases and biomineralization ceases, demonstrating that LSM34 function is essential for the formation of the calcareous endoskeletal spicule of the embryo. Since LSM34 is found primarily in a specialized extracellular matrix surrounding the spicule, it is probable that this matrix is important for the biomineralization process.

Animals↗
PubMed1994

Immunogenetic studies on HLA-DR in German coal miners with and without coal worker's pneumoconiosis.

Coal worker's pneumoconiosis is caused by the pulmonary deposition of coal dust, including silica particles. Several factors such as chemical composition and physical properties of silica-containing dust, particle size distribution, intensity, and duration of exposure influence the disease development. Genetic factors may also be involved. To define whether HLA-DRB may function as a genetic factor for predisposition to coal worker's pneumoconiosis, we determined DRB1, 3, 4, 5 alleles. For this purpose, DRB typing with sequence-specific oligonucleotide probes in 204 German miners with pneumoconiosis and in 52 German miners without pneumoconiosis was used. The miners had worked under comparable conditions. The frequency of DR8 (1*0801-0804) was increased in patients developing pneumoconiosis during the first 15 years of mining (p = 0.047). The frequency of DR1 (1*0101-0103) was elevated (p = 0.022) and that of DR52 (3*0101, 3*0201, 3*0202, and 3*0301) was reduced (p = 0.026) in miners without pneumoconiosis. Our data show that the presence of DR1 and the absence of DR52 support the resistance to coal worker's pneumoconiosis. Furthermore, DR8 may be involved in the rapid development of coal worker's pneumoconiosis.

Adult↗
PubMed1996

Hypoxia-inducible protein binding to vascular endothelial growth factor mRNA and its modulation by the von Hippel-Lindau protein.

Hypoxia induces an increase in the stability of the mRNA encoding vascular endothelial growth factor (VEGF). We have previously demonstrated that a 500-base region of the 3'-untranslated region of VEGF mRNA that is critical for stabilization of VEGF mRNA in an in vitro degradation assay forms a RNA-protein complex in a hypoxia-inducible fashion. We report here the identification of three adenylate-uridylate-rich RNA elements within this region that form an identical or closely related hypoxia-inducible RNA-protein complex. This complex is constitutively elevated in a tumor cell line lacking the wild type von Hippel-Lindau tumor suppressor gene and in which VEGF mRNA is constitutively stabilized. Furthermore, the glucose transporter-1 mRNA, which is also stabilized by hypoxia, forms a hypoxia-inducible RNA-protein complex with similar sequence and protein binding characteristics to that described for VEGF mRNA. Finally, RNA affinity purification and UV cross-linking were used to identify three proteins of 32, 28, and 17 kDa that are derived from this hypoxia-inducible RNA-protein complex.

Adenine↗
PubMed2004

Morphogenesis during Xenopus gastrulation requires Wee1-mediated inhibition of cell proliferation.

Major developmental events in early Xenopus embryogenesis coincide with changes in the length and composition of the cell cycle. These changes are mediated in part through the regulation of CyclinB/Cdc2 and they occur at the first mitotic cell cycle, the mid-blastula transition (MBT) and at gastrulation. In this report, we investigate the contribution of maternal Wee1, a kinase inhibitor of CyclinB/Cdc2, to these crucial developmental transitions. By depleting Wee1 protein levels using antisense morpholino oligonucleotides, we show that Wee1 regulates M-phase entry and Cdc2 tyrosine phosphorylation in early gastrula embryos. Moreover, we find that Wee1 is required for key morphogenetic movements involved in gastrulation, but is not needed for the induction of zygotic transcription. In addition, Wee1 is positively regulated by tyrosine autophosphorylation in early gastrula embryos and this upregulation of Wee1 activity is required for normal gastrulation. We also show that overexpression of Cdc25C, a phosphatase that activates the CyclinB/Cdc2 complex, induces gastrulation defects that can be rescued by Wee1, providing additional evidence that cell cycle inhibition is crucial for the gastrulation process. Together, these findings further elucidate the developmental function of Wee1 and demonstrate the importance of cell cycle regulation in vertebrate morphogenesis.

Animals↗
PubMed1998

A comparison of in vivo gene delivery methods for antisense therapy in ligament healing.

To determine the most efficient in vivo delivery method of oligonucleotides for antisense therapy in ligament healing, fluorescence-labelled phosphorothioate oligodeoxynuleotides (ODN) were introduced into 12 rabbit ligament scars 2 weeks after injury using haemagglutinating virus of Japan (Sendai virus: HVJ)-conjugated liposomes. We compared the efficiency of cellular uptake of fluorescence as a percentage of all cells in each scar using three delivery procedures: (1) direct free-hand injection into the ligament scar using a conventional syringe; (2) systematic direct sca injection using a repeating 10 microliters dispenser and a square mesh grid system; and (3) injection into the feeding (femoral) artery. Results showed that there was a significant difference in fluorescence uptake by scar cells on day 1 after injection between the three delivery methods: (1) direct free-hand, 9.7 +/- 7.6% (average +/- s.d.); (2) systematic direct, 58.4 +/- 15.9%; and (3) intra-arterial, 0.2 +/- 0.1%. Systematic direct injection was most efficient and it resulted in 25.9 +/- 13.0% of scar cells being labeled at 7 days after transfection. We then introduced antisense ODN for the rabbit proteoglycan, decorin, into ligament scars with this delivery method and confirmed a significant inhibition of decorin mRNA expression in antisense-treated scar tissues in vivo both at 2 days (42.3 +/- 14.7% of sense control +/- s.d.; P < 0.0025) and 3 weeks (60.5 +/- 28.2% of sense control +/- s.d.; P < 0.024) after treatment, compared with sense ODN-treated scars. Decorin was significantly suppressed also at protein level in antisense-treated scars at 4 weeks (66.6 +/- 35.7% of sense control +/- s.d.; P < 0.045) after treatment. These results demonstrate that in vivo transfection efficiency in ligament scars is 'delivery system dependent' and that introduction of antisense ODN for the small proteoglycan, decorin, with this delivery method can lead to significant suppression of its expression over 3 weeks both at mRNA and protein levels. Thus, an effective model for the potential manipulation of scar composition and quality in ligament healing has been established.

Animals↗
PubMed1980

Hamster mitochondrial transfer RNA lacks T and the universal GUUCG sequence.

Earlier inferences (based on incorporation of radio-activity from methyl-labeled methionine) that mammalian mitochondrial tRNA lacks ribothymidine ('T') have been confirmed using [14C]uridine as precursor. Moreover, oligonucleotide fingerprint analysis of 32P-labeled samples have shown that hamster mitochondrial tRNA lacks the 'universal' pentanucleotide of conventional tRNA in which T normally occurs, CTpsiCG, in modified or unmodified form.

Animals↗
PubMed1990

Identification and sequence analysis of the maize stripe virus major noncapsid protein gene.

The maize stripe virus (MStV) major noncapsid protein (NCP) gene was characterized, and the location of the NCP gene was identified among the 5-RNA, 18-kb genome. A 12-amino-acid sequence of the NCP was compared with nucleotide sequence data for MStV RNAs 3 and 4 and was found to align perfectly within a 528-nucleotide open reading frame (ORF) of RNA 4. The amino acid composition of purified NCP was almost identical to that deduced from the putative coding region. The deduced NCP molecular weight was 19,815, very similar to that determined by SDS-PAGE analysis of the purified NCP. In vitro transcription and translation analysis of the cDNA representing this region showed unequivocally that this region encoded the NCP. Primer extension analysis using a synthetic oligonucleotide complementary to a sequence near the 5' end of the coding region revealed that the NCP ORF is located 61 nucleotides from the 5' end of RNA 4.

Amino Acid Sequence↗
PubMed1999

Hydration of lipoplexes commonly used in gene delivery: follow-up by laurdan fluorescence changes and quantification by differential scanning calorimetry.

Lipoplexes, which are formed spontaneously between cationic liposomes and negatively charged nucleic acids, are commonly used for gene and oligonucleotide delivery in vitro and in vivo. Being assemblies, lipoplexes can be characterized by various physicochemical parameters, including size distribution, shape, physical state (lamellar, hexagonal type II and/or other phases), sign and magnitude of electrical surface potential, and level of hydration at the lipid-DNA interface. Only after all these variables will be characterized for lipoplexes with a broad spectrum of lipid compositions and DNA/cationic lipid (L(+)) mole (or charge) ratios can their relevance to transfection efficiency be understood. Of all these physicochemical parameters, hydration is the most neglected, and therefore the focus of this study. Cationic liposomes composed of DOTAP without and with helper lipids (DOPC, DOPE, or cholesterol) or of DC-Chol/DOPE were complexed with pDNA (S16 human growth hormone) at various DNA(-)/L(+) charge ratios (0.1-3.2). (DOTAP=N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride; DC-Chol=(3beta-[N-(N',N'-dimethylaminoethane)-carbamoyl]-cholester ol; DOPC=1, 2-dioleoyl-sn-glycero-3-phosphocholine; DOPE=1, 2-dioleoyl-sn-glycero-3-phosphoethanolamine). The hydration levels of the different cationic liposomes and the DNA separately are compared with the hydration levels of the lipoplexes. Two independent approaches were applied to study hydration. First, we used a semi-quantitative approach of determining changes in the 'generalized polarization' (GP) of laurdan (6-dodecanoyl-2-dimethylaminonaphthalene). This method was recently used extensively and successfully to characterize changes of hydration at lipid-water interfaces. Laurdan excitation GP at 340 nm (GP(340)DOTAP. The GP(340) of lipoplexes of all lipid compositions (except those based on DC-Chol/DOPE) was higher than the GP(340) of the cationic liposomes alone and increased with increasing DNA(-)/L(+) charge ratio, reaching a plateau at a charge ratio of 1. 0, suggesting an increase in dehydration at the lipid-water interface with increasing DNA(-)/L(+) charge ratio. Confirmation was obtained from the second method, differential scanning calorimetry (DSC). DOTAP/DOPE lipoplexes with charge ratio 0.44 had 16.5% dehydration and with charge ratio 1.5, 46.4% dehydration. For DOTAP/Chol lipoplexes with these charge ratios, there was 17.9% and 49% dehydration, respectively. These data are in good agreement with the laurdan data described above. They suggest that the dehydration occurs during lipoplex formation and that this is a prerequisite for the intimate contact between cationic lipids and DNA.

2-Naphthylamine↗
PubMed1988

Four novel U RNAs are encoded by a herpesvirus.

Marmoset T lymphocytes transformed by herpesvirus saimiri contain the first virally encoded U RNAs (called HSURs) to be identified. HSURs assemble into small nuclear ribonucleoproteins of low abundance (less than or equal to 2 x 10(4) copies/cell). They bind proteins with Sm determinants and acquire a 5' trimethylguanosine cap structure. The sequences of HSUR 1 (143 nucleotides), HSUR 2 (115 nucleotides), HSUR 3 (76 nucleotides), and HSUR 4 (106 nucleotides) are related to each other but are distinct from any previously characterized cellular U RNA. The viral genes encoding the HSURs possess conserved enhancer, promoter, and 3' end formation signals unique to U RNA genes. HSUR 1 and HSUR 2 have a similar 5' end sequence that exhibits perfect complementarity to the highly conserved AAUAAA polyadenylation signal. Oligonucleotide directed RNAase H degradation indicates that this 5' end region is available for base pairing interactions within the HSUR 1 and HSUR 2 snRNP particles.

Base Composition↗
PubMed1998

Molecular cloning and characterization of a rabbit eIF2C protein.

Rabbit eIF2C (94kDa) has been shown to play important roles in the eukaryotic peptide chain initiation process. In this study, the primary structure of rabbit eIF2C is determined by cDNA cloning. Based on the partial amino acid sequences of Endolys C cleaved fragments, degenerate oligonucleotides were synthesized and used as primers for the polymerase chain reaction to amplify the corresponding cDNA fragment from a rabbit liver cDNA library. This fragment was subsequently used to screen for larger cDNAs. Marathon cDNA amplification and 5'-rapid amplification of cDNA ends were used to confirm the translation start site. Sequences from the overlapping clones were assembled into a 3599-bp composite sequence, which contains a single open reading frame that translates into a 813-deduced amino acid sequence. Northern blot analysis of rabbit liver ploy(A)+ RNA yielded a single message species at approximately 4.6kb. Western blot analysis of rabbit reticulocyte lysate using polyclonal antibody against the 94kDa eIF2C detected a higher-molecular-weight polypeptide (140kDa). No 94kDa polypeptide was detected. The cloned cDNA was further characterized by in-vitro transcription-coupled translation in reticulocyte lysate. The translated product was precipitated with antibodies against eIF2C. Genomic Southern blot analysis indicates that the rabbit eIF2C is a single copy gene. Sequence analysis reveals that rabbit eIF2C has strong homology with a hypothetical protein in Caenorhabditis elegans.

Amino Acid Sequence↗
PubMed1997

Effects of oligodeoxynucleotides on the physicochemical characteristics and cellular uptake of liposomes.

We studied the effects of a phosphodiester oligodeoxynucleotide (ODN), which is antisense to the site in the neighborhood of the AUG initiation codon of the mouse tumor necrosis factor alpha gene (TNF-alpha), on the physicochemical characteristics and the cellular association of three types of liposomes with different surface charges. The physicochemical characteristics of the liposomes changed after adding ODN. When the ODN/lipid molar ratio was approximately 0.15 in cationic (TMAG) liposomes [consisting of N-(alpha-trimethylammonioacetyl)didodecyl-D-glutamate chloride (TMAG), dilauroylphosphatidylcholine (DLPC), and dioleolylphosphatidylethanolamine (DOPE) in a 1:2:2 ratio], but not in neutral and negatively charged liposomes, then the liposomes aggregated and fused. At higher molar ratios, these changes in TMA liposomes were not evident. In addition, ODN inverted the zeta-potential of TMAG liposomes from positive to negative at an ODN/lipid molar ratio of approximately 0.15. Therefore, the aggregation and fusion induced by ODN could be explained by a lower surface charge repulsion between TMAG liposomes. On the other hand, the association of ODN with RAW264.7 cells, a mouse macrophage-like cell line, was very slight. The cellular association of ODN was significantly enhanced compared with neutral and negatively charged liposomes by encapsulation in TMAG liposomes. The ODN added to liposome suspensions did not affect the rate and extent of TMAG liposome cellular association, even at an ODN/lipid molar ratio of approximately 0.15. These results indicate that the lipid composition and ODN/lipid molar ratio are critical for the physicochemical characteristics of cationic liposomes. However, the changes had less influence on the cellular uptake properties of cationic liposomes.

Animals↗
PubMed1988

Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide.

A method for achieving strand specific nicking of DNA has been developed. Phosphorothioate groups were incorporated enzymatically into the (-)strand of M13 RF IV DNA. When such DNA is reacted with restriction endonucleases in the presence of ethidium bromide nicked DNA (RF II) is produced. All of the restriction enzymes tested linearised phosphorothioate-containing DNA in the absence of this dye. The strand specificity of the reaction was investigated by employing the ethidium bromide mediated nicking reaction in the phosphorothioate-based oligonucleotide-directed mutagenesis method. The mutational efficiencies obtained were in the region of 64-89%, indicating that these restriction enzymes hydrolyse the phosphodiester bond at the cleavage site of the unsubstituted (+)strand.

Base Composition↗
PubMed2004

Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers.

Landfill sites are responsible for 6-12% of global methane emission. Methanotrophs play a very important role in decreasing landfill site methane emissions. We investigated the methane oxidation capacity and methanotroph diversity in lysimeters simulating landfill sites with different plant vegetations. Methane oxidation rates were 35 g methane m-2 day-1 or higher for planted lysimeters and 18 g methane m-2 day-1 or less for bare soil controls. Best methane oxidation, as displayed by gas depth profiles, was found under a vegetation of grass and alfalfa. Methanotroph communities were analysed at high throughput and resolution using a microbial diagnostic microarray targeting the particulate methane monooxygenase (pmoA) gene of methanotrophs and functionally related bacteria. Members of the genera Methylocystis and Methylocaldum were found to be the dominant members in landfill site simulating lysimeters. Soil bacterial communities in biogas free control lysimeters, which were less abundant in methanotrophs, were dominated by Methylocaldum. Type Ia methanotrophs were found only in the top layers of bare soil lysimeters with relatively high oxygen and low methane concentrations. A competetive advantage of type II methanotrophs over type Ia methanotrophs was indicated under all plant covers investigated. Analysis of average and individual results from parallel samples was used to identify general trends and variations in methanotroph community structures in relation to depth, methane supply and plant cover. The applicability of the technology for the detection of environmental perturbations was proven by an erroneous result, where an unexpected community composition detected with the microarray indicated a potential gas leakage in the lysimeter being investigated.

Base Sequence↗
PubMed2004

Silencing the jasmonate cascade: induced plant defenses and insect populations.

We transformed the native tobacco, Nicotiana attenuata, to silence its lipoxygenase, hydroperoxide lyase, and allene oxide synthase genes in order to inhibit oxylipin signaling, known to mediate the plant's direct and indirect defenses. When planted into native habitats, lipoxygenase-deficient plants were more vulnerable to N. attenuata's adapted herbivores but also attracted novel herbivore species, which fed and reproduced successfully. In addition to highlighting the value of genetically silencing plants to study ecological interactions in nature, these results show that lipoxygenase-dependent signaling determines host selection for opportunistic herbivores and that induced defenses influence herbivore community composition.

Acetates↗