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At least 757 records · Page 42Linked to original sources
PubMed2006

[HLA-DQA1 genotyping by using oligonucleotide microarrays].

In order to fabricate the HLA-DQA1 genotyping chip and develop an integrated, parallel technical platform to type HLA system, a pair of primers and a set of probes were designed according to the sequences of HLA-DQA1 exon 2, where the polymorphism is concentrated. The oligonucleotide chip was made with the methods developed in our laboratory. The target DNA was asymmetrically amplified with the labeled sense primer. The signals were scanned and analyzed after the hybridization between microarray and PCR product. The allele types of the samples were identified. The result was verified by the standard DNA and DNA sequencing. The results showed that the genotyping was successfully carried out in 50 standard DNA samples and 50 clinical samples. Among them, results of the 50 standard DNA samples matched their templates. In the other 50 samples, results of the randomly selected 10 matched their sequencing results except that two of them got the incompletely result. In reproducible tests, the signal reappear rate was 95%. It is concluded that HLA-DQA1 genotyping by using our array system is simple and convenient with satisfied accuracy and reproducibility.

Genotype↗
PubMed1994

Expression of an antisense dihydrofolate reductase transcript in transfected mosquito cells: effects on growth and plating efficiency.

Novel approaches to control of vector-borne disease include potential use of transgenic insects, in which molecular mechanisms will be induced to prevent transmission of pathogenic organisms. The infrastructure essential to this technology includes the cloning of essential genes from vector insects, and the development of efficient transformation strategies. In this study, we use a continuous mosquito (Aedes albopictus) cell line and a cloned mosquito dihydrofolate reductase gene to demonstrate a transgenic approach that may be used to select for the presence or absence of particular gene functions in transfected cells. Plasmids containing the dihydrofolate reductase gene in sense and antisense orientation, under the regulation of a temperature-inducible promoter, were expressed in stably transfected mosquito cells. At the normal growth temperature of 28 degrees C, or after mild heat induction at 34 degrees C, expression of the dihydrofolate reductase construct in sense orientation had little effect on cell growth. In contrast, recovery of clones transfected with the antisense construct was reduced, and induction of antisense transcripts at 34 degrees C further compromised cell growth and viability. Clones transfected with the sense construct retained significantly higher copy numbers of foreign DNA than did cells transfected with the antisense construct. These studies provide a basis for use of sense and antisense dihydrofolate reductase constructs to recover transfected mosquito cells with specific desired phenotypes, based on the relative expression of cloned genes of interest.

Aedes↗
PubMed1984

Faithful initiation of ribosomal RNA transcription from cloned DNA by purified RNA polymerase I.

A faithful transcription system for ribosomal RNA genes has been developed by using components from the small free-living amoeba Acanthamoeba castellanii. The system utilizes protein-free recombinant DNA as a template and in addition requires a crude cell-free extract containing RNA polymerase I and a transcription initiation factor (TIF-I). The transcript is initiated at the same position as the in vivo precursor ribosomal RNA: templates truncated at various sites downstream of the transcription start site give rise to only the predicted runoff RNA transcripts, and the runoff transcript produced has a 5'-terminus identical with the 5'-terminus of the isolated ribosomal RNA precursor. Faithful initiation can be elicited by the DNA sequence extending from -55 to +19 in the template. Subclones containing this sequence yield only the predicted runoff RNAs regardless of the orientation of this fragment in the cloning vector DNA; thus, only the in vivo sense strand of the template is specifically transcribed in the in vitro system. The system is specific for the RNA polymerase responsible for the transcription of ribosomal RNA genes in vivo. Faithful transcription, like RNA polymerase I from Acanthamoeba, is insensitive to alpha-amanitin inhibition, and transcription is greatly stimulated by highly purified RNA polymerase I but not by RNA polymerases II or III. Conditions for optimal transcription were determined.

Amoeba↗
PubMed2001

What controls the length of noncoding DNA?

Several recent studies of genome evolution indicate that the rate of DNA loss exceeds that of DNA gain, leading to an underlying mutational pressure towards collapsing the length of noncoding DNA. That such a collapse is not observed suggests opposing mechanisms favoring longer noncoding regions. The presence of transposable elements alone also does not explain observed features of noncoding DNA. At present, a multidisciplinary approach--using population genetics techniques, large-scale genomic analyses, and in silico evolution--is beginning to provide new and valuable insights into the forces that shape the length of noncoding DNA and, ultimately, genome size. Recombination, in a broad sense, might be the missing key parameter for understanding the observed variation in length of noncoding DNA in eukaryotes.

Animals↗
PubMed1988

Inhibition of cellular proliferation by antisense oligodeoxynucleotides to PCNA cyclin.

The proliferating cell nuclear antigen (PCNA or cyclin) is a nuclear protein recently identified as a cofactor of DNA polymerase delta. When exponentially growing Balb/c3T3 cells are exposed to antisense oligodeoxynucleotides to PCNA, both DNA synthesis and mitosis are completely suppressed. A corresponding sense oligodeoxynucleotide has no inhibitory effects. These experiments indicate that PCNA (cyclin) is important in cellular DNA synthesis and in cell cycle progression.

Animals↗
PubMed1994

Robotic automation of dideoxyribonucleotide sequencing reactions.

We developed a robot to carry out standard Sanger dideoxyribonucleotide sequencing reactions efficiently and with minimal human intervention. A commercial robot was adapted to our design and specifications, and we programmed it to perform up to 240 sequencing reactions in a single unattended run of 7 h. The robot configuration can be easily altered to allow 480 reactions to be performed in an unattended run of 14 h. The special features of our robot include cooled reagent reservoirs and cooled chambers for storage of DNA templates and completed reactions as well as reproducible aspiration of small volumes by using a sensing algorithm. The robot has successfully performed over 3500 DNA reactions in about 30 separate runs in our DNA core facility.

DNA-Directed DNA Polymerase↗
PubMed1996

A familial syndrome of hypocalcemia with hypercalciuria due to mutations in the calcium-sensing receptor.

BACKGROUND: The calcium-sensing receptor regulates the secretion of parathyroid hormone in response to changes in extracellular calcium concentrations, and mutations that result in a loss of function of the receptor are associated with familial hypocalciuric hypercalcemia. Mutations involving a gain of function have been associated with hypocalcemia in two kindreds. We examined the possibility that the latter type of mutation may result in a phenotype of familial hypocalcemia with hypercalciuria. METHODS: We studied six kindreds given a diagnosis of autosomal dominant hypoparathyroidism on the basis of their hypocalcemia and normal serum parathyroid hormone concentrations, a combination that suggested a defect of the calcium-sensing receptor. The hypocalcemia was associated with hypercalciuria, and treatment with vitamin D resulted in increased hypercalciuria, nephrocalcinosis, and renal impairment. Mutations in the calcium-sensing-receptor gene were identified by DNA-sequence analysis and expressed in human embryonic kidney cells (HEK-293). RESULTS: Five heterozygous missense mutations (Asn118Lys, Phe128Leu, Thr151Met, Glu191Lys, and Phe612Ser) were detected in the extracellular domain of the calcium-sensing-receptor gene and shown to cosegregate with the disease. Analysis of the functional expression of three of the mutant receptors in HEK-293 cells demonstrated shifts in the dose-response curves so that the extracellular calcium concentrations needed to produce half-maximal increases in total inositol phosphate in the cells were significantly (P=0.02 to P<0.001) lower than those required for the wild-type receptor. CONCLUSIONS: Gain-of-function mutations in the calcium-sensing receptor are associated with a familial syndrome of hypocalcemia with hypercalciuria that needs to be distinguished from hypoparathyroidism.

Adolescent↗
PubMed1992

Structural and functional analysis of the Bz2 locus of Zea mays: characterization of overlapping transcripts.

Analysis of the transcription pattern of the Bz2 locus revealed that overlapping transcripts are derived from opposite DNA strands. The most abundant transcript (sense transcript) has an open reading frame coding for a protein of 241 amino acids, whilst in the antisense orientation no open reading frame has been detected; the antisense transcripts are detected only in those tissues that show high levels of sense transcript. Particle gun experiments indicate that the sense transcript is sufficient to provide the Bz2 function. The promoter driving the sense transcript contains the elements usually found in front of eukaryotic genes. In addition an element with similarity to the C1 and R binding sites identified in the Bz1 promoter is found. Further upstream in the promoter region a transposon-like insertion has been identified. This element has features similar to members of the Ac/Ds transposable element family. The putative Bz2 protein shows similarity to various other plant proteins and to an Escherichia coli protein. All related proteins have in common the fact that they are involved in stress responses.

Amino Acid Sequence↗
PubMed2003

The evolution of homing endonuclease genes and group I introns in nuclear rDNA.

Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.

Amino Acid Sequence↗
PubMed2003

Tyr212: a key residue involved in strand discrimination by the DNA mismatch repair endonuclease MutH.

The molecular mechanism of how the dam-methylation status of the DNA is recognized during DNA mismatch repair by the strand discrimination endonuclease MutH is not known. A comparison of the crystal structure of MutH with those of co-crystal structures of several restriction endonucleases, together with a multiple sequence alignment of MutH and related proteins suggested that Phe94, Arg184 and Tyr212 could be involved in discrimination between a methylated or unmethylated adenine in the d(GATC) sequence. A mutational analysis revealed that the variants R184A and Y212S, but not F94A, were substantially reduced in their ability to complement a mismatch repair deficiency in a mutH(-) Escherichia coli strain. In vitro, R184A displayed a strongly reduced endonuclease activity, whereas the Y212S variant has almost completely lost its preference for cleaving the unmethylated strand at hemimethylated d(GATC) sites. Furthermore, the Y212 variant can cleave fully methlyated d(GATC) sites at a comparable rate to unmethylated d(GATC) sites. This demonstrates that Tyr212 is an important, if not the only amino acid residue in MutH for sensing the methylation status of the DNA.

Amino Acid Sequence↗
PubMed1986

The binding of the antitumor antibiotic chartreusin to poly(dA-dT).poly(dA-dT), poly(dG-dC).poly(dG-dC), calf thymus DNA, transfer RNA, and ribosomal RNA.

Chartreusin binds cooperatively to poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Both the site-exclusion model and the specific site model yield cooperative binding constants of about 5 X 10(5) M-1 and 3 X 10(5) M-1 for the AT and GC polymers, respectively, and the same stoichiometry and intrinsic binding constant for both polymers of 5 nucleotides per binding site and 3.1 X 10(4) M-1. The Scatchard plot for calf thymus DNA is curved in the opposite sense from that of cooperative binding. These binding data did not fit the site-exclusion model with the cooperative binding parameter as a variable nor the specific site, negative-cooperative binding model. The site-exclusion model with a cooperative binding parameter of unity yielded a binding constant of about 4 X 10(4) M-1 and a stoichiometry of about 5 nucleotides per binding site. The same model for transfer and ribosomal RNA yielded binding constants of 5 X 10(3) M-1 and 7 X 10(3) M-1 and stoichiometries of about 13 and 6 nucleotides per binding site, respectively.

Antibiotics, Antineoplastic↗
PubMedDate not supplied

Effects of sense tankyrase transfection on smooth muscle cells of corpus cavernosum in rat.

This study was conducted to construct the eukaryotic expression vectors for sense tankyrase and to investigate the effects of tankyrase transfection on smooth muscle cells of corpus cavernosum in the rat. After the eukaryotic expression vectors for sense tankyrase were constructed and identified smooth muscle cells of rat corpus cavernosum were transfected with the recombinant plasmids of sense tankyrase (pcDNA-TNKS). Levels of DNA and RNA were then evaluated. Measurement of telomerase activity was conducted by TRAP-ELISA assay, the length of telomere by Southern blot and the growth curve by MTT assay. We have found that the eukaryotic expression vectors for sense tankyrase were constructed and the recombinant plasmids of sense tankyrase were transfected into smooth muscle cells of rat corpus cavernosum successfully; no significant differences in telomerase activity were observed between TNKS-transfected cells (SMC-TANKS), zero-load- transfected cells (SMC-Zeo), and non-transfected cells (SMC) (P > 0.05). The length of telomere in SMC-TANKS was longer than that in SMC-Zeo or SMC (P < 0.01), and the OD value of TNKS-transfected cell was significantly higher than that of the non-transfected cells (P < 0.01). These results suggested that the eukaryotic expression vectors for sense tankyrase were constructed successfully, which provides the basis for gene therapy. Transfection of recombinant plasmids of sense tankyrase helps change the telomerase length of smooth muscle cells of corpus cavernosum and extend the cell life span.

Animals↗
PubMed1992

Ornithine decarboxylase activity is critical for cell transformation.

The enzyme ornithine decarboxylase is the key regulator of the synthesis of polyamines which are essential for cell proliferation. Expression of this enzyme is transiently increased upon stimulation by growth factors, but becomes constitutively activated during cell transformation induced by carcinogens, viruses or oncogenes. To test whether ornithine decarboxylase could be a common mediator of transformation and oncogenic itself, we transfected NIH3T3 cells with expression vectors carrying the complementary DNA encoding human ornithine decarboxylase in sense and antisense orientations. The increased expression of the enzyme (50-100-times endogenous levels) induced not only cell transformation, but also anchorage-independent growth in soft agar and increased tyrosine phosphorylation of a protein of M(r) 130K. Expression of ornithine decarboxylase antisense RNA was associated with an epithelioid morphology and reduced cell proliferation. Moreover, blocking the endogenous enzyme using specific inhibitor or synthesizing antisense RNA prevented transformation of rat fibroblasts by temperature-sensitive v-src oncogene. Our results imply that the gene encoding ornithine decarboxylase is a proto-oncogene central for regulation of cell growth and transformation.

3T3 Cells↗
PubMedDate not supplied

Performance of interdigitated nanoelectrodes for electrochemical DNA biosensor.

An electrochemical methodology for bio-molecule sensing using an array of well-defined nanostructures is presented. We describe the fabrication by e-beam lithography of nanoelectrodes consisting of a 100 micro m x 50 micro m area containing interdigitated electrodes of 100 nm in width and interelectrode distance of 200 nm. Sensitivity and response time of the nanoelectrodes are compared to the responses of macro- and microelectrodes. The specificity of the sensor is studied by modifying the gold electrodes with DNA. The technique enables to characterize both single and double-stranded DNA of 15 nucleotides. A special electrochemical cell is adapted to control the temperature and measure the DNA concentration by UV analysis. The electrochemical method requires no label on the DNA, only redox mediators were used.

Adsorption↗
PubMed1995

The BCL2 major breakpoint region is a sequence- and cell-cycle-specific binding site of the Ku antigen.

The majority of translocations involving BCL2 are very narrowly targeted to three breakpoint clusters evenly spaced over a 100-bp region of the gene's terminal exon. We have recently shown that the immediate upstream boundary of this major breakpoint region (mbr) is a specific recognition site for single-strand DNA (ssDNA) binding proteins on the sense and antisense strands. The downstream flank of the mbr is a helicase binding site. In this report we demonstrate that the helicase and ssDNA binding proteins show reciprocal changes in binding activity over the cell cycle. The helicase is maximally active in G1 and early S phases; the ssDNA binding proteins are maximally active in late S and G2/M phases. An inhibitor of helicase binding appears in late S and G2/M. Finally, at least one component of the helicase binding complex is the Ku antigen. Thus, a protein with helicase activity implicated in repair of double-strand breaks, variable (diversity) joining recombination, and, potentially, cell-cycle regulation is targeted to the BCL2 mbr.

Antigens, Nuclear↗
PubMed1994

Homologous cysteine proteinase genes located on two different chromosomes from Trypanosoma rangeli.

DNA fragments were obtained by the polymerase chain reaction (PCR) using genomic DNA from T. rangeli as template and oligonucleotide primers encoding the active site amino acids of cysteine proteinase. After amplification by PCR, several DNA products were observed. These were purified and used as templates for a second round of PCR. This resulted in two DNA products of 475 and 498 bp. The 498 bp DNA (Tr-CP) contained both the sense and antisense primer sequences, and encoded a polypeptide having substantial homology with eukaryotic cysteine proteinases. The other product (Tr-DMR), which lacked the antisense primer sequence, encoded a polypeptide having homology with the DNA mismatch repair gene from Saccharomyces cerevisiae. The overall homology of the Tr-CP-encoded polypeptide to the cysteine proteinases from other trypanosome species was 69% identity (T. cruzi) and 73% identity (T. brucei), respectively. Northern blot analysis revealed that the Tr-CP gene was specifically expressed in T. rangeli as a 1.7 kb mRNA. A karyotype map of the chromosomes was also performed using pulsed-field gradient gel electrophoresis and Southern blot hybridization with these genes. T. rangeli has 14 chromosome bands ranging from 350 kb to 1.6 Mb, which were fewer in number and smaller in size compared with those from T. cruzi. The Tr-CP fragment and the Tr-DMR fragment hybridized with equal intensity on chromosome 1 (350 kb) and chromosome 2 (470 kb), respectively. These results suggest that non-pathogenic T. rangeli contains a conserved gene corresponding to the cysteine proteinase or a closely related enzyme, and that there is more than one copy of this gene, each found on different chromosomes.

Amino Acid Sequence↗
PubMed1999

Tiam1 is involved in the regulation of bufalin-induced apoptosis in human leukemia cells.

Bufalin, a component of the Chinese medicine chan'su, induces apoptosis in various lines of human tumor cells, such as leukemia HL60 and U937 cells, by altering the expression of apoptosis-related genes, for example, bcl-2 and c-myc. In this study, we characterized a gene that is involved in bufalin-induced apoptosis by the differential display (DD) technique. The partial nucleotide sequence of one of the differentially expressed clones obtained after treatment with bufalin was identical to that of the human gene for Tiam1. When U937 cells were treated with 10(-7) M bufalin, expression of both Tiam1 mRNA and the protein was induced 1 h after the start of the treatment. The increase of Tiam1 mRNA was transient but the level of Tiam1 protein continued to increase at least for 6 h. In addition, the activities of Rac1 and p21-activated kinase (PAK) were also stimulated by bufalin treatment. To evaluate the role of Tiam1 in the apoptotic process, we examined the effects of the expression of sense and antisense RNA for Tiam1 in U937 cells. Apoptosis was strongly induced by bufalin in cells that expressed sense RNA for Tiam1 as compared to apoptosis in control cells treated with bufalin only. Cells expressing antisense RNA for Tiaml were significantly more resistant than the control bufalin-treated cells to induction of DNA fragmentation in response to bufalin. Moreover, sense transformants had elevated activities of PAK and c-Jun NH2-terminal kinase (JNK). These results suggest that Tiaml might play a critical role in bufalin-induced apoptosis through the activation of Rac1, PAK, and JNK pathway.

Antineoplastic Agents↗
PubMed1998

Identification and localization of the extracellular calcium-sensing receptor in human breast.

The extracellular calcium (Ca2+o)-sensing receptor (CaR) plays a critical role in maintaining Ca2+o homeostasis in mammals by virtue of its presence in parathyroid gland and kidney. The breast is well recognized as a Ca(2+)-handling organ, and the effects of altering Ca2+o on the proliferation of breast epithelial cells are well documented. To date there are no data regarding the expression and localization of CaR in breast tissue. In the present study, we assessed the distribution of CaR messenger ribonucleic acid (mRNA) and protein in normal and fibrocystic human breast tissue as well as in ductal carcinoma of the breast using RT-PCR, Northern analysis, and immunohistochemistry with CaR-specific antisera. In all tissues, RT-PCR performed using sense and antisense primers based on the sequence of the human parathyroid CaR complementary DNA amplified a product of the size expected (425 bp) for genuine CaR transcripts. Nucleotide sequencing of RT-PCR products confirmed more than 99% homology with human parathyroid CaR complementary DNA. Although insufficient quantities of mRNA were isolated from normal and fibrocystic tissue for Northern analysis, a single 5.2-kb CaR transcript was expressed in malignant breast tissue similar to the major CaR transcript in human parathyroid. Localization of CaR protein by immunohistochemistry showed specific CaR staining of the ductal epithelial cells of the breast in all three tissue types. These findings indicate the presence of CaR mRNA and protein in the breast, providing indirect evidence that the CaR may have some role(s) in the control of Ca2+ transport, epithelial cell proliferation, and/or other processes in normal and abnormal breast tissue.

Base Sequence↗