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At least 739 records · Page 41Linked to original sources
PubMed1984

Cloning of the rat endogenous helper leukemia virus DNA sequence and expression of the helper activity encoded by the cloned DNA sequence in normal rat kidney cells by microinjection.

By the use of recombinant DNA technology and microinjection in cultured cells, the molecular genetic elements involved in the evolution of a retrovirus with the multipotential to infect, transform and replicate in host cell, have been critically examined in this investigation. Recently we have identified and purified the integrated and proviral DNA sequences specific for two rat endogenous helper leukemia viruses, WR- RaLV , originated from a chemically induced wild rat fibrosarcoma, and RHHV , isolated from a chemically induced rat hepatoma, HTC-H1 (1). By using a multidisciplinary approach combining restriction endonuclease analysis, reverse phase V-column chromatography, agarose gel electrophoresis, Southern blot transfer and filter nucleic acid hybridization, we were able to demonstrate that the rat helper leukemia viral DNA sequence was approximately 8.4-8.8 kb. The 8.8 kb RHHV DNA was molecularly cloned via the EK-1 certified vector pBR 322 plasmid into E. coli RRI cells. A successful recombinant clone, 8/32, that carried one entire RHHV 8.8 kb DNA sequence was mapped by restriction endonuclease analyses. Restricted DNA fragments of various sizes throughout the complete RHHV genome were isolated and purified for intranuclear microinjection into normal rat kidney cells. Release of type C infectious helper virus in these microinjected cells was investigated by superinfection on K-NRK, Kirsten sarcoma transformed non-producer cells. Recombination of the helper viral DNA sequence, en toto or of subgenomic sizes, carried in microinjected cells, with the sarcomagenic DNA sequence, carried in K-NRK cells, was also studied by genome-rescue and cell-transformation experiments. Our observations led to the conclusion that all critical genetic elements including the 5' LTR helper DNA sequence, gag, pol, and env genes, encoded for the biological activity of the type C helper virus resided within the 6.0 kb proximal to the 5' terminus of the endogenous rat type C helper virus DNA. They proved vitally essential for the recombination with the Src sequence during the evolution of an infectious, transforming and replication-competent retrovirus.

Animals↗
PubMed1994

Complete Nucleotide Sequence of Mouse Mammary Tumor Virus from JYG Chinese Wild Mice: Absence of Bacterial Insertion Sequences in the Cloned Viral gag Gene.

Mammary tumors of a newly isolated strain of Chinese wild mouse (JYG mouse) harbor exogenous mouse mammary tumor virus (MMTV). The complete nucleotide sequence of exogenous JYG-MMTV was determined on the proviral 5' long terminal repeat (LTR)(partial)-gag-pol-env-3' LTR (partial) fragment cloned into a plasmid vector and the cDNA sequence from JYG-MMTV producing cells. Similarly to the other MMTV species the LTR of JYG-MMTV contains an open reading frame (ORF). The amino acid sequence of the JYG-MMTV ORF resembles that of SW-MMTV (92% identity) and endogenous Mtv-7 (93% identity) especially at the C-terminal region. Thus, a functional similarity in T-cell receptor V beta recognition as a superantigen is implicated among these MMTV species. Analysis of the viral gag nucleotide sequence revealed that this gene is not disrupted by the bacterial insertion sequence IS1 or IS2, which have been reported to be present in the majority of the plasmids containing the gag region. Comparison of amino acid sequences of JYG-MMTV with those of BR6-MMTV showed that over 96% of the amino acids of gag, pol, protease and env products are identical. These results suggest the intact nature of the nucleotide sequence of the near full-length MMTV genome cloned in the plasmid.

Journal Article↗
PubMed1996

Feedback shift register sequences versus uniformly distributed random sequences for correlation chromatography.

Two alternative input sequences are commonly employed in correlation chromatography (CC). They are sequences derived according to the algorithm of the feedback shift register (i.e., pseudo random binary sequences (PRBS)) and sequences derived by using the uniform random binary sequences (URBS). These two sequences are compared. By applying the "cleaning" data processing technique to the correlograms that result from these sequences, we show that when the PRBS is used the S/N of the correlogram is much higher than the one resulting from using URBS.

Algorithms↗
PubMed2005

Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences.

A genome-wide view of sequence mutability in mice is still limited, although biologists usually assume the same scenario for mice as for humans. In this study, we examined the sequence context in the local environment of 482,528 mouse single nucleotide polymorphisms (SNPs). We found that CpG-containing short sequences, in general, had more representation in the local sequences of SNPs compared to the genome sequences. The extent of this overrepresentation was stronger in mice than in humans, which is inconsistent with previous observations of the weaker neighboring-nucleotide biases on mouse SNPs. To exclude the CpG effect, we compared the distribution patterns of short sequences among the six categories of SNPs. The results revealed an even stronger pattern in the CpG-containing group for C/G substitution compared to for A/G or C/T substitutions. We next performed the first genome-wide sequence context analysis of SNPs in the mouse CpG islands. SNPs occurring at CpG sites were 3.14-fold less prevalent than expected, suggesting the suppression of methylation-dependent deamination in the CpG islands. The extent of this suppression was less in mice than in humans. Finally, compared with humans, the observations of a greater deficit of CpG dinucleotides, a stronger overrepresentation of CpG-containing n-mers surrounding the polymorphic sites, and a higher SNP/genome ratio of CpG dinucleotides in the mouse genome support the "loss of CpG islands" model in the mouse lineage.

Animals↗
PubMed2000

International Rice Genome Sequencing Project: the effort to completely sequence the rice genome.

The International Rice Genome Sequencing Project (IRGSP) involves researchers from ten countries who are working to completely and accurately sequence the rice genome within a short period. Sequencing uses a map-based clone-by-clone shotgun strategy; shared bacterial artificial chromosome/P1-derived artificial chromosome libraries have been constructed from Oryza sativa ssp. japonica variety 'Nipponbare'. End-sequencing, fingerprinting and marker-aided PCR screening are being used to make sequence-ready contigs. Annotated sequences are immediately released for public use and are made available with supplemental information at each IRGSP member's website. The IRGSP works to promote the development of rice and cereal genomics in addition to producing genome sequence data.

Chromosome Mapping↗
PubMed2001

Integration of telomere sequences with the draft human genome sequence.

Telomeres are the ends of linear eukaryotic chromosomes. To ensure that no large stretches of uncharacterized DNA remain between the ends of the human working draft sequence and the ends of each chromosome, we would need to connect the sequences of the telomeres to the working draft sequence. But telomeres have an unusual DNA sequence composition and organization that makes them particularly difficult to isolate and analyse. Here we use specialized linear yeast artificial chromosome clones, each carrying a large telomere-terminal fragment of human DNA, to integrate most human telomeres with the working draft sequence. Subtelomeric sequence structure appears to vary widely, mainly as a result of large differences in subtelomeric repeat sequence abundance and organization at individual telomeres. Many subtelomeric regions appear to be gene-rich, matching both known and unknown expressed genes. This indicates that human subtelomeric regions are not simply buffers of nonfunctional 'junk DNA' next to the molecular telomere, but are instead functional parts of the expressed genome.

Chromosomes, Artificial, Bacterial↗
PubMed1997

Optimal MR protocol for hepatic hemangiomas. Comparison of conventional spin-echo sequences with T2-weighted turbo spin-echo and serial gradient-echo (FLASH) sequences with gadolinium enhancement.

PURPOSE: To compare conventional spin-echo (SE) sequences with T2-weighted turbo SE and serial gadolinium-enhanced T1-weighted FLASH sequences in the detection and characterization of hepatic hemangiomas, and to describe the enhancement characteristics of the lesions on dynamic MR imaging. MATERIAL AND METHODS: Forty-two patients with 66 hemangiomas were studied at 1.0 T or 1.5 T by using conventional SE sequences (T1-weighted, T2-weighted, and heavily T2-weighted), T2-weighted turbo SE sequences, and breath-hold T1-weighted FLASH sequences acquired before, immediately after, and 1, 2, 3, 5, and 10 min after injection of a bolus of gadopentetate dimeglumine. Images were quantitatively analyzed for lesion-to-liver contrast-to-noise (C/N) ratios, and qualitatively analyzed for lesion conspicuity. The enhancement pattern and the rapidity of enhancement were analyzed in small (<15 mm), medium (15-39 mm), and large (>39 mm) hemangiomas. RESULTS: In T2-weighted images, T2-weighted turbo SE and heavily T2-weighted SE images had higher C/N ratios than T2-weighted SE images (p=0.003). Lesion conspicuity was not significantly different in these 3 sequences (p=0.307). In T1-weighted images, T1-weighted FLASH images had higher C/N (p<0.001) and also better lesion conspicuity (p<0.001) than T1-weighted SE images. Immediate uniform enhancement was seen in 43% of small hemangiomas (9 of 21 lesions), and persistent central hypointensity was seen in 73% of large hemangiomas (11 of 15 lesions). Rapid enhancement was seen in 62% of small hemangiomas (13 of 21 lesions) and in 31% of medium or large hemangiomas (14 of 45 lesions). CONCLUSION: Further clinical study is needed for evaluating the differential diagnostic advantages of turbo SE T2-weighted imaging compared to the calculation of T2-values by means of a SE T2-weighted sequence. However, the results of the present study suggest that T2-weighted turbo SE imaging and precontrast and serial gadolinium-enhanced FLASH imaging have the potential to replace conventional SE imaging in the evaluation of hepatic hemangiomas.

Contrast Media↗
PubMed2001

Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins.

As an extension of a sequencing project of human cDNA clones which encode large proteins of unidentified genes, we herein present the entire sequences of 60 cDNA clones for the genes named KIAA1879-KIAA1938. The cDNA clones were isolated from size-fractionated cDNA libraries derived from human fetal brain, adult whole brain and amygdala, and their protein-coding sequences were predicted. Thirty-seven cDNA clones entirely sequenced in this study were selected as cDNAs which have coding potentiality by in vitro transcription/translation experiments, and the remaining 23 cDNA clones were chosen by computer-assisted analysis of terminal sequences of cDNAs. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here were 4.5 kb and 2.2 kb (733 amino acid residues), respectively. Sequence analyses against the public databases enabled us to annotate the functions of the predicted products of the 25 genes; 84% of these predicted gene products (21 gene products) were classified into proteins related to cell signaling/communication, nucleic acid management, and cell structure/motility. In addition to the sequence information about these 60 genes, their expression profiles were also studied in some human tissues including brain regions by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗
PubMed1997

Osteogenic protein-1 up-regulation of the collagen X promoter activity is mediated by a MEF-2-like sequence and requires an adjacent AP-1 sequence.

Bone morphogenetic proteins induce chondrogenesis and osteogenesis in vivo. To investigate molecular mechanisms involved in chondrocyte induction, we examined the effect of osteogenic protein (OP)-1/bone morphogenetic protein-7 on the collagen X promoter. In rat calvaria-derived chondrogenic C5.18 cells, OP-1 up-regulates collagen X mRNA levels and its promoter activity in a cell type- specific manner. Deletion analysis localizes the OP-1 response region to 33 bp (-310/-278), which confers OP-1 responsiveness to both the minimal homologous and heterologous Rous sarcoma virus promoter. Transforming growth factor-beta2 or activin, which up-regulates the expression of a transforming growth factor-beta-inducible p3TP-Lux construct, has little effect on collagen X mRNA and on this 33-bp region. Mutational analysis shows that both an AP-1 like sequence (-294/-285, TGAATCATCA) and an A/T-rich myocyte enhancer factor (MEF)-2 like sequence (-310/-298, TTAAAAATAAAAA) in the 33-bp region are necessary for the OP-1 effect. Gel shift assays show interaction of distinct nuclear proteins from C5.18 cells with the AP-1-like and the MEF-2-like sequences. OP-1 rapidly induces nuclear protein interaction with the MEF-2-like sequence but not with the AP-1 like sequence. MEF-2-like binding activity induced by OP-1 is distinct from the MEF-2 family proteins present in C2C12 myoblasts, in which OP-1 does not induce collagen X mRNA or up-regulate its promoter activity. In conclusion, we identified a specific response region for OP-1 in the mouse collagen X promoter. Mutational and gel shift analyses suggest that OP-1 induces nuclear protein interaction with an A/T-rich MEF-2 like sequence, distinct from the MEF-2 present in myoblasts, and up-regulates collagen X promoter activity, which also requires an AP-1 like sequence.

Activins↗
PubMed1999

MR imaging of the liver using an ultrafast 3D multi-shot EPI sequence. Comparison with four other T1-weighted sequences.

PURPOSE: To compare a 3D echo planar imaging (EPI) sequence with four other T1-weighted sequences for imaging of the liver at 1 T. MATERIAL AND METHODS: Twenty volunteers were included in our imaging protocol. Spin-echo (SE), turbo SE (TSE), turbo field echo (TFE) in 2D and 3D acquisition mode, fast field echo (T1-FFE) and 3D EPI sequences were applied. Signal-to-noise (S/N) ratio of the liver, contrast-to-noise (C/N) ratio and relative contrast (ReCon) between the liver and the spleen, scanning time per slice and artifact levels were evaluated. RESULTS: 3D EPI provided a statistically equivalent S/N ratio of the liver with SE and T1-FFE sequences (p>0.05), while it provided a statistically higher S/ N ratio of the liver compared to TFE sequences (p<0.05). The TSE technique provided a statistically higher S/N ratio of the liver compared to 3D EPI (p<0.05). With regard to the liver-spleen C/N ratio, 3D EPI provided statistically equivalent results compared to all sequences except T1-FFE, where 3D EPI was superior. With regard to liver-spleen ReCon, 3D EPI was statistically equivalent to SE, TSE and T1-FFE, while it provided significantly higher liver-spleen ReCon than 3D TFE and significantly lower than 2D TFE. CONCLUSION: 3D EPI provided sufficient ReCon and C/N ratio and produced motion-free images in one breath-hold period. Further clinical studies are required to estimate the sensitivity, specificity and accuracy of the sequence.

Adult↗
PubMed2000

Microsatellite instability of dinucleotide tandem repeat sequences is higher than trinucleotide, tetranucleotide and pentanucleotide repeat sequences in prostate cancer.

In order to investigate whether the change in length of simple repetitive genomic sequences (microsatellite instability) is associated with prostate cancer, we analyzed 40 prostate cancer samples with 44 microsatellite loci markers on chromosomes 1, 3, 5, 6, 8, 9, 11, 13, 16, 17 and X. DNA was extracted from normal and tumor cells of 40 microdissected cancer samples, amplified by PCR and analyzed for microsatellite instability using 44 primers for dinucleotide, trinucleotide, tetranucleotide and pentanucleotide repeat sequences. The results of this study demonstrate that 45% of the prostate cancer specimens (18 out of 40) showed microsatellite instability (MSI) at a minimum of one locus using dinucleotide repeat sequences. Two out of 40 samples (5%) showed MSI at a minimum of one locus using three different trinucleotide repeat primers (AR, SR and TBP). Ten out of 40 (25%) samples showed MSI at a minimum of one locus using five different tetranucleotide repeat primers (HPRT1, HPRTII, MYCL1, RB, REN). There were no MSI observed in samples using pentanucleotide repeat sequences. There were no MSI in benign prostatic hyperplasia samples (25 samples). These experiments suggest that the microsatellite instability of dinucleotide tandem repeat sequences is much higher than trinucleotide, tetranucleotide and pentanucleotide repeat sequences in prostate cancer. The MSI with different lengths of nucleotide repeat sequences did not correlate with the stage and grades of prostate cancer.

Dinucleotide Repeats↗
PubMed1999

The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2.

An international consortium has been formed to sequence the entire genome of the human malaria parasite Plasmodium falciparum. We sequenced chromosome 2 of clone 3D7 using a shotgun sequencing strategy. Chromosome 2 is 947 kb in length, has a base composition of 80.2% A + T, and contains 210 predicted genes. In comparison to the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, a greater proportion of genes containing introns, and nearly twice as many proteins containing predicted non-globular domains. A group of putative surface proteins was identified, rifins, which are encoded by a gene family comprising up to 7% of the protein-encoding gene in the genome. The rifins exhibit considerable sequence diversity and may play an important role in antigenic variation. Sixteen genes encoded on chromosome 2 showed signs of a plastid or mitochondrial origin, including several genes involved in fatty acid biosynthesis. Completion of the chromosome 2 sequence demonstrated that the A + T-rich genome of P. falciparum can be sequenced by the shotgun approach. Within 2-3 years, the sequence of almost all P. falciparum genes will have been determined, paving the way for genetic, biochemical, and immunological research aimed at developing new drugs and vaccines against malaria.

Animals↗
PubMed2003

Distinct mechanisms for processing spatial sequences and pitch sequences in the human auditory brain.

Perception of the acoustic world requires the simultaneous processing of the acoustic patterns associated with sound objects and their location in space. In this functional magnetic resonance experiment, we investigated the human brain areas engaged in the analysis of pitch sequences and sequences of acoustic spatial locations in a paradigm in which both could be varied independently. Subjects were presented with sequences of sounds in which the individual sounds were regular interval noises with variable pitch. Positions of individual sounds were varied using a virtual acoustic space paradigm during scanning. Sound sequences with changing pitch specifically activated lateral Heschl's gyrus (HG), anterior planum temporale (PT), planum polare, and superior temporal gyrus anterior to HG. Sound sequences with changing spatial locations specifically activated posteromedial PT. These results demonstrate directly that distinct mechanisms for the analysis of pitch sequences and acoustic spatial sequences exist in the human brain. This functional differentiation is evident as early as PT: within PT, pitch pattern is processed anterolaterally and spatial location is processed posteromedially. These areas may represent human homologs of macaque lateral and medial belt, respectively.

Acoustic Stimulation↗
PubMed1990

The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation.

CD spectra were obtained for eight synthetic double-stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A-C).d(G-T)] and poly[d(A-G).d(C-T)], (b) poly[d(A-C-C).d(G-G-T)] and poly[d(A-C-G).d(C-G-T)], and (c) poly[d(A).d(T)], poly[d(A-T).d(A-T)], poly[d(A-A-T).d(A-T-T)], and poly[d(A-A-T-T).d(A-A-T-T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G.C)-containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180-191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right-handed conformations. Among the set of sequences containing only A.T base pairs, poly[d(A).d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A.T)-rich polymers and was absent from two first-neighbor estimations of the poly[d(A).d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A.T)-rich polymers was due in part to the fact that poly[d(A).d(T)] exists in a noncanonical B conformation.

Base Composition↗
PubMed1982

The nucleotide sequence of the mouse immunoglobulin epsilon gene: comparison with the human epsilon gene sequence.

We have determined the nucleotide sequence of the immunoglobulin epsilon gene cloned from newborn mouse DNA. The epsilon gene sequence allows prediction of the amino acid sequence of the constant region of the epsilon chain and comparison of it with sequences of the human epsilon and other mouse immunoglobulin genes. The epsilon gene was shown to be under the weakest selection pressure at the protein level among the immunoglobulin genes although the divergence at the synonymous position is similar. Our results suggest that the epsilon gene may be dispensable, which is in accord with the fact that IgE has only obscure roles in the immune defense system but has an undesirable role as a mediator of hypersensitivity. The sequence data suggest that the human and murine epsilon genes were derived from different ancestors duplicated a long time ago. The amino acid sequence of the epsilon chain is more homologous to those of the gamma chains than the other mouse heavy chains. Two membrane exons, separated by an 80-base intron, were identified 1.7 kb 3' to the CH4 domain of the epsilon gene and shown to conserve a hydrophobic portion similar to those of other heavy chain genes. RNA blot hybridization showed that the epsilon membrane exons are transcribed into two species of mRNA in an IgE hybridoma.

Amino Acid Sequence↗
PubMed1997

alpha B-crystallin TATA sequence mutations: lens-preference for the proximal TATA box and the distal TATA-like sequence in transgenic mice.

The mouse alpha B-crystallin promoter is active in lens (preferentially), heart and skeletal muscle, and contains a proximal (-28/-22) and distal (-76/-69) TATA sequence. The present investigation explores by site-specific mutagenesis of alpha B-crystallin promoter-chloramphenicol acetyltransferase (cat) reporter gene constructs the function of these two potential TATA boxes in transfected lens cells and transgenic mice. Unexpectedly, mutagenesis of either or both TATA sequences had no effect on promoter activity in transfected lens cells. By contrast, in transgenic mice mutagenesis of the proximal, distal or both TATA sequences preferentially reduced promoter activity in the lens, with minimal effect in the heart or muscle. 5' RACE analysis of lens and muscle RNA of transgenic mice showed that elimination of the proximal TATA box led to transcription initiation at position -48. This upstream initiation site was apparently not due to the utilization of the distal TATA sequence, since the transgene carrying mutations in both TATA sequences also initiated at position -48. The preferential function of the distal TATA sequence in the lens is probably due to the binding of a transcription factor unrelated to transcription initiation, while the preferential lens function of the proximal TATA box appears to involve transcription initiation.

Animals↗
PubMed1998

A Bayes-optimal sequence-structure theory that unifies protein sequence-structure recognition and alignment.

A rigorous Bayesian analysis is presented that unifies protein sequence-structure alignment and recognition. Given a sequence, explicit formulae are derived to select (1) its globally most probable core structure from a structure library; (2) its globally most probable alignment to a given core structure; (3) its most probable joint core structure and alignment chosen globally across the entire library; and (4) its most probable individual segments, secondary structure, and super-secondary structures across the entire library. The computations involved are NP-hard in the general case (3D-3D). Fast exact recursions for the restricted sequence singleton-only (1D-3D) case are given. Conclusions include: (a) the most probable joint core structure and alignment is not necessarily the most probable alignment of the most probable core structure, but rather maximizes the product of core and alignment probabilities; (b) use of a sequence-independent linear or affine gap penalty may result in the highest-probability threading not having the lowest score; (c) selecting the most probable core structure from the library (core structure selection or fold recognition only) involves comparing probabilities summed over all possible alignments of the sequence to the core, and not comparing individual optimal (or near-optimal) sequence-structure alignments; and (d) assuming uninformative priors, core structure selection is equivalent to comparing the ratio of two global means.

Amino Acid Sequence↗
PubMed1984

Sequence of a cDNA coding for a rat class II A alpha chain: extensive DNA and protein sequence identity to H-2 A alpha and HLA-DC1 alpha chains.

The rat major histocompatibility complex (RT1-B region) codes for two sets of class II molecules (Ia antigens) referred to as A and E. Each class II molecule is composed of two glycoprotein chains called the A alpha and A beta or E alpha and E beta. Two cDNA clones encoding rat A alpha chains were identified from cDNA derived from rat spleen mRNA using a combination of mRNA selection and colony hybridization techniques. The complete nucleotide sequence of the cDNA insert of one of these cDNA clones, pRIa.2, was determined. This sequence codes for the carboxy-terminal 129 amino acids of the rat A alpha chain and 293 nucleotides of 3' untranslated sequence. The rat A alpha chain was shown to be highly homologous in terms of both protein and DNA sequence identities to HLA-DC1 alpha and H-2 A alpha chains. Comparison between the coding regions of the cDNA insert of pRIa.2 and the corresponding region of a cDNA insert encoding an HLA-DC1 alpha chain showed sequence identities of 85% and 81% at the protein and DNA levels, respectively. Comparison between pRIa.2 and cDNA encoding an H-2 A alpha chain sequence showed identities of 91% for both protein and DNA. Results are discussed which strongly suggest that the class II A and E primordial genes arose by gene duplication prior to the evolutionary divergence of the mammals.

Amino Acid Sequence↗