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PubMed2000

Sequence learning in Parkinson's disease: a comparison of spatial-attention and number-response sequences.

The serial reaction time (SRT) task has been frequently used to assess procedural learning of sequences. Patients with Parkinson's disease (PD) have been reported to show deficits on this task, but it is as yet unclear whether this impairment reflects a general sequencing deficit or a deficit in the sequencing of motor-output responses. In order to examine this issue, PD patients and controls were administered an SRT task which allowed the simultaneous and independent assessment of the procedural learning of spatial regularities and the learning of motor-response regularities. PD patients were unimpaired at learning a sequence of spatial locations, but showed a deficit at learning a stimulus-to-motor-response sequence. The results suggest that sequencing impairments in PD are not general, but specific to the type of sequential information inherent in a task.

Aged↗
PubMed1996

Spatial attention and implicit sequence learning: evidence for independent learning of spatial and nonspatial sequences.

This research investigated whether regular spatial orienting sequences can be learned implicitly and independently of response requirements. In a new version of a serial response task introduced by M. J. Nissen and P. Bullemer (1987) participants had to discriminate between objects that could occur at different locations. Independent sequences determined the succession of locations and objects. Even participants who were not aware of any regularities exhibited evidence for learning of both sequences (Experiment 1). Experiment 2 showed that the joint learning of spatial and object sequences was as efficient as learning of single sequences and that it even occurred when learning required memory for past sequence elements and attention was blocked through a secondary tone-counting task. Results are consistent with the idea that independent systems may exist for the implicit acquisition of spatial and nonspatial regularities.

Adult↗
PubMed2000

[MRI of osteomyelitis: sensitivity and specificity of STIR sequences in comparison with contrast-enhaned T1 spin echo sequences].

PURPOSE: To evaluate the need for additional MR sequences including administration of Gd-DTPA after inconspicuous Short-Tau Inversion-Recovery (STIR) sequence to exclude the diagnosis of osteomyelitis. MATERIAL AND METHODS: 112 MR examinations of 79 patients acquired for the detection of possible osteomyelitis were analyzed retrospectively. All examinations were performed at 0.5 T including STIR, T1-weighted spin echo sequences (T1 SE) before and after application of Gd-DTPA. Additionally, 93 T2-weighted spin echo sequences were available. The examinations were analyzed by two experienced radiologists. First, the STIR sequences were studied, followed by the T1 SE images before and after administration of contrast material. Finally, the T2-weighted images were evaluated. Diagnoses were confirmed by operation (22), biopsy (10), and follow-up (80). RESULTS: In 53 cases osteomyelitis was diagnosed, while the remaining 59 cases suffered from another disease. The sensitivity of the STIR sequence was 100% while the specificity for osteomyelitis was 49.2%. The specificity increased to 79.7% by including T1 SE images into the analysis and reached 83.1% after considering the contrast enhanced images. T2-weighted images yielded no additional information. CONCLUSION: The combination of STIR and T1SE images shows a high sensitivity and specificity for osteomyelitis, thus obviating the need for any additional examinations.

Adolescent↗
PubMed1977

Novel mechanism for RNA maturation: the leader sequences of simian virus 40 mRNA are not transcribed adjacent to the coding sequences.

The 5'-terminal 100-200 ribonucleotides of late simian virus 40 (SV40) mRNAs are not transcribed immediately adjacent to their coding sequences. This conclusion is based on the following observations. The major late SV40 cytoplasmic RNA species, 16S and 19S, were purified from poly(A)-containing cytoplasmic RNA by hybridization to and elution from an SV40 DNA fragment that maps between 0.67 and 0.76. This fragment is remote from the DNA fragments that include the coding sequences. The RNA transcripts from the fragment located between 0.67 and 0.76 were found in abundance. Even though selected on oligo(dT)-cellulose columns, the 5'-terminal sequences did not contain poly(A) tails directly adjacent to their 3' termini. The 5' terminus of the 16S mRNA, as monitored by hybridization of the sequences adjacent to the "cap" structure, was found adjacent to the coding sequences when intact [3H]methyl-labeled RNA was hybridized with restriction fragments. However, after fragmentation, the methyl label of this same RNA hybridized with a fragment that is remote from the coding sequences and maps between 0.67 and 0.73. These results imply a novel mechanism for biosynthesis of SV40 mRNA.

DNA Restriction Enzymes↗
PubMed2005

Characterization and phylogenetic relationships among microsporidia infecting silkworm, Bombyx mori, using inter simple sequence repeat (ISSR) and small subunit rRNA (SSU-rRNA) sequence analysis.

This study is the first report on the genetic characterization and relationships among different microsporidia infecting the silkworm, Bombyx mori, using inter simple sequence repeat PCR (ISSR-PCR) analysis. Six different microsporidians were distinguished through molecular DNA typing using ISSR-PCR. Thus, ISSR-PCR analysis can be a powerful tool to detect polymorphisms and identify microsporidians, which are difficult to study with microscopy because of their extremely small size. Of the 100 ISSR primers tested, only 28 primers had reproducibility and high polymorphism (93%). A total of 24 ISSR primers produced 55 unique genetic markers, which could be used to differentiate the microsporidians from each other. Among the 28 SSRs tested, the most abundant were (CA)n, (GA)n, and (GT)n repeats. The degree of band sharing was used to evaluate genetic similarity between different microsporidian isolates and to construct a phylogenetic tree using Jaccard's similarity coefficient. The results indicate that the DNA profiles based on ISSR markers can be used as diagnostic tools to identify different microsporidia with considerable accuracy. In addition, the small subunit ribosomal RNA (SSU-rRNA) sequence gene was amplified, cloned, and sequenced from each of the 6 microsporidian isolates. These sequences were compared with 20 other microsporidian SSU-rRNA sequences to develop a phylogenetic tree for the microsporidia isolated from the silkworms. This method was found to be useful in establishing the phylogenetic relationships among the different microsporidians isolated from silkworms. Of the 6 microsporidian isolates, NIK-1s revealed an SSU-rRNA gene sequence similar to Nosema bombycis, indicating that NIK-1s is similar to N. bombycis; the remaining 5 isolates, which differed from each other and from N. bombycis, were considered to be different variants belonging to the species N. bombycis.

Animals↗
PubMed2002

DNA sequence conservation between the Bacillus anthracis pXO2 plasmid and genomic sequence from closely related bacteria.

BACKGROUND: Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs). Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity to B. anthracis, as determined by amplified fragment length polymorphism (AFLP) analysis, were examined by PCR for the presence of sequences similar to 47 pXO2 ORFs. RESULTS: The two most distantly related isolates examined, B. thuringiensis 33679 and B. thuringiensis AWO6, produced the greatest number of ORF sequences similar to pXO2; 10 detected in 33679 and 16 in AWO6. No more than two of the pXO2 ORFs were detected in any one of the remaining isolates. Dot-blot DNA hybridizations between pXO2 ORF fragments and total genomic DNA from AWO6 were consistent with the PCR assay results for this isolate and also revealed nine additional ORFs shared between these two bacteria. Sequences similar to the B. anthracis cap genes or their regulator, acpA, were not detected among any of the examined isolates. CONCLUSIONS: The presence of pXO2 sequences in the other Bacillus isolates did not correlate with genomic relatedness established by AFLP analysis. The presence of pXO2 ORF sequences in other Bacillus species suggests the possibility that certain pXO2 plasmid gene functions may also be present in other closely related bacteria.

Journal Article↗
PubMed1996

Sequences of topotecan and cisplatin: phase I, pharmacologic, and in vitro studies to examine sequence dependence.

PURPOSE: A phase I and pharmacologic study was performed to evaluate the feasibility of administering the topoisomerase I (topo I) inhibitor topotecan (TPT) in combination with cisplatin (CDDP) in minimally pretreated adults with solid tumors. The study was designed to evaluate the magnitude of the toxicologic and pharmacologic differences between the two sequences of drug administration. MATERIALS AND METHODS: TPT was administered as a 30-minute infusion daily for 5 days and CDDP was given either before TPT on day 1 or after TPT on day 5. Each patient was treated with both schedules on an alternating basis every 3 weeks. Sequential dose escalation of TPT or CDDP resulted in three dosage permutation of TPT/CDDP (mg/m2): 0.75/50, 1/50, and 0.75/75. After the maximum-tolerated dose (MTD) level was achieved, the feasibility of using granulocyte colony-stimulating factor (G-CSF) to permit further dose escalation was studied. To examine the interaction of TPT and CDDP in vitro, human A549 lung cancer cells were exposed to these agents concurrently and sequentially. RESULTS: Dose-limiting neutropenia and thrombocytopenia resulted after the doses of TPT or CDDP were increased to greater than 0.75 and 50 mg/m2, respectively, without and with G-CSF. The sequence of CDDP before TPT induced significantly worse neutropenia and thrombocytopenia than the alternate sequence. In vitro studies failed to provide any evidence for the differences in the cytotoxicity of these two sequences. Instead, pharmacokinetic studies suggested that the differences in toxicity were due, in part, to lower TPT clearance and exposure when CDDP preceeds TPT, possibly due to subclinical renal tubular toxicity induced by CDDP. CONCLUSION: The sequence of CDDP before TPT at doses of 50 and 0.75 mg/m2, respectively, is recommended for subsequent clinical trials in tumor types in which both agents have significant single-agent activity. The potential for sequence-dependent cytotoxic, toxicologic, and pharmacologic effects should be evaluated in concurrent clinical and laboratory studies in the course of developing combination chemotherapy regimens that consist of topo I-targeting agents and other antineoplastic agents, particularly DNA-damaging agents.

Adenocarcinoma↗
PubMed2006

Phylogenetic analysis of gamma-proteobacteria inferred from nucleotide sequence comparisons of the house-keeping genes adk, aroE and gdh: comparisons with phylogeny inferred from 16S rRNA gene sequences.

Nucleotide sequence comparisons of three house-keeping genes, adenylate kinase (adk), shikimate dehydrogenase (aroE), and glucose-6-phosphate dehydrogenase (gdh), were used to infer the phylogeny of 33 gamma-proteobacteria. Phylogenetic trees inferred from each gene, and from the concatenated sequences of all three genes, are, in general, similar to a 16S rRNA gene-inferred tree. Similar grouping of bacteria are revealed at the family, genus, species and strain levels in all five trees. The house-keeping genes, however, show a higher rate of nucleotide sequence substitutions. Consequently, they can possibly probe deeper branches of a phylogenetic tree than the 16S rRNA gene. However, because their nucleotide sequences are not as highly conserved among gamma-proteobacteria, family- or genus-specific primers would need to be designed for the amplification of any of these three house-keeping genes. Since these genes are used in multilocus sequence typing, it is expected that the number of sequences publicly available for many taxa will increase over time proving them very useful either at complementing 16S rRNA-inferred phylogenies or for specific, targeted, phylogenetic analysis.

Adenylate Kinase↗
PubMedDate not supplied

Optimal pulse sequence for ferumoxides-enhanced MR imaging used in the detection of hepatocellular carcinoma: a comparative study using seven pulse sequences.

OBJECTIVE: To identify the optimal pulse sequence for ferumoxides-enhanced magnetic resonance (MR) imaging in the detection of hepatocelluar carcinomas (HCCs). MATERIALS AND METHODS: Sixteen patients with 25 HCCs underwent MR imaging following intravenous infusion of ferumoxides. All MR studies were performed on a 1.5-T MR system, using a phased-array coil. Ferumoxides (Feridex IV) at a dose of 15 micromol/Kg was slowly infused intravenously, and axial images of seven sequences were obtained 30 minutes after the end of infusion. The MR protocol included fast spin-echo (FSE) with two echo times (TR3333-8571/TE18 and 90-117), singleshot FSE (SSFSE) with two echo times (TRinfinity/TE39 and 98), T2*-weighted gradient- recalled acquisition in the steady state (GRASS) (TR216/TE20), T2*-weighted fast multiplanar GRASS (FMPGR) (TR130/TE8.4-9.5), and T2*-weighted fast multiplanar spoiled GRASS (FMPSPGR) (TR130/TE8.4-9.5). Contrast-to-noise ratios (CNRs) of HCCs determined during the imaging sequences formed the basis of quantitative analysis, and images were qualitatively assessed in terms of lesion conspicuity and image artifacts. The diagnostic accuracy of all sequences was assessed using receiver operating characteristic (ROC) analysis. RESULTS: Quantitative analysis revealed that the CNRs of T2*-weighted FMPGR and T2*-weighted FMPSPGR were significantly higher than those of the other sequences, while qualitative analysis showed that image artifacts were prominent at T2*-weighted GRASS imaging. Lesion conspicuity was statistically significantly less clear at SSFSE imaging. In term of lesion detection, T2*-weighted FMPGR, T2*- weighted FMPSPGR, and proton density FSE imaging were statistically superior to the others. CONCLUSION: T2*-weighted FMPGR, T2*- weighted FMPSPGR, and proton density FSE appear to be the optimal pulse sequences for ferumoxidesenhanced MR imaging in the detection of HCCs.

Adult↗
PubMed2002

A H(2)(15)O positron emission tomography study on mental imagery of movement sequences--the effect of modulating sequence length and direction.

Motor imagery is a state of mental rehearsal of single movements or movement patterns and has been shown to recruit motor networks overlapping with those activated during movement execution. We wished to examine whether the brain areas subserving control of sequential processes could be delineated by pure mental imagery, their activation levels reflecting the processing demands of a sequential task. We studied six right-handed volunteers (39.0 +/- 14 years) with H(2)(15)O positron emission tomography (PET) while they continuously mentally pursued with their right hand one of five sequences differing in complexity (i.e., increases in sequence length, single-finger repetitions, and reversals). Conditions were repeated twice, alternating with two rest scans. Each imagined single motor element was paced at a frequency of 1 Hz. Significant activation increases (P < 0.05, corrected) associated with imagination of right finger movement sequences (conditions I to V combined)--compared to the rest condition--were observed in left sensorimotor cortex (M1/S1) and the adjacent inferior parietal cortex. Further activation increases (P < 0.001, uncorrected) occurred in bilateral dorsal premotor (PMd) cortex, left caudal supplementary motor area, bilateral ventral premotor cortex, right M1, left superior parietal cortex, left putamen, and right cerebellum. Activation decreases occurred in bilateral prefrontal and right temporo-occipital cortex. Activation increases that correlated with sequence complexity were observed only in specific areas of the activated network, notably in left PMd, right superior parietal cortex, and right cerebellar vermis (P < 0.05, corrected). In conclusion, our study, by varying the sequence structure of imagined finger movements, identified task-related activity changes in parietopremotor-cerebellar structures, reflecting their role in mediating sequence control.

Adult↗
PubMed1989

Structural polymorphism of homopurine--homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.

In this paper, we have analysed the conformational behaviour shown by the homopurine--homopyrimidine alternating d(GA.CT)22 sequence cloned into SV40. Our results show that, in the presence of zinc ions, the d(GA.CT)22 sequence adopts an altered secondary DNA structure (*H-DNA) which differs from either B-DNA or H-DNA. Formation of *H-DNA is facilitated by negative supercoiling and does not appear to require base protonation, since it is induced at neutral pH by approximately 0.4 mM ZnCl2. The patterns of OsO4 and DEPC modification obtained in the presence of zinc are compatible with a homopurine--homopurine--homopyridimine triplex, though other structural models for *H-DNA are also possible. The hypersensitivity to S1-cleavage of the d(GA.CT)22 sequence is reinterpreted in terms of the equilibria between the B-, H- and *H-forms of the sequence. These results reveal the high degree of structural polymorphism shown by homopurine-homopyrimidine sequences. Its biological relevance is discussed.

Animals↗
PubMed2004

Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica.

We have developed and evaluated sequence-tagged site (STS) primers based on expressed sequence-tag information derived from sugi (Cryptomeria japonica) for use in hinoki (Chamaecyparis obtusa), a species that belongs to a different family (although it appears to be fairly closely related to sugi). Of the 417 C. japonica STS primer pairs we screened, 120 (approximately 30%) were transferable and provided specific PCR amplification products from 16 C. obtusa plus trees. We used haploid megagametophytes to investigate the homology of 80 STS fragments between C. obtusa and C. japonica and to identify orthologous loci. Nearly 90% of the fragments showed high (>70%) degrees of similarity between the species, and 35 STSs indicated homology to entries with the same putative function in a public DNA database. Of the 120 STS fragments amplified, 72 showed restriction fragment length polymorphisms; in addition, the CC2430 primers detected amplicon length polymorphism. We assessed the inheritance pattern of 27 cleaved amplified polymorphic sequence markers, using 20 individuals from the segregation population. All the markers analyzed were consistent with the marker inheritance patterns obtained from the screening panel, and no markers (except CC2716) showed significant (P<0.01) deviation from the expected segregation ratio. In total, 136 polymorphic markers were developed using C. japonica-based STS primers without any sequence modification. In addition, the applicability of STS-based markers developed in one species to other species was found to closely reflect the evolutionary distance between the species, which is roughly concordant with the difference between their rbcL sequences. We plan to use these markers for genetic studies in C. obtusa. Most of the markers should also provide reliable anchor loci for comparative mapping studies of the C. obtusa and C. japonica genomes.

Base Sequence↗
PubMed1998

Nucleotide sequence of the 5'-terminus of Newcastle disease virus and assembly of the complete genomic sequence: agreement with the "rule of six".

We have determined the sequences of the 5' ends of three strains of Newcastle disease virus, permitting the assembly of the entire genomic sequence, which amounts to 15,186 nucleotides. This length is in agreement with the rule of six, which has been shown to determine replication efficiency in similar viruses. Comparison of the extreme 5' end of the trailer sequence with that of the 3'-terminal leader sequence of the virus reveals a high degree of complementarity. Variation between the 5'-terminal sequences of the different strains reveals the presence of alternative L gene polyadenylation signals, leading to correspondingly different trailer lengths.

Animals↗
PubMed1990

Comparative gas phase and pulsed liquid phase sequencing on a modified Applied Biosystems 477A sequencer.

A simple and inexpensive modification of the Applied Biosystems 477A sequencer, to run in the pulsed liquid-phase and in the gas-phase mode of the Edman chemistry, is described. This modification is especially useful for sequencing samples on polyvinylidene difluoride (PVDF) membranes. Additional carriers are required if a sample on a PVDF membrane is sequenced with the pulsed liquid-phase degradation program of the 477A. In the gas-phase mode no such carriers are needed. This eliminates time-consuming preconditioning sequencer cycles and reduces the sequencer background. In addition, initial coupling yields in the gas-phase mode exceeded those in the pulsed liquid-phase mode, whereas the average repetitive yields were similar. Samples spotted onto glass fiber filters pretreated with polybrene and samples spotted or electroblotted onto PVDF membranes were examined. A number of advantages of the gas-phase mode are presented.

Amino Acid Sequence↗
PubMed1985

DNA sequence for cloned cDNA for murine amelogenin reveal the amino acid sequence for enamel-specific protein.

Enamel is the unique and highly mineralized extracellular matrix that covers vertebrate teeth. Amelogenin proteins represent the predominate subfamily of gene products found in developing mammalian enamel, and are implicated in the regulation of the formation of the largest hydroxyapatite crystals in the vertebrate body. Previous attempts to isolate, purify and characterize amelogenins extracted from developing matrix have proven difficult. We now have determined the DNA sequence for a cDNA for the 26-kDa class of murine amelogenin and deduced its corresponding amino acid sequence. The murine amino acid sequence is homologous to bovine or porcine amelogenins extracted from developing enamel matrices. However, an additional 10-residues were found at the carboxy terminus of the murine amelogenin. This is the most complete sequence database for amelogenin peptides and the only DNA sequence for enamel specific genes.

Amelogenin↗
PubMed1986

Nucleotide sequence of the 26 S mRNA of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and deduced sequence of the encoded structural proteins.

A cDNA clone containing all of the 26 S mRNA coding region of the RNA genome of Venezuelan equine encephalitis (VEE) virus, virulent strain Trinidad donkey (TRD), has been constructed and sequenced. The nucleotide and deduced amino acid sequences of the 26 S RNA of VEE virus conform to the general organization of the alphavirus subgenomic mRNA. Excluding the poly(A) tail, the VEE 26 S RNA is 3913 nucleotides long with a protein coding region of 3762 nucleotides. Codon usage in the translated region is nonrandom and correlates well with that reported for Sindbis (SIN), Semliki Forest (SF), and Ross River (RR) alphaviruses. Highly conserved sequences of 19 to 22 nucleotides representing putative replicase recognition sites occur at the 26 S RNA junction region of the 42 S genomic RNA and at the 3' terminus immediately preceding the poly(A) tail. The conserved sequence at the 26 S/42 S junction region of VEE virus differs from that of other alphaviruses in that an ochre termination codon (UAA) is substituted for a GGU (Gly) codon present in the other viruses. The 5' and 3' noncoding regions (30 and 121 nucleotides, respectively) of the VEE 26 S RNA are shorter than has been reported for several other alphaviruses. The approximate transmembrane domains of the VEE E1 and E2 envelope glycoproteins have been identified. VEE E1 contains a single asparagine-linked glycosylation site, whereas E2 has three such sites, all of which are apparently glycosylated. The deduced amino acid sequence of the VEE polyprotein shows an overall homology of 44 to 46% with the precursor polyproteins of SIN, SF, and RR viruses. VEE virus capsid, E1, and E2 structural proteins show 43 to 46%, 50 to 53%, and 36 to 41% homology, respectively, with the cognate proteins of SIN, SF, and RR viruses.

Amino Acid Sequence↗
PubMed1982

Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence.

We have cloned and sequenced a cDNA copy of in vitro-polyadenylated 7SL RNA of HeLa cells. The cloned fragment is 303 bp long and has a composite structure. A central block of 140 bp is homologous to a new set of human middle-repetitive sequences. This block appears to be inserted in an Alu consensus sequence, 100 bp from the 5' end and 40 bp from the 3' end of the Alu monomer. Two 6 bp direct repeats are found at the junction between the Alu flanking sequences and the central element. The analysis of several clones shows the existence of sequence microheterogeneity in the 5' portion of the molecule. The 7L DNA probably represents a subset of the Alu family of DNA, highly conserved in evolution.

Base Sequence↗
PubMed1983

Nucleotide sequence of the herpes simplex virus type 2 (HSV-2) thymidine kinase gene and predicted amino acid sequence of thymidine kinase polypeptide and its comparison with the HSV-1 thymidine kinase gene.

To analyze the boundaries of the functional coding region of the HSV-2(333) thymidine kinase gene (TK gene), deletion mutants of hybrid plasmid pMAR401 H2G, which contains the 17.5 kbp BglII-G fragment of HSV-2 DNA, were prepared and tested for capacity to transform LM(TK-) cells to the thymidine kinase-positive phenotype. These studies showed that hybrid plasmids containing 2.2-2.4 kbp subfragments of HSV-2 BglII-G DNA transformed LM(TK-) cells to the thymidine kinase-positive phenotype and suggested that the region critical for transformation might be less than 2 kbp. That the activity expressed in the transformants was HSV-2 thymidine kinase was shown by experiments with type-specific enzyme-inhibiting rabbit antisera and by disc-polyacrylamide gel electrophoresis analyses. DNA fragments of the HSV-2 TK gene were subcloned in phage M13mp9 and M13mp8. A sequence of 1656 bp containing the entire coding region of the TK gene and the flanking sequences was determined by the dideoxynucleotide chain termination method. Comparisons with the HSV-1(Cl 101) TK gene revealed that PstI, PvuII, and EcoRI cleavage sites had homologous locations as did promoter, translational start and stop, and polyadenylation signals. Extensive homology was observed in the nucleotide sequence preceding the ATG translational start signal and in portions of the coding region of the genes. Comparisons of the predicted amino acid sequences of the HSV-1 and HSV-2 thymidine kinase polypeptides revealed that both were enriched in alanine, arginine, glycine, leucine, and proline residues and that clear, but interrupted homology existed within several regions of the polypeptide chains. Stretches of 15-30 amino acid residues were identical in conserved regions. The possibility is suggested that domains containing some of the conserved amino acid sequences might have a role in substrate binding and as major antigenic determinants.

Amino Acid Sequence↗