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PubMed2005

The implicit sequence learning deficit in patients with Parkinson's disease: a matter of impaired sequence integration?

Despite the wealth of research investigating the serial reaction time (SRT) learning abilities of people with Parkinson's disease (PD), the role of the basal ganglia in implicit sequence learning remains largely unclear. The present research sought to examine the ability of people with PD to implicitly learn simultaneously operating sequences and integrate patterned information from each sequence dimension. Using a version of the SRT which reduced motor demands, the present experiment investigated the implicit learning of a spatial sequence, a stimulus-response sequence, and an integrated spatial/stimulus-response sequence, all of which are usually confounded in the standard SRT task. Whereas both PD and control groups demonstrated robust learning for the individual spatial and response sequences, only control participants evidenced learning for the integrated sequence. Further, unlike implicit learning for the spatial and object sequences, impaired integrated sequence acquisition was specifically related to the severity of patients' PD symptomatology. The implicit learning deficits of PD patients are discussed with regard to the role played by the basal ganglia in integrative sequence learning in the SRT.

Aged↗
PubMed2004

Comparison of MR imaging sequences for liver and head and neck interventions: is there a single optimal sequence for all purposes?

RATIONALE AND OBJECTIVES: To compare the appropriate pulse sequences for interventional device guidance during magnetic resonance (MR) imaging at 0.2 T and to evaluate the dependence of sequence selection on the anatomic region of the procedure. MATERIALS AND METHODS: Using a C-arm 0.2 T system, four interventional MR sequences were applied in 23 liver cases and during MR-guided neck interventions in 13 patients. The imaging protocol consisted of: multislice turbo spin echo (TSE) T2w, sequential-slice fast imaging with steady precession (FISP), a time-reversed version of FISP (PSIF), and FISP with balanced gradients in all spatial directions (True-FISP) sequences. Vessel conspicuity was rated and contrast-to-noise ratio (CNR) was calculated for each sequence and a differential receiver operating characteristic was performed. RESULTS: Liver findings were detected in 96% using the TSE sequence. PSIF, FISP, and True-FISP imaging showed lesions in 91%, 61%, and 65%, respectively. The TSE sequence offered the best CNR, followed by PSIF imaging. Differential receiver operating characteristic analysis also rated TSE and PSIF to be the superior sequences. Lesions in the head and neck were detected in all cases by TSE and FISP, in 92% using True-FISP, and in 84% using PSIF. True-FISP offered the best CNR, followed by TSE imaging. Vessels appeared bright on FISP and True-FISP imaging and dark on the other sequences. CONCLUSION: In interventional MR imaging, no single sequence fits all purposes. Image guidance for interventional MR during liver procedures is best achieved by PSIF or TSE, whereas biopsies in the head and neck are best performed using FISP or True-FISP sequences.

Adult↗
PubMed2003

Collagen XI sequence variations in nonsyndromic cleft palate, Robin sequence and micrognathia.

Cleft palate is a common birth defect, but its etiopathogenesis is mostly unknown. Several studies have shown that cleft palate has a strong genetic component. Robin sequence consists of three of the following four findings: micrognathia, glossoptosis, obstructive apnea, and cleft palate. While cleft palate is mainly nonsyndromic, about 80 percent of Robin sequence cases are associated with syndromes. Mutations in genes coding for cartilage collagens II and XI, COL2A1, COL11A1 and COL11A2, have been shown to cause chondrodysplasias that are commonly associated with Robin sequence, micrognathia or cleft palate. We therefore analyzed a cohort of 24 patients with nonsyndromic Robin sequence, 17 with nonsyndromic cleft palate and 21 with nonsyndromic micrognathia for mutations in COL11A2. A total of 23 Robin sequence patients were also analyzed for mutations in COL2A1 and COL11A1. We detected two disease-associated mutations in patients with Robin sequence, an Arg to stop codon mutation in COL11A2 and a splicing mutation in COL11A1. Two putatively disease-associated sequence variations were found in COL11A1 in Robin sequence patients, one in COL11A2 in a patient with micrognathia and one in COL2A1 in two patients with Robin sequence. The results showed that sequence variations in these genes can play a role in the etiology of Robin sequence, cleft palate and micrognathia but are not common causes of these phenotypes.

Cleft Palate↗
PubMed1990

Reproductive senescence in domestic fowl: effects on egg production, sequence length and inter-sequence pause length.

1. Age-related changes in egg production, oviposition sequence length and inter-sequence pause length were studied by analysis of oviposition records of 50 individually-caged broiler breeders from 24 to 62 weeks of age. 2. The 44 surviving hens exhibited a production profile characteristic of broiler breeders (184 eggs per hen), with a peak mean sequence length of 19 eggs at 32 weeks of age. Inter-sequence pause length was maximum (1.6 d) at 54 weeks of age. Overall, the hens averaged 48 sequences, with a mean sequence length of 4.1 d. 3. Most hens had a single characteristically long sequence about the time of peak egg production (average: 24.3 d). The term 'prime' is suggested to denote this sequence. 4. Sorting the hens into groups on the basis of total egg output (upper and lower 50% and upper and lower 25%) indicated that high producing hens (upper 50% and 25%) had a very long prime sequence early in lay, and had few inter-sequence pauses of greater than 1 d duration. The converse was true for low producers (lower 50% and 25%). 5. The length of the prime sequence may be a good indicator of reproductive efficiency of hens later in life.

Aging↗
PubMed2003

Evidence for lasting sequence segmentation in the discrete sequence-production task.

It is well known that movement sequences are initiated and executed more slowly as they become longer. Those effects of sequence length, which have been found to lessen with practice, have been attributed to the development of a single motor chunk that represents the entire sequence. But an increasingly efficient distribution of programming can also explain the effects. To examine the mechanisms underlying skill in executing keying sequences, the authors examined the performance of participants (N = 18) who practiced a discrete sequence-production task involving fixed sequences of 3 and 6 key presses. Detailed examination of the effects of extensive practice, of regularities in key pressing order, and of a preceding choice RT task on the production of those sequences showed that most participants executed the 6-key sequence as 2 or more successive segments and continued to do so in the various conditions. The preceding choice RT task restored the sequence-length effect in latency that had disappeared with practice. The present results suggest that practice induces the development of motor chunks, each representing a short segment, and with longer sequences a control scheme for concatenating the motor chunks. Segmentation of longer sequences appeared to be concealed by individual segmentation differences unless there were regularities that imposed a common segmentation pattern.

Adult↗
PubMedDate not supplied

The value of fast and ultrafast T2-weighted MR imaging sequences in hepatic enhancement with ferumoxides: comparison with conventional spin-echo sequence.

PURPOSE: The efficacy of superparamagnetic iron oxide (SPIO) was evaluated with fast T2-weighted imaging sequences such as turbo spin-echo (TSE), half-Fourier single shot turbo spin echo (HASTE), and echo-planar imaging (EPI) in comparison with the conventional spin-echo (SE) sequence on a 1.5 Tesla MR unit. MATERIALS AND METHODS: In a phantom study, we prepared vials containing different concentrations of ferumoxides (0, 0.25, 0.5, 0.75, and 1 micromol Fe) in 2% agarose simulating the liver. In an animal study, contrast medium in doses of 10, 20, and 30 micromol/kg of ferumoxides was injected into the ear vein of rabbits weighing 3.0-4.0 kg under general anesthesia. MR imaging of the phantom and liver of the rabbits was obtained with the T2-weighted SE sequence (TR/TE=2000/20, 80), TSE sequences (TR/effective TE=2000/90, echo train length=7), HASTE (effective TE=64, 90 msec), and EPI (effective TE=64, 90 msec). Three rabbits in each group were imaged before and 1 hour after ferumoxides administration for in-vivo study. The Signal intensity of pre- and postcontrast imaging of the phantom or rabbits' livers was measured with operator-defined regions of interest, and signal-to-noise ratios (SNR) were obtained. Immediately after imaging, the rabbits were sacrificed and the livers were removed at autopsy, followed by ex-vivo study. In a clinical study, 10 micromol/kg of ferumoxides was given in 34 consecutive patients with 31 solid tumors. The liver SNR were evaluated for all 34 patients, and tumor to-liver contrast-to-noise ratios (CNR) were evaluated for all 31 solid lesions. The same series of imaging techniques as in the experimental studies was performed for quantitative and qualitative analyses. RESULTS: In both in-vitro and in-vivo studies, SNR of the phantom or rabbits' livers significantly decreased after ferumoxides administration. The decrease in SNR on excised rabbits' livers was 72% for EPI, 36% for HASTE, 61% for SE, and 51% for TSE at a dose of 10 micromol/kg of ferumoxides. In the clinical study, HASTE and TSE showed significant improvement in CNRs after ferumoxides administration (p<0.05). Visual analysis revealed improvement in tumor detection for all sequences. On EPI, although contrast was excellent, severe image distortion was seen. Although the signal decrease with HASTE and TSE was somewhat inferior to those with EPI and SE, respectively, the effect of contrast enhancement on HASTE and TSE was marked on visual analysis. CONCLUSION: Although TSE sequences and HASTE sequences are less susceptible to magnetic field inhomogeneities than SE and EPI sequences, the decrease in liver signal on HASTE and TSE sequences was comparable to that on EPI and SE sequences, respectively. These sequences are useful clinically for ferumoxides imaging, because they are less sensitive to motion artifacts.

Adult↗
PubMed1992

A micronucleus-limited sequence family in Tetrahymena thermophila: organization and sequence conservation.

During macronuclear development in the ciliated protozoan Tetrahymena thermophila, sequence reorganization including sequence loss occurs. Addressing questions about the organization and nucleotide sequence of micronucleus limited regions can lead to insights about mechanisms of DNA rearrangements during macronuclear development as well as mechanisms for the maintenance of the stability of micronucleus-limited sequence families. We have previously identified a moderately repetitive micronucleus-limited sequence family called X-H (family members hybridize to an approximately 450 bp Xbal-HindIII restriction fragment), completely absent from macronuclear DNA. The first member of this family which we isolated is associated with terminal sequences characteristic of a Tel-1 element, a putative micronuclear transposable element. Two additional family members have been isolated which are not closely associated with Tel-1 terminal sequences. We have nucleotide sequence data for three cloned members of the X-H family. This analysis has demonstrated that the longest cloned members of the X-H family share a region of homology of approximately 2,400 bp and are highly conserved, differing only by small insertions or deletions of 100 bp or less. The sequences from one of the sequenced family members flanking the region of homology are themselves mostly micronucleus-limited.

Animals↗
PubMed1996

"Doublex" fluorescent DNA sequencing: two independent sequences obtained simultaneously in one reaction with internal labeling and unlabeled primers.

The novel "doublex" DNA sequencing technique that makes it possible to obtain simultaneously two independent sequences from one sequencing reaction with the use of unlabeled primers and internal labeling is described. The different sequencing products are labeled in parallel with fluorescein-15-dATP and Texas red-5-dCTP present in the same tube. The characteristics of T7 DNA polymerase are exploited to ensure that only either of the labeled dNTPs is incorporated into the corresponding sequencing products. Specificity of labeling is ensured by the selection of primers. One of the unlabeled primers is chosen to be followed by an "A," the other by a "C" to be incorporated immediately downstream from the primer binding site. The doublex sequencing technique is applicable to the simultaneous sequencing of either the same DNA template/strand or a mixture of different templates. Combinations of unlabeled and labeled primers in the same sequencing reaction are also possible. The two sequences can be determined in parallel and on-line in the same lanes of a gel with a novel automated DNA sequencer, which was previously described for use with labeled primers.

Autoanalysis↗
PubMed1991

Purification and amino-terminal sequence of the bovine cardiac sodium-calcium exchanger: evidence for the presence of a signal sequence.

The Na(+)-Ca2+ exchange carrier was purified from bovine cardiac tissue by a new procedure which relies principally upon anion-exchange chromatography. The purified protein exhibited two major bands on sodium dodecyl sulfate gels, at 120 and 160 kDa. The relative intensities of the two bands could be altered by variations in the procedures used for preparing the samples for electrophoresis, suggesting that they represent two different conformational states of the same protein. The NH2-terminal amino acid sequences of the 120- and 160-kDa bands were identical and agreed closely with a region of the deduced amino acid sequence of the recently cloned canine cardiac exchanger. The NH2-terminal sequence was preceded in the deduced sequence by a 32-residue segment that exhibited the characteristics of a signal sequence; the initial amino acid in the NH2-terminal sequence followed immediately after the predicted cleavage site for the signal sequence. The Na(+)-Ca2+ exchanger appears to be unique among membrane transport carriers in encoding a cleaved signal sequence. The characteristics of the sequences flanking the first putative transmembrane segment of the mature exchanger suggest that the signal sequence is necessary to ensure the correct topological orientation of the exchanger in the membrane.

Amino Acid Sequence↗
PubMed1984

Bacillus megaterium spore protein C-3: nucleotide sequence of its gene and the amino acid sequence at its spore protease cleavage site.

The nucleotide sequence of the Bacillus megaterium gene coding for spore-specific protein C-3 has been determined. The gene codes for 65 amino acids and the coding sequence is preceded by an efficient ribosome-binding site. The predicted protein C-3 sequence agrees with both the amino acid composition and the amino terminal sequence of protein C-3, and shows homology (approx. 65% of all residues are identical) with the sequences of the analogous proteins A and C of B. megaterium. Protein C-3 is cleaved by the sequence-specific B. megaterium spore protease, and the amino acid sequence at the new amino-terminus generated is identical to that predicted from the gene sequence, and homologous to the spore protease cleavage sites in the A and C proteins. The protein C-3 gene also shares a number of features with the previously sequenced protein C gene in both upstream and downstream flanking sequence.

Amino Acid Sequence↗
PubMed1994

Error-tolerant identification of peptides in sequence databases by peptide sequence tags.

We demonstrate a new approach to the identification of mass spectrometrically fragmented peptides. A fragmentation spectrum usually contains a short, easily identifiable series of sequence ions, which yields a partial sequence. This partial sequence divides the peptide into three parts-regions 1, 2, and 3-characterized by the added mass m1 of region 1, the partial sequence of region 2, and the added mass m3 of region 3. We call the construct, m1 partial sequence m3, a "peptide sequence tag" and show that it is a highly specific identifier of the peptide. An algorithm developed here that uses the sequence tag to find the peptide in a sequence database is up to 1 million-fold more discriminating than the partial sequence information alone. Peptides can be identified even in the presence of an unknown posttranslational modification or an amino acid substitution between an entry in the sequence database and the measured peptide. These concepts are demonstrated with model and practical examples of electrospray mass spectrometry/mass spectrometry of tryptic peptides. Just two to three amino acid residues derived by fragmentation are enough to identify these peptides. In peptide mapping applications, even less information is necessary.

Algorithms↗
PubMed1995

Sequence-specific DNA binding by a rhodium complex: recognition based on sequence-dependent twistability.

The chemical construction of small molecules targeted to DNA depends upon the sequence-dependent structure of the double helix. Here we describe a new structural element to be considered in the sequence-specific recognition of DNA, sequence-dependent DNA twistability. The importance of sequence-dependent DNA twistability is demonstrated in the DNA recognition properties of a novel synthetic rhodium intercalator, lambda-1-Rh(MGP)2phi5+. This metallointercalator, containing pendant guanidinium groups, binds in the major groove of DNA at subnanomolar concentrations to the 6 base pair sequence 5'-CATATG-3' with enantiospecificity. An essential feature of this recognition is the sequence-specific unwinding of the DNA helix, which permits direct contacts between guanidinium functionalities on the metal complex and guanine residues. Through an assay developed to test for sequence-specific DNA unwinding, a 70 +/- 10 degrees unwinding of the sequence 5'-CATATG-3' is established with specific binding by the metal complex. This sequence-dependent twistability may be an essential feature of the recognition of sequences by DNA-binding proteins and may be exploited in future design.

Base Composition↗
PubMed1987

Sequence-specific interactions of nuclear factors with conserved sequences of human class II major histocompatibility complex genes.

All class II major histocompatibility complex genes contain two highly conserved sequences, termed X and Y, within the promoter regions(s), which may have a role in regulation of expression. To study trans-acting factors that interact with these sequences, sequence-specific DNA binding activity has been examined by the gel electrophoresis retardation assay using the HLA-DQ2 beta gene 5' flanking DNA and nuclear extracts derived from various cell types. Several specific protein-binding activities were found using a 45-base-pair (bp) HinfI/Sau96I (-142 to -98 bp) and a 38-bp Sau96I/Sau96I (-97 to -60 bp) fragment, which include conserved sequence X (-113 to -100 bp) and conserved sequence Y (-80 to -71 bp), respectively. Competition experiments, methylation interference analysis, and DNase I foot-printing demonstrated that distinct proteins in a nuclear extract of Raji cells (a human B lymphoma line) bind to sequence X, to sequence Y, and to DNA 5' of the X sequence (termed sequence W). The factor binding site in the W sequence is also found to be conserved among beta-chain genes and is suggested to be a gamma-interferon control region.

B-Lymphocytes↗
PubMed1996

Sequence scanning: A method for rapid sequence acquisition from large-fragment DNA clones.

A strategy of "sequence scanning" is proposed for rapid acquisition of sequence from clones such as bacteriophage P1 clones, cosmids, or yeast artificial chromosomes. The approach makes use of a special vector, called LambdaScan, that reliably yields subclones with inserts in the size range 8-12 kb. A number of subclones, typically 96 or 192, are chosen at random, and the ends of the inserts are sequenced using vector-specific primers. Then long-range spectrum PCR is used to order and orient the clones. This combination of shotgun and directed sequencing results in a high-resolution physical map suitable for the identification of coding regions or for comparison of sequence organization among genomes. Computer simulations indicate that, for a target clone of 100 kb, the scanning of 192 subclones with sequencing reads as short as 350 bp results in an approximate ratio of 1:2:1 of regions of double-stranded sequence, single-stranded sequence, and gaps. Longer sequencing reads tip the ratio strongly toward increased double-stranded sequence.

Animals↗
PubMed1988

The sequence of the human epidermal 58-kD (#5) type II keratin reveals an absence of 5' upstream sequence conservation between coexpressed epidermal keratins.

We report the isolation and sequencing of cDNA and genomic clones encoding the complete sequence of the human 58-kD epidermal keratin (#5). The sequence specifies a protein of 62,471 daltons that contains a central alpha-helical segment capable of forming a coiled-coil structure flanked by regions that are not alpha-helical. A comparison of the primary sequence with the known sequences of other intermediate filament proteins reveals many common motifs. The 58-kD keratin is highly similar to other type II keratins and less similar to type I keratins and other intermediate filament proteins. The 58-kD keratin is regulated by retinoids in several tissues and is one of four keratins abundantly expressed in epidermal keratinocytes, where it may be important in maintaining structural integrity of the integument. A comparison of the keratin 5 sequence with coexpressed keratin 14 reveals an absence of sequence conservation in regulatory regions and suggests that common sequence elements may not be necessary for coordinate expression of type I and type II keratin partners. Interestingly, keratin 5 contains only one region weakly resembling the SV40 enhancer-like sequence found in some other keratins indicating that this sequence motif may not be necessary for regulation or abundant expression of all epidermal keratins.

Base Sequence↗
PubMed1996

Identification of sequence motifs causing band compressions on human cDNA sequencing.

In order to characterize DNA sequences leading to band compressions in an automated dideoxy-DNA sequencing system which uses fluorescent dye primers, we compiled DNA sequences at compression sites from accumulated sequence data of human cDNAs (about 205 kb in total length). The results clearly showed that almost all the 3'-end regions at the compression sites (> 98%) carried two types of common sequence motifs. The predominant one (about 68%) contained a sequence of 5'-Y'GN1-2AR'-3' (Y' and R': pyrimidine and purine residues capable of base pairing). The remainder (about 32%) carried a hairpin motif with a relatively stable GC-rich stem (> or = 3 bp) connected by a loop consisting of 3 or 4 nucleotides. The occurrence of compressions at these motif sites was further confirmed by using synthetic DNAs with random sequences (about 58 kb in total length). Since DNA sequences at compression sites analyzed so far shared either of the type of motifs in the sequencing system employed here, it was possible to predict the nucleotide residue to be located at a compression site by carefully checking the sequence preceding the site.

Artifacts↗
PubMed1991

The primary structure of skeletal muscle myosin heavy chain: IV. Sequence of the rod, and the complete 1,938-residue sequence of the heavy chain.

In the preceding paper [Maita, T., Miyanishi, T., Matsuzono, K., Tanioka, Y., & Matsuda, G. (1991) J. Biochem. 110, 68-74], we reported the amino-terminal 837-residue sequence of the heavy chain of adult chicken pectoralis muscle myosin. This paper describes the carboxyl terminal 1,097-residue sequence and the linkage of the two sequences. Rod obtained by digesting myosin filaments with alpha-chymotrypsin was redigested with the protease at high KCl concentration, and two fragments, subfragment-2 and light meromyosin, were isolated and sequenced by conventional methods. The linkage of the two fragments was deduced from the sequence of an overlapping peptide obtained by cleaving the rod with cyanogen bromide. The rod contained 1,039 amino acid residues, but lacked the carboxyl-terminal 58 residues of the heavy chain. A carboxyl-terminal 63-residue peptide obtained by cleaving the whole heavy chain with cyanogen bromide was sequenced. Thus, the carboxyl terminal 1,097-residue sequence of the heavy chain was completed. The linkage of subfragment-1 and the rod was deduced from the sequence of an overlapping peptide between the two which was obtained by cleaving heavy meromyosin with cyanogen bromide. Comparing the sequence of the adult myosin thus determined with that of chicken embryonic myosin reported by Molina et al. [Molina, M.I., Kropp, K.E., Gulick, J., & Robbins, J. (1987) J. Biol. Chem. 262, 6478-6488], we found that the sequence homology is 94%.

Amino Acid Sequence↗
PubMed1990

Analysis of integrated human papillomavirus type 16 DNA in cervical cancers: amplification of viral sequences together with cellular flanking sequences.

We have isolated four clones of integrated human papillomavirus type 16 (HPV-16) DNA from four different primary cervical cancer specimens. All clones were found to be monomeric or dimeric forms of HPV-16 DNA with cellular flanking sequences at both ends. Analysis of the viral sequences in these clones showed that E6/E7 open reading frames and the long control region were conserved and that no region specific for the integration was detected. Analysis of the cellular flanking sequences revealed no significant homology with any known human DNA sequences, except Alu sequences, and no homology among the clones, indicating no cellular sequence specific for the integration. By probing with single-copy cellular flanking sequences from the clones, it was demonstrated that the integrated HPV-16 DNAs, with different sizes in the same specimens, shared the same cellular flanking sequences at the ends. Furthermore, it was shown that the viral sequences together with cellular flanking sequences were amplified. The possible process of viral integration into cell chromosomes in cervical cancer is discussed.

Base Sequence↗