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PubMed1995

Identification and characterization of a novel conserved DNA repeat.

Homozygous In(10)17Rk mice contain a paracentric inversion within Chromosome (Chr) 10 and exhibit a pygmy phenotype, suggesting that the distal inversion breakpoint is within the pygmy (pg) locus. In order to obtain the pygmy gene by positional cloning procedures, In(10)17Rk DNA was subjected to RFLP analysis with single-copy probes derived from the wild-type pygmy locus. This analysis identified a DNA polymorphism in the DBA/2J mouse strain on which the In(10)17Rk mutation was originally induced. A detailed characterization of this polymorphism revealed the presence of a novel, tandemly repeated DNA element. Copy number estimation experiments indicate that there are approximately 100,000 copies of this element in the haploid DBA/2J genome. PCR typing studies revealed the presence of the repeat at the pygmy locus of 6 of the 18 Mus domesticus strains analyzed. The absence of the repeat from the pygmy locus of 12 strains of the M. domesticus species and from the M. caroli, M. spretus, M. castaneus, and M. molossinus species suggests that the repeat could serve as a strain-specific hybridization probe in genetic mapping studies. Finally, the novel tandem DNA repeat is conserved in both rat and human genomes as indicated by Southern hybridization experiments.

Alleles↗
PubMed1988

Abnormal sequence of expression of differentiation markers in psoriatic epidermis: inversion of two steps in the differentiation program?

This immunohistologic study was undertaken to compare epidermal differentiation in normal and psoriatic skin. Although basal cells retain a normal phenotype in this disease, suprabasal layers exhibit abnormal sets of differentiation markers. The 67-kD keratin and Bd5 antigen, which are found in normal epidermis immediately above the basal layer, appear several layers higher in involved psoriatic epidermis. On the contrary, KF2 antigen, which is found in the upper spinous layers of normal epidermis, appears more precociously in psoriatic epidermis. Paradoxically, in this disease characterized by the absence of a granular layer, some markers specific for this layer in normal skin, such as involucrin and transglutaminase, appear in lower skin cell layers, while other granular markers, such as filaggrin, are either absent or found in the parakeratotic scales. These results point out the existence in psoriasis of a suprabasal cell population characterized by a set of markers that are never coexpressed in normal epidermis. The existence of this abnormal population of cells can be explained as the result of the inversion of two steps in the differentiation program. Thus, instead of an inability to express a given differentiation marker, psoriasis seems to be characterized by an abnormal sequence of expression of these markers.

Adult↗
PubMed2005

Molecular characterization of the pericentric inversion of chimpanzee chromosome 11 homologous to human chromosome 9.

In addition to the fusion of human chromosome 2, nine pericentric inversions are the most conspicuous karyotype differences between humans and chimpanzees. In this study we identified the breakpoint regions of the pericentric inversion of chimpanzee chromosome 11 (PTR 11) homologous to human chromosome 9 (HSA 9). The break in homology between PTR 11p and HSA 9p12 maps to pericentromeric segmental duplications, whereas the breakpoint region orthologous to 9q21.33 is located in intergenic single-copy sequences. Close to the inversion breakpoint in PTR 11q, large blocks of alpha satellites are located, which indicate the presence of the centromere. Since G-banding analysis and the comparative BAC analyses performed in this study imply that the inversion breaks occurred in the region homologous to HSA 9q21.33 and 9p12, but not within the centromere, the structure of PTR 11 cannot be explained by a single pericentric inversion. In addition to this pericentric inversion of PTR 11, further events like centromere repositioning or a second smaller inversion must be assumed to explain the structure of PTR 11 compared with HSA 9.

Animals↗
PubMed2005

Sequence determinants of a transmembrane proton channel: an inverse relationship between stability and function.

The driving forces behind the folding processes of integral membrane proteins after insertion into the bilayer, is currently under debate. The M2 protein from the influenza A virus is an ideal system to study lateral association of transmembrane helices. Its proton selective channel is essential for virus functioning and a target of the drug amantadine. A 25 residue transmembrane fragment of M2, M2TM, forms a four-helix bundle in vivo and in various detergents and phospholipid bilayers. Presented here are the energetic consequences for mutations made to the helix/helix interfaces of the M2TM tetramer. Analytical ultracentrifugation has been used to determine the effect of ten single-site mutations, to either alanine or phenylalanine, on the oligomeric state and the free energy of M2TM in the absence and the presence of amantadine. It was expected that many of these mutations would perturb the M2TM stability and tetrameric integrity. Interestingly, none of the mutations destabilize tetramerization. This finding suggests that M2 sacrifices stability to preserve its functions, which require rapid and specific interchange between distinct conformations involved in gating and proton conduction. Mutations might therefore restrict the full range of conformations by stabilizing a given native or non-native conformational state. In order to assess one specific conformation of the tetramer, we measured the binding of amantadine to the resting state of the channel, and examined the overall free energy of assembly of the amantadine bound tetramer. All of the mutations destabilized amantadine binding or were isoenergetic. We also find that large to small residue changes destabilize the amantadine bound tetramer whereas mutations to side-chains of similar volume stabilize this conformation. A structural model of the amantadine bound state of M2TM was generated using a novel protocol that optimizes a structure for an ensemble of neutral and disruptive mutations. The model structure is consistent with the mutational data.

Amantadine↗
PubMed1995

Molecular characterization of a deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.

A 93-kb region (D region) of plasmid pAE1 of Alcaligenes eutrophus H1 has been found to have a high rate of spontaneous deletion. In this study, we constructed a restriction endonuclease map and carried out limited sequencing of an approximately 100-kb region from pAE1 which includes the D region (the deleted region) in order to detect and characterize repetitive sequences. Two types of repetitive sequences, the R1 and R2 sequences, were observed to flank the D region; within the D region are three copies of insertion element ISAE1. The R1 and R2 sequences are arranged in direct and inverted orientations, respectively. Molecular analysis of the end product of the deletion is consistent with the hypothesis that the loss of the D-region DNA is the result of recombination between two copies of the R1 sequence. The R1 sequence encodes a 415-amino-acid protein which exhibits substantial sequence similarity to the lambda integrase family of site-specific recombinases. Its genetic function remains to be determined.

Alcaligenes↗
PubMed1997

Inversion of Moraxella lacunata type 4 pilin gene sequences by a Neisseria gonorrhoeae site-specific recombinase.

A plasmid library of Neisseria gonorrhoeae sequences was screened for the ability to mediate recombinations on a sequence containing the Moraxella lacunata type 4 pilin gene invertible region in Escherichia coli. A plasmid containing the N. gonorrhoeae sequence encoding the putative recombinase (gcr) was identified and sequenced. Plasmids containing gcr were able to mediate site-specific recombinations despite a weak amino acid homology to Piv, the native M. lacunata pilin gene invertase. The gcr gene is present only in pathogenic strains of Neisseria tested; however, in our assays gene knockouts of gcr did not alter the variation of surface features that play a role in the pathogenesis of N. gonorrhoeae.

Amino Acid Sequence↗
PubMed1987

Concerted deletions and inversions are caused by mitotic recombination between delta sequences in Saccharomyces cerevisiae.

Deletions of a tyrosine tRNA suppressor gene, SUP4-o, are mediated by recombination between short repeated delta sequences in Saccharomyces cerevisiae. The arrangement of the five solo delta sequences that surround the SUP4 locus was established by DNA sequence analysis. Seven deletion classes were identified by genomic blotting. DNA sequence analysis also showed that the delta sequences within a 6.5-kilobase region of the SUP4 locus were the endpoints of these events. In three of these classes, an adjacent interval surrounded by delta sequences was inverted in concert with the deletion. The frequency of all deletion classes decreased in strains that contained mutations in the recombination and repair gene RAD52. We present two gene conversion mechanisms by which these rearrangements could have been generated. These models may also explain deletions between repeated sequences in other systems.

Base Sequence↗
PubMed1995

Structure and function of the selenium translation element in the 3'-untranslated region of human cellular glutathione peroxidase mRNA.

In eukaryotes, incorporation of selenocysteine into the polypeptide chain at a UGA codon requires a unique sequence motif, or "selenium translation element" (STE), located in the 3'-untranslated region of the mRNA. The present study examines structure-function relationships of conserved sequence elements and of the putative stem-loop secondary structure in the STE of human GPX1 mRNA, which encodes the important antioxidant enzyme cellular glutathione peroxidase (EC 1.11.1.9). Deletion of the basal stem, upper stem, or apical loop of the stem-loop structure eliminated the ability of the STE to direct selenocysteine incorporation at the UGA codon of an epitope-tagged GPX1 reporter construct transfected into COS1 cells. However, mutations that change the primary nucleotide sequence of nonconserved portions of the stem-loop, but preserve its overall secondary structure, by inversion of apical loop sequences or exchange of 5' and 3' sides of stem segments, had little or no effect on selenocysteine incorporation. Effects of single- and double-nucleotide substitutions in three short, highly conserved elements in the GPX1 STE depended in large part on their computer-predicted perturbation of the stem-loop and its midstem bulge. Only in the conserved "AAA" apical loop sequence did mutations show major effects on function without predicted changes in secondary structure. Our results demonstrate the critical role of the three short, highly conserved sequences. However, outside of these elements, the function of the human GPX1 STE appears to depend strongly on the stem-loop secondary structure.

Animals↗
PubMed1994

[Magnetic resonance imaging in denervated muscle. A preliminary study].

Ten patients with various forms of peripheral neuropathy and spinal radiculopathy were examined with MRI using a low-field permanent magnet (0.2 T) and spin echo (SE)/inversion recovery (IR) sequences, with an adequate inversion time to suppress healthy muscle signal. In acute denervation MR sensitivity was low on both sequences; in subacute denervation the damaged muscle was more intense than the healthy muscle only on IR sequences. MRI adequately depicted fatty infiltration in chronic denervation. In conclusion, MRI is a promising tool for mapping and noninvasively monitoring denervated motor units in skeletal muscles, whose role is currently complementary to that of electromyography.

Acute Disease↗
PubMed1994

Four novel PEPD alleles causing prolidase deficiency.

Mutations at the PEPD locus cause prolidase deficiency (McKusick 170100), a rare autosomal recessive disorder characterized by iminodipeptiduria, skin ulcers, mental retardation, and recurrent infections. Four PEPD mutations from five severely affected individuals were characterized by analysis of reverse-transcribed, PCR-amplified (RT-PCR) cDNA. We used SSCP analysis on four overlapping cDNA fragments covering the entire coding region of the PEPD gene and detected abnormal SSCP bands for the fragment spanning all or part of exons 13-15 in three of the probands. Direct sequencing of the mutant cDNAs showed a G-->A, 1342 substitution (G448R) in two patients and a 3-bp deletion (delta E452 or delta E453) in another. In the other two probands the amplified products were of reduced size. Direct sequencing of these mutant cDNAs revealed a deletion of exon 5 in one patient and of exon 7 in the other. Intronic sequences flanking exons 5 and 7 were identified using inverse PCR followed by direct sequencing. Conventional PCR and direct sequencing then established the intron-exon borders of the mutant genomic DNA revealing two splice acceptor mutations: a G-->C substitution at position -1 of intron 4 and an A-->G substitution at position -2 of intron 6. Our results indicate that the severe form of prolidase deficiency is caused by multiple PEPD alleles. In this report we attempt to begin the process of describing these alleles and cataloging their phenotypic expression.

Alleles↗
PubMed1995

Inverse PCR-mediated cloning of the promoter for the rat vasopressin V2 receptor gene.

The adenylyl cyclase-coupled vasopressin V2 receptor has been cloned recently and shown, in rats, to be produced from the predominant form of two alternate spliced variants. To begin to unravel the transcriptional regulation of this receptor, we have isolated the 5' flanking region of the rat vasopressin V2 receptor gene and characterized its promoter sequence. The method of inverse polymerase chain reaction (PCR), which allows the amplification of DNA fragments adjacent to a segment of known sequence, was used as an alternative approach to genomic DNA library screening. Using a probe encompassing part of the coding region, first we identified by Southern blot analysis, a single BstX I hybridizing fragment of 2.3 kilobases (kb). This size predicted a BstX I restriction site 1.5 kb upstream to the gene coding region. Cloning of this fragment was accomplished through circularization of BstX I restriction digests and inverse PCR-mediated amplification. Sequence analysis of the gene 5' flanking domain enabled the design of oligonucleotide primers with the usual forward/reverse orientation, and additional clones were generated from native genomic DNA using a high fidelity thermoresistant DNA polymerase. Reverse transcription-PCR (RT-PCR) and primer extension analysis mapped the major transcription start site 422 nucleotides upstream to the translation initiation codon. The promoter region lacks a TATA box but contains a CAAT box and a consensus binding site for transcription factor Sp1. Multiple potential binding sites for the transcription factor PEA3 are clustered in two DNA portions located 0.6 kb and 1 kb upstream to the coding region. In addition, sequences homologous to glucocorticoid response elements are present and might be responsible for the regulation by adrenal steroids of vasopressin-dependent adenylyl cyclase activity in the kidney.

Amino Acid Sequence↗
PubMed1999

Lesion load measurements in multiple sclerosis: the effect of incorporating magnetization transfer contrast in fast-FLAIR sequence.

We compared the ability and reproducibility of a fast fluid-attenuated inversion recovery (fast-FLAIR) sequence with and without a magnetization transfer (MT) pulse for detecting and measuring multiple sclerosis (MS)-related abnormalities on magnetic resonance imaging (MRI) scans from 20 patients. The Contrast-to-Noise ratios between lesions and normal-appearing white matter, lesion numbers, lesion volumes and the variability of such measurements were similar for the two sequences. This suggests that the addition of MT to FLAIR sequences as currently implemented on standard MRI scanners does not improve the detection of MS lesions.

Adult↗
PubMed2001

T(1) quantification with inversion recovery TrueFISP.

A snapshot FLASH sequence can be used to acquire the time course of longitudinal magnetization during its recovery after a single inversion pulse. However, excitation pulses disturb the exponential recovery of longitudinal magnetization and may produce systematic errors in T(1) estimations. In this context the possibility of using the TrueFISP sequence to detect the recovery of longitudinal magnetization for quantitative T(1) measurements was examined. Experiments were performed on different Gd-doped water phantoms and on humans. T(1) values derived from inversion recovery TrueFISP were in excellent agreement with the single-point method even for flip angles up to 50 degrees. In terms of T(1) accuracy and SNR, the proposed method seems to be superior to the conventional inversion recovery snapshot FLASH technique. Magn Reson Med 45:720-723, 2001.

Brain↗
PubMed1996

Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein.

In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-beta protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to "fit" the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.

Algorithms↗
PubMed2003

Honeybee (Apis mellifera L.) mrjp gene family: computational analysis of putative promoters and genomic structure of mrjp1, the gene coding for the most abundant protein of larval food.

Mrjp1 gene belongs to the honeybee mrjp gene family encoding the major royal jelly proteins (MRJPs), secreted by nurse bees into the royal jelly. In this study, we have isolated the genomic clone containing the entire mrjp1 gene and determined its sequence. The mrjp1 gene sequence spans over 3038 bp and contains six exons separated by five introns. Seven mismatches between the mrjp1 gene sequence and two previously independently published cDNA sequences were found, but these differences do not lead to any change in the deduced amino acid sequence of MRJP1. With the aid of inverse polymerase chain reaction we obtained sequences flanking the 5' ends of other mrjp genes (mrjp2, mrjp3, mrjp4 and mrjp5). Putative promoters were predicted upstream of all mrjp genes (including mrjp1). The predicted promoters contain the TATA motif (TATATATT), highly conserved both in sequence and position. Ultraspiracle (USP) transcription factor (TF) binding sites in putative promoter regions and clusters of dead ringer TF binding sites upstream of these promoters were predicted computationally. We propose that USP, as a juvenile hormone (JH) binding TF, might possibly act as a mediator of mrjp expression in response to JH. Mrjp1's genomic locus is predicted to encode an antisense transcript, partially overlapping with five mrjp1 exons and entirely overlapping with the putative promoter and predicted transcriptional start point of mrjp1. This finding may shed light on the mechanisms of regulation of mrjps expression. Southern blot analysis of genomic DNA revealed that all so far known members of mrjp gene family (mrjp1, mrjp2, mrjp3, mrjp4 and mrjp5) are present as single-copy genes per haploid honeybee genome. Although MRJPs and the yellow protein of Drosophila melanogaster share a certain degree of similarity in aa sequence and although it has been shown that they share a common evolutionary origin, neither structural similarities in the gene organization, nor significant similarities between intron sequences of mrjp1 gene and fourteen yellow-like genes of D. melanogaster were found.

Animals↗
PubMed1998

Double inversion recovery imaging of the brain: initial experience and comparison with fluid attenuated inversion recovery imaging.

The purpose of this study was to evaluate the diagnostic efficacy of the double inversion recovery fast spin echo (DIR-FSE) sequence for brain imaging compared to the fluid-attenuated inversion recovery (FLAIR) sequence. DIR-FSE and FLAIR-FSE sequences were obtained and compared side by side. Image assessment criteria included lesion conspicuity, contrast between different types of normal tissue, image quality, and artifacts. In addition, contrast ratios and contrast-to-noise ratios were determined. Scan time of DIR-FSE was 33% longer than scan time of FLAIR-FSE. Overall lesion conspicuity was equal on DIR-FSE and FLAIR-FSE; however, DIR-FSE showed particular advantages for infratentorial lesions and lesions with only poor contrast on T2-weighted images, whereas FLAIR was slightly superior for small superficial cerebral abnormalities. Gray-white differentiation was better with DIR-FSE. Cerebrospinal fluid suppression was equal on both sequences; cerebrospinal fluid pulsation artifacts were more pronounced on DIR-FSE but did not cause diagnostic difficulties on these images. We conclude that DIR-FSE might be obtained if infratentorial lesions and abnormalities with only slightly prolonged T2 relaxation times are suspected. Otherwise, FLAIR-FSE seems preferable.

Adolescent↗
PubMed2005

Electron-transfer ion/ion reactions of doubly protonated peptides: effect of elevated bath gas temperature.

In this study, the electron-transfer dissociation (ETD) behavior of cations derived from 27 different peptides (22 of which are tryptic peptides) has been studied in a 3D quadrupole ion trap mass spectrometer. Ion/ion reactions between peptide cations and nitrobenzene anions have been examined at both room temperature and in an elevated temperature bath gas environment to form ETD product ions. From the peptides studied, the ETD sequence coverage tends to be inversely related to peptide size. At room temperature, very high sequence coverage (approximately 100%) was observed for small peptides (< or =7 amino acids). For medium-sized peptides composed of 8-11 amino acids, the average sequence coverage was 46%. Larger peptides with 14 or more amino acids yielded an average sequence coverage of 23%. Elevated-temperature ETD provided increased sequence coverage over room-temperature experiments for the peptides of greater than 7 residues, giving an average of 67% for medium-sized peptides and 63% for larger peptides. Percent ETD, a measure of the extent of electron transfer, has also been calculated for the peptides and also shows an inverse relation with peptide size. Bath gas temperature does not have a consistent effect on percent ETD, however. For the tryptic peptides, fragmentation is localized at the ends of the peptides suggesting that the distribution of charge within the peptide may play an important role in determining fragmentation sites. A triply protonated peptide has also been studied and shows behavior similar to the doubly charged peptides. These preliminary results suggest that for a given charge state there is a maximum size for which high sequence coverage is obtained and that increasing the bath gas temperature can increase this maximum.

Amino Acid Sequence↗
PubMed1989

Characterization of the staphylococcal beta-lactamase transposon Tn552.

The staphylococcal beta-lactamase transposon Tn552 is a member of a novel group of transposable elements. The organization of genes in Tn552 resembles that of members of the Tn21 sub-group of Tn3 family transposons, which transpose replicatively by cointegrate formation and resolution. Thus, a possible resolution site ('resL') and a resolvase gene (tnpR or 'binL') have been identified. However, consistent with the fact that Tn552 generates 6 bp (rather than 5 bp) flanking direct repeats of target DNA, neither the putative transposase protein, nor the terminal inverted repeats of Tn552 are homologous to those of Tn3 elements. Tn552, like phage Mu and retroelements, is defined by the terminal dinucleotides 5' TG .. CA 3'. A naturally occurring staphylococcal plasmid, pI9789, contains a Tn552-derived resolution system ('resR-binR') that acts as a 'hotspot' for Tn552 transposition; insertion creates a segment of DNA flanked by inversely repeated resolution sites, one (resR) on pI9789 and the other (resL) on Tn552. The putative Tn552 resolvase, the most closely related of known resolvases to the homologous DNA invertases, initially was identified as a DNA invertase ('Bin') as a result of its ability to mediate efficient inversion of this segment in vivo.

Amino Acid Sequence↗