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PubMed1996

A targeted mutation of the D3 dopamine receptor gene is associated with hyperactivity in mice.

While most effects of dopamine in the brain are mediated by the D1 and D2 receptor subtypes, other members of this G protein-coupled receptor family have potentially important functions. D3 receptors belong to the D2-like subclass of dopamine receptors, activation of which inhibits adenylyl cyclase. Using targeted mutagenesis in mouse embryonic stem cells, we have generated mice lacking functional D3 receptors. A premature chain-termination mutation was introduced in the D3 receptor gene after residue Arg-148 in the second intracellular loop of the predicted protein sequence. Binding of the dopamine antagonist [125I]iodosulpride to D3 receptors was absent in mice homozygous for the mutation and greatly reduced in heterozygous mice. Behavioral analysis of mutant mice showed that this mutation is associated with hyperactivity in an exploratory test. Homozygous mice lacking D3 receptors display increased locomotor activity and rearing behavior. Mice heterozygous for the D3 receptor mutation show similar, albeit less pronounced, behavioral alterations. Our findings indicate that D3 receptors play an inhibitory role in the control of certain behaviors.

Amino Acid Sequence↗

PubMed1996

Thrombin receptor activating mutations. Alteration of an extracellular agonist recognition domain causes constitutive signaling.

Constitutively active thrombin receptors were generated while constructing chimeric receptors to identify the structural basis for thrombin receptor agonist specificity. Substitution of eight amino acids from the Xenopus receptor's second extracellular loop (XECL2B) for the cognate sequence in the human thrombin receptor was sufficient to confer robust constitutive activity. Smaller substitutions within the XECL2B site yielded less constitutive activation, and substitution of several unrelated sequences at this site caused no activation. Expression of the XECL2B receptor caused high basal 45Ca efflux in Xenopus oocytes and high basal phosphoinositide hydrolysis and reporter gene induction in COS cells. Of note, a mutant receptor in which all four of the Xenopus thrombin receptor's extracellular segments replaced the cognate human sequences showed much less constitutive activity than XECL2B and preserved responsiveness to agonist. This partial complementation of the XECL2B phenotype by addition of other Xenopus extracellular structures suggests that the XECL2B mutation causes constitutive activation by altering interactions among the human receptor's extracellular domains. Thus, a change in an extracellular loop of a G protein-coupled receptor can transmit information across the cell membrane to cause signaling, perhaps via a conformational change similar to that caused by agonist binding. Indeed, the site of the activating mutation in XECL2B coincides with a putative agonist-docking site, supporting the hypothesis that agonist interactions with the thrombin receptor's extracellular loops contribute to receptor activation.

Amino Acid Sequence↗

PubMed2000

Duplicated downstream enhancers control expression of the human apolipoprotein E gene in macrophages and adipose tissue.

Two distal enhancers that specify apolipoprotein (apo) E gene expression in isolated macrophages and adipose tissue were identified in transgenic mice that were generated with constructs of the human apoE/C-I/C-I'/C-IV/C-II gene cluster. One of these enhancers, multienhancer 1, consists of a 620-nucleotide sequence located 3.3 kilobases (kb) downstream of the apoE gene. The second enhancer, multienhancer 2, is a 619-nucleotide sequence located 15.9 kb downstream of the apoE gene and 5.9 kb downstream of the apoC-I gene. The two enhancers are 95% identical in sequence, and they are likely to have arisen as a consequence of the gene duplication event that yielded the apoC-I gene and the apoC-I' pseudogene. Both enhancer sequences appear to have equivalent activity in directing apoE gene expression in peritoneal macrophages and in adipocytes, suggesting that their activity in specific cell types may be determined by common regulatory elements.

Adipose Tissue↗

PubMed2005

MagicMatch--cross-referencing sequence identifiers across databases.

MOTIVATION: At present, mapping of sequence identifiers across databases is a daunting, time-consuming and computationally expensive process, usually achieved by sequence similarity searches with strict threshold values. SUMMARY: We present a rapid and efficient method to map sequence identifiers across databases. The method uses the MD5 checksum algorithm for message integrity to generate sequence fingerprints and uses these fingerprints as hash strings to map sequences across databases. The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer.

Algorithms↗

PubMed2003

Revisiting the mouse mitochondrial DNA sequence.

The existence of reliable mtDNA reference sequences for each species is of great relevance in a variety of fields, from phylogenetic and population genetics studies to pathogenetic determination of mtDNA variants in humans or in animal models of mtDNA-linked diseases. We present compelling evidence for the existence of sequencing errors on the current mouse mtDNA reference sequence. This includes the deletion of a full codon in two genes, the substitution of one amino acid on five occasions and also the involvement of tRNA and rRNA genes. The conclusions are supported by: (i) the re-sequencing of the original cell line used by Bibb and Clayton, the LA9 cell line, (ii) the sequencing of a second L-derivative clone (L929), and (iii) the comparison with 12 other mtDNA sequences from live mice, 10 of them maternally related with the mouse from which the L cells were generated. Two of the latest sequences are reported for the first time in this study (Balb/cJ and C57BL/6J). In addition, we found that both the LA9 and L929 mtDNAs also contain private clone polymorphic variants that, at least in the case of L929, promote functional impairment of the oxidative phosphorylation system. Consequently, the mtDNA of the strain used for the mouse genome project (C57BL/6J) is proposed as the new standard for the mouse mtDNA sequence.

Animals↗

PubMed1991

Identification of T-cell epitopes without B-cell activity in the first and second conserved regions of the HIV Env protein.

We have previously hypothesized that an effective vaccine against HIV should elicit cell-mediated immunity without antiviral antibody production. As a first step towards this goal we have identified potential T-cell epitopes, without B-cell activity against the native protein, from the first and second conserved sequences, and from three functionally important regions of the HIV-1 envelope protein gp160. For this approach, short peptide sequences selected by established computer programs were synthesized and chemically modified to generate either polymers with disulfide bonds, or micelles with two palmitic acid residues attached to the amino-terminal lysine. In both configurations several peptides were immunogenic without the need for coupling to carrier molecules. Of the 19 peptides we tested in our present studies, seven induced good T-cell proliferative response in mice representing four major histocompatibility complex haplotypes. None of these seven peptides produced antibodies that could recognize the envelope protein gp160.

Amino Acid Sequence↗

PubMed1997

Identification of a second endogenous Porphyromonas gingivalis insertion element.

In this study a second endogenous Porphyromonas gingivalis insertion element (IS element) that is capable of transposition within P. gingivalis was identified. Nucleotide sequence analysis of the Tn4351 insertion site in a P. gingivalis Tn4351-generated transconjugant showed that a complete copy of the previously unidentified IS element, designated PGIS2, had inserted into IS4351R in Tn4351. PGIS2 is 1,207 bp in length with 19-bp imperfect terminal inverted repeats, and insertion resulted in a duplicated 10-bp target sequence. Results of Southern hybridization of chromosomal DNA isolated from several P. gingivalis strains with a PGIS2-specific probe demonstrated that the number of copies of PGIS2 per genome varies among different P. gingivalis strains. Computer analysis of the putative polypeptide encoded by PGIS2 revealed strong homologies to the products encoded by IS1358 from Vibrio cholerae, ISAS1 from Aeromonas salmonicida, and H-rpt in Escherichia coli K-12.

Amino Acid Sequence↗

PubMed1997

Inhibition of gonadotropin-releasing hormone receptor signaling by expression of a splice variant of the human receptor.

GnRH binds to a specific G protein-coupled receptor in the pituitary to regulate synthesis and secretion of gonadotropins. Using RT-PCR and human pituitary poly(A)+ RNA as a template, the full-length GnRH receptor (wild type) and a second truncated cDNA characterized by a 128-bp deletion between nucleotide positions 522 and 651 were cloned. The deletion causes a frame shift in the open reading frame, thus generating new coding sequence for further 75 amino acids. The truncated cDNA arises from alternative splicing by accepting a cryptic splicing acceptor site in exon 2. Distinct translation products of approximately 45-50 and 42 kDa were immunoprecipitated from COS-7 cells transfected with cDNA coding for wild type GnRH receptor and the truncated splice variant, respectively. Immunocytochemical and enzyme-linked immunosorbent assay studies revealed a membranous expression pattern for both receptor isoforms. Expression of the splice variant, however, occurred at a significantly lower cell surface receptor density. In terms of ligand binding and phospholipase C activation, the wild type receptor showed characteristics of a typical GnRH receptor, whereas the splice variant was incapable of ligand binding and signal transduction. Coexpression of wild type and truncated proteins in transiently or stably transfected cells, however, resulted in impaired signaling via the wild type receptor by reducing maximal agonist-induced inositol phosphate accumulation. The inhibitory effect depended on the amount of splice variant cDNA cotransfected and was specific for the GnRH receptor because signaling via other G(q/11)-coupled receptors, such as the thromboxane A2, M5 muscarinic, and V1 vasopressin receptors, was not affected. Immunological studies revealed that coexpression of the wild type receptor and the truncated splice variant resulted in impaired insertion of the wild type receptor into the plasma membrane. Thus, expression of truncated receptor proteins may highlight a novel principle of specific functional inhibition of G protein-coupled receptors.

Alternative Splicing↗

PubMed2006

Construction of MMR plasmid substrates and analysis of MMR error correction and excision.

We describe simple and efficient construction of mismatch repair (MMR) substrates, by generation of gapped plasmids using one sequence-specific nicking endonuclease (N.BstNBI), ligation of synthetic oligomers into the gaps, and introduction of defined single nicks for initiation of MMR excision using a second such endonuclease (N.AlwI). We further describe measurement of completed mismatch correction and a sensitive quantitative assay for MMR excision intermediates. These methods can be easily adapted for construction of substrates containing defined DNA lesions, for analysis of MMR responses to DNA damage and for studies of other DNA repair pathways.

Base Pair Mismatch↗

PubMed2000

Nonspecific, nested suppression PCR method for isolation of unknown flanking DNA.

We report the development of a simple, sensitive and robust two-step PCR method for the isolation of unknown sequences flanking characterized regions of genomic DNA or cDNA. The method requires 100 bp or less of a known sequence upstream of an oligonucleotide primer binding site. A first round of suppression PCR is conducted at low stringency with a polymerase lacking exonuclease activity to generate a mixture of products including fragments of the desired flanking sequence that are often greater than 1 kb in length. The desired fragments are then amplified from the mixture in a second round of suppression PCR using an extended oligonucleotide in combination with a polymerase exhibiting exonuclease activity. These fragments are subsequently identified by hybridization with the 100 bp of known sequence or simply by cloning and sequencing. The method is widely applicable and allows isolation of novel cDNA from very low abundance transcripts.

Alkalies↗

PubMed2003

Vaccine development for potential bioterrorism agents.

Vaccines are considered to be one of the most effective ways of combating disease caused by bioterrorism agents. Such vaccines must be able to provide protection against pathogens which might enter the body by a number of routes, including the respiratory tract. They should also be able to induce protective immunity rapidly and would ideally be given non-invasively. There are few vaccines which currently meet these requirements. In part, this reflects the low level of research on many bioterrorism agents over the past few decades. Little is known about basic mechanisms of pathogenicity of many of these agents. However, by their very nature these agents cause serious disease, and must be handled in high containment laboratories. This requirement also limits the speed and ease with which research on these pathogens can now take place. Against this background, research on vaccines against potential bioterrorism agents is likely to proceed along two lines. Firstly because the genome sequences of most of the principal bioterrorism agents have either been completed or are close to completion, there is likely to be reliance on the exploitation of this information to devise improved vaccines. A number of groups are working on methodologies to identify vaccine antigens directly from genome sequences. Secondly, there will be a need to formulate such vaccines appropriately for the rapid induction of protective immunity after non-invasive delivery. The prospects for the development of a new generation of bioterrorism vaccines which exploit these technologies are reviewed in this manuscript.

Bioterrorism↗

PubMed2001

Organizer and axes formation as a self-organizing process.

It is a widely held view that axis formation is based essentially on pre-localized determinants. However, the robustness of early development, the pattern regulation observed after experimental interferences and the existence of systems that don't require maternal determinants suggest that self-regulating pattern forming systems are also involved. A model is proposed that allows axes formation by a chain of reactions based on local self-enhancement and long-range inhibition. Their appropriate linkage ensures that the intermediary patterns emerge in the correct sequence and have the correct spatial relation to each other. Specifically, the model comprises the following events: the generation of a pole by a pattern-forming process, the formation of a second organizer eccentric to the pole (e.g. the Nieuwkoop center), the ecto-meso-endo subdivision, the generation of the Spemann-Mangold organizer with its anterior-posterior subdivision under the influence of the Nieuwkoop center, the conversion of the Spemann-Mangold organizer (a hot spot) into the notochord (a hot stripe), and the marking of the left side of the organism by a patterning reaction influenced by the midline. The pattern forming reactions do not depend on but can make use of maternally pre-localized determinants or asymmetries. Comparison with known genes and molecules reveals that many of the expected ingredients are present. Computer simulations show that the model accounts for many regulatory features reported in the literature. The computer simulations are available in an animated form at.

Animals↗

PubMed1992

[Eye movement: experimental and clinical study using cine mode MRI].

As a special lecture at the 96th Annual Congress of the Japanese Ophthalmological Society in 1992, we presented experimental and clinical studies on eye movement using magnetic resonance imaging (MRI). MRI is more valuable than X-ray CT in defining external muscle anatomy in the orbit in a variety of pathological changes, and is free from the danger of radiation. Cine mode MRI, which was originally developed to observe cardiovascular function, was utilized experimentally for observation of eye movement. We invented two methods to produce a series of photographs. In the first method, "the moving eye method", the subjects were asked to perform 256 or 512 vertical and horizontal eye movements in synchronization with a sound trigger. In the second, "the fixed eye method", the subjects were asked to gaze at individual points in a 5 to 7 point sequence as indicated by the investigator. In both methods MRI data was generated and the resulting series of photographs were observed in cine mode on a television monitor. Displaying the MRI generated photographs in cine mode enables direct observation of the movement of the eye, optic nerve and extraocular muscles within the orbit. The moving eye method was more accurate in its portrayal of the actual movement of the eye, but the large number of eye movements, at least 256 movements, required about 5 minutes, and caused physical and mental fatigue for the subjects. The fixed eye method did not show actual movement of the eye, but was less fatiguing than the former method, and avoided several of its problems. A large number of ophthalmoplegia cases such as abducens palsy, oculomotor palsy, fracture of the orbital wall, foreign bodies in the orbit, Duane's syndrome, endocrine myopathy, esotropia, exotropia, etc., were examined using the fixed eye method of cine mode MRI. Using this technique, anatomical changes, such as atrophy or hypertrophy and the functional state demonstrated by the contraction and relaxation of the extraocular muscles could be investigated. Transposition of the extraocular muscles, an effective treatment for paralytic squint, was reexamined and a new surgical procedure was developed for abducens palsy. The measurement of the length, thickness and weight of the extraocular muscles from the MRI-generated photographs allowed for more accurate analysis. The three dimensional reconstructive method of MRI is very valuable for diagnosis in the orbit and is expected to contribute to future progress.

Adult↗

PubMed1997

Use of a C-arm system to generate true three-dimensional computed rotational angiograms: preliminary in vitro and in vivo results.

PURPOSE: To evaluate the potential use of a C-arm mounted X-ray image intensifier (XRII) system to generate three-dimensional computed rotational angiograms during interventional neuroradiologic procedures. METHODS: A clinical angiographic system was modified to allow collection of sufficient views during selective intraarterial contrast injections for CT reconstruction of a 15 x 15 x 15-cm3 volume. Image intensifier distortion and C-arm instabilities were corrected by using image-based techniques. The impact of the pulsatile nature of the vessels during image data acquisition and of the presence of bone on the 3-D reconstructions was investigated by generating 3-D reconstructions of an anesthetized 20-kg pig and of a human skull phantom. RESULTS: A sequence of images sufficient for 3-D reconstruction was acquired in less than 5 seconds. Image intensifier distortion and C-arm instabilities were corrected to subpixel accuracy (0.035 mm and 0.07 mm, respectively). Both the intracranial vessels of the pig and the small, high-contrast structures in the skull were reconstructed with negligible artifacts. CONCLUSIONS: Using a C-arm mounted XRII system, computed rotational angiography can provide true 3-D images of diagnostic quality.

Animals↗

PubMed1997

Time course of hexachlorobenzene-induced alterations of lipid metabolism and their relation to porphyria.

A great deal of information concerning the effects of hexachlorobenzene on the haem metabolic pathway has been obtained but little is known about the effects of the drug on lipid metabolism. Consequently, the time course of phospholipid metabolism alteration caused by this xenobiotic was evaluated as related to changes in porphyrin metabolism with the aim to understand better the interregulation of both metabolisms. Female Wistar rats were treated with HCB (1 g/kg) over a 1-8 week period. Individual phospholipid content, [32P] incorporation, total lipid content, lipid peroxidation, uroporphyrinogen decarboxylase activity, its inhibitor generation and porphyrin content, were the parameters measured in the liver of treated rats. Phospholipid metabolism-with the exception of sphingomyelin-presents a biphasic behaviour, in both the endogenous contents and de novo synthesis. The turning point between both phases is the time at which levels of porphyrin and conjugated dienes increase, the latter compounds being involved in oxidative processes. On the other hand, sphingomyelin decreases continuously during the 8 weeks of treatment. It was also found that the malondialdehyde content increased during the early stages. The time sequence for haem metabolism parameters showed that the accumulation of porphyrins occurs after the decrease in uroporphyrinogen decarboxylase activity and the enzyme inhibitor formation, which are early events (first and second weeks). Porphyrins could not by themselves exacerbate uroporphyrinogen decarboxylase impairment or inhibitor generation. This study shows that hexachlorobenzene alters simultaneously phospholipid and porphyrin metabolisms from the early stages, and generates an oxidative environment that favours porphyrinogens and lipid oxidation at later stages. So, this oxidative environment links the alterations on both metabolisms.

Animals↗

PubMed1996

Identification of the dipteran Leu-callatostatin peptide family: characterisation of the prohormone gene from Calliphora vomitoria and Lucilia cuprina.

The prohormone gene encoding the Leu-callatostatin peptides has been isolated from a Calliphora vomitoria genomic DNA library and its homologue was cloned from genomic and cDNA libraries of another blowfly species, Lucilia cuprina. Gene and prohormone structure and organisation are essentially identical in the two species. The Leu-callatostatin gene consists of at least 3 exons. The prohormone is encoded on exons two and three and the two blocks of putative Leu-callatostatin peptides are carried on separate exons. It is 180 amino-acids long, begins with a short signal peptide and contains two blocks of tandemly arranged Leu-callatostatin peptides separated by an acidic spacer region. The prohormone contains 5 copies of the C-terminal sequence -YX FGL characteristic of the Leu-callatostatin family. Complete endoproteolytic processing at all possible pairs of basic amino acids would generate 5 different Leu-callatostatin octapeptides. Two larger Leu-callatostatins could be released if processing was not complete at two of the sites. None of the 3 peptides encoded in the first block was identified in previous purification studies of the callatostatin peptides. The second block, located at the carboxyl end of the prohormone, contains two peptide sequences identical to the previously isolated Leu-callatostatins 1 and 4. The absence of independent copies of Leu-callatostatins 2 and 3 on the prohormone establishes that endoproteolytic cleavage of the precursor does not invariably proceed to completion and that Leu-callatostatin 2 must be derived by N-terminal processing of the parent peptide Leu-callatostatin 1. Reverse transcriptase PCR analysis of mRNA from brain and midgut, the two major sites of Leu-callatostatin expression, shows that the prohormone sequence at these two sites is identical, ruling out the possibility that different populations of peptides are expressed in these two tissues as a result of alternative RNA splicing.

Amino Acid Sequence↗

PubMed1990

A second isoform of chicken brush border myosin I contains a 29-residue inserted sequence that binds calmodulin.

Chicken brush border myosin I (CBB-MI) is a single-headed, nonfilamentous, myosin-like mechanoenzyme which, as isolated, has 3 mol of calmodulin (CAM) 'light chains' bound per mole of 119 kDa heavy chain. We have isolated a partial cDNA clone for CBB-MI that encodes the C-terminal approximately 35 kDa of the heavy chain. The sequence of this clone is identical to that of an authentic, near-full-length CBB-MI cDNA clone reported recently, except for an 87-bp/29-residue insertion occurring approximately 32 kDa from the C-terminus. This insert, which is probably generated by an alternate splicing event, is expressed in brush border as part of a message of the size predicted for the CBB-MI heavy chain, although the steady state level of this transcript is approximately 8-fold lower than for transcripts lacking the insert. 125I-CAM overlays of this cDNA clone (expressed as a trpE fusion protein in E. coli) indicate that it binds one more calmodulin than does a second cDNA clone that lacks the 29-residue insert. A synthetic peptide corresponding to the insert sequence binds tightly to CAM-Sepharose, demonstrates a shift and enhancement of fluorescence in the presence of CAM, and binds CAM in solution with a KD of 190 nM (in 100 mM KCl). We conclude that a second, low-abundance isoform of CBB-MI contains an additional (and possibly fourth) CAM binding site as a result of a 29-residue peptide that is inserted into the tail domain by an apparent alternate splicing event.

Amino Acid Sequence↗

PubMed1997

Integration of 101 DNA markers across human Xp11 using a panel of somatic cell hybrids.

One hundred and one DNA markers previously assigned to the short arm of the human X chromosome were localized on a hybrid mapping panel consisting of ten radiation-reduced, and four classical somatic cell hybrids. Of the 101 DNA markers, 16 are genes, two are pseudogenes, 13 are expressed sequence tags, 32 are simple tandem repeats (STRs), four are restriction fragment length polymorphisms, one is a variable number of tandem repeats, and 33 are sequence tagged sites (STSs). Three of these markers, two STSs and one STR, were generated from the products of an inter-Alu PCR library of a radiation-reduced hybrid containing Xp11.4-->p11.22 as its only human DNA content. A second STR was isolated from a region-specific cosmid containing the gene ZNF21. The 101 DNA markers fell into 22 bins based on their retention on the hybrids of this panel, which, in combination with YAC contig data, could be further resolved into 24 bins. This hybrid map of Xp11 has an average resolution of approximately 0.8 Mb.

Animals↗