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Biomedical subjects

M Lovett

Publications and source records attributed to M Lovett.

At least 73 records · Page 4Linked to original sources

Fishing for complements: finding genes by direct selection.

Deriving a saturated gene map of a complex genome is a daunting undertaking. By current methods, finding all the genes in even a single megabase of the human genome is technically difficult. Direct selection is a technique focussed upon the isolation of cDNAs encoded by such large genomic regions and involves hybridization-based selection and PCR methods. It is particularly useful in the positional cloning of loci associated with genetic disease and for rapidly searching large genomic regions for transcriptional units that are normally expressed at low levels. Direct selection can produce up to 100,000-fold enrichment of specific cDNAs, and allows simultaneous searches to be conducted on many complex tissues. The applications of this technique extend to many approaches that involve cDNA cloning, including isolating related genes from complex pools of cDNA.

Chromosome Mapping↗

An immunoglobulin switchlike sequence is linked with canine narcolepsy.

Canine narcolepsy is an animal model of the human disorder that is transmitted as a single autosomal recessive gene with full penetrance (canarc-1) in Dobermans and Labradors. In previous experiments, we have identified a very tight linkage marker for canarc-1. This marker, a 0.85-kb band cross reacting with a human mu-switch Heavy-Chain Immunoglobulin probe (maximum logarithm of odds [LOD] score Zmax = 10.8 at 0% recombination), has now been cloned and sequenced. The gene, composed of GC rich repeats, is 75% homologous to the human mu-switch gene and is similar in organization to immunoglobulin switch genes. Curiously, however, this mu-switchlike segment appears to be unlinked with other switchlike polymorphisms detected at high stringency with the human mu-switch probe. Because in most animal species all switch genes are located within 300-500 kb and show tight linkage in families, this result suggests two possible hypotheses: 1) Our 0.85 kb is a true immunoglobulin switch segment, but the map of the canine Variable Heavy-Chain loci is organized in unlinked clusters, or 2) our 0.85-kb segment is not an immunoglobulin switch segment and is located elsewhere in the genome in all species. We are now using chromosome walking and Yeast Artificial Chromosome Cloning techniques, together with corresponding studies in humans to identify the pathological gene.

Alleles↗

Magnetic bead capture of expressed sequences encoded within large genomic segments.

Magnetic bead capture utilizes biotin-streptavidin magnetic bead technology to isolate cDNAs rapidly from large genomic intervals, giving several thousand-fold enrichment of the selected cDNAs. The technique can allow parallel analysis of several large genomic segments of varying complexities and can be applied to the isolation of expressed sequences from various tissue sources.

Bacterial Proteins↗

A physical map of 15 loci on human chromosome 5q23-q33 by two-color fluorescence in situ hybridization.

The q23-q33 region of human chromosome 5 encodes a large number of growth factors, growth factor receptors, and hormone/neurotransmitter receptors. This is also the general region into which several disease genes have been mapped, including diastrophic dysplasia, Treacher Collins syndrome, hereditary startle disease, the myeloid disorders that are associated with the 5q-syndrome, autosomal-dominant forms of hereditary deafness, and limb girdle muscular dystrophy. We have developed a framework physical map of this region using cosmid clones isolated from the Los Alamos arrayed chromosome 5-specific library. Entry points into this library included 14 probes to genes within this interval and one anonymous polymorphic marker locus. A physical map has been constructed using fluorescence in situ hybridization of these cosmids on metaphase and interphase chromosomes, and this is in good agreement with the radiation hybrid map of the region. The derived order of loci across the region is cen-IL4-IL5-IRF1-IL3-IL9-EGR1-CD1 4-FGFA-GRL-D5S207-ADRB2-SPARC-RPS14+ ++-CSF1R- ADRA1, and the total distance spanned by these loci is approximately 15 Mb. The framework map, genomic clones, and contig expansion within 5q23-q33 should provide valuable resources for the eventual isolation of the clinically relevant loci that reside in this region.

Chromosome Mapping↗

Genetic and physical mapping of the Treacher Collins syndrome locus with respect to loci in the chromosome 5q3 region.

Treacher Collins syndrome is an autosomal dominant, craniofacial developmental disorder, and its locus (TCOF1) has been mapped to chromosome 5q3. To refine the location of the gene within this region, linkage analysis was performed among the TCOF1 locus and 12 loci (IL9, FGFA, GRL, D5S207, D5S210, D5S376, CSF1R, SPARC, D5S119, D5S209, D5S527, FGFR4) in 13 Treacher Collins syndrome families. The highest maximum lod score was obtained between loci TCOF1 and D5S210 (Z = 10.52; theta = 0.02 +/- 0.07). The best order, IL9-GRL-D5S207/D5S210-CSF1R-SPARC-++ +D5S119, and genetic distances among these loci were determined in the 40 CEPH families by multipoint linkage analysis. YAC clones were used to establish the order of loci, centromere-5'GRL3'-D5S207-D5S210-D5S376-CSF1R -SPARC-D5S119-telomere. By combining known physical mapping data with ours, the order of chromosome 5q3 markers is centromere-IL9-FGFA-5'GRL3'-D5S207-D5S210- D5S376-CSF1R-SPARC-D5S119-D5S209- FGFR4-telomere. Based on this order, haplotype analysis suggests that the TCOF1 locus resides distal of CSF1R and proximal to SPARC within a region less than 1 Mb in size.

Base Sequence↗

Usefulness of atrial electrograms recorded via central venous catheters in the diagnosis of complex cardiac arrhythmias.

OBJECTIVE: To assess the role of intravascular atrial electrograms in improving the diagnosis of complex cardiac arrhythmias in critically ill patients. DESIGN: Prospective, clinical study comparing the accuracy of cardiac rhythm diagnosis using standard surface electrocardiogram (EKG) and intravascular atrial electrograms. SETTING: Intensive care unit of a university teaching hospital. PATIENTS: A total of 57 critically ill patients (44 cardiothoracic surgery, five acute myocardial infarction, two septic shock, six miscellaneous) with 85 complex cardiac arrhythmias that were unable to be diagnosed with certainty using the surface EKG. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The intravascular atrial electrogram altered diagnosis based on the surface EKG in 11 (13%) patients and confirmed rhythm diagnosis in 60 (71%) of 85 patients with arrhythmia. Of 61 patients with wide complex tachycardia, 40 (66%) were diagnosed as ventricular tachycardia (atrioventricular dissociation demonstrated on the atrial electrogram), and 11 (18%) as supraventricular tachycardia with aberrant conduction. Ten (16%) wide complex tachycardias could not be diagnosed with confidence using both surface EKG and intravascular electrogram. There were no adverse effects with this technique. CONCLUSIONS: Intravascular atrial electrograms recorded via central venous catheters are useful in the diagnosis of complex cardiac arrhythmias, particularly ventricular tachycardia. The technique is safe, simple, and quick.

Arrhythmias, Cardiac↗

The selective isolation of novel cDNAs encoded by the regions surrounding the human interleukin 4 and 5 genes.

We have developed modifications to direct cDNA selection that allow the rapid and reproducible isolation of low abundance cDNAs encoded by large genomic clones. Biotinylated, cloned genomic DNAs are hybridized in solution with amplifiable cDNAs. The genomic clones and attached cDNAs are captured on streptavidin coated magnetic beads, the cDNAs are eluted and amplified. We have applied this protocol to a 425kb YAC that contains the human IL4 and IL5 genes. After two cycles of enrichment twenty-four cDNAs were evaluated, all of which were homologous to the YAC. DNA sequencing revealed that nine cDNAs were 100% homologous to the interferon regulatory factor 1 (IRF1) gene. Six clones were 70% homologous to the murine P600 gene, which is coexpressed with IL4 and IL5 in mouse Th2 cells. The nine remaining clones were unique within the sequence databases and were non redundant. All of the selected cDNAs were initially present at very low abundance and were enriched by as much as 100,000-fold in two cycles of enrichment. This modified selection technique should be readily applicable to the isolation of many candidate disease loci as well as the derivation of detailed transcription maps across large genomic regions.

Amino Acid Sequence↗

Isolation of region-specific cosmids from chromosome 5 by hybridization with microdissection clones.

A method is described for the isolation of chromosome region specific cosmids. The 5q35 region of the long arm of human chromosome 5 was microdissected, digested with MboI, ligated to oligonucleotide adaptors, amplified by the polymerase chain reaction and cloned into a plasmid vector. Inserts which did not contain highly repetitive sequences were used to screen a chromosome 5 cosmid library by direct hybridization. There were 33 positive cosmid clones identified with 4 microclones. Individual cosmid clones were biotinylated and used as probes for fluorescence in situ hybridization to metaphase chromosomes. Of the 33 cosmids that were mapped, 29 localized to q35 and 4 to q34, demonstrating the specificity of the microdissection library and the cosmids.

Base Sequence↗

Reassignment of the human macrophage colony stimulating factor gene to chromosome 1p13-21.

Macrophage colony stimulating factor (CSF-1) is a member of a family of glycoproteins that are necessary for the normal proliferation and differentiation of myeloid progenitor cells. The human CSF-1 gene has previously been assigned to chromosome 5 using somatic cell hybrids, and further localized to 5q33 by in situ hybridization with a 3H labelled cDNA probe. However, the murine macrophage colony stimulating factor gene (csfm) has been localized to a region on mouse chromosome 3 which was previously shown to be syntenic with the proximal region of 1p and not 5q. Using a human genomic DNA clone that contains the CSF-1 gene, we have localized CSF-1 to chromosome 1p13-21 by fluorescence in situ hybridization. The reassignment of the CSF-1 gene argues against its involvement in myeloid disorders with deletions of the long arm of chromosome 5.

Animals↗

A radiation hybrid map of 18 growth factor, growth factor receptor, hormone receptor, or neurotransmitter receptor genes on the distal region of the long arm of chromosome 5.

The distal portion of the long arm of human chromosome 5 contains an impressive number of genes encoding growth factors, growth factor receptors, and hormone/neurotransmitter receptors. The order of and relative distance between 18 of these genes was determined by radiation hybrid mapping. There is only a single gap in a contiguous radiation map from 5q22-5q35. For this set of radiation hybrids, one map unit (centiray) corresponds to 20-50 kb of DNA. Close physical proximity for several pairs of loci was predicted by the map. Two sets of these were found to be contained in single YAC clones. The physical map produced by radiation hybrid mapping should prove useful in efforts to identify four disease genes that have been assigned to distal 5q by linkage studies.

Base Sequence↗

New strategies for isolation of low abundance viral and host cDNAs: application to cloning of the hepatitis E virus and analysis of tissue-specific transcription.

The ability to clone viruses molecularly has led to dramatic advances in our understanding of this diverse group of agents at the molecular level. These insights are critical to the development of experimental strategies for the containment and control of the various viral pathogens that cause hepatitis in man. Knowledge of the genes and gene products have, for example, assisted in the design of expression systems that have been useful for the cell-free expression and production of viral constituents in the development of a subunit (recombinant) vaccine for HBV. Of particular advantage to the experimenter would be the ability to clone the virus directly from the infectious source without the need to resort to biologic amplification systems that require costly investments of money and manpower. This would obviate the need for the time-intensive development of a tissue culture propagation or the expensive cost of developing an animal model. The methods described here have applications to the discovery and isolation of low abundance transcripts from host (cellular) genes. These host encoded products may have important roles in virus replication and certainly by themselves constitute a growing area of study. The direct selection protocol has already proven its value in the isolation of novel (previously undescribed) gene sequences from complex cellular sources. The application of these methodologies should, at the single cell level, aid in the delineation of those important host-encoded gene products that are critical for the efficient in vitro propagation of hepatotropic viruses. The identification of these low abundance cellular genes will elucidate the biologic interplay between host and obligate intracellular parasite (virus) and potentially lead to the development of new strategies for virus control that take into consideration the role of the cell as host.

Base Sequence↗

Examining the function and regulation of hsp 70 in cells subjected to metabolic stress.

Members of the heat-shock protein (hsp) 70 family, distributed within various cellular compartments, have been implicated in facilitating protein maturation events. In particular, related hsp 70 family members appear to bind nascent polypeptides which are in the course of synthesis and/or translocation into organelles. We previously reported that in normal, unstressed cells, cytosolic hsp 70 (hsp 72/73) interacted transiently with nascent polypeptides. We suspect that such interactions function to prevent or slow down the folding of the nascent polypeptide chain. Once synthesis is complete, and now with all of the information for folding present, the newly synthesized protein appears to commence along its folding pathway, accompanied by the ATP-dependent release of hsp 72/73. Herein, we examined how these events occur in cells subjected to different types of metabolic stress. In cells exposed to either an amino acid analog or sodium arsenite, two potent inducers of the stress response, newly synthesized proteins bind to but are not released from hsp 70. Under these conditions of metabolic stress, we suspect that the newly synthesized proteins are unable to commence proper folding and consequently remain bound to their hsp 70 chaperone. In cells subjected to heat shock, a large number of both newly synthesized as well as mature proteins are rendered insoluble. Within this insoluble material are appreciable amounts of hsp 72/73. Finally, we show that in cells depleted of ATP, the release of hsp 70 from maturing proteins is inhibited. Thus, in cells experiencing metabolic stress, newly synthesized proteins unable to properly fold, as will as mature proteins which begin to unfold become stably bound to hsp 72/73. As a consequence and over time, the free or available levels of pre-existing hsp 72/73 are reduced. We propose that this reduction in the available levels of hsp 72/73 is the trigger by which the stress response is initiated.

Adenosine Triphosphate↗

Cytokine gene expression in rejecting cardiac allografts.

Heart transplantation is now a viable therapeutic option for patients with certain end-stage cardiac diseases. However, episodes of rejection, opportunistic infection, and life-threatening side effects of generalized immunosuppression remain very real problems for these patients. A better understanding of the molecular mechanisms underlying rejection may provide the basis for the development of more specific, less toxic immunosuppressive therapies. While cytokines have long been implicated in the pathogenesis of rejection, the precise role of each cytokine in this process has yet to be defined. We report here the application of the polymerase chain reaction (PCR) to the detection of cytokine mRNA in biopsies obtained from heterotopic abdominal cardiac allografts in cynomolgus monkeys. With the exception of IL-6 and IL-8, cytokine transcripts were undetectable in samples obtained from the donor heart pretransplant. In contrast, IFN-gamma transcripts were detected in all transplants two days after surgery before evidence of rejection was demonstrable by histopathologic analysis. IL-1 beta, IL-2, and IL-6 transcripts were detected when minimal rejection was noted. At later times, IL-1 alpha, IL-1 beta, IL-2, IL-6, IL-8, TNF-beta, and IFN-gamma transcripts were detectable. Further characterization of the spectrum of cytokines expressed at various stages of rejection may lead to insights into the biology of transplant rejection and to the development of more specific and potent reagents to diagnose and/or treat rejection.

Animals↗

Direct selection: a method for the isolation of cDNAs encoded by large genomic regions.

We have developed a strategy for the rapid enrichment and identification of cDNAs encoded by large genomic regions. The basis of this "direct selection" scheme is the hybridization of an entire library of cDNAs to an immobilized genomic clone. Nonspecific hybrids are eliminated and selected cDNAs are eluted. These molecules are then amplified and are either cloned or subjected to further selection/amplification cycles. This scheme was tested using a 550-kilobase yeast artificial chromosome clone that contains the EPO gene. Using this clone and a fetal kidney cDNA library, we have achieved a 1000-fold enrichment of EPO cDNAs in one cycle of enrichment. More significantly, we have further investigated one of the "anonymous" cDNAs that was selectively enriched. We confirmed that this cDNA was encoded by the yeast artificial chromosome. Its frequency in the starting library was 1 in 1 x 10(5) cDNAs and after selection comprised 2% of the selected library. DNA sequence analysis of this cDNA and of the yeast artificial chromosome clone revealed that this gene encodes the beta 2 subunit of the human guanine nucleotide-binding regulatory proteins. Restriction mapping and hybridization data position this gene (GNB2) to within 30-70 kilobases of the EPO gene. The selective isolation and mapping of GNB2 confirms the feasibility of this direct selection strategy and suggests that it will be useful for the rapid isolation of cDNAs, including disease-related genes, across extensive portions of the human genome.

Base Sequence↗

Genetic linkage of autosomal recessive canine narcolepsy with a mu immunoglobulin heavy-chain switch-like segment.

Identification of genes determining narcolepsy susceptibility is important not only for understanding that disorder but also for possible clues to general sleep-control mechanisms. Studies in humans reveal at least one such gene related to the major histocompatibility complex and in dog an as-yet-unmapped single, autosomal recessive gene canarc-1. Gene markers for canarc-1 were therefore sought by DNA restriction fragment length polymorphisms in our colony of narcoleptic dogs. A human mu-switch immunoglobulin probe and the enzyme Hae III identified a gene cosegregating with canarc-1 in backcrossed animals (logarithm of odds scores: m = 24, Z max = 7.2 at theta = 0%). canarc-1 was also shown not to be tightly linked with the dog major histocompatibility complex (m = 40, Z less than -2 at theta less than 4.8%). These results represent the mapping of a non-major histocompatibility complex narcolepsy gene and strongly suggest involvement of the immune system in the pathophysiology of that disease.

Animals↗

Radiation hybrid map of 13 loci on the long arm of chromosome 5.

Radiation hybrid mapping was used in conjunction with a natural deletion mapping panel to predict the order of and distance between 13 loci in the distal portion of the long arm of human chromosome 5. A panel of irradiation hybrids containing fragments of 5q was generated from an HPRT+ Chinese hamster-human cell hybrid containing a derivative chromosome 5 [der(5)t(4;5)(5qter----5p15.1::4p15.1----4pter)] as its only human DNA. One hundred nine radiation hybrids containing human DNA were screened with polymerase chain reaction primer sets representing nine genes encoding growth factors, growth factor receptors, or hormone receptors (IL3, IL4, IL5, CSF1R, FGFA, ADRB2, GRL, GABRA1, and DRD1) as well as four other loci (FER, SPARC, RPS14, and CD14) to generate a radiation hybrid map of the area 5q21-q35. A physical map predicting the order of and distance between the 13 loci was constructed based on segregation of the 13 loci in hybrid clones. The radiation hybrid panel will be useful as a mapping tool for determining the location and order of other genes and polymorphic loci in this region as well as for generating new DNA probes from specific regions.

Animals↗

Isolation and DNA sequence of a gene encoding alpha-trichosanthin, a type I ribosome-inactivating protein.

alpha-Trichosanthin (alpha-TCS) is a ribosome-inactivating protein that has recently been shown to inhibit the replication of human immunodeficiency virus. We have isolated a gene encoding alpha-TCS and have determined its DNA sequence. The data indicate that alpha-TCS is synthesized as a preproprotein consisting of 289 amino acids, the first 23 residues of which comprise a putative secretory signal peptide. The last 19 residues comprise a carboxyl extension that has not been reported to be associated with the mature protein and that may be processed in the endoplasmic reticulum or Golgi apparatus of cells producing alpha-TCS. The mature protein consists of 247 amino acids. The sequence predicted by translation of the DNA sequence agrees with and confirms the primary sequence determined recently on the protein. The molecular clone for alpha-TCS will facilitate directed mutational analyses that may provide information on how this peptide, and other ribosome-inactivating proteins, function. These studies may also lead to the development of therapeutic agents with altered activities and/or improved properties for in vivo use.

Amino Acid Sequence↗

Localization of a human T-cell-specific gene, RANTES (D17S136E), to chromosome 17q11.2-q12.

We report here the localization of the gene for a human T-cell-specific molecule, designated RANTES, to human chromosome region 17q11.2-q12 by in situ hybridization and analysis of somatic cell hybrids using a cDNA probe to the gene. We have recently shown that this gene, which encodes a small, secreted, putative lymphokine, is a member of a larger gene family some of whose members reside on chromosome 4 but most of whose members have not to date been mapped. A secondary hybridization peak was noted on the region of human chromosome 5q31-q34, which may represent the location of other members of the gene family. Interestingly, this latter region overlaps with the location of an extended linked cluster of growth factor and receptor genes, some of which may be coregulated with members of the RANTES gene family.

Amino Acid Sequence↗