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Biomedical subjects

C B Lawrence

Publications and source records attributed to C B Lawrence.

At least 19 recordsLinked to original sources
PubMed1995

Fat mobilisation in short days is not associated with altered noradrenergic sensitivity of adipocytes in Djungarian hamsters.

One of the primary physiological responses of the Djungarian hamster to short photoperiods is a reduction in body weight with fat mobilisation. The depletion of fat to a minimum level may be regulated either in the periphery, through the sensitivity of adipocytes to hormonal stimulation, or centrally, via adjustments in efferent activity. To investigate this, we examined the lipolytic pathway in fat cells from animals at various stages of entrainment to long or short photoperiod. Short photoperiod exposure of up to a 10-week duration was without effect on basal glycerol release by unstimulated cells or on the ability of norepinephrine or an adenosine analogue to stimulate or inhibit lipolysis, respectively. Prolonged exposure to short photoperiod reduced basal glycerol release, but adipocytes retained their sensitivity to hormonal stimulation. Short photoperiod had no effect on the density or affinity of membrane-bound beta-adrenergic or adenosine receptors, or upon the ability of isoproterenol or forskolin to stimulate adenylate cyclase in adipocyte membranes. This suggests that the regulation of fat depletion in short photoperiod is determined centrally and does not involve alterations in adipocyte sensitivity and, in particular, the desensitisation of the adipocyte beta-adrenergic receptor-linked adenylate cyclase pathway.

Adenylyl Cyclase Inhibitors↗
PubMed1995

Hypothalamic NPY and prepro-NPY mRNA in Djungarian hamsters: effects of food deprivation and photoperiod.

Two catabolic states leading to loss of body weight were compared in the Djungarian hamster (Phodopus sungorus campbelli). Hypothalamic neuropeptide Y (NPY) and gene expression for NPY and corticotropin-releasing factor (CRF) were examined after withdrawal of food for 48 h or exposure to short photoperiod for 10 or 20 wk. Food deprivation was accompanied by increases in both NPY and prepro-NPY mRNA in the hypothalamic arcuate nucleus (ARC). Increases in gene expression were limited compared with published data from the rat and were inversely related to predeprivation body weight. Exposure to short photoperiod for 20 wk reduced body weight by 39%, but the activity of the NPY-ergic system was not affected; peptide concentration and gene expression were similar in short photoperiod hamsters and long photoperiod controls. The hypothalamic NPY-ergic system of the Djungarian hamster is sensitive to weight loss due to imposed manipulations of energy balance, but the catabolism observed in short photoperiod gives rise to a body weight that is appropriate to the season encoded by the photoperiod. CRF gene expression was not affected by food deprivation or short photoperiod.

Animals↗
PubMed1995

Identification of human gene structure using linear discriminant functions and dynamic programming.

Development of advanced technique to identify gene structure is one of the main challenges of the Human Genome Project. Discriminant analysis was applied to the construction of recognition functions for various components of gene structure. Linear discriminant functions for splice sites, 5'-coding, internal exon, and 3'-coding region recognition have been developed. A gene structure prediction system FGENE has been developed based on the exon recognition functions. We compute a graph of mutual compatibility of different exons and present a gene structure models as paths of this directed acyclic graph. For an optimal model selection we apply a variant of dynamic programming algorithm to search for the path in the graph with the maximal value of the corresponding discriminant functions. Prediction by FGENE for 185 complete human gene sequences has 81% exact exon recognition accuracy and 91% accuracy at the level of individual exon nucleotides with the correlation coefficient (C) equals 0.90. Testing FGENE on 35 genes not used in the development of discriminant functions shows 71% accuracy of exact exon prediction and 89% at the nucleotide level (C = 0.86). FGENE compares very favorably with the other programs currently used to predict protein-coding regions. Analysis of uncharacterized human sequences based on our methods for splice site (HSPL, RNASPL), internal exons (HEXON), all type of exons (FEXH) and human (FGENEH) and bacterial (CDSB) gene structure prediction and recognition of human and bacterial sequences (HBR) (to test a library for E. coli contamination) is available through the University of Houston, Weizmann Institute of Science network server and a WWW page of the Human Genome Center at Baylor College of Medicine.

Algorithms↗
PubMed1995

Viewing genome data as objects for application development.

Genomics is becoming a data-intensive science, and an increasing number of laboratories are generating data which swamps storage in traditional paper-and-ink notebooks. Capturing the data flow requires large systems with multiple applications manipulating the same or similar data. Large systems often have conflicting requirements for data representation. Consistency across applications is a prime consideration, and appropriate data representation is an important issue in developing practical systems for molecular biologists. Graphs are a natural representation for describing genome data, while objects are good for modeling the behavior necessary for laboratory applications. We present a method for translating graph descriptions of genome data into objects using objects as views on graphs. Graph representations describe genome concepts while objects capture individual views for application development insuring consistency across genome applications.

Chromosome Mapping↗
PubMed1994

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.

Algorithms↗
PubMed1994

The genome reconstruction manager: a software environment for supporting high-throughput DNA sequencing.

A new software system designed for use in high-throughput DNA sequencing laboratories is described. The Genome Reconstruction Manager (GRM) was developed from requirements derived from ongoing large-scale DNA sequencing projects. Object-oriented principles were followed in designing the system, and tools supporting object-oriented system development were employed for its implementation. GRM provides several advances in software support for high-throughput DNA sequencing: support for random, directed, and mixed sequencing strategies; a novel system for fragment assembly; a commercial object data-base management system for data storage; a client/server architecture for using network computational servers; and an underlying data model that can evolve to support fully automatic sequence reconstruction. GRM is currently being deployed for production use in high-throughput DNA sequencing projects.

Algorithms↗
PubMed1994

Effect of photoperiod on mitochondrial GDP binding and adenylate cyclase activity in brown adipose tissue of Djungarian hamsters.

Experiments were designed to investigate the involvement of brown adipose tissue (BAT) thermogenesis in the weight loss exhibited by Djungarian hamsters (Phodopus sungorus campbelli) in response to a short photoperiod. Significant decreases in body weight preceded reductions in food intake, suggesting a photoperiod-induced change in energy expenditure. Sixteen weeks exposure to short photoperiod resulted in large decreases in body weight and interscapular BAT mass that were accompanied by an increase in the thermogenic activity of BAT (estimated by mitochondrial GDP binding). However, exposure to short photoperiod for 8 weeks, that induced smaller but significant reductions in body weight, was without effect on the BAT parameters measured. This suggests that increased BAT thermogenesis is unlikely to initiate, or contribute to, the early stages of photoperiod-induced weight loss. In addition, short photoperiod failed to induce any change in the specific activity or sensitivity of adenylate cyclase in BAT membranes, in contrast to the downregulation of catecholamine-stimulated cAMP production observed in BAT following cold exposure.

Adenylyl Cyclases↗
PubMed1994

Novel estrogen response elements identified by genetic selection in yeast are differentially responsive to estrogens and antiestrogens in mammalian cells.

A powerful and versatile system for the identification of novel response elements for members of the intracellular receptor family is presented as applied to the human estrogen receptor. In the past, a limited number of estrogen response elements (EREs) have been functionally identified in the promoter regions of estrogen-regulated genes. From these a consensus ERE has been defined that is identical to the ERE of the Xenopus laevis vitellogenin gene, i.e., 5'-GGTCA NNN TGACC-3'. In order to investigate without bias the range of sequences that could function as EREs in vivo, we have developed a genetic selection in yeast expressing the human estrogen receptor (hER) and transformed with a random oligonucleotide library in a vector where expression of a selectable marker requires insertion of an upstream activating sequence. More than 1,000,000 transformants were screened and of 726 clones that contained activating sequences, 65 were found to be hormone-dependent. Sequencing revealed that the majority contained at least one 4/5 match to a canonical ERE half-site, but only one contained a full consensus ERE as previously defined. Some contained half-sites arranged as direct repeats. Twelve elements were further characterized to compare estrogen activation in yeast and mammalian cells and in vitro binding to hER. The results of these studies reveal that sequences that bind weakly to hER in vitro are fully functional as EREs in yeast and are conditionally responsive to estrogen in mammalian cells. In addition, an element was identified that is more sensitive to the partial agonist activities of tamoxifen and nafoxidine than is the consensus ERE, indicating that not only promoter context but the sequence of the binding site itself can allow distinction between receptor activated by agonist and that activated by antagonist.

Base Sequence↗
PubMed1994

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

Discriminant analysis is applied to the problem of recognition 5'-, internal and 3'-exons in human DNA sequences. Specific recognition functions were developed for revealing exons of particular types. The method based on a splice site prediction algorithm that uses the linear Fisher discriminant to combine the information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions (Solovyev, Lawrence, 1994). The accuracy of our splice site recognition function is about 97%. A discriminant function for 5'-exon prediction includes hexanucleotide composition of upstream region, triplet composition around the ATG codon, ORF coding potential, donor splice site potential and composition of downstream intron region. For internal exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79% and a level of pseudoexon ORF prediction of 99.96%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. A discriminant function for 3'-exon prediction includes octanucleotide composition of upstream intron region, triplet composition around the stop codon, ORF coding potential, acceptor splice site potential and hexanucleotide composition of downstream region.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Simulation↗
PubMed1993

G-protein coupling of vagal CCK binding sites and comparisons of transport rates.

The ability of nanomolar concentrations of guanine, but not adenine, nucleotides to inhibit specific 125I-Bolton-Hunter CCK binding to ligated rat vagus nerve demonstrated that vagal CCK binding sites were linked to G-proteins during axonal transport. The GTP analogue, GTP[S], reduced specific binding to both anterogradely and retrogradely transported binding sites by more than 90% at 1 microM. Transport of these putative receptor-G-protein complexes was examined under conditions of food deprivation or physiological hyperphagia induced by either lactation or genetic obesity. None of the physiological or imposed manipulations of food intake had any effect on the axonal transport of CCK binding sites. Transection of the cervical vagus resulted in an accumulation of binding sites at the lesion site that was indistinguishable from that seen following ligation for the same period.

Animals↗
PubMed1993

Identification of human gene functional regions based on oligonucleotide composition.

Accurate recognition of coding and intron regions within large regions of uncharacterized genomic DNA is an unsolved problem. A data base of more than 4,240,791 bp coding and 7,790,682 bp noncoding human sequences was extracted from GenBank to develop a function for locating coding regions in anonymous sequences. Several coding measures based on oligonucleotide preferences were tested on a control set that including 1/3 of all extracted sequences. An accuracy of separation of coding/noncoding regions is 87% for 9 bp oligonucleotides on 54 bp windows and 91% on 108 bp windows, respectively. For separation of coding/intron regions the accuracy is 89-90% for 8 bp oligonucleotides on 54 bp windows and up to 95% on 108 bp windows. Using the information about preferences of octanucleotides in protein coding and intron regions and significant triplet frequencies as a function of position near splice junctions, a joint splice site prediction scheme was developed. The accuracy of the joint scheme for predicting splice site positions on the test set was about 96-97%, which exceeds the accuracy of the previously reported splice site selection method based on a more complex artificial neural network approach. A model of splicing using poly-G(C) rich exon flanking sequences is suggested. A remarkable difference of oligonucleotide composition 5'- and 3'- gene regions is displayed and applied in a gene structure predictive system.

Exons↗
PubMed1992

Selectivity of cholecystokinin (CCK) receptor antagonists, MK-329 and L-365,260, for axonally-transported CCK binding sites on the rat vagus nerve.

The ability of the cholecystokinin (CCK) receptor antagonists, MK-329 and L-365,260, to selectively inhibit 125I-Bolton-Hunter-CCK8 binding to ligated rat vagus nerve in vitro was examined at concentrations ranging from 10(-10) M to 10(-6) M. Both antagonists inhibited binding to CCK binding sites accumulating proximal to ligatures on the cervical vagus. Incubation of nerve sections in the presence of both antagonists produced an additive effect, indicating that both CCK-A and CCK-B binding sites are transported towards the periphery. In contrast, CCK binding sites accumulating distal to the ligature possessed the pharmacological characteristics of the CCK-B receptor sub-type only.

Animals↗
PubMed1992

Effect of neonatal capsaicin treatment on cholecystokinin-(CCK8) satiety and axonal transport of CCK binding sites in the rat vagus nerve.

Cholecystokinin (CCK) binding sites which accumulate at ligatures placed on the rat vagus nerve may mediate the satiety actions of CCK. Treatment of neonatal rats with capsaicin attenuated the satiety effect of injected CCK in adult life. Capsaicin pretreatment also reduced, but did not eliminate, the accumulation of CCK binding sites proximal and distal to ligatures on either cervical trunk. A similar effect was observed following ligation of subdiaphragmatic vagal trunks. The CCK receptor antagonists, MK-329 and L-365,260, inhibited binding to capsaicin- and vehicle-treated nerves to a similar degree. Densities of CCK binding sites in the nucleus tractus solitarius and area postrema were also markedly affected by neonatal capsaicin treatment.

Animals↗
PubMed1991

RNA secondary structure analysis of the packaging signal for Moloney murine leukemia virus.

We have examined the cis-acting RNA packaging signal (psi) from Moloney murine leukemia virus using a combination of chemical and primary sequence analysis techniques. For our chemical analyses, we used dimethyl sulfate, kethoxal, and 1-cyclohexyl-3-(2-morpholinoethyl)-carbodiimide metho-p-toluene sulfonate as probes for RNA secondary structure. The structural information obtained from these studies was used to constrain computer algorithms for prediction of RNA secondary structure. In addition, we generated and analyzed a phylogenetic comparison of homologous sequences from related retroviruses. From these data, we have developed two models for the RNA secondary structure of the packaging signal psi. Both of these models suggest the presence of secondary structure elements in a region of the psi RNA known to be required for function.

Aldehydes↗
PubMed1990

Use of homology domains in sequence similarity detection.

We have found the detection of homology domains using a nonlinear similarity score and the DD algorithm to be a useful approach for identifying similarity between sequences and evaluating potential homology. There are several reasons for the success of the method. (i) Homology domains are identified by a rigorous method that guarantees they will be locally optimal. (ii) The relative significance of different homology domains can be directly compared using the nonlinear similarity score. (iii) Different cost matrices can be used in the calculation of the similarity score. (iv) Relatively long sequences can be compared in a single pass as storage requirements are proportional to the shorter of the two sequences being compared. (v) The method has proved to be very sensitive in practice. (vi) The boundaries of authentic regions of homology are accurately identified. (vii) The information required to define a homology domain (its location, size, similarity score, etc.) can be stored in a compact data structure, facilitating the sharing of homology domain data among different software tools. (viii) The method can be applied to similarity searches of the nucleotide and protein sequence data banks. These properties make the identification of homology domains for studying sequence similarity a useful companion to other accepted methods, such as dynamic programming based analyses.

Animals↗
PubMed1989

Infection of bovine cells of embryonic origin by amphotropic retroviral vectors.

Two amphotropic-based mouse retroviral vectors carrying the neomycin-resistance gene were used to infect four bovine cell lines. Two cell lines, bovine kidney and spleen cells, were refractory to the infection while two independent bovine cells of apparent embryonic origin were infected by the amphotropic retroviral vectors at a measurable titer. Southern blot analysis reveals the presence of neomycin-resistance gene in the G418-resistant bovine cells. The results demonstrate the successful transfer of a gene to bovine cells of embryonic origin using a murine retroviral vector system.

Animals↗
PubMed1989

Two new members of the OmpR superfamily detected by homology to a sensor-binding core domain.

The OmpR superfamily includes proteins that act as transcriptional regulators of operons that respond to environmental stimuli. A homologous domain near the N-terminus, termed a sensor-binding core domain, is thought to play a role in recognition of a signal transduction protein. We have identified two previously unrecognized members of this regulator family of proteins: a 23.8-kd protein transcribed from the uvrC transcription unit and the PgtA gene product, which is a phosphoglycerate transport regulatory protein. The sensor-binding core domain is also present in four proteins that regulate bacterial sporulation and chemotaxis. The 23.8-kd protein also has sequence similarity to elongation factor Tu and two regulatory proteins: HtpR, the heat-shock regulatory protein, and TraJ, a regulator of expression of genes involved in conjugation. There is a 77-amino acid region near the C-terminus of the 23.8-kd protein that has 30% similarity with a 28.1-kd protein coded for by an open reading frame 5' to the reading frame of the 23.8-kd protein in the uvrC transcription unit. Genetic distance analysis of amino acid sequences of proteins with a sensor-binding core domain suggests that the 23.8-kd protein and the chemotaxis regulatory proteins are distantly related to the other regulatory proteins in the OmpR superfamily.

Amino Acid Sequence↗