Biomedical subjects

C E Lawrence

Publications and source records attributed to C E Lawrence.

At least 37 records · Page 2Linked to original sources

PubMed1998

Bayesian adaptive sequence alignment algorithms.

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.

Adenylate Kinase↗

PubMed1998

Bayesian protein family classifier.

A Bayesian procedure for the simultaneous alignment and classification of sequences into subclasses is described. This Gibbs sampling algorithm iterates between an alignment step and a classification step. It employs Bayesian inference for the identification of the number of conserved columns, the number of motifs in each class, their size, and the size of the classes. Using Bayesian prediction, inter-class differences in all these variables are brought to bare on the classification. Application to a superfamily of cyclic nucleotide-binding proteins identifies both similarities and differences in the sequence characteristics of the five subclasses identified by the procedure: 1) cNMP-dependent kinases, 2) prokaryotic cAMP-dependent regulatory proteins, CRP-type, 3) prokaryotic regulatory proteins, FNR-type, 4) cAMP gated ion channel proteins of animals, and 5) cAMP gated ion channels of plants.

Algorithms↗

PubMed1997

Value of alpha 1-acid glycoprotein in the diagnosis of feline infectious peritonitis.

Feline infectious peritonitis (FIP) is notoriously difficult to differentiate from the many other diseases with similar clinical signs and at present the only conclusive diagnostic test is the histopathological examination of a biopsy. The potential value of raised levels of the acute phase reactants, alpha 1-acid glycoprotein (AGP) and haptoglobin in the diagnosis of the disease was investigated. The concentrations of the two proteins were determined in serum samples from healthy cats and gave reference ranges of 0.1 to 0.48 g/litre and 0.04 to 3.84 g/litre, respectively. Levels of AGP greater than 1.5 g/litre in serum, plasma or effusion samples were found to be of value in distinguishing field cases of FIP from cats with similar clinical signs and differentiated these two groups of cats more effectively than the albumin:globulin ratio. The concentration of haptoglobin was higher in cats with FIP than in the group of healthy cats, but this protein was not of value in the diagnosis of FIP. Serum samples from feline immunodeficiency virus-infected cats were also analysed for these proteins and their concentrations were significantly elevated, illustrating that raised levels of AGP and haptoglobin are not pathognomonic for FIP.

Animals↗

PubMed1997

Extracting protein alignment models from the sequence database.

Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called Probe fully automates this process of model construction starting from a single sequence. Central to this program is a powerful new method to locate and align only those, often subtly, conserved patterns essential to the family as a whole. When applied to randomly chosen proteins, Probe found on average about four times as many relationships as a pairwise search and yielded many new discoveries. These include: an obscure subfamily of globins in the roundworm Caenorhabditis elegans ; two new superfamilies of metallohydrolases; a lipoyl/biotin swinging arm domain in bacterial membrane fusion proteins; and a DH domain in the yeast Bud3 and Fus2 proteins. By identifying distant relationships and merging families into superfamilies in this way, this analysis further confirms the notion that proteins evolved from relatively few ancient sequences. Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences.

Algorithms↗

PubMed1997

Identification and characterization of two groups of congenital hypothyroid infants: implications for newborn screening.

A retrospective analysis of 400 newborns diagnosed with congenital primary hypothyroidism between 1983 and 1987 was conducted. Two distinct groups of cases were identified and characterized based on their newborn screening TSH value. The two groups are separated at a TSH concentration of 50 mU/l of serum by a normal probability plot. This finding is in agreement with the 1993 recommendation from the American Academy of Pediatrics that infants with a low T4 level and a TSH concentration greater than 40 mU/l be considered to have primary hypothyroidism until proven otherwise. The group of infants with TSH less than 50 mU/l have a higher proportion of males and low birthweight infants. For this group, T4 increases with increasing TSH. We find that screening TSH, T4, and birthweight are predictive of follow-up serum TSH level for the cases with TSH > 50 mU/l but not for cases with TSH < 50 mU/l. An optimal rule for selecting screening cutoff levels is presented based on only T4, TSH and their interaction. Adjustments for sex, birthweight or age at which sample was taken did not aid in distinguishing cases from controls for newborns whose age of sample is 2 days or greater.

Congenital Hypothyroidism↗

PubMed1997

Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers.

A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contracts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue-residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue-residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy.

Crystallization↗

PubMed1996

Detection of likely transmembrane beta strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler.

The mitochondrial channel VDAC is presumed to fold as a beta-barrel although the number and identity of transmembrane beta-strands in the protein are controversial. Previously, a novel multiple alignment algorithm called the Gibbs sampler was used to detect a residue-frequency motif in sequences of bacterial outer-membrane proteins that corresponds to transmembrane beta-strands in bacterial porins of known structure (Neuwald et al., 1995, Protein Science, 4, 1618. In the present study, this bacterial motif has been used to screen sets of mitochondrial membrane protein sequences, with matches occurring in only two classes of proteins: VDACs and the outer-membrane protein import pore (1SP42, M0M38). These results suggest a structural (and perhaps evolutionary) relatedness between the bacterial and mitochondrial pore proteins, with the mitochondrial subsequences that match the bacterial motif corresponding to transmembrane beta-strands as in the porins.

Amino Acid Sequence↗

PubMed1995

Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles.

Algorithms↗

PubMed1995

Cytokine production by cats infected with feline immunodeficiency virus: a longitudinal study.

The immune responsiveness of cats naturally or experimentally infected with feline immunodeficiency virus (FIV) was studied. Peripheral blood mononuclear cells (PBMC) from naturally infected, symptomatic animals displayed depressed proliferation and interleukin-2 (IL-2) production in response to mitogens, which was accompanied by a significant increase in IL-1, IL-6 and tumour necrosis factor (TNF) production. Longitudinal studies were performed over a period of 4 years in experimentally infected animals. The responses of cells from these cats to concanavalin A (Con A) were consistently less than those from uninfected cats throughout the period but, owing to variation between cats, were significantly lower on only a few occasions. By contrast, the responses of cells to pokeweed mitogen (PWM) were severely affected and declined progressively throughout the 4-year period. In general, responses to Con A but not PWM could be restored by the addition of exogenous IL-2. The decline in immune responsiveness was concurrent with a decline in feline (f)CD4+ cells and an inversion in the CD4:CD8 ratio. Peak production of IL-1, IL-6 and TNF coincided with periods of depressed immune responses. Additionally, immunodeficient responses and elevated levels of proinflammatory cytokines were concurrent with the presence of clinical signs. We conclude that, like human immunodeficiency virus (HIV), FIV infection results in significant perturbation of the immune response. Responses to PWM appear to correlate with disease progression which suggests that the CD3 pathway is affected in the earlier stages of the disease and that additional activation pathways such as CD2 may not be affected until the animal enters the acquired immune deficient syndrome (AIDS) stage of the disease.

Animals↗

PubMed1994

Quantitative analysis of ribosome binding sites in E.coli.

185 clones with randomized ribosome binding sites, from position -11 to 0 preceding the coding region of beta-galactosidase, were selected and sequenced. The translational yield of each clone was determined; they varied by more than 3000-fold. Multiple linear regression analysis was used to determine the contribution to translation initiation activity of each base at each position. Features known to be important for translation initiation, such as the initiation codon, the Shine/Dalgarno sequence, the identity of the base at position -3 and the occurrence of alternative ATGs, are all found to be important quantitatively for activity. No other features are found to be of general significance, although the effects of secondary structure can be seen as outliers. A comparison to a large number of natural E.coli translation initiation sites shows the information profile to be qualitatively similar although differing quantitatively. This is probably due to the selection for good translation initiation sites in the natural set compared to the low average activity of the randomized set.

Base Sequence↗

PubMed1994

Immune response profiles in responsive and non-responsive mouse strains infected with Heligmosomoides polygyrus.

The immune response to a primary infection with Heligmosomoides polygyrus was monitored in three strains of mice (SJL, BALB/c, CBA) with different degrees of susceptibility to the infection. Parameters measured included circulating leucocyte numbers, T and B cell numbers in the mesenteric lymph nodes, the mucosal mast cell response, and quantitative and qualitative antibody responses to parasite antigens. From these data it would appear that resistance was governed by the relative speed and magnitude of the immune response mounted by the host. The possible immunological mechanisms governing this process are discussed.

Animals↗

PubMed1994

Immunosuppressive proteins secreted by the gastrointestinal nematode parasite Heligmosomoides polygyrus.

Experiments are described in which the conditions for the production, assay and isolation of immunomodulatory factors from the excretory-secretory (ES) products of Heligmosomoides polygyrus have been standardized. For the inhibition of an in vitro antibody response to keyhole limpet haemocyanin, immunosuppressive activity was most reproducibly produced by 10-20-day-old adult worms maintained in culture for 24 h. This activity was relatively stable at room temperature, at 50 degrees C and pH 2, but was destroyed by boiling. Immunosuppressive activity was eluted from Sephadex G-100 in fractions preceding those containing the bulk of ES proteins, and resolved on sodium dodecyl sulphate-polyacrylamide gel electrophoresis with molecular masses of 67, 54 and 20 kDa. The relative purity of these factors was confirmed by iso-electric focusing, where immunosuppressive activity was associated with proteins of pI values of approximately 4.2 and 4.35.

Animals↗

PubMed1994

Polyclonal B-cell activation in cats infected with feline immunodeficiency virus.

The specificity of the antibody response following natural or experimental infection of domestic cats with feline immunodeficiency virus (FIV) was examined. The antibody response to a range of non-viral antigens, including trinitrophenol (TNP), ovalbumin, beta-galactosidase, deoxyribonucleic acid (DNA) and keyhole limpet haemocyanin (KLH), was measured in 220 cats naturally infected with FIV. Infected cats had higher antibody levels to these antigens, in particular TNP, KLH and beta-galactosidase, than non-infected control cats. Competition binding studies demonstrated that this response was not due to the presence of cross-reacting epitopes on recombinant FIV p17 or p24 antigens, suggesting that the B-cell activation associated with infection was polyclonal rather than entirely virus specific. Studies on cats experimentally infected with FIV revealed a similar pattern, with infected cats developing an antibody response to heterologous non-viral antigens at 6-8 weeks post-infection. There were two discernible peaks of antibody activity, the first occurring 10-20 weeks post-infection and the second peak 40-60 weeks post-infection. The antibody response to KLH, DNA and beta-galactosidase remained elevated throughout the 90-week study period, whereas the antibody levels to the other antigens declined to levels approaching those observed in normal cats.

Animals↗

PubMed1993

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to deciphering these sequences and understanding the relations among them is the difficulty of detecting subtle local residue patterns common to multiple sequences. Such patterns frequently reflect similar molecular structures and biological properties. A mathematical definition of this "local multiple alignment" problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling. This algorithm finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations, and allows the simultaneous detection and optimization of multiple patterns and pattern repeats. The method is illustrated as applied to helix-turn-helix proteins, lipocalins, and prenyltransferases.

Algorithms↗

PubMed1993

An empirical energy function for threading protein sequence through the folding motif.

In this paper we present a new residue contact potential derived by statistical analysis of protein crystal structures. This gives mean hydrophobic and pairwise contact energies as a function of residue type and distance interval. To test the accuracy of this potential we generate model structures by "threading" different sequences through backbone folding motifs found in the structural data base. We find that conformational energies calculated by summing contact potentials show perfect specificity in matching the correct sequences with each globular folding motif in a 161-protein data set. They also identify correct models with the core folding motifs of hemerythrin and immunoglobulin McPC603 V1-domain, among millions of alternatives possible when we align subsequences with alpha-helices and beta-strands, and allow for variation in the lengths of intervening loops. We suggest that contact potentials reflect important constraints on nonbonded interaction in native proteins, and that "threading" may be useful for structure prediction by recognition of folding motif.

Amino Acid Sequence↗

PubMed1993

Risk profile for Chlamydia infection in women from public health clinics in New York State.

The prevalence of chlamydial infection and associated risk factors were studied in 1531 women from ten clinics in New York State excluding New York City. Overall Chlamydia infection rates were 13.6%; 17.6% in eight high risk family planning and STD clinics, and 5.7% in two low risk college and private clinics. Risk factors for Chlamydia infection included: age < 20 years (odds ratio 1.6), use of oral contraceptives (odds ratio 2.0), a history of having more than one sexual partner (odds ratio 1.7) and, in one clinic where data was available, inflammation on Papanicolaou smears (odds ratio 2.1). These data helped secure funding for Chlamydia preventive services and permitted development of a risk profile (score card) of Chlamydia for each age group. Use of such a score card can be most helpful in assigning which patients could benefit most from Chlamydia cultures, especially in those areas where testing is unavailable or too costly to screen all patients.

Adolescent↗

PubMed1993

Differential secretion of acetylcholinesterase and proteases during the development of Heligmosomoides polygyrus.

The development of the gastrointestinal nematode Heligmosomoides polygyrus was studied in the mouse. Levels of production of acetylcholinesterase and proteases were measured in excretory/secretory products of various stages of the parasite. The production of acetylcholinesterase was found to be maximal between days 4 and 6 post-infection, corresponding to the fourth larval stage of the parasite's life-cycle. Analysis of proteolytic activity revealed both quantitative and qualitative differences between the stages. Quantitative examination showed a maximal concentration of proteolytic enzymes in the early third larval stage (L3). Qualitative analysis revealed L3-associated molecules at 96, 15 and 8 kDa, L4-associated molecules at 58 and 33 kDa and adult-associated molecules at 116, 102, 39 and 25 kDa. A number appeared to be shared by all stages (18, 16 and 13 kDa), whilst others (76 and 42 kDa) appeared to be associated with the late L4/early adult parasite. The biological and immunological implications of variation in the production of proteases and acetylcholinesterase during the development of H. polygyrus are discussed.

Acetylcholinesterase↗

PubMed1992

Lymphosarcoma in experimentally induced feline immunodeficiency virus infection [corrected].

A cat experimentally infected with feline immunodeficiency virus (FIV) but known to be free of feline leukaemia virus (FeLV) developed lymphosarcoma. The lesions in the liver and kidneys were present nine months after infection, when the cat was 21 months old. The cat had no overt signs of immunodeficiency and it is suggested that the B cell activation induced shortly after FIV infection produced a large pool of proliferating lymphocytes from which the malignant cells emerged.

Animals↗