A test of the negative discriminative stimulus as a reinforcer of observing

Five pigeons were used to test the hypothesis that the source of reinforcement for observing behavior is the information that it provides concerning the schedule of primary reinforcement. On a variable-interval schedule, pecking the left-hand key produced a 30-sec display of such information. During this 30-sec period, when pecking the right-hand key was reinforced on a random-interval schedule, both keys were green; when no reinforcement was scheduled (extinction) both keys were red. Later, this baseline procedure, in which both red and green were available, was replaced for blocks of sessions by procedures in which either (a) the red was eliminated and only the green could be produced; or (b) the green was eliminated and only the red could be produced. The results were that green maintained rates of pecking on the left key that were as high or higher than when both colors were available and that red maintained no responding. It was concluded that the reinforcing value of a stimulus depends on the positive or negative direction of its correlation with primary reinforcement, rather than upon the amount of information that it conveys.

Mast cell production of IL-4 and TNF may be required for protective and pathological responses in gastrointestinal helminth infection

Expulsion of the gastrointestinal nematode Trichinella spiralis is associated with Th2 responses and intestinal inflammation, which correlate with a marked mast cell (MC) response. To address the role of MC-derived cytokines in the induction of protective responses, WBB6F1-KitW/KitW-v (W/W(v)) mice were reconstituted with wild-type, tumor necrosis factor (TNF)-alpha(-/-), or interleukin (IL)-4(-/-) bone marrow (BM) prior to infection with T. spiralis. W/W(v) mice reconstituted with TNF-alpha(-/-) or IL-4(-/-) BM expelled the parasite less efficiently and showed diminished enteropathy, whereas protective responses were normal in W/W(v) mice reconstituted with wild-type BM and were accompanied by intestinal pathology. MC responses were reduced in W/W(v) mice reconstituted with IL-4(-/-) BM and to a lesser extent when reconstituted with TNF-alpha(-/-). These results suggest that MC-derived IL-4 and TNF may regulate the induction of protective Th2 responses and intestinal inflammation associated with the expulsion of T. spiralis. Significantly, these studies suggest a role for MC-derived cytokines as autocrine growth factors.

The role of IL-4, IL-13 and IL-4Ralpha in the development of protective and pathological responses to Trichinella spiralis

T helper type 2 (Th2) responses have been shown to be important in protective responses to gastrointestinal (GI) helminth infections and in the development of the intestinal pathology accompanying expulsion of the parasite. Different inbred mouse strains have been shown to develop different cytokine profiles following infection with GI helminths with increased resistance observed in those strains where Th2 cytokines predominate. The aim of this study was to determine the role of IL-4, IL-13 and IL-4Ralpha and the impact of host background on the development of the protective and pathological responses induced by infection with the gastrointestinal helminth Trichinella spiralis. IL-4, IL-13 and IL-4Ralpha were required for the generation of Th2 responses to T. spiralis; however, the role these responses play in the development of protection and enteropathy was less clear. IL-4Ralpha-deficiency mice resulted in substantially reduced parasite expulsion, intestinal pathology and Th2 responses. Similarly, lack of IL-13 resulted in inhibited expulsion and the development of enteropathy. Although Th2 responses were reduced in BALB/c IL-4-/- mice, neither expulsion nor enteropathy were different from wild-type mice. In contrast, C57BL/6 IL-4-/- exhibited delayed expulsion and reduced pathology, suggesting that host genetics are important in the function of individual cytokines. Thus, differences in background genotype may be an important component in the development host protection and the development of intestinal pathology accompanying the loss of GI helminths.

Contrasting effects of acute and chronic gastro-intestinal helminth infections on a heterologous immune response in a transgenic adoptive transfer model

We have previously found that co-immunisation with ovalbumin (OVA) and the body fluid of the helminth Ascaris suum inhibited an OVA-specific delayed type hypersensitivity (DTH) response by reducing OVA-specific CD4+ T lymphocyte proliferation via an IL-4 independent mechanism. In the present study, we determined whether parasite infections themselves could induce similar changes to peripheral immunisation by examining the modulation of OVA-specific immune responses during acute and chronic helminth infections. Surprisingly, an acute infection with Trichinella spiralis, but not a chronic infection with Heligmosomoides polygyrus, inhibited the OVA-specific DTH reaction. Correspondingly, the T helper 1 (Th1) OVA-specific response was decreased in mice infected with T. spiralis, but not with H. polygyrus. Inhibition of the Th1 response may be a result of a shift in the Th1/Th2 balance as although both H. polygyrus and T. spiralis infected mice induced a Th2 OVA-specific response, that exhibited by T. spiralis was more potent. Furthermore, although IL-10 secretion upon OVA restimulation was similarly increased by both infections, production of this immunoregulatory cytokine may play a role in the suppression of immune responses observed with T. spiralis infection depending on the context of its release. Interestingly, analysis of the OVA-specific T lymphocyte division by carboxyfluorescein diacetate succinimidyl ester (CFSE) staining revealed that gastro-intestinal infection with the acute helminth T. spiralis, but not with chronic H. polygyrus, inhibited the systemic immune response by significantly inhibiting the antigen-specific T cell proliferation during the primary response, a mechanism similar to that observed when A. suum parasite extracts were directly mixed with the OVA during immunisation in our previous studies.

Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

Coordinated Muc2 and Muc3 mucin gene expression in Trichinella spiralis infection in wild-type and cytokine-deficient mice

Mucin hypersecretion is an important component of the immune response to gastrointestinal nematode infection. Two discrete types of mucin proteins exist in the mouse intestine, secretory Muc2 and membrane-bound Muc3. We examined Muc2 and Muc3 expression in wild-type mice and mice lacking gamma interferon receptor (IFNgammaR-/-), tumor necrosis factor receptor 1 (TNFR1-/-) and interleukin 4 (IL4-/-) infected with Trichinella spiralis. Infected wild-type mice demonstrated significant goblet cell hyperplasia and increased mucin glycoprotein. In situ hybridization showed this was accompanied by increases in Muc2 and Muc3 mRNA. Total intestinal mucin protein and Muc2 and Muc3 mRNA levels were also significantly increased in cytokine-deficient mice. These data demonstrate the coordinated up-regulation of two types of mucin genes in response to T. spiralis infection and may form the basis of an innate mucosal response independent of IFN-gamma, TNF, and IL-4.

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

Single-stranded regions in RNA secondary structure are important for RNA-RNA and RNA-protein interactions. We present a probability profile approach for the prediction of these regions based on a statistical algorithm for sampling RNA secondary structures. For the prediction of phylogenetically-determined single-stranded regions in secondary structures of representative RNA sequences, the probability profile offers substantial improvement over the minimum free energy structure. In designing antisense oligonucleotides, a practical problem is how to select a secondary structure for the target mRNA from the optimal structure(s) and many suboptimal structures with similar free energies. By summarizing the information from a statistical sample of probable secondary structures in a single plot, the probability profile not only presents a solution to this dilemma, but also reveals 'well-determined' single-stranded regions through the assignment of probabilities as measures of confidence in predictions. In antisense application to the rabbit beta-globin mRNA, a significant correlation between hybridization potential predicted by the probability profile and the degree of inhibition of in vitro translation suggests that the probability profile approach is valuable for the identification of effective antisense target sites. Coupling computational design with DNA-RNA array technique provides a rational, efficient framework for antisense oligonucleotide screening. This framework has the potential for high-throughput applications to functional genomics and drug target validation.

Anatomy of a preferred target site for the bacterial insertion sequence IS903

Like many transposons the bacterial insertion sequence IS903 was thought to insert randomly. However, using both genetic and statistical approaches, we have derived a target site for IS903 that is used 84% of the time. Computational and genetic analyses of multiple IS903 insertion sites predicted a preferred target consisting of a 21 bp palindromic pattern centered on the 9 bp target duplication generated during transposition. Here we show that targeting can be dissected into four components: the 5 bp flanking sequences, the most important sequences required for site-specific insertion; the 7 bp palindromic core within the target duplication; the dinucleotide pair at the transposon-target junction; and the local DNA context. Finally, using a substrate with multiple target sites we show that a target site is more likely found by a local bind-and-slide model and not by extended DNA tracking.

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.

Delayed expulsion of the nematode Trichinella spiralis in mice lacking the mucosal mast cell-specific granule chymase, mouse mast cell protease-1

Expulsion of gastrointestinal nematodes is associated with pronounced mucosal mast cell (MMC) hyperplasia, differentiation, and activation, accompanied by the systemic release of MMC granule chymases (chymotrypsin-like serine proteases). The beta-chymase mouse mast cell protease-1 (mMCP-1) is expressed predominantly by intraepithelial MMCs, and levels in the bloodstream and intestinal lumen are maximal at the time of worm expulsion in parasitized mice. To address the in vivo functions of MMC-specific beta-chymases, we have generated transgenic mice that lack the mMCP-1 gene. They were backcrossed onto a congenic BALB/c background to investigate the response to nematode infection. The deletion of the mMCP-1 gene is associated with significantly delayed expulsion of Trichinella spiralis and increased deposition of muscle larvae in BALB/c mice despite the presence of normal and sometimes increased numbers of MMCs. Neither worm fecundity nor worm burdens were altered in Nippostrongylus-infected mMCP-1(-/)- BALB/c mice. These data demonstrate, for the first time, that the ablation of an MMC-derived effector molecule compromises the expulsion process.

Immunopathology of intestinal helminth infection

The relationship between intestinal pathology and immune expulsion of gastrointestinal nematodes remains controversial. Parasite expulsion is associated with intestinal pathology in several model systems and both of these phenomena are T cell dependent. However, while immune expulsion of gastrointestinal helminth parasites is usually associated with Th2 responses, the effector mechanisms directly responsible for parasite loss have not been elucidated. In contrast, the intestinal pathology observed in many other disease models closely resembles that seen in helminth infections, but has been attributed to Th1 cytokines. We have used infection with the nematode Trichinella spiralis in mice defective for cytokines to demonstrate that although parasite expulsion is indeed IL-4 dependent, contrary to expectations, the enteropathy is also regulated by IL-4. Furthermore, abrogation of severe pathology in iNOS deficient and TNF receptor defective animals does not prevent parasite expulsion. TNF and iNOS are therefore involved in intestinal pathology in nematode infections, apparently under regulation by IL-4 and Th2 mediated responses. Therefore, it appears that the IL-4-dependent protective response against the parasite operates by a mechanism other than merely the gross degradation of the parasite's environment brought about by the immune enteropathy. However, it remains important to elucidate the protective mechanisms involved in parasite expulsion, which are still unclear.

Human-mouse genome comparisons to locate regulatory sites

Elucidating the human transcriptional regulatory network is a challenge of the post-genomic era. Technical progress so far is impressive, including detailed understanding of regulatory mechanisms for at least a few genes in multicellular organisms, rapid and precise localization of regulatory regions within extensive regions of DNA by means of cross-species comparison, and de novo determination of transcription-factor binding specificities from large-scale yeast expression data. Here we address two problems involved in extending these results to the human genome: first, it has been unclear how many model organism genomes will be needed to delineate most regulatory regions; and second, the discovery of transcription-factor binding sites (response elements) from expression data has not yet been generalized from single-celled organisms to multicellular organisms. We found that 98% (74/75) of experimentally defined sequence-specific binding sites of skeletal-muscle-specific transcription factors are confined to the 19% of human sequences that are most conserved in the orthologous rodent sequences. Also we found that in using this restriction, the binding specificities of all three major muscle-specific transcription factors (MYF, SRF and MEF2) can be computationally identified.

Database search based on Bayesian alignment

The size of protein sequence database is getting larger each day. One common challenge is to predict protein structures or functions of the sequences in databases. It is easy when a sequence shares direct similarity to a well-characterized protein. If there is no direct similarity, we have to rely on a third sequence or a model as intermediate to link two proteins together. We developed a new model based method, called Bayesian search, as a means to connect two distantly related proteins. We compared this Bayesian search model with pairwise and multiple sequence comparison methods on structural databases using structural similarity as the criteria for relationship. The results show that the Bayesian search can link more distantly related sequence pairs than other methods, collectively and consistently over large protein families. If each query made one error on average against SCOP database PDB40D-B, Bayesian search found 36.5% of related pairs, PSI-Blast found 32.6%, and Smith-Waterman method found 25%. Examples are presented to show that the alignments predicted by the Bayesian search agree well with structural alignments. Also false positives found by Bayesian search at low cutoff values are analyzed.

Nitric oxide mediates intestinal pathology but not immune expulsion during Trichinella spiralis infection in mice

The relationship between intestinal pathology and immune expulsion of gastrointestinal (GI) nematodes remains controversial. Although immune expulsion of GI helminth parasites is usually associated with Th2 responses, the effector mechanisms directly responsible for parasite loss have not been identified. We have previously shown that while the intestinal pathology accompanying the expulsion of the GI parasite Trichinella spiralis may be dependent on IL-4 and mediated by TNF, parasite loss is independent of TNF. In contrast, intestinal pathology in other disease models has been attributed to Th1 cytokines, although it closely resembles that seen in helminth infections. Whereas production of inducible NO synthase (iNOS) in the gut is important for both homeostasis of the epithelial layer and in protection against pathogenic microorganisms, overproduction of NO has been implicated in the pathogenesis of a number of inflammatory conditions. We therefore investigated the role of NO in T. spiralis infection using iNOS-deficient mice. iNOS-/- and iNOS-/+ mice were infected with T. spiralis, and parasite expulsion and intestinal pathology were followed. Parasite expulsion proceeded similarly in both groups of animals, but significant intestinal pathology was only observed in the heterozygous mice. Thus it appears that, although the protective effects of Th2 responses in GI helminth infection do not require NO, this mediator contributes substantially to the associated enteropathy. NO may therefore be an important mediator of enteropathy in both Th1- and Th2-inducing conditions.

Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis

We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification. In addition to the known cNMP-binding proteins (cNMP-dependent kinases, cNMP-gated channels, cAMP-guanine nucleotide exchange factors, and bacterial cAMP-dependent transcription factors), new functional groups of cNMP-binding proteins were identified, including putative ABC-transporter subunits, translocases, and esterases. Classification of the nucleotide cyclases revealed subtle differences in sequence conservation of the active site that distinguish the five classes of cyclases: the multicellular eukaryotic adenylyl cyclases, the eukaryotic receptor-type guanylyl cyclases, the eukaryotic soluble guanylyl cyclases, the unicellular eukaryotic and prokaryotic adenylyl cyclases, and the putative prokaryotic guanylyl cyclases. Phylogenetic distribution of the cNMP-binding proteins and cyclases was analyzed, with particular attention to the 22 complete archaeal and eubacterial genome sequences. Mycobacterium tuberculosis H37Rv and Synechocystis PCC6803 were each found to encode several more putative cNMP-binding proteins than other prokaryotes; many of these proteins are of unknown function. M. tuberculosis also encodes several more putative nucleotide cyclases than other prokaryotic species.

A bayesian statistical algorithm for RNA secondary structure prediction

A Bayesian approach for predicting RNA secondary structure that addresses the following three open issues is described: (1) the need for a representation of the full ensemble of probable structures; (2) the need to specify a fixed set of energy parameters; (3) the desire to make statistical inferences on all variables in the problem. It has recently been shown that Bayesian inference can be employed to relax or eliminate the need to specify the parameters of bioinformatics recursive algorithms and to give a statistical representation of the full ensemble of probable solutions with the incorporation of uncertainty in parameter values. In this paper, we make an initial exploration of these potential advantages of the Bayesian approach. We present a Bayesian algorithm that is based on stacking energy rules but relaxes the need to specify the parameters. The algorithm returns the exact posterior distribution of the number of destabilizing loops, stacking energy matrices, and secondary structures. The algorithm generates statistically representative structures from the full ensemble of probable secondary structures in exact proportion to the posterior probabilities. Once the forward recursions for the algorithm are completed, the backward recursive sampling executes in O(n) time, providing a very efficient approach for generating representative structures. We demonstrate the utility of the Bayesian approach with several tRNA sequences. The potential of the approach for predicting RNA secondary structures and presenting alternative structures is illustrated with applications to the Escherichia coli tRNA(Ala) sequence and the Xenopus laevis oocyte 5S rRNA sequence.

Differential mRNA display cloning and characterization of a Cryptosporidium parvum gene expressed during intracellular development

Differential mRNA display was used to detect differences in gene expression between mock-infected and Cryptosporidium parvum-infected human adenocarcinoma cells. A reproducible band present only in C. parvum-infected cells, ddHC-10 was isolated and cloned. Northern blot analysis was used to confirm the differential expression of the HC-10 mRNA. As differential mRNA display does not differentiate between parasite and host mRNAs, Southern blot analysis was used to demonstrate that ddHC-10 represented a C. parvum gene. Northern blot analysis demonstrated that HC-10 mRNA is expressed by sporozoites prior to invasion of host cells. Screening of a C. parvum genomic library identified 2 different genomic clones, HC-10-13C and HC-10-6C. The combined genomic sequence contained a predicted open reading frame of 2,952 base pairs (bp), coding for a protein of 984 amino acids with a predicted molecular weight of approximately 106 kDa. Reverse transcription polymerase chain reaction mapping of the HC-10 transcript demonstrated that the HC-10 gene lacks introns, and the approximately 4,789-bp mRNA contains relatively large 5' (approximately 1,390-bp) and 3' (approximately 440-bp) untranslated regions. The predicted polypeptide contained a high proportion of polar amino acids, with the most abundant amino acids being serine (10.5%), threonine (9.8%), and cysteine (7.6%). The C-terminal region of the predicted polypeptide is characterized by a threonine-rich region containing multiple repeats of the sequence TTTTRP. This repeat motif is similar to that found in the mucin-like genes of vertebrates and lower eukaryotes that have been shown to play important roles in cell-cell interactions in multicellular organisms and invasion of host cells by unicellular parasites.

Bayesian inference on biopolymer models

MOTIVATION

Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics.

RESULTS

The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described.

AVAILABILITY

Software and a set of transparencies for a tutorial describing these ideas are available at http://www.wadsworth.org/res&res/bioinfo/

Feline immunodeficiency virus (FIV)-associated lymphoma: a potential role for immune dysfunction in tumourigenesis

To determine the potential role of immune dysfunction in feline immunodeficiency virus (FIV)-associated lymphomagenesis, we present the results of immunological monitoring during the chronic phase of experimental FIV infection in two cats which subsequently developed lymphoma. In one cat, C1, cell-mediated immunity was depressed throughout the monitoring period but particularly from 125-200 weeks post-infection (pi), when this cat demonstrated profoundly impaired lymphocyte blastogenesis and markedly increased interleukin-1 (IL-1) production compared to age-matched, uninfected control cats. Lymphocyte function in the other cat, C2, was preserved to a greater degree. Alterations in the levels of immunoglobulin isotypes M, A and G in CD4+-, CD8+- and CD21+-lymphocyte sub-sets were demonstrated in both cats. Southern blot analysis revealed the presence of integrated FIV-provirus in tumour DNA from C2 but not C1 indicating a possible direct role for the virus in the former case only. In this study we have characterised, for the first time, the FIV-induced immune dysfunction in cats which developed lymphoma, demonstrating potential indirect mechanisms of tumourigenesis.

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.

IL-4-regulated enteropathy in an intestinal nematode infection

The relationship between intestinal pathology and immune expulsion of gastrointestinal nematodes remains controversial. Parasite expulsion is associated with intestinal pathology in several model systems and both of these phenomena are T cell dependent. Immune expulsion of gastrointestinal helminth parasites is usually associated with Th2 responses, but the effector mechanisms directly responsible for parasite loss have not been elucidated. In contrast, the intestinal pathology observed in many other disease models closely resembles that seen in helminth infections, but has been attributed to Th1 cytokines. We have used infection with the nematode Trichinella spiralis in mice defective for cytokines or their receptors to investigate cytokine regulation of both immunopathology and parasite rejection. Consistent with previous findings, we found that parasite expulsion is IL-4 dependent. Contrary to expectations, however, the enteropathy is not regulated by IFN-gamma but by IL-4. Moreover, abrogation of severe pathology in TNF receptor-defective animals does not prevent parasite expulsion. TNF is therefore involved in intestinal pathology in nematode infections, apparently under regulation by IL-4- and Th2-mediated responses. This work therefore not only reveals a novel interplay between IL-4 and TNF, but also that the IL-4-dependent protective response against the parasite operates by a mechanism other than merely the gross degradation of the parasite's environment brought about by the immune enteropathy.

Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase

The pyridoxal-P binding sites of the two isoforms of human glutamate decarboxylase (GAD65 and GAD67) were modeled by using PROBE (a recently developed algorithm for multiple sequence alignment and database searching) to align the primary sequence of GAD with pyridoxal-P binding proteins of known structure. GAD's cofactor binding site is particularly interesting because GAD activity in the brain is controlled in part by a regulated interconversion of the apo- and holoenzymes. PROBE identified six motifs shared by the two GADs and four proteins of known structure: bacterial ornithine decarboxylase, dialkylglycine decarboxylase, aspartate aminotransferase, and tyrosine phenol-lyase. Five of the motifs corresponded to the alpha/beta elements and loops that form most of the conserved fold of the pyridoxal-P binding cleft of the four enzymes of known structure; the sixth motif corresponded to a helical element of the small domain that closes when the substrate binds. Eight residues that interact with pyridoxal-P and a ninth residue that lies at the interface of the large and small domains were also identified. Eleven additional conserved residues were identified and their functions were evaluated by examining the proteins of known structure. The key residues that interact directly with pyridoxal-P were identical in ornithine decarboxylase and the two GADs, thus allowing us to make a specific structural prediction of the cofactor binding site of GAD. The strong conservation of the cofactor binding site in GAD indicates that the highly regulated transition between apo- and holoGAD is accomplished by modifications in this basic fold rather than through a novel folding pattern.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Decreased mitogen responsiveness and elevated tumor necrosis factor production in cats shortly after feline immunodeficiency virus infection

We present the results of an investigation into the effects of feline immunodeficiency virus (FIV) infection on the response to mitogens and cytokine production in the first month of infection. We were able to demonstrate a depression of response of peripheral blood mononuclear cells to the mitogens concanavalin A, phytohaemagglutinin and pokeweed mitogen, with the response to pokeweed mitogen being most severely affected. The response of the cells of the spleen were affected by 10 days post infection and these could not be augmented by the addition of exogenous interleukin-2 (IL-2). The response of mesenteric lymph node cells was not affected until 20 days post infection and this could be partially restored by the addition of exogenous IL-2. IL-2 production was unaffected in peripheral blood mononuclear cells, slightly depressed in mesenteric lymph node cells and slightly elevated in spleen cells. Tumor necrosis factor levels were significantly elevated with respect to controls within 10 days of infection. These studies suggest that there are a number of changes in the immune response of FIV infected cats early in infection and this may determine the subsequent outcome of the infection.

Clinical and pathological findings in feline immunodeficiency virus experimental infection

A study is described of the clinical and pathological findings in 20 specific pathogen free cats infected when 1 year old with feline immunodeficiency virus and monitored over 12 months. Cats were divided into two groups (A and B). The clinical and clinicopathological features were studied in Group A. In Group B, at 1, 2, 4, 9 and 12 months post infection two cats were necropsied. Clinically all cats developed generalised lymphadenopathy, six cats were neutropenic and five cats lymphopenic. Three cats became febrile with conjunctivitis and anterior uveitis and one of these cats ultimately developed jaundice. Postmortem examinations confirmed a generalised lymphadenopathy involving peripheral and visceral lymph nodes with concurrent stimulation of splenic white matter and mucosal lymphoid tissue of the digestive tract and conjunctiva. Within the lymph nodes there was a reactive follicular hyperplasia accompanied by a paracortical hyperplasia with an increased paracortical vascularity. Unusual features were the presence of lymphoid follicles in the bone marrow, thymus and parathyroid tissue. In addition, aggregates of lymphoid cells were found within salivary glands, kidneys, sclera and choroid of the eye. One cat developed a lymphosarcoma affecting the liver and kidneys at 36 weeks post infection. The cat with jaundice had a cholangitis with marked biliary epithelial hyperplasia.

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.

Estimating serum polychlorinated biphenyl levels in highly exposed workers: an empirical model

A regression model estimating high-homolog polychlorinated biphenyl (PCB) serum concentration on the basis of job exposure categorizations was developed. The model assumes first-order kinetics with a half-life determined empirically and uses variables that incorporate both intensity and duration of exposure over a 30-yr period. In order to compare the efficiency of these regression-based exposure estimates relative to often-used epidemiological parameters, models with dichotomized, ordinal, and continuous exposure surrogates were also investigated. Among the alternative exposure categorizations the most straightforward measure, ever versus never direct, was a particularly poor predictor of serum PCB level (r2 = .01). Nearly all of the candidate exposure measures we tried predicted serum levels poorly. The best of these after the fact was with total months employed in direct-exposure jobs (r2 = .43). None of the logical deductive models approached the predictability of the empirical model developed here (r2 = .69).

Modelling length bias in a longitudinally-linked record system of HIV cases

We compare numbers of hospital admissions for intravenous drug using (IVDU) HIV patients and other HIV patients in acute-care facilities in New York State. Data consist of routinely collected hospital-discharge reports from New York's Statewide Planning and Research Cooperative System, linked into longitudinal case histories. Because recognition of an IVDU depends on an opioid diagnosis on any record in the case history, the observed distribution of the number of admissions per case for recognized IVDU's is biased towards greater numbers of admissions. We develop and apply a model to overcome this biasing. Our findings reveal that the mean numbers of admissions for the two groups differ significantly, but less so than without recognition of the length biasing.

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

A statistical analysis of ion pairs in protein crystal structures shows that their abundance with respect to uncharged controls is accurately predicted by a Boltzmann-like function of electrostatic potential. It appears that the mechanisms of protein folding and/or evolution combine to produce a "thermal" distribution of local nonbonded interactions, as has been suggested by statistical-mechanical theories. Using this relationship, we develop a maximum likelihood methodology for estimation of apparent energetic parameters from the data base of known structures, and we derive electrostatic potential functions that lead to optimal agreement of observed and predicted ion-pair frequencies. These are similar to potentials of mean force derived from electrostatic theory, but departure from Coulombic behavior is less than has been suggested.

Immunogenetic correlates of susceptibility to infection with Heligmosomoides polygyrus in outbred mice

Outbred MF1 mice were characterized with respect to their susceptibility to infection with Heligmosomoides polygyrus (Nematoda) on the basis of faecal egg counts after 8 weeks of repeated infection (50 larvae/week). Selective breeding for resistance and susceptibility was carried out over 3 generations. The H-2 type of a sample of the mice was determined, and antigen recognition assessed on the basis of Western blots against adult and larval H. polygyrus homogenate. The selective breeding programme yielded very strong evidence for the heritability of susceptibility to infection. The results were consistent with a model of single gene control with resistance dominant over susceptibility. The presence of the H-2k haplotype was significantly associated with susceptibility, as was the recognition of a 17 kDa antigen in blots against both larval and adult worm homogenate. The proportion of mice phenotypically susceptible to infection, the proportion bearing the H-2k haplotype, and the proportion recognizing the 17 kDa antigen, were all approximately 0.25.

Identification of the most significant amphipathic helix with application to HIV and MHV envelope proteins

Amphipathic helices, which play important roles in protein structure, occur in a wide variety of lengths. Yet existing methods employ fixed window lengths. We present a hierarchical procedure that identifies the Q most significant amphipathic helices regardless of length. Since the observed hydrophobicities are not normally distributed, test statistics usually employed for least-squares regression are inappropriate for assessing statistical significance of amphipathic helices. We show that an adjusted F statistic provides a good test. An application to the envelope protein of HIV finds an unexpected long amphipathic helix in gp41.