RosettaSurf—A surface-centric computational design approach

Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted with geometric (shape) and chemical (electrostatics) features of the underlying protein structure. Protein surfaces are dependent on their chemical composition and, ultimately determine protein function, acting as the interface that engages in interactions with other molecules. In the past, such representations were utilized to compare protein structures on global and local scales and have shed light on functional properties of proteins. Here we describe RosettaSurf, a surface-centric computational design protocol, that focuses on the molecular surface shape and electrostatic properties as means for protein engineering, offering a unique approach for the design of proteins and their functions. The RosettaSurf protocol combines the explicit optimization of molecular surface features with a global scoring function during the sequence design process, diverging from the typical design approaches that rely solely on an energy scoring function. With this computational approach, we attempt to address a fundamental problem in protein design related to the design of functional sites in proteins, even when structurally similar templates are absent in the characterized structural repertoire. Surface-centric design exploits the premise that molecular surfaces are, to a certain extent, independent of the underlying sequence and backbone configuration, meaning that different sequences in different proteins may present similar surfaces. We benchmarked RosettaSurf on various sequence recovery datasets and showcased its design capabilities by generating epitope mimics that were biochemically validated. Overall, our results indicate that the explicit optimization of surface features may lead to new routes for the design of functional proteins.

Finely orchestrated protein-protein interactions are at the heart of virtually all fundamental cellular processes. Altering these processes or encoding new functions in proteins has been a long-standing goal in computational protein design. Protein design methods commonly rely on scoring functions that seek to identify amino acid sequences that optimize structural configurations of atoms while minimizing a variety of physics-based and statistical terms. The objectives of the large majority of computational design protocols have been focused on obtaining a predefined structural conformation. However, routinely introducing a functional aspect on designer proteins has been more challenging. Our results suggest that the molecular surface features can be a useful optimization parameter to guide the design process towards functional surfaces that mimic known protein binding sites and interact with their intended targets. Specifically, we demonstrate that our design method can optimize experimental libraries through computational screening, creating a basis for highly specific protein binders, as well as design a potent immunogen that engages with site-specific antibodies. The ability to create proteins with novel functions will be transformative for biomedical applications, providing many opportunities for the design of novel immunogens, protein components for synthetic biology, and other protein-based biotechnologies.

Stationary time-vertex signal processing

This paper considers regression tasks involving high-dimensional multivariate processes whose structure is dependent on some known graph topology. We put forth a new definition of time-vertex wide-sense stationarity, or joint stationarity for short, that goes beyond product graphs. Joint stationarity helps by reducing the estimation variance and recovery complexity. In particular, for any jointly stationary process (a) one reliably learns the covariance structure from as little as a single realization of the process and (b) solves MMSE recovery problems, such as interpolation and denoising, in computational time nearly linear on the number of edges and timesteps. Experiments with three datasets suggest that joint stationarity can yield accuracy improvements in the recovery of high-dimensional processes evolving over a graph, even when the latter is only approximately known, or the process is not strictly stationary.

Flavored e-cigarette use: Characterizing youth, young adult, and adult users

The purpose of this study is to investigate how the use of flavored e-cigarettes varies between youth (12-17 years old), young adults (18-29 years old), and older adults (30 + years old). Cross-sectional surveys of school-going youth (n = 3907) and young adult college students (n = 5482) in Texas, and young adults and older adults (n = 6051) nationwide were administered in 2014-2015. Proportions and 95% confidence intervals were used to describe the percentage of e-cigarette use at initiation and in the past 30 days that was flavored, among current e-cigarette users. Chi-square tests were applied to examine differences by combustible tobacco product use and demographic factors. Most e-cigarette users said their first and "usual" e-cigarettes were flavored. At initiation, the majority of Texas school-going youth (98%), Texas young adult college students (95%), and young adults (71.2%) nationwide said their first e-cigarettes were flavored to taste like something other than tobacco, compared to 44.1% of older adults nationwide. Fruit and candy flavors predominated for all groups; and, for youth, flavors were an especially salient reason to use e-cigarettes. Among adults, the use of tobacco flavor at initiation was common among dual users (e-cigarettes + combustible tobacco), while other flavors were more common among former cigarette smokers (P = 0.03). Restricting the range of e-cigarette flavors (e.g., eliminating sweet flavors, like fruit and candy) may benefit youth and young adult prevention efforts. However, it is unclear what impact this change would have on adult smoking cessation.

Identifying the immunomodulatory components of helminths

Immunomodulatory components of helminths offer great promise as an entirely new class of biologics for the treatment of inflammatory diseases. Here, we discuss the emerging themes in helminth-driven immunomodulation in the context of therapeutic drug discovery. We broadly define the approaches that are currently applied by researchers to identify these helminth molecules, highlighting key areas of potential exploitation that have been mostly neglected thus far, notably small molecules. Finally, we propose that the investigation of immunomodulatory compounds will enable the translation of current and future research efforts into potential treatments for autoimmune and allergic diseases, while at the same time yielding new insights into the molecular interface of host-parasite biology.

A multivalent chimeric vaccine composed of Schistosoma mansoni SmTSP-2 and Sm29 was able to induce protection against infection in mice

Schistosoma mansoni is a blood fluke parasite responsible for schistosomiasis. The best long-term strategy to control schistosomiasis is through immunization combined with drug treatment. In this study, we cloned, expressed and purified SmTSP-2 fused to the N- and C-terminal halves of Sm29 and tested these chimeras as vaccine candidates using an adjuvant approved to be used in humans. The results demonstrated that vaccination with SmTSP-2 fused to N- or C-terminus of Sm29-induced reduction in worm burden and liver pathology when compared to control animals. Additionally, we detected high levels of mouse-specific IgG, IgG1 and IgG2a against both chimeras and significant amounts of IFN-γ and TNF-α and no IL-4. Finally, studies with sera from patients resistant to infection and living in schistosomiasis endemic areas revealed high levels of specific IgG to both chimeras when compared to healthy individuals. In conclusion, SmTSP-2/Sm29 chimeras tested here induced partial protection against infection and might be a potential vaccine candidate.

The immunology of human hookworm infections

Hookworms are one of the most prevalent parasites of humans in developing countries, but we know relatively little about the immune response generated to hookworm infection. This can be attributed to a lack of permissive animal models and a relatively small research community compared with those of the more high-profile parasitic diseases. However, recently, research has emerged on the development of vaccines to control hookworm infection and the use of hookworm to treat autoimmune and allergic disorders, contributing to a greater understanding of the strategies used by hookworms to modulate the host's immune response. A substantial body of research on the immunobiology of hookworms originates from Australia, so this review will summarize the current status of the field with a particular emphasis on research carried out 'down under'.

A portrait of the "SCP/TAPS" proteins of eukaryotes--developing a framework for fundamental research and biotechnological outcomes

A wide range of proteins belonging to the SCP/TAPS "family" has been described for various eukaryotic organisms, including plants and animals (vertebrates and invertebrates, such as helminths). Although SCP/TAPS proteins have been proposed to play key roles in a number of fundamental biological processes, such as host-pathogen interactions and defence mechanisms, there is a paucity of information on their genetic relationships, structures and functions, and there is no standardised nomenclature for these proteins. A detailed analysis of the relationships of members of the SCP/TAPS family of proteins, based on key protein signatures, could provide a foundation for investigating these areas. In this article, we review the current state of knowledge of key SCP/TAPS proteins of eukaryotes, with an emphasis on those from parasitic helminths, and undertake a comprehensive, systematic phylogenetic analysis of currently available full-length protein sequence data (considering characteristic protein signatures or motifs) to infer relationships and provide a framework (based on statistical support) for the naming of these proteins. This framework is intended to guide genomic and molecular biological explorations of key SCP/TAPS molecules associated with infectious diseases of plants and animals. In particular, fundamental investigations of these molecules in parasites and the integration of structural and functional data could lead to new and innovative approaches for the control of parasitic diseases, with important biotechnological outcomes.

Exploring transcriptional conservation between Ancylostoma caninum and Haemonchus contortus by oligonucleotide microarray and bioinformatic analyses

In this study, we identified, using an established oligonucleotide microarray platform for the parasitic nematode Haemonchus contortus, transcripts that are 'conserved' between serum-activated and non-activated L3s of Ancylostoma caninum (aL3 and L3, respectively) and H. contortus by cross-species hybridization (CSH) at high stringency and conducted extensive bioinformatic analyses of the cross-hybridizing expressed sequence tags (ESTs). The microarray analysis revealed significant differential hybridization between aL3 and L3 for 32 molecules from A. caninum, of which 29 were shown to have homologues/orthologues in the free-living nematode Caenorhabditis elegans and/or A. caninum and the other three molecules had no homologues in current gene databases. 'Non-wildtype' RNAi phenotypes were recorded for 13 of the C. elegans homologues. A subset of 16 C. elegans homologues/orthologues (i.e. genes abce-1, act-2, C08H9.2, C55F2.1, calu-1, col-181, cpr-6, elo-2, asp-1, K07E3.4, rpn-2, sel-9, T28C12.4, hsb-1, Y57G11C.15 and ZK593.1) were predicted to interact genetically with a total of 156 (range 1-88) other genes. Gene ontology (GO) analysis of the interacting genes revealed that the most common subcategories were signal transduction (7%), intracellular protein transport and glycolysis (6.2%) within 'biological process'; nuclear (25.7%) and intracellular (19.8%) within 'cellular component'; and ATP-binding (14.4%) and protein-binding (8.4%) within 'molecular function'. The potential roles of key molecules in the two blood-feeding parasitic nematodes are discussed in relation to the known roles of their homologues/orthologues in C. elegans. The CSH approach used may provide a tool for the screening of genes conserved across a range of different taxa of parasites for which DNA microarray platforms are not available.

Molecular and phylogenetic characterization of cytochromes c from Haemonchus contortus and Trichostrongylus vitrinus (Nematoda: Trichostrongylida)

Although cytochrome c genes (cyt c) and proteins (CYT C) have been relatively well studied in mammals, very little is known about them in parasitic helminths. In the present study, we investigated this group of molecules in Haemonchus contortus (barber's pole worm) and Trichostrongylus vitrinus (black scour worm), two parasitic nematodes of small ruminants. The cyt c gene (512 bp) of H. contortus had one intron and encoded a transcript of 345 nucleotides, whilst that of T. vitrinus (792 bp) had two introns and encoded a transcript of 360 nucleotides. The transcription of cyt c in T. vitrinus was substantially greater in adult males compared with females, although no such gender-enrichment was evident in adults of H. contortus. These findings were supported at the protein level by immunoblot analyses. The inferred proteins (designated Hc-CYT C and Tv-CYT C, respectively) shared nucleotide and amino acid identities of 78% and 85%, respectively. The alignment of these and other CYT C sequences from nematodes, flatworms, insects and mammals identified conserved motifs associated with CYT C oxidase- and reductase- as well as haem-binding. One residue (histidine-26) was conserved for mammals, whereas this residue was absent from all nematodes; the functional significance of this difference is not yet known. Both phylogenetic analysis and protein modelling revealed that CYT C proteins of nematodes are structurally distinct from those of mammals and other organisms, suggesting their potential as targets for parasite intervention.

Vaccines against blood-feeding nematodes of humans and livestock

This paper summarises the progress towards vaccine development against the major blood-feeding nematodes of man and livestock, the hookworms and Haemonchus contortus, respectively. The impact of the diseases and the drivers for vaccine development are summarized as well as the anticipated impact of the host immune response on vaccine design. The performance requirements are discussed and progress towards these objectives using defined larval and adult antigens, many of these being shared between species. Specific examples include the Ancylostoma secreted proteins and homologues in Haemonchus as well as proteases used for digestion of the blood meal. This discussion shows that many of the major vaccine candidates are shared between these blood-feeding species, not only those from the blood-feeding stages but also those expressed by infective L3s in the early stages of infection. Challenges for the future include: exploiting the expanding genome information for antigen discovery, use of different recombinant protein expression systems, formulation with new adjuvants, and novel methods of field testing vaccine efficacy.

Saposin-like proteins from the intestine of the blood-feeding hookworm, Ancylostoma caninum

Hookworms feed on blood, utilizing haemoglobin for nutrition, growth and reproduction. The haemoglobin digestion cascade has been partially elucidated, but the process immediately preceding this event, haemolysis, has received considerably less attention. We have cloned and expressed Ancylostoma caninum mRNAs encoding 2 proteins belonging to the saposin-like protein (SAPLIP) family, termed Ac-slp-1 and Ac-slp-2. The open reading frames of SLP-1 and SLP-2 were used to identify expressed sequence tags encoding SAPLIPs from the 4 major clades of animal parasitic nematodes. Both Ac-slp-1 and slp-2 mRNAs were shown to be expressed in all life stages assessed, with slp-1 predominantly being expressed in third-stage larvae (L3) before and after activation with dog serum. Recombinant SLP-1 and SLP-2 were expressed in insect cells and used to raise specific antisera in mice. These antisera were used as probes in fluorescence microscopy to localize the anatomic expression sites of both proteins to small, punctate organelles or vesicles within the intestinal cells of adult worms; weak staining was detected on the microvillar brush border of the intestine. Using transmission electron microscopy, both proteins were localized to similar vesicles in the intestinal cells of the L3. Recombinant proteins contained C-terminal purification tags that potentially precluded dimerization and possibly interfered with the subsequent detection of haemolytic activity. Their expression in the gut of the L3 and adult stages suggests a role for these hookworm SAPLIPs in the lysis of host cells during tissue migration and/or feeding.

A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy

The gastrointestinal tracts of multi-cellular blood-feeding parasites are targets for vaccines and drugs. Recently, recombinant vaccines that interrupt the digestion of blood in the hookworm gut have shown efficacy, so we explored the intestinal transcriptomes of the human and canine hookworms, Necator americanus and Ancylostoma caninum, respectively. We used Laser Microdissection Microscopy to dissect gut tissue from the parasites, extracted the RNA and generated cDNA libraries. A total of 480 expressed sequence tags were sequenced from each library and assembled into contigs, accounting for 268 N. americanus genes and 276 A. caninum genes. Only 17% of N. americanus and 36% of A. caninum contigs were assigned Gene Ontology classifications. Twenty-six (9.8%) N. americanus and 18 (6.5%) A. caninum contigs did not have homologues in any databases including dbEST-of these novel clones, seven N. americanus and three A. caninum contigs had Open Reading Frames with predicted secretory signal peptides. The most abundant transcripts corresponded to mRNAs encoding cholesterol-and fatty acid-binding proteins, C-type lectins, Activation-Associated Secretory Proteins, and proteases of different mechanistic classes, particularly astacin-like metallopeptidases. Expressed sequence tags corresponding to known and potential recombinant vaccines were identified and these included homologues of proteases, anti-clotting factors, defensins and integral membrane proteins involved in cell adhesion.

Transcriptome profiling of lung schistosomula,in vitro cultured schistosomula and adult Schistosoma japonicum

The schistosomulum is the main target of vaccine-induced protective immunity; however, most studies have utilized schistosomula produced by mechanical transformation of infective larvae followed by in vitro culture rather than larvae isolated directly from the lungs of infected mammals. Using transmission electron microscopy, we demonstrated that there was little difference in the ultrastructure of Schistosoma japonicum schistosomula obtained by the two methods. However, significant differences in gene expression profiles were apparent when we used an oligonucleotide microarray to compare the gene expression profiles of schistosomula obtained in vivo from lung tissue with those maintained in vitro, and with adult worms of S. japonicum. It is likely that host environmental factors, which cannot be reliably reproduced in vitro, do influence the growth, development and overall biology of schistosomes. Thus caution is urged when using in vitro-cultured schistosomes and mechanically transformed/cultured schistosomula in molecular, biochemical and immunological studies.

Minors' tobacco possession law violations and intentions to smoke: implications for tobacco control

OBJECTIVES

To test: (1) whether citation under the Minors in Possession (MIP) law, vicarious citation (knowing someone who was cited), and threat of driving licence suspension are associated with decreased intentions to smoke next year; and (2) whether the policy is differentially enforced.

SUBJECTS

28,249 white, Hispanic, and African American students in grades 6-12 (11-18 years old) participated in the study.

METHOD

The 86 item anonymous Texas Youth Tobacco Survey was completed by students attending 37 schools in 14 east and central Texas communities.

RESULTS

Hierarchical linear modelling showed that MIP citation was unrelated to the future smoking intentions of most youth. However, there was a negative association between citation and smoking intentions for ever daily smoking youth at four schools. Threat of licence suspension was associated with a lower likelihood of future smoking intentions among ever daily smoking youth and vicarious citation did not deter youth from future smoking. African American and Hispanic youth had a higher probability of being cited than their peers.

CONCLUSIONS

Threat of driving licence suspension has the intended effect upon youth who are/were committed smokers and MIP citation has the intended effect upon committed smokers at only four schools. However, differential enforcement of the law based on ethnicity may be occurring. Before drawing firm conclusions, current findings must be replicated with longitudinal data to determine the consequences of citation on subsequent tobacco use.

Hookworm cathepsin D aspartic proteases: contributing roles in the host-specific degradation of serum proteins and skin macromolecules

Cathepsin D aspartic proteases of hookworms were recently implicated in the host-specific digestion of haemoglobin by adult parasites. Ac-APR-1 from the dog hookworm, Ancylostoma caninum and Na-APR-1 from the human hookworm, Necator americanus, were shown to be expressed in the infective larval stage (L3) as well as adult worms. We now show that both proteases degraded skin macromolecules and serum proteins, some of which were cleaved more readily from permissive definitive hosts as opposed to non-permissive hosts. Na-APR-1 degraded human collagens more efficiently than did Ac-APR-1, and Ac-APR-1 degraded canine serum albumin more efficiently than did Na-APR-1. On the other hand, both enzymes degraded human serum proteins (albumin and fibrinogen) with approximately equal efficiency under the conditions of our assays in vitro. Molecular models of these 2 orthologous, aspartic proteases showed that, despite having active site clefts with identical primary sequences, residues in the S3 pocket adopted different conformations, likely accounting for different substrate preferences reported previously. Antisera raised to both proteases partially inhibited (16-26%) migration of hookworm L3 through hamster skin in vitro, further implying a connective tissue invasive role for these enzymes in addition to digestion of serum and erythrocyte proteins for nutrition.

Hemoglobin-degrading, aspartic proteases of blood-feeding parasites: substrate specificity revealed by homology models

Blood-feeding parasites, including schistosomes, hookworms, and malaria parasites, employ aspartic proteases to make initial or early cleavages in ingested host hemoglobin. To better understand the substrate affinity of these aspartic proteases, sequences were aligned with and/or three-dimensional, molecular models were constructed of the cathepsin D-like aspartic proteases of schistosomes and hookworms and of plasmepsins of Plasmodium falciparum and Plasmodium vivax, using the structure of human cathepsin D bound to the inhibitor pepstatin as the template. The catalytic subsites S5 through S4' were determined for the modeled parasite proteases. Subsequently, the crystal structure of mouse renin complexed with the nonapeptidyl inhibitor t-butyl-CO-His-Pro-Phe-His-Leu [CHOHCH(2)]Leu-Tyr-Tyr-Ser- NH(2) (CH-66) was used to build homology models of the hemoglobin-degrading peptidases docked with a series of octapeptide substrates. The modeled octapeptides included representative sites in hemoglobin known to be cleaved by both Schistosoma japonicum cathepsin D and human cathepsin D, as well as sites cleaved by one but not the other of these enzymes. The peptidase-octapeptide substrate models revealed that differences in cleavage sites were generally attributable to the influence of a single amino acid change among the P5 to P4' residues that would either enhance or diminish the enzymatic affinity. The difference in cleavage sites appeared to be more profound than might be expected from sequence differences in the enzymes and hemoglobins. The findings support the notion that selective inhibitors of the hemoglobin-degrading peptidases of blood-feeding parasites at large could be developed as novel anti-parasitic agents.

Immune responses in hookworm infections

Hookworms infect perhaps one-fifth of the entire human population, yet little is known about their interaction with our immune system. The two major species are Necator americanus, which is adapted to tropical conditions, and Ancylostoma duodenale, which predominates in more temperate zones. While having many common features, they also differ in several key aspects of their biology. Host immune responses are triggered by larval invasion of the skin, larval migration through the circulation and lungs, and worm establishment in the intestine, where adult worms feed on blood and mucosa while injecting various molecules that facilitate feeding and modulate host protective responses. Despite repeated exposure, protective immunity does not seem to develop in humans, so that infections occur in all age groups (depending on exposure patterns) and tend to be prolonged. Responses to both larval and adult worms have a characteristic T-helper type 2 profile, with activated mast cells in the gut mucosa, elevated levels of circulating immunoglobulin E, and eosinophilia in the peripheral blood and local tissues, features also characteristic of type I hypersensitivity reactions. The longevity of adult hookworms is determined probably more by parasite genetics than by host immunity. However, many of the proteins released by the parasites seem to have immunomodulatory activity, presumably for self-protection. Advances in molecular biotechnology enable the identification and characterization of increasing numbers of these parasite molecules and should enhance our detailed understanding of the protective and pathogenetic mechanisms in hookworm infections.

Receptor for Fc on the surfaces of schistosomes

Schistosoma mansoni masks its surface with adsorbed host proteins including erythrocyte antigens, immunoglobulins, major histocompatibility complex class I, and beta(2)-microglobulin (beta(2)m), presumably as a means of avoiding host immune responses. How this is accomplished has not been explained. To identify surface receptors for host proteins, we biotinylated the tegument of live S. mansoni adults and mechanically transformed schistosomula and then removed the parasite surface with detergent. Incubation of biotinylated schistosome surface extracts with human immunoglobulin G (IgG) Fc-Sepharose resulted in purification of a 97-kDa protein that was subsequently identified as paramyosin (Pmy), using antiserum specific for recombinant Pmy. Fc also bound recombinant S. mansoni Pmy and native S. japonicum Pmy. Antiserum to Pmy decreased the binding of Pmy to Fc-Sepharose, and no proteins bound after removal of Pmy from extracts. Fluoresceinated human Fc bound to the surface, vestigial penetration glands, and nascent oral cavity of mechanically transformed schistosomula, and rabbit anti-Pmy Fab fragments ablated the binding of Fc to the schistosome surface. Pmy coprecipitated with host IgG from parasite surface extracts, indicating that complexes formed on the parasite surface as well as in vitro. Binding of Pmy to Fc was not inhibited by soluble protein A, suggesting that Pmy does not bind to the region between the CH2 and CH3 domains used by many other Fc-binding proteins. beta(2)m did not bind to the schistosome Fc receptor (Pmy), a finding that contradicts reports from earlier workers but did bind to a heteromultimer of labeled schistosomula surface proteins. This is the first report of the molecular identity of a schistosome Fc receptor; moreover it demonstrates an additional aspect of the unusual and multifunctional properties of Pmy from schistosomes and other parasitic flatworms.

A cDNA encoding Tc-MUC-5, a mucin from Toxocara canis larvae identified by expression screening

Toxocara canis is an ascarid nematode parasite of canids. Larvae infect a wide range of accidental hosts including humans, in whom they are the aetiologic agent of visceral and ocular Larva migrans. The labile surface coat of T. canis larvae consists of a family of mucin glycoproteins termed TES-120, for which the cDNAs have recently been cloned. In this paper, we describe the identification of a novel cDNA (Tc-muc-5) encoding an apomucin by expression screening of a cDNA library with antiserum raised to T. canis excretory/secretory products, and compare the predicted Tc-MUC-5 protein with those of other T. canis mucins (Tc-MUC-1-Tc-MUC-4) that include the TES-120 surface coat glycoproteins. Tc-MUC-5 has both a larger open reading frame and a more divergent sequence than the other T. canis mucins. It contains a putative signal peptide followed by two six-cysteine (SXC) domains, an extended threonine-rich central mucin core domain and two C-terminal SXC domains. Amino acid composition analysis of secreted TES-120 glycoproteins revealed a distinct lack of lysine residues; while this finding is in agreement with the primary sequences of Tc-MUC-1-Tc-MUC-4, Tc-MUC-5 is conspicuous by its relative abundance of lysines (6.7%), suggesting that this protein is not part of the TES-120 family of surface coat proteins.

Parental alcoholism and co-occurring antisocial behavior: prospective relationships to externalizing behavior problems in their young sons

The hypothesis that parental alcoholism and co-occurring antisocial behavior would be indirectly linked to child externalizing behavior problems through child lack of control, current levels of parent depression, family conflict, and parent-child conflict was tested using manifest variable regression analysis. Participants were a community sample of 125 families with an alcoholic father and 83 ecologically matched but nonsubstance abusing families involved in the first 2 waves of an ongoing longitudinal study (with 3 years between each wave). All families had a biological son who was 3-5 years old at study onset. Results revealed that child lack of control mediated the relation between paternal alcoholism and the son's subsequent externalizing behavior problems. Family conflict was a significant mediator of maternal and paternal lifetime antisocial behavior effects and father-son conflict mediated paternal lifetime antisocial behavior effects. Study implications are discussed within the context of parental socialization of antisocial behavior.

Schistosoma japonicum cathepsin D aspartic protease cleaves human IgG and other serum components

Recombinant cathepsin D aspartic protease of Schistosoma japonicum cleaved human IgG in vitro in a time and dose-dependent manner. Optimal cleavage was seen at pH 3.6-4.5; modest cleavage remained at pH 5.0, and no cleavage was detected above pH 5.0. Amino terminal sequencing of the major cleavage fragments of human IgG identified a Fab fragment from the VH1 domain, and 2 cleavage sites in the CH2 domain below the hinge region. The P1 and P1' residues at the 2 CH2 cleavage sites were Phe254-Leu255 and Leu325-Thr326, indicating a preference by the schistosome protease for bulky hydrophobic residues flanking the scissile bond. No cleavage of the immunoglobulin light chain was detected. In addition, the recombinant schistosome protease indiscriminately degraded the human serum proteins complement C3 and serum albumin into numerous small fragments. These results demonstrate specific cleavage of human IgG by the recombinant schistosome aspartic protease, and highlight the broad range digestive specificity of the enzyme which may play a role in the degradation of host serum proteins ingested as part of the schistosome bloodmeal.

Gulliver, a long terminal repeat retrotransposon from the genome of the oriental blood fluke Schistosoma japonicum

We characterized the consensus sequence and structure of a long terminal repeat (LTR) retrotransposon from the genome of the human blood fluke, Schistosoma japonicum, and have named this element, Gulliver. The full length, consensus Gulliver LTR retrotransposon was 4788 bp, and it was flanked at its 5'- and 3'-ends by LTRs of 259 bp. Each LTR included RNA polymerase II promoter sequences, a CAAT signal and a TATA box. Gulliver exhibited features characteristic of a functional LTR retrotransposon including two read through (termination) ORFs encoding retroviral gag and pol proteins of 312 and 1071 amino acid residues, respectively. The gag ORF encoded motifs conserved in nucleic acid binding proteins, while the pol ORF encoded conserved domains of aspartic protease, reverse transcriptase (RT), RNaseH and integrase, in that order, a pol pattern conserved in the gypsy lineage of LTR retrotransposons. Whereas the sequence and structure of Gulliver was similar to that of gypsy, phylogenetic analysis revealed that Gulliver did not group particularly closely with the gypsy family. Rather, its closest relatives were a LTR retrotransposon from Caenorhabditis elegans, mag from Bombyx mori and, to a lesser extent, easel from the salmon Oncorhynchus keta. Dot blot hybridizations indicated that Gulliver was present at between 100 and several thousand copies in the S. japonicum genome, and Southern hybridization analysis suggested its probable presence in the genome of Schistosoma mansoni. Transcripts encoding the RT domain of Gulliver were detected by RT-PCR in larval and adult stages of S. japonicum, indicating that (at least) the RT domain of Gulliver is transcribed. This is the first report of the sequence and structure of an LTR retrotransposon from any schistosome or indeed from any species belonging to the phylum Platyhelminthes.

A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs

Infective larvae of the parasitic nematode Toxocara canis secrete a family of mucin-like glycoproteins, which are implicated in parasite immune evasion. Analysis of T. canis expressed sequence tags identified a family of four mRNAs encoding distinct apomucins (Tc-muc-1-4), one of which had been previously identified in the TES-120 family of glycoproteins secreted by this parasite. The protein products of all four cDNAs contain signal peptides, a repetitive serine/threonine-rich tract, and varying numbers of 36-amino acid six-cysteine (SXC) domains. SXC domains are found in many nematode proteins and show similarity to cnidarian (sea anemone) toxins. Antibodies to the SXC domains of Tc-MUC-1 and Tc-MUC-3 recognize differently migrating members of TES-120. TES-120 proteins separated by chromatographic methods showed distinct amino acid composition, mass, and sequence information by both Edman degradation and matrix-assisted laser desorption ionization/time of flight mass spectrometry on peptide fragments. Tc-MUC-1, -2, and -3 were shown to be secreted mucins with real masses of 39.7, 47.8, and 45.0 kDa in contrast to their predicted peptide masses of 15.7, 16.2, and 26.0 kDa, respectively. The presence of SXC domains in all mucin products supports the suggestion that the SXC motif is required for mucin assembly or export. Homology modeling indicates that the six-cysteine domains of the T. canis mucins adopt a similar fold to the sea anemone potassium channel-blocking toxin BgK, forming three disulfide bonds within each subunit.

Purification of a diagnostic, secreted cysteine protease-like protein from the hookworm Ancylostoma caninum

The enteric infection of humans with the canine hookworm Ancylostoma caninum varies in its clinical presentation, ranging from asymptomatic to eosinophilic gastroenteritis requiring surgical intervention. Infections are not patent, but can be diagnosed immunologically by detecting antibodies to an immunodominant secreted hookworm protein termed Ac68. To characterise Ac68, we purified the native protein from A. caninum excretory/secretory products using size exclusion followed by anion exchange chromatography. The epitopes in the purified protein recognised by human infection sera were shown to be proteins and not carbohydrates. The N-terminal amino acid sequence of the purified Ac68 was determined and six of the 11 residues obtained were shared with a previously characterised cysteine protease of A. caninum, AcCP1.

The relation of personality to alcohol abuse/dependence in a high-risk sample

The current study had two goals. The first goal was to test the mediational role of young adult personality in the relation between parental alcoholism and young adult alcoholism. The second was to examine the associations between personality and alcohol use motives and reasons to limit drinking in order to explore possible mechanisms by which personality may influence alcohol abuse/dependence. Multilevel modeling techniques were used to analyze data obtained from a community sample of young adult children of alcoholics and demographically matched controls. Results revealed that young adult neuroticism and agreeableness each, in part, mediated the effect of parental alcoholism on young adult alcoholism. Moreover, individuals high in neuloticism reported stronger coping motives to use alcohol, individuals low in agreeableness reported stronger coping motives and weaker upbringing reasons to limit drinking, and individuals low in conscientiousness reported stronger coping and enhancement motives to use alcohol, and weaker performance reasons to limit drinking.

Identification of a new C-type lectin, TES-70, secreted by infective larvae of Toxocara canis, which binds to host ligands

Infective larvae of the dog roundworm Toxocara canis survive in the tissues of their hosts for extended periods in a state of developmental arrest, successfully evading immune destruction. This survival strategy is thought to be mediated by T. canis excretory/secretory (TES) products which downregulate or divert the immune response. We purified one of the major TES products, TES-70 and gained amino acid sequence from 4 tryptic peptides. These peptides were matched to a predicted protein from a cDNA that was isolated by expression screening a T. canis cDNA library with mouse anti-TES serum. The predicted protein (Tc-CTL-4) is similar to, but larger than, Tc-CTL-1, a 32-kDa C-type lectin secreted by T. canis larvae. Tc-CTL-4 has a signal peptide, 2 Cys-rich domains and a C-terminal calcium-dependent C-type lectin domain that shares sequence similarity with host immune cell receptors such as macrophage mannose receptor and CD23. The lectin domain was expressed in bacteria and antiserum to the purified recombinant protein was used to confirm that Tc-ctl-4 did encode the native TES-70 glycoprotein. TES-70 selectively bound to ligands on the surface of Madin-Darby Canine Kidney cells in vitro in a calcium-dependent manner, inhibitable by mammalian serum, indicating that a host glycan is the native ligand for this new parasite lectin.

Helminth C-type lectins and host-parasite interactions

C-type lectins (C-TLs) are a family of carbohydrate-binding proteins intimately involved in diverse processes including vertebrate immune cell signalling and trafficking, activation of innate immunity in both vertebrates and invertebrates, and venom-induced haemostasis. Helminth C-TLs sharing sequence and structural similarity with mammalian immune cell lectins have recently been identified from nematode parasites, suggesting clear roles for these proteins at the host-parasite interface, notably in immune evasion. Here, Alex Loukas and Rick Maizels review the status of helminth lectin research and suggest ways in which parasitic worms might utilize C-TLs during their life history.

Sjalpha elements, short interspersed element-like retroposons bearing a hammerhead ribozyme motif from the genome of the oriental blood fluke Schistosoma japonicum

Smalpha is a short interspersed element (SINE)-like retroposon that occurs in high copy number of the genome of the human blood fluke Schistosoma mansoni. The sequence of the consensus Smalpha element includes the hallmark features of SINE-like elements including a promoter region for RNA polymerase III, an AT-rich stretch at its 3'-terminus, a short length of 500 bp or less, and short direct repeat sequences flanking the insertion site. Interestingly, the sequence of Smalpha also encodes an active ribozyme bearing a hammerhead domain. Contrary to the recent findings of Ferbeyre et al. (Mol. Cell. Biol. 18 (1998) 3880-8) that indicated that Smalpha-like elements were absent from the genome of the Oriental blood fluke Schistosoma japonicum, we report here that the genome of S. japonicum does contain a family of Smalpha-like retroposons, elements that we have named the Sjalpha family. Like Smalpha, Sjalpha elements are SINE-like in structure and sequence, are present at high copy number interspersed throughout the S. japonicum genome, and contain an ostensibly functional, hammerhead ribozyme motif. The presence of these elements in all species of Schistosoma so far examined suggests that the hammerhead domain was acquired by vertical transmission from a common schistosome ancestor.

Toxocara canis: genes expressed by the arrested infective larval stage of a parasitic nematode

Toxocara canis is a widely distributed nematode parasite which reaches maturity in dogs. However, eggs voided by canid animals are infective to a very wide range of paratenic hosts including humans. In noncanid hosts, infective larvae emerge from the eggs and invade the soft tissues, often entering the brain and musculature. Such larvae may remain for many months or years in these tissues without further growth or differentiation, and yet appear to evade inflammatory reactions or other modes of immune attack. To understand the ability of T. canis larvae to survive in the immunocompetent host, we have undertaken a molecular analysis of the major genes expressed at this stage. By a combination of protein sequencing, gene identification, and expressed sequence tag (EST) analysis we have characterised a range of potentially important gene products from this parasite. Some of these are homologues of prominent mammalian proteins such as C-type lectins (represented by the secreted products TES-32 and TES-70), and mucins (TES-120), and additional products show strong similarities to known cysteine proteases, phosphatidylethanolamine-binding proteins and other ligands. A number of these proteins include a conspicuous 36-amino acid motif containing six cysteines. This domain (termed NC6 or SXC) appears to be an evolutionarily mobile module, which in T. canis is combined with a spectrum of diverse functional domains in different genes. In addition, we have identified a set of novel gene sequences that show no resemblance to any genes encoded by the free-living nematode C. elegans. Four of these are designated abundant novel transcripts, and collectively these account for nearly 20% of the cDNA isolated from the arrested infective stage. Such parasite-specific genes expressed at a high level by a stage that shows remarkable endurance may represent critical products necessary for the success of the parasitic mode of life.

A survey of genes expressed in adults of the human hookworm, Necator americanus

Hookworms are gut-dwelling, blood-feeding nematodes that infect hundreds of millions of people, particularly in the tropics. As part of a program aiming to define novel drug targets and vaccine candidates for human parasitic nematodes, genes expressed in adults of the human hookworm Necator americanus were surveyed by the expressed sequence tag approach. In total 161 new hookworm genes were identified. For the majority of these, a function could be assigned by homology. The dataset includes proteases, protease inhibitors, a lipid binding protein, C-type lectins, an anti-bacterial factor, globins and other genes of interest from a drug or vaccine development viewpoint. Three different classes of small, secreted proteins were identified that may be involved in the host-parasite interaction, including potential potassium channel blocking peptides. One third of the genes were novel. These included highly expressed, secreted (glyco)proteins which may be part of the excretory-secretory products of these important pathogens. Of particular interest are a family of 9 genes with similarity to the immunomodulatory protein, neutrophil inhibitory factor, that may play a role in establishing an immunocompromised niche for this successful parasite.

Cloning and characterisation of a prohibitin gene from infective larvae of the parasitic nematode Toxocara canis

Infective larvae of the parasitic nematode Toxocara canis express an mRNA (Tc-pro-1) encoding a predicted protein that shares significant homology with prohibitin, a protein involved in inhibition of cell proliferation - The closest homologues of Tc-pro-1 include an expressed sequence tag (EST) from Caenorhabditis elegans and Drosophila L2Cc, a protein thought to be essential for larval development and moulting. Other homologues include prohibitin from rat and human and an EST from Saccharomyces cerevisiae. Parasite life cycles generally include periods of developmental arrest, which in the larvae of T. canis may persist for many years without loss of metabolic activity. This report of the first full-length gene encoding prohibitin from a parasitic nematode raises interesting suggestions about the potential role of prohibitin in diapause and in the regulation of moulting in development.

Identification of abundantly expressed novel and conserved genes from the infective larval stage of Toxocara canis by an expressed sequence tag strategy

Larvae of Toxocara canis, a nematode parasite of dogs, infect humans, causing visceral and ocular larva migrans. In noncanid hosts, larvae neither grow nor differentiate but endure in a state of arrested development. Reasoning that parasite protein production is orientated to immune evasion, we undertook a random sequencing project from a larval cDNA library to characterize the most highly expressed transcripts. In all, 266 clones were sequenced, most from both 3' and 5' ends, and similarity searches against GenBank protein and dbEST nucleotide databases were conducted. Cluster analyses showed that 128 distinct gene products had been found, all but 3 of which represented newly identified genes. Ninety-five genes were represented by a single clone, but seven transcripts were present at high frequencies, each composing >2% of all clones sequenced. These high-abundance transcripts include a mucin and a C-type lectin, which are both major excretory-secretory antigens released by parasites. Four highly expressed novel gene transcripts, termed ant (abundant novel transcript) genes, were found. Together, these four genes comprised 18% of all cDNA clones isolated, but no similar sequences occur in the Caenorhabditis elegans genome. While the coding regions of the four genes are dissimilar, their 3' untranslated tracts have significant homology in nucleotide sequence. The discovery of these abundant, parasite-specific genes of newly identified lectins and mucins, as well as a range of conserved and novel proteins, provides defined candidates for future analysis of the molecular basis of immune evasion by T. canis.

A hookworm allergen which strongly resembles calreticulin

Immmoglobulin E-rich plasma from patients from Papua New Guinea infected with Necator americanus has been used to probe an adult N. americanus cDNA library for the presence of hookworm allergens. Using this approach, one hookworm allergen has been identified as calreticulin, which was subsequently expressed in Escherichia coli. Little serological cross reactivity was seen between the recombinant calreticulins of this hookworm and its host. Prospective roles for hookworm calreticulin in the host-parasite relationship are discussed in depth.

A novel C-type lectin secreted by a tissue-dwelling parasitic nematode

Many parasitic nematodes live for surprisingly long periods in the tissues of their hosts, implying sophisticated mechanisms for evading the host immune system. The nematode Toxocara canis survives for years in mammalian tissues, and when cultivated in vitro, secretes antigens such as TES-32. From the peptide sequence, we cloned TES-32 cDNA, which encodes a 219 amino-acid protein that has a domain characteristic of host calcium-dependent (C-type) lectins, a family of proteins associated with immune defence. Homology modelling predicted that TES-32 bears remarkable structural similarity to mammalian immune-system lectins. Native TES-32 acted as a functional lectin in affinity chromatography. Unusually, it bound both mannose- and galactose-type monosaccharides, a pattern precluded in mammalian lectins by a constraining loop adjacent to the carbohydrate-binding site. In TES-32, this loop appeared to be less obtrusive, permitting a broader range of ligand binding. The similarity of TES-32 to host immune cell receptors suggests a hitherto unsuspected strategy for parasite immune evasion.

The organization of a galectin gene from Teladorsagia circumcincta

Galectins are a family of soluble beta-galactoside-binding lectins that are conserved amongst a broad range of organisms. We have previously isolated cDNA clones coding for galectins from the sheep gastrointestinal nematode parasites Teladorsagia circumcincta, Haemonchus contortus and Trichostrongylus colubriformis, revealing a high level of identity between these molecules. This subsequent study reports the organization of the T. circumcincta Tci-gal-1 galectin gene. The coding region is broken into eight exons covering 6.6 kbp, with introns ranging in size from 55 base pairs (bp) to 2.8 kbp. Comparisons with recently reported galectin structures from Caenorhabditis elegans reveal strong architectural similarity between galectins from the parasitic and free-living nematodes, but this structure is not conserved in mammalian galectins.

Characterisation of Tc-cpl-1, a cathepsin L-like cysteine protease from Toxocara canis infective larvae

Cysteine proteases play vital biological roles in both intracellular and extracellular environments. A cysteine protease migrating at 30 kDa was identified in somatic extracts of Toxocara canis larvae (TEX), by its binding to the biotinylated inhibitor Phe-Ala-CH2F. TEX proteases readily cleaved the cathepsin L- and B-specific peptide substrate Z-Phe-Arg-AMC and to a lesser extent, the cathepsin B-specific peptide Z-Arg-Arg-AMC. Excretory/secretory (TES) products of T. canis larvae did not cleave either substrate. Partial sequence encoding the 5' end of a cysteine protease cDNA from infective T. canis larvae was then obtained from an expressed sequence tag (EST) project. The entire cDNA (termed Tc-cpl-1) was subsequently sequenced and found to encode a preproenzyme similar to cathepsin L-like proteases (identities between 36 and 69%), the closest homologues being two predicted proteins from Caenorhabditis elegans cosmids, a cathepsin L-like enzyme from Brugia pahangi and a range of parasite and plant papain-like proteases. Sequence alignment with homologues of known secondary structure indicated several charged residues in the S1 and S2 subsites involved in determining substrate specificity. Some of these are shared with human cathepsin B, including Glu 205 (papain numbering), known to permit cleavage of Arg-Arg peptide bonds. The recombinant protease (rTc-CPL-1) was expressed in bacteria for immunisation of mice and the subsequent antiserum shown to specifically react with the 30 kDa native protease in TEX. Sera from mice infected with the parasite also contained antibodies to rTc-CPL-1 as did sera from nine patients with proven toxocariasis; control sera did not. Larger scale studies are underway to investigate the efficacy of rTc-CPL-1 as a diagnostic antigen for human toxocariasis, the current test for which relies on whole excretory/secretory antigens of cultured parasites.

Immunoglobulin G subclass antibodies against excretory/secretory antigens of Ancylostoma caninum in human enteric infections

Most patients with proven or suspected enteric infection with the common hookworm of dogs, Ancylostoma caninum, produce immunoglobulin G (IgG) and IgE antibodies to an immunodominant excretory/secretory antigen (Ac68) of the parasite. These antibodies were detected in both enzyme-linked immunosorbent assay (ELISA) and Western blots; the Western blot to detect IgG antibodies to Ac68 was the most specific and sensitive. The subclasses of IgG of the antibody response to the parasite were analyzed using Western blots with anti-IgG subclass-specific monoclonal antibodies as marker systems in an attempt to further improve the specificity of the assay. Eight patients with confirmed enteric infections with A. caninum (positive controls) were tested; six had antibodies in all IgG subclasses against Ac68. Twenty sera from patients with suspected enteric infection with A. caninum (manifested as eosinophilic enteritis or unexplained abdominal pain with peripheral eosinophilia) were tested; 16 had total IgG antibodies to Ac68, while IgG1, IgG2, IgG3, and IgG4 responses were found in 11, 10, 9, and 12 of these sera, respectively. Small numbers of sera from groups of patients infected with other helminths and from healthy blood donors had various combinations of IgG, IgG1, IgG2, and IgG3 antibodies to Ac68, but none of these sera had IgG4 antibodies to Ac68. Sera from all nine patients with human hookworm infection had IgG, IgG1, IgG2, and IgG3 antibodies to Ac68 and eight of the nine were also positive for IgG4 antibodies. These results indicate the Western blot to detect IgG4 antibodies to Ac68 is the most reliable immunodiagnostic test yet described for enteric infection with A. caninum, although this test does not discriminate between infections with human and canine hookworms.

A distinctive aphthous ileitis linked to Ancylostoma caninum

Ileal ulceration is diagnosed commonly at colonoscopy in northeastern Australia. This observation has occurred contemporaneously with the description of a painful enteritis caused through supposedly rare infections by Ancylostoma caninum, the cosmopolitan dog hookworm. In this study, we describe the morphology and prevalence of ileal ulcers and investigate their cause. There were 182 patients with a distinctive aphthous ileitis highlighted by haemorrhage into the tips of surrounding villi. The annual rate reached 4.7% of ileal examinations. Eosinophilic enteritis was the characteristic, but inconsistent, histological appearance. Ulceration was linked to infection by A. caninum through serological testing and, in three patients, by the retrieval of single hookworms. Affected patients were also more likely to own a dog (53%) than the total colonoscopic population (43%; P < 0.02). The monthly rates of diagnosis were related to climate with fewest recordings during winter. Pain was the chief indication for colonoscopy (49%), proportionally higher than in controls (28%; P < 0.0001). Patients with ulcers had increased blood eosinophil, immunoglobulin E and serological values. These results were higher still in the subset with pain compared with the rest. Most patients, however, had colonoscopy performed for unrelated reasons, such as bowel cancer surveillance, and were identified as having subclinical ulceration (rate 3.2%). The findings establish a distinctive aphthous ileitis characterized by tissue eosinophilia. The cause has been tentatively linked to canine hookworms. It is proposed that infection in this geographic region is common and only rarely does a painful enteritis develop as a consequence of hypersensitization.

Eosinophilic enteritis in northeastern Australia. Pathology, association with Ancylostoma caninum, and implications

While eosinophilic gastroenteritis is considered a rare condition, eosinophilic enteritis without gastric involvement is quite common in northeastern Australia. We present 79 patients with biopsy-proven eosinophilic enteritis, 70 seen since 1987. In 10 patients, eosinophilic enteritis was associated with infection by single, sexually immature, adult hookworms, most positively identified as the common dog hookworm Ancylostoma caninum. An additional 22 patients (of 34 tested) had serological evidence of A. caninum exposure. The essential pathology, i.e., edema and eosinophilic infiltration of the gut wall, ascites, and regional lymphadenopathy, was identical to that seen in eosinophilic gastroenteritis. Additional, more specific features included pathological reactions centered on attached worms, mucosal alterations and ulcers considered to be hookworm bite sites, and submucosal and lymph node granulomas with central eosinophil degranulation and degradation products. Since A. caninum has an almost worldwide distribution, it is probable that A. caninum-induced eosinophilic enteritis occurs outside Australia. We show that the worm is easily overlooked in pathological specimens and that care is required to preserve worms intact for specific parasitological identification. The clinical and pathological features were similar to those seen in another human enteric helminthic zoonosis, anisakiasis. The possibility that there are yet other undiscovered intestinal zoonoses remains.