Threshold effects on the lectin-mediated aggregation of liposomes: Influence of the diameter of the liposomes

Summary It had previously been found that small unilamellar liposomes of ca. 0.03 m diameter which bear synthetic cholesterol-containing glycolipids may be aggregated by an appropriate lectin [8]. Where studied, threshold effects have been observed in that the amount of glycolipid incorporated in the liposomes must exceed a certain minimum concentration in order for aggregation to occur [3, 8, 9, 13, 14]. Threshold effects of this type may be important in mediating cell-cell and virus-cell interactions. However, before studies with small unilamellar liposomes are useful as a model for these recognition and binding phenomena, it must be shown that the observed threshold effects are not associated with the very small radius of curvature of these liposomes. This article reports that larger liposomes of average diameter 0.26 and 0.45 m which contain the synthetic glycolipidl also show threshold effects when aggregated with the galactose binding lectin ricin agglutinin. Under conditions where more than 1% (mole) glycolipid is required to support the aggregation of the smallest liposomes, those of intermediate size require only 0.18% (mole) while the largest liposomes examined require between 0.095 and 0.15% (mole) depending on the method of preparation.     

What signals do herbivore-induced plant volatiles provide conspecific herbivores?

Herbivore-induced plant volatiles (HIPVs) have been opined as ‘indirect or direct defenses’ of plants and are extensively studied. In contrast, HIPVs may also indicate that plant defenses have been overcome by herbivores infesting the plant; however, studies on this aspect have so far received little attention. Using the interaction of Capsicum annum (Bell pepper) with its pest Scirtothrips dorsalis (Chilli thrips) as a model system, we studied the role of HIPVs in this selected insect–plant interaction. Multiple-choice olfactometer assays with headspace volatiles collected from different growth stages of un-infested C. annum plants represented by pre-flowering (PF), flowering (FL) and fruiting stages (FR) proved FR volatiles to be highly attractive to S. dorsalis. Further, FR plants were infested with S. dorsalis adults and HIPVs released by infested plants were collected and subjected to multiple-choice olfactometer bioassays. Thrips were significantly attracted to HIPVs than to headspace volatiles of un-infested FR plants or thrips body odour. Coupled GC-EAG with S. dorsalis and HIPVs or FR plant volatile revealed specific compounds that elicited an EAG response. Individual EAG-active compounds were less attractive to thrips, however, synthetic blends of EAG-active compounds at the ratio similar to headspace samples were found to be highly attractive. However, when given a choice between synthetic blends of HIPVs and FR, thrips were significantly attracted to synthetic blend of HIPVs. Our study provides empirical data on signals HIPVs may provide to conspecific herbivores and suggests that the role of HIPVs, mostly generalized as defense, may vary based on the interaction and must be studied closely to understand their ecological functions.     

Rare Variants Create Synthetic Genome-Wide Associations

Genome-wide association studies (GWAS) have now identified at least 2,000 common variants that appear associated with common diseases or related traits (http://www.genome.gov/gwastudies), hundreds of which have been convincingly replicated. It is generally thought that the associated markers reflect the effect of a nearby common (minor allele frequency >0.05) causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites. We propose as an alternative explanation that variants much less common than the associated one may create “synthetic associations” by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings. Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. We show that they are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies. We also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations, in the latter case extending over a 2.5-Mb interval encompassing scores of “blocks” of associated variants. In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals.     

Surface-active lipids in rhodococci

Like other hydrocarbon-oxidising bacteria, rhodococci respond to the presence of alkanes by producing biosurfactant molecules to improve their ability to utilise these hydrophobic compounds as growth substrates. In the rhodococci these surfactants are predominantly glycolipids, the majority of which remain cell-bound during unrestricted growth. Most work has been done on the trehalose mycolates formed by Rhodococcus erythropolis, but nitrogen- limited conditions lead to the production of anionic trehalose tetraesters also.As surfactants, these compounds, whether purified or in crude form, are able to reduce the surface tension of water from 72 mN m-1 to a low of 26, thus making them among the most potent biosurfactants known. They are also able to reduce the interfacial tension between water and a hydrophobic phase (e.g. n- hexadecane) from 43 mN m-1 to values less than one (Table 1). Biosurfactants have about a ten- to 40-fold lower critical micelle concentration than synthetic surfactants. Such properties suggest a range of industrial applications, where a variety of surface-active characteristics are appropriate. Interest in biosurfactants as industrial chemicals results from the toxicity of many petrochemical-derived surfactants. Currently world-wide surfactant production is on a very large scale, and the demand for them is increasing. However, the drive towards less environmentally damaging chemicals makes biosurfactants attractive as they have lower toxicity.The reason they have not achieved a significant market share is the cost of production, which is considerably higher than for synthetic surfactants. This problem is being addressed using several strategies. An approach where there is great scope for improvement with the rhodococci is an understanding of the genetic basis of glycolipid production, which is largely unknown. They may find applications in the near future in the environmental remediation industries, where the requirement for purified molecules is of less importance.This review summarises knowledge of the chemistry, biochemistry and production of Rhodococcus surface-active lipids. Where they have been used, or there is potential for use, in industrial applications is discussed.     

Use of synthetic peptides for the detection and quantification of autoantibodies

Summary and conclusions The rapid progress made over the last 10 years in the identification of individual autoantigens and in the localization of the epitopes involved, has resulted in a parallel reduction in the complexity of the antigen required for the detection of autoantibodies. The ability to use synthetic peptides as antigens is a remarkable culmination of this process considering that many antigenic particles contain multiple proteins (eg. Sm consist of 8 or more individual proteins).Despite the fact that patients with SLE have a polyclonal hypergammaglobulinemia, excellent correlations between ELISAs utilizing the P2 or SmB/B synthetic peptides, ELISAs utilizing r proteins and immunoblotting were obtained [28, 38, 50]. However, false positive/non-specific binding to a P2-BSA-glutaraldehyde conjugate has been observed with serum from old MRL/lpr mice (unpublished observations). In addition, some of the results obtained in human autoimmune diseases suggest that non-specific binding may be problematic in some instances. It is difficult, at present, to know whether the higher frequencies of detection of autoantibodies to certain synthetic peptide antigens reflect increased sensitivity or decreased specificity.Synthetic peptide antigens have beeen used to detect autoantibodies in both organ specific and multisystem autoimmune diseases. In only a small number of cases have these reagents been rigorously tested for sensitivity and specificity. Despite this, synthetic peptides have been shown to be valuable for detection and quantification of autoantibodies in certain clinical situations. Undoubtedly, further progress in epitope mapping of autoantigens coupled with technological advances in protein synthesis and improved prediction of protein structure will lead to a large number of synthetic peptide antigens for research and clinical applications. It is unlikely that short synthetic peptides will substitute for native proteins in all instances since some autoantibodies show a striking preference for conformational epitopes.Abbreviations r recombinant - SLE systemic lupus erythematosus     

Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation

Genome-wide association studies (GWAS) have in recent years discovered thousands of associated markers for hundreds of phenotypes. However, associated loci often only explain a relatively small fraction of heritability and the link between association and causality has yet to be uncovered for most loci. Rare causal variants have been suggested as one scenario that may partially explain these shortcomings. Specifically, Dickson et al. recently reported simulations of rare causal variants that lead to association signals of common, tag single nucleotide polymorphisms, dubbed "synthetic associations". However, an open question is what practical implications synthetic associations have for GWAS. Here, we explore the signatures exhibited by such "synthetic associations" and their implications based on patterns of genetic variation observed in human populations, thus accounting for human evolutionary history -a force disregarded in previous simulation studies. This is made possible by human population genetic data from HapMap 3 consisting of both resequencing and array-based genotyping data for the same set of individuals from multiple populations. We report that synthetic associations tend to be further away from the underlying risk alleles compared to "natural associations" (i.e. associations due to underlying common causal variants), but to a much lesser extent than previously predicted, with both the age and the effect size of the risk allele playing a part in this phenomenon. We find that while a synthetic association has a lower probability of capturing causal variants within its linkage disequilibrium block, sequencing around the associated variant need not extend substantially to have a high probability of capturing at least one causal variant. We also show that the minor allele frequency of synthetic associations is lower than of natural associations for most, but not all, loci that we explored. Finally, we find the variance in associated allele frequency to be a potential indicator of synthetic associations.     

Nests as ornaments: revealing construction by male sticklebacks

Nests are built by animals from a variety of taxa, and serveas receptacles for eggs and developing offspring. Where nestsare built solely or mainly by one sex, they also have the potentialto serve as extended ornaments, because aspects of constructionpotentially reveal or amplify characteristics of the builderto prospective mates. Here, we develop novel indices to quantifynest structure and examine variation in temporal and structuralaspects of nest construction in relation to morphological,immunological, and physiological traits in male three-spinedsticklebacks, Gasterosteus aculeatus. Wild-caught male sticklebacksthat began construction within 3 days of being transferredto the laboratory built "neater" nests than fish that tooklonger to start, and we present alternative testable hypothesesthat could explain this pattern. Various characteristics ofnest-building males correlated with nest structure. The relativeweight of the building male's kidney—which secretes aglue-like protein used in nest building and whose developmentis androgen-dependent—correlated positively with nest "neatness." We also found males with enlarged spleens (an indicatorof immune stress) to construct less "compact" nests. The structureof a nest may therefore be important not only in determiningits functional capacity, but may also act as a quality-revealingornament. We suggest that females may gain valuable informationregarding male health status and androgen levels from nestinspection.     

Chance and serendipity in science: two examples from my own career

The usual scientific paper follows a rather narrowly (but not ever rigidly) defined pattern. Both the author and the journal like to see a linear logical presentation of a "story." Seldom does the paper give the reader the "backstory." Where did the idea come from in the first place? How many false leads led down blind alleys? What happened by chance and what by logical planning? Was there an element of serendipity involved? Perhaps as we enter the paperless era and do not have to count words quite so religiously, it may be possible to encourage a more freewheeling scientific paper, but for now, we have to rely on the historians of science and/or those who "tell all" about their own research. "Reflections" seems an appropriate space for the latter. I have chosen two scenarios from my own career in which happy accidents played important roles but, unhappily, received little recognition in my published papers.     

Expert systems in treating substance abuse.

Computer programs can assist humans in solving complex problems that cannot be solved by traditional computational techniques using mathematic formulas. These programs, or "expert systems," are commonly used in finance, engineering, and computer design. Although not routinely used in medicine at present, medical expert systems have been developed to assist physicians in solving many kinds of medical problems that traditionally require consultation from a physician specialist. No expert systems are available specifically for drug abuse treatment, but at least one is under development. Where access to a physician specialist in substance abuse is not available for consultation, this expert system will extend specialized substance abuse treatment expertise to nonspecialists. Medical expert systems are a developing technologic tool that can assist physicians in practicing better medicine.     

Phenotype-dependent response of cultured aortic smooth muscle to serum mitogens

Smooth muscle cells from the aortic media of adult pigs and monkeys have been grown in primary culture by plating cells enzymatically dissociated from the intact aorta. During the first 6 d these cells are in the "contractile" phenotype. That is, they contract slowly in response to angiotensin II and their cytoplasm is filled with both thick and thin myofilaments. In this state they do not incorporate [3H]thymidine into DNA or proliferate in response to normolipemic or hyperlipemic whole blood serum (WBS). After 7 d in culture the cells undergo a spontaneous modulation of phenotype to a "synthetic" state where they cannot be stimulated to contract and their cytoplasm is filled with organelles usually associated with synthesis of secretory protein. Thick myosin-containing filaments can no longer be demonstrated. When challenged with normolipemic or hyperlipemic WBS the cells incorporate [3H]thymidine into DNA and undergo logarithmic growth. It is suggested that when smooth muscle is the contractile phenotype (as normally exists for most cells in the aortic media of adult animals) it does not divide when challenged with serum mitogens but can undergo a change of phenotype to a synthetic state in which division can be stimulated.     

Selenium and its' role in the maintenance of genomic stability

Selenium (Se) is an essential micronutrient for humans, acting as a component of the unusual amino acids, selenocysteine (Se-Cys) and selenomethionine (Se-Met). Where Se levels are low, the cell cannot synthesise selenoproteins, although some selenoproteins and some tissues are prioritised over others. Characterised functions of known selenoproteins, include selenium transport (selenoprotein P), antioxidant/redox properties (glutathione peroxidases (GPxs), thioredoxin reductases and selenoprotein P) and anti-inflammatory properties (selenoprotein S and GPx4). Various forms of Se are consumed as part of a normal diet, or as a dietary supplement. Supplementation of tissue culture media, animal or human diets with moderate levels of certain Se compounds may protect against the formation of DNA adducts, DNA or chromosome breakage, and chromosome gain or loss. Protective effects have also been shown on mitochondrial DNA, and on telomere length and function. Some of the effects of Se compounds on gene expression may relate to modulation of DNA methylation or inhibition of histone deacetylation. Despite a large number of positive effects of selenium and selenoproteins in various model systems, there have now been some human clinical trials that have shown adverse effects of Se supplementation, according to various endpoints. Too much Se is as harmful as too little, with animal models showing a "U"-shaped efficacy curve. Current recommended daily allowances differ among countries, but are generally based on the amount of Se necessary to saturate GPx enzymes. However, increasing evidence suggests that other enzymes may be more important than GPx for Se action, that optimal levels may depend upon the form of Se being ingested, and vary according to genotype. New paradigms, possibly involving nutrigenomic tools, will be necessary to optimise the forms and levels of Se desirable for maximum protection of genomic stability in all humans.     

Malaria in Nottingham children.

In five and a half years 16 children were admitted to hospital in Nottingham suffering from malaria. Thirteen cases were caused by Plasmodium vivax and two by P falciparum, and in one the type was not identified. All were children of immigrant parents, predominantly from Pakistan, although most were born in England but had been visiting Asia. Three children were ill on or soon after arrival, but in the others the onset of symptoms was delayed by up to nine months. All made an uneventful recovery, although two children with P vivax infections had a further relapse after chloroquine treatment only. The question "Where have you been?" should be put to all immigrant parents whose children have a febrile illness. Agencies who provide travel for Asian immigrant families returning home for a visit should be encouraged to provide instructions about malaria prophylaxis.     

A novel and efficient method for synthetic carbohydrate conjugate vaccine preparation: synthesis of sialyl Tn-KLH conjugate using a 4-(4-N-maleimidomethyl) cyclohexane-1-carboxyl hydrazide (MMCCH) linker arm

STn (NeuAc26GalNAc-O-Ser/Thr) is a carbohydrate epitope overexpressed in various human carcinomas. Clinical trials are underway using synthetic STn or STn trimeric glycopeptides [STn, cluster; STn(c) conjugated with keyhole limpet hemocyanin (KLH) as active specific immunotherapy for these cancers. These vaccines have been prepared by conjugating a crotyl ethyl amide derivative of STn or STn(c) to KLH by direct reductive amination after ozonolysis. In the case of STn(c) the conjugation efficiency and the resulting epitope ratios were low. This may be due to steric hinderance of the short spacer arm. To overcome these difficulties, without resynthesis, the STn(c) glycopeptide was modified by attachment of an MMCCH (4-(4-N-maleimidomethyl) cyclohexane-1-carboxyl hydrazide) spacer arm to the aldehyde derivative, and then conjugated with thiolated KLH. This method gave a higher epitope ratio and yield than the direct method. The STn(c)-MMCCH-KLH conjugate induced high titer antibodies in mice against STn(c). This method may be generally applicable for large synthetic oligosaccharides.     

Design and construction of "synthetic species"

Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr's Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term "synthetic species" to distinguish it from "natural species", not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity.     

Growth of Cryptococcus neoformans in a thiamine-free medium

The growth of Cryptococcus neoformans in a minimal liquid synthetic medium with or without thiamine (10 g/ml) was investigated. In these media the presence or absence of thiamine had no effect on the development of C. neoformans. To check these results, we performed a series of experiments on a solid form of the minimal synthetic medium. In this study a series of six serial transfers were carried out to starve the cells of nutrients that may have been carried over from their growth on rich media. In each of the transfers on the solid synthetic medium, C. neoformans showed a similar and scarce growth. This finding indicates that C. neoformans could be autotrophic in respect to thiamine.     

Establishment by the rat lymph node method of epitope-defined monoclonal antibodies recognizing the six different α chains of human type IV collagen

A group of rat monoclonal antibodies recognizing the six different chains of human type IV collagen have been established by our novel method. The method is designated the rat lymph node method in which enlarged medial iliac lymph nodes of a rat injected with an antigen emulsion via hind footpads are used as a source of B cells for cell fusion to produce hybridomas. The immunogens used were synthetic peptides having non-consensus amino acid sequences near the carboxyl termini of type IV collagen chains. Hybridomas were screened both by ELISA with synthetic peptides and by indirect immunofluorescence with cryostat sections of human kidneys. Because the epitopes of all antibodies were determined by multipin-peptide scanning, they were confirmed to be isoform-specific. They are useful for identification of chains of type IV collagen at the protein level in normal and abnormal conditions. The combined use of synthetic peptides as immunogens, the rat lymph node method as making monoclonal antibodies, and the multipin-peptide scanning as epitope mapping is found to be a strong tool for identification of peptides and proteins whose amino acid sequences are known or have been deduced.     

Entrainment of circadian programs

Of the three defining properties of circadian rhythmicity--persisting free-running rhythm, temperature compensation, and entrainment--the last is often poorly understood by many chronobiologists. This paper gives an overview of entrainment. Where have we been? Where are we now? Whence should we be going? Particular emphasis is given to a discussion of the Discrete vs. Continuous models for entrainment. We provide an integrated mechanism for entrainment from a limit-cycle perspective.     

Working together to respond to the challenges of EU policy to replace animal testing

This paper presents a personal perspective on efforts during the past 15 years to replace animal testing for assessing the safety of chemicals and products. It is based on an invited lecture--the FRAME Annual Lecture--given in October 2005, with the theme of "making progress by working together" (government-industry-academia-NGOs). Where we have achieved some successes, these have clearly been due to effective cooperation and collaboration between the relevant stakeholders. In recent times, there has not been this same level of active commitment and coordination. This needs to change, since, if we are to make good progress in the years to come in responding to the new challenges of the EU policy to replace animal testing, this will undoubtedly require us to work together, hopefully facilitated by effective leadership and coordination from the EU policy-makers themselves.