Defining the complementarities between antibodies and haptens to refine our understanding and aid the prediction of a successful binding interaction.

BACKGROUND: Low molecular weight haptens (<1000 Da) cannot be recognized by the immune system unless conjugated to larger carrier molecules. Antibodies to these exceptionally small antigens can still be generated with exquisite sensitivity. A detailed understanding at the molecular level of this incredible ability of antibodies to recognize haptens, is still limited compared to other antigen classes. METHODS: Different hapten targets with a broad range of structural flexibility and polarity were conjugated to carrier proteins, and utilized in sheep immunization. Three antibody libraries were constructed and used as potential pools to isolate specific antibodies to each target. The isolated antibodies were analysed in term of CDR length, canonical structure, and binding site shape and electrostatic potential. RESULTS: The simple, chemically naïve structure of squalane (SQA) was recognized with micromolar sensitivity. An increase in structural rigidity of the hydrophobic and cyclic coprostane (COP) did not improve this binding sensitivity beyond the micromolar range, whilst the polar etioporphyrin (POR) was detected with nanomolar sensitivity. Homoserine lactone (HSL) molecules, which combine molecular flexibility and polarity, generated super-sensitive (picomolar) interactions. To better understand this range of antibody-hapten interactions, analyses were extended to examine the binding loop canonical structures and CDR lengths of a series of anti-hapten clones. Analyses of the pre and post- selection (panning of the phage displayed libraries) sequences revealed more conserved sites (123) within the post-selection sequences, when compared to their pre-selection counterparts (28). The strong selection pressure, generated by panning against these haptens resulted in the isolation of antibodies with significant sequence conservation in the FW regions, and suitable binding site cavities, representing only a relatively small subset of the available full repertoire sequence and structural diversity. As part of this process, the important influence of CDR H2 on antigen binding was observed through its direct interaction with individual antigens and indirect impact on the orientation and the pocket shape, when combined with CDRs H3 and L3. The binding pockets also displayed electrostatic surfaces that were complementary to the hydrophobic nature of COP, SQA, and POR, and the negatively charged HSL. CONCLUSIONS: The best binding antibodies have shown improved capacity to recognize these haptens by establishing complementary binding pockets in terms of size, shape, and electrostatic potential.

High-sensitivity monoclonal antibodies specific for homoserine lactones protect mice from lethal Pseudomonas aeruginosa infections.

A number of bacteria, including pathogens like Pseudomonas aeruginosa, utilize homoserine lactones (HSLs) as quorum sensing (QS) signaling compounds and engage in cell-to-cell communication to coordinate their behavior. Blocking this bacterial communication may be an attractive strategy for infection control as QS takes a central role in P. aeruginosa biology. In this study, immunomodulation of HSL molecules by monoclonal antibodies (MAbs) was used as a novel approach to prevent P. aeruginosa infections and as tools to detect HSLs in bodily fluids as a possible first clue to an undiagnosed Gram-negative infection. Using sheep immunization and recombinant antibody technology, a panel of sheep-mouse chimeric MAbs were generated which recognized HSL compounds with high sensitivity (nanomolar range) and cross-reactivity. These MAbs retained their nanomolar sensitivity in complex matrices and were able to recognize HSLs in P. aeruginosa cultures grown in the presence of urine. In a nematode slow-killing assay, HSL MAbs significantly increased the survival of worms fed on the antibiotic-resistant strain PA058. The therapeutic benefit of these MAbs was further studied using a mouse model of Pseudomonas infection in which groups of mice treated with HSL-2 and HSL-4 MAbs survived, 7 days after pathogen challenge, in significantly greater numbers (83 and 67%, respectively) compared with the control groups. This body of work has provided early proof-of-concept data to demonstrate the potential of HSL-specific, monoclonal antibodies as theranostic clinical leads suitable for the diagnosis, prevention, and treatment of life-threatening bacterial infections.

Wide screening of phage-displayed libraries identifies immune targets in planta.

Microbe-Associated Molecular Patterns and virulence effectors are recognized by plants as a first step to mount a defence response against potential pathogens. This recognition involves a large family of extracellular membrane receptors and other immune proteins located in different sub-cellular compartments. We have used phage-display technology to express and select for Arabidopsis proteins able to bind bacterial pathogens. To rapidly identify microbe-bound phage, we developed a monitoring method based on microarrays. This combined strategy allowed for a genome-wide screening of plant proteins involved in pathogen perception. Two phage libraries for high-throughput selection were constructed from cDNA of plants infected with Pseudomonas aeruginosa PA14, or from combined samples of the virulent isolate DC3000 of Pseudomonas syringae pv. tomato and its avirulent variant avrRpt2. These three pathosystems represent different degrees in the specificity of plant-microbe interactions. Libraries cover up to 2 × 10(7) different plant transcripts that can be displayed as functional proteins on the surface of T7 bacteriophage. A number of these were selected in a bio-panning assay for binding to Pseudomonas cells. Among the selected clones we isolated the ethylene response factor ATERF-1, which was able to bind the three bacterial strains in competition assays. ATERF-1 was rapidly exported from the nucleus upon infiltration of either alive or heat-killed Pseudomonas. Moreover, aterf-1 mutants exhibited enhanced susceptibility to infection. These findings suggest that ATERF-1 contains a microbe-recognition domain with a role in plant defence. To identify other putative pathogen-binding proteins on a genome-wide scale, the copy number of selected-vs.-total clones was compared by hybridizing phage cDNAs with Arabidopsis microarrays. Microarray analysis revealed a set of 472 candidates with significant fold change. Within this set defence-related genes, including well-known targets of bacterial effectors, are over-represented. Other genes non-previously related to defence can be associated through this study with general or strain-specific recognition of Pseudomonas.

Synthesis and characterisation of immunogens for the production of antibodies against small hydrophobic molecules with biosignature properties.

In the present study, five different classes of small hydrophobic molecular targets, atypical for antibody generation, were structurally modified in order to introduce suitable reactive functionalities and/or spacers which allow covalent coupling to a carrier protein resulting in a stable carrier-hapten complex. These targets were chosen to serve as markers of extant and/or extinct life in the context of the development of the Life Marker Chip (LMC), an antibody-based instrument, which is being developed by a UK-led international consortium for flight to Mars on board the joint ESA/NASA Mars exploration ExoMars mission. The hapten-protein conjugates were designed to be used as immunogens for antibody generation and immunoassay reagents in subsequent stages of the LMC development. The extent of protein modification due to covalent attachment of hapten was determined by two independent methods, i.e. trinitrobenzenesulfonic acid (TNBSA) titrations of remaining protein reactive groups and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of the resultant hapten-protein conjugates. In a further quality validation step, the conjugates were presented to an animal's immune system and polyclonal antibody titres with moderate specificity were obtained. These results suggest that conjugates synthesized as described herein can successfully be used in the generation of antibodies targeting small hydrophobic molecules.

Serine/threonine protein kinase SGK1 in glucocorticoid-dependent transdifferentiation of pancreatic acinar cells to hepatocytes.

Elevated glucocorticoid levels result in the transdifferentiation of pancreatic acinar cells into hepatocytes through a process that requires a transient repression of WNT signalling upstream of the induction of C/EBP-ß. However, the mechanism by which glucocorticoid interacts with WNT signalling is unknown. A screen of microarray data showed that the serine/threonine protein kinase SGK1 (serum- and glucocorticoid-regulated kinase 1) was markedly induced in the model B-13 pancreatic rat acinar cell line after glucocorticoid treatment (which converts them into hepatocyte-like 'B-13/H' cells) and this was confirmed at the level of mRNA (notably an alternatively transcribed SGK1C form) and protein. Knockdown of SGK1 using an siRNA designed to target all variant transcripts inhibited glucocorticoid-dependent transdifferentiation, whereas overexpression of the human C isoform (and also the human SGK1F isoform, for which no orthologue in the rat has been identified) alone - but not the wild-type A form - inhibited distal WNT signalling Tcf/Lef transcription factor activity, and converted B-13 cells into B-13/H cells. These effects were lost when the kinase functions of SGK1C and SGK1F were mutated. Inhibition of SGK1 kinase activity also inhibited glucocorticoid-dependent transdifferentiation. Expression of SGK1C and SGK1F resulted in the appearance of phosphorylated ß-catenin, and recombinant SGK1 was shown to directly phosphorylate purified ß-catenin in vitro in an ATP-dependent reaction. These data therefore demonstrate a crucial role for SGK1 induction in B-13 cell transdifferentiation to B-13/H hepatocytes and suggest that direct phosphorylation of ß-catenin by SGK1C represents the mechanism of crosstalk between glucocorticoid and WNT signalling pathways.

AR42J-B-13 cell: an expandable progenitor to generate an unlimited supply of functional hepatocytes.

Hepatocytes are the preparation of choice for Toxicological research in vitro. However, despite the fact that hepatocytes proliferate in vivo during liver regeneration, they are resistant to proliferation in vitro, do not tolerate sub-culture and tend to enter a de-differentiation program that results in a loss of hepatic function. These limitations have resulted in the search for expandable rodent and human cells capable of being directed to differentiate into functional hepatocytes. Research with stem cells suggests that it may be possible to provide the research community with hepatocytes in vitro although to date, significant challenges remain, notably generating a sufficiently pure population of hepatocytes with a quantitative functionality comparable with hepatocytes. This paper reviews work with the AR42J-B-13 (B-13) cell line. The B-13 cell was cloned from the rodent AR42J pancreatic cell line, express genes associated with pancreatic acinar cells and readily proliferates in simple culture media. When exposed to glucocorticoid, 75-85% of the cells trans-differentiate into hepatocyte-like (B-13/H) cells functioning at a level quantitatively similar to freshly isolated rat hepatocytes (with the remaining cells retaining the B-13 phenotype). Trans-differentiation of pancreatic acinar cells also appears to occur in vivo in rats treated with glucocorticoid; in mice with elevated circulating glucocorticoid and in humans treated for long periods with glucocorticoid. The B-13 response to glucocorticoid therefore appears to be related to a real pathophysiological response of a pancreatic cell to glucocorticoid. An understanding of how this process occurs and if it can be generated or engineered in human cells would result in a cell line with the ability to generate an unlimited supply of functional human hepatocytes in a cost effective manner.

Shark novel antigen receptors--the next generation of biologic therapeutics?

Over recent decades we have witnessed a revolution in health care as new classes of therapeutics based on natural biological molecules have become available to medical practitioners. These promised to target some of the most serious conditions that had previously evaded traditional small molecule drugs, such as cancers and to alleviate many of the concerns of patients and doctors alike regarding adverse side effects and impaired quality of life that are often associated with chemo-therapeutics. Many early 'biologics' were based on antibodies, Nature's answer to invading pathogens and malignancies, derived from rodents and in many ways failed to live up to expectations. Most of these issues were subsequently negated by technological advances that saw the introduction of human or "humanized' antibodies and have resulted in a number of commercial 'block-busters'. Today, most of the large pharmaceutical companies have product pipelines that include an increasing proportion of biologic as opposed to small molecule compounds. The limitations of antibodies or other large protein drugs are now being realized however and ever more inventive solutions are being sought to develop equally efficacious but smaller, more soluble, more stable and less costly alternatives to broaden the range of drug-able targets and therapeutic options. The aim of this chapter is to introduce the reader to one such novel approach that seeks to exploit a unique antibody-like protein evolved by ancestral sharks over 450 M years ago and that may lead to a host of new therapeutic opportunities and help us to tackle some of the pressing clinical demands of the 21 st century.

A Chiropracticness Test.

BACKGROUND: There is little homogeneity of opinion in the chiropractic profession about its essence and identity. Matters compromising the establishment of a coherent identity include the issue of vertebral subluxation, philosophy, mercantilism, poverty of qualifications in some chiropractic college faculty, and lack of intellectual productivity in some chiropractic college faculty. DISCUSSION: The Chiropractic profession has mislabeled rhetoric, supposition and cant as philosophy, whilst showing sparse evidence for the existence of more than a few chiropractors writing in philosophy as a discipline. There is no evidence for "Chiropractic Philosophy". I propose, however, that a better use of the discipline of philosophy can be of great use to the Chiropractic profession. Various thinkers throughout the ages have written about deduction, induction and falsificationism as methods to discover more reliably the nature of things in the world about us. Each method has strengths and frailties, but some of the latter are insurmountable for our purposes. SUMMARY: Using a contrivance of that method which seems most suited, sui generis, for the purpose, I propose a Chiropracticness Test as a tool to assist the search for essence and identity in Chiropractic.

Subluxation: dogma or science?

Subluxation syndrome is a legitimate, potentially testable, theoretical construct for which there is little experimental evidence. Acceptable as hypothesis, the widespread assertion of the clinical meaningfulness of this notion brings ridicule from the scientific and health care communities and confusion within the chiropractic profession. We believe that an evidence-orientation among chiropractors requires that we distinguish between subluxation dogma vs. subluxation as the potential focus of clinical research. We lament efforts to generate unity within the profession through consensus statements concerning subluxation dogma, and believe that cultural authority will continue to elude us so long as we assert dogma as though it were validated clinical theory.

Generation of a monoclonal human single chain antibody fragment to hepatic stellate cells--a potential mechanism for targeting liver anti-fibrotic therapeutics.

BACKGROUND/AIMS: Hepatic stellate cells are pivotal to fibrogenesis in the liver and many potential anti-fibrotic therapeutics are required to act on targets within hepatic stellate cells. The aim of this study was to generate a human antibody fragment to hepatic stellate cells. METHODS: Phage display was used to generate a human monoclonal antibody fragment to a peptide sequence present on an extracellular domain of synaptophysin, a protein expressed on the surface of hepatic stellate cells. RESULTS: An antibody fragment was isolated (termed C1-3), expressed in bacteria and purified. Fluorescently-labelled C1-3 antibody associated with human hepatic stellate cells but not hepatocytes in culture. Binding of fluorescently labelled C1-3 to hepatic stellate cells was blocked by the extracellular synaptophysin peptide sequence and uptake of the antibody intracellularly was inhibited by monensin. The toxin tributyl tin-when conjugated to C1-3-retained the ability to kill hepatic stellate cells confirming that C1-3 is sequestered intracellularly. CONCLUSIONS: This antibody fragment may be an effective means to target therapeutics to human hepatic stellate cells.

Identification of a truncated ratp28-related protein expressed in kidney.

An RT-PCR based strategy to clone the membrane-associated steroid binding protein ratp28 additionally amplified a novel sequence-related PCR product termed HC5. The HC5 PCR product was cloned and sequenced and showed 94% nucleotide sequence similarity to ratp28. The HC5 cDNA sequence open reading frame encodes a predicted 75 amino acid (8.0kDa) protein, and is therefore truncated compared to ratp28 (195 amino acids, 21.6kDa). In vitro transcription and translation of the HC5 cDNA resulted in the production of 2 proteins of approximately 8 and 6kDa. Restriction digests from various tissues demonstrated that liver and heart expressed primarily ratp28 mRNA whereas kidney and blood contained both ratp28 and HC5 transcripts. Phage display was employed to generate an antibody fragment to a peptide sequence conserved in ratp28 and HC5. Western blotting identified a 10kDa protein in cytosolic fractions of rat kidney. The function of HC5 remains to be determined.