Abstract P5-08-04: Defining chromatin accessibility profiles of partial and reversible EMT

The epithelial-to-mesenchymal transition (EMT) reversible cellular reprogramming event, used repeatedly throughout development, is hypothesized to be involved in the cell migration and consequently metastasis that ultimately contributes to most breast cancer-related fatalities. In this process, cuboidal epithelial cells, marked by the presence of tight junction proteins and cell-cell adhesions, lose their apicobasal polarity and acquire a spindle-like morphology and migratory traits. EMT was originally regarded to have only two states, with cells exhibiting either epithelial or mesenchymal phenotypes; however, recently, researchers have demonstrated the existence of a dual epithelial/mesenchymal state, termed hybrid- or partial-EMT. Due to its inherent plasticity, it is believed that EMT and its reversal mesenchymal-to-epithelial transition (MET) is, at least, partly regulated by epigenetic means such as alterations in chromatin structure. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a novel technique that employs the use of a mutant Tn5 transposase to cleave nucleosome-free DNA regions in a non-biased manner. In this investigation, we induced MCF10A mammary epithelial cells to undergo a short-term (<4 days) or long-term (>4 days) EMT. Addition and withdrawal of exogenous TGFβ1 produced partial- or full-EMT and MET conditions which were interrogated by ATAC- and RNA-seq. Hierarchical clustering of ATAC cleavage peaks revealed that pre-EMT and short- and long-term MET conditions demonstrate similar chromatin accessibility profiles with cleavage sites enriched for specific binding motifs. Notably, transcription factors typically not associated with EMT displayed dynamic enrichment in the accessible chromatin at various timepoints in our assay. Correlation with RNA-seq data reveals highly dynamic changes in gene expression suggesting dynamic and reversible use of regulatory programs. Importantly, partial-EMT cells were characterized by unique accessibility patterns, motif enrichment, and gene expression supporting the conclusion that this is not merely an intermediate but a unique state.

Citation Format: Johnson KS, Hussein S, Lin Y, Taube JH. Defining chromatin accessibility profiles of partial and reversible EMT [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-08-04.

Southern Ocean Biogeochemical Float Deployment Strategy, With Example From the Greenwich Meridian Line (GO-SHIP A12)

Biogeochemical Argo floats, profiling to 2,000-m depth, are being deployed throughout the Southern Ocean by the Southern Ocean Carbon and Climate Observations and Modeling program (SOCCOM). The goal is 200 floats by 2020, to provide the first full set of annual cycles of carbon, oxygen, nitrate, and optical properties across multiple oceanographic regimes. Building from no prior coverage to a sparse array, deployments are based on prior knowledge of water mass properties, mean frontal locations, mean circulation and eddy variability, winds, air-sea heat/freshwater/carbon exchange, prior Argo trajectories, and float simulations in the Southern Ocean State Estimate and Hybrid Coordinate Ocean Model (HYCOM). Twelve floats deployed from the 2014-2015 Polarstern cruise from South Africa to Antarctica are used as a test case to evaluate the deployment strategy adopted for SOCCOM's 20 deployment cruises and 126 floats to date. After several years, these floats continue to represent the deployment zones targeted in advance: (1) Weddell Gyre sea ice zone, observing the Antarctic Slope Front, and a decadally-rare polynya over Maud Rise; (2) Antarctic Circumpolar Current (ACC) including the topographically steered Southern Zone chimney where upwelling carbon/nutrient-rich deep waters produce surprisingly large carbon dioxide outgassing; (3) Subantarctic and Subtropical zones between the ACC and Africa; and (4) Cape Basin. Argo floats and eddy-resolving HYCOM simulations were the best predictors of individual SOCCOM float pathways, with uncertainty after 2 years of order 1,000 km in the sea ice zone and more than double that in and north of the ACC.

OSIRIS-REx Contamination Control Strategy and Implementation

OSIRIS-REx will return pristine samples of carbonaceous asteroid Bennu. This article describes how pristine was defined based on expectations of Bennu and on a realistic understanding of what is achievable with a constrained schedule and budget, and how that definition flowed to requirements and implementation. To return a pristine sample, the OSIRIS-REx spacecraft sampling hardware was maintained at level 100 A/2 and <180 ng/cm² of amino acids and hydrazine on the sampler head through precision cleaning, control of materials, and vigilance. Contamination is further characterized via witness material exposed to the spacecraft assembly and testing environment as well as in space. This characterization provided knowledge of the expected background and will be used in conjunction with archived spacecraft components for comparison with the samples when they are delivered to Earth for analysis. Most of all, the cleanliness of the OSIRIS-REx spacecraft was achieved through communication among scientists, engineers, managers, and technicians.

Phenylpropenoid phenolics in sweetbay magnolia as chemical determinants of host use in saturniid silkmoths (Callosamia)

Host plant chemistry can play an important role in determining the evolution of host use patterns in herbivorous insects by influencing host selection, consumption, and assimilation of foliage. We used a comparative approach to test the hypothesis that specialist herbivores of sweetbay magnolia (Magnolia virginiana) possess adaptations that allow them to overcome chemical deterrents or toxins that prevent herbivory by unadapted herbivores. The three silkmoth species in the genusCallosamia can be collectively regarded as specialists on magnoliaceous hosts; however, only the monophagousC. securifera is able to complete development on sweetbay magnolia, its natural host. In laboratory assays with intact foliage, bothC. angulifera and the polyphagousC. promethea fed readily on sweetbay but were unable to survive past the third instar. Two neolignan compounds, magnolol and a biphenyl ether, were found to reduce neonate growth and survival of unadapted herbivore species when painted on acceptable host leaves at concentrations similar to those found in sweetbay foliage. Both compounds significantly reduced neonate growth ofC. angulifera andC. promethea but had no effect on the sweetbay specialist,C. securifera, indicating that the latter species possesses the unique ability in the genus to tolerate, metabolize, or otherwise circumvent the phytochemical defenses of this host.

Schedule-induced defecation: No-food and massed-food baselines

Defecation rate was monitored during daily 30-min periods as 16 rats were exposed to different sequences of the following three experimental conditions: (a) a fixed-time 60-s food delivery schedule, (b) a massed-food presentation baseline, and/or (c) a no-food baseline. All food delivery was response independent. Rate of defecation increased during fixed-time 60-s food delivery when compared to baseline rates of defecation established during no-food and massed-food baselines. This effect was present for 12 of 16 rats during four alternative sequences of experimental conditions. Within-subject reversals established reliability of this effect. Schedule induction of defecation is clearly demonstrated under these conditions.

Comparative analysis of urban atmospheric aerosol by particle-induced X-ray emission (PIXE), proton elastic scattering analysis (PESA), and aerosol mass spectrometry (AMS)

A multifaceted approach to atmospheric aerosol analysis is often desirable in field studies where an understanding of technical comparability among different measurement techniques is essential. Herein, we report quantitative intercomparisons of particle-induced X-ray emission (PIXE) and proton elastic scattering analysis (PESA), performed of fline under a vacuum, with analysis by aerosol mass spectrometry (AMS) carried out in real-time during the MCMA-2003 Field Campaign in the Mexico City Metropolitan Area. Good agreement was observed for mass concentrations of PIXE-measured sulfur (assuming it was dominated by SO4(2-)) and AMS-measured sulfate during most of the campaign. PESA-measured hydrogen mass was separated into sulfate H and organic H mass fractions, assuming the only major contributions were (NH4)2SO4 and organic compounds. Comparison of the organic H mass with AMS organic aerosol measurements indicates that about 75% of the mass of these species evaporated under a vacuum. However approximately 25% of the organics does remain under a vacuum, which is only possible with low-vapor-pressure compounds, and which supports the presence of high-molecular-weight or highly oxidized organics consistent with atmospheric aging. Approximately 10% of the chloride detected by AMS was measured by PIXE, possibly in the form of metal-chloride complexes, while the majority of Cl was likely present as more volatile species including NH4Cl. This is the first comparison of PIXE/PESA and AMS and, to our knowledge, also the first report of PESA hydrogen measurements for urban organic aerosols.

A massive phytoplankton bloom induced by an ecosystem-scale iron fertilization experiment in the equatorial Pacific Ocean

The seeding of an expanse of surface waters in the equatorial Pacific Ocean with low concentrations of dissolved iron triggered a massive phytoplankton bloom which consumed large quantities of carbon dioxide and nitrate that these microscopic plants cannot fully utilize under natural conditions. These and other observations provide unequivocal support for the hypothesis that phytoplankton growth in this oceanic region is limited by iron bioavailability.

Assessment of bony resection margins in oral cancer using elastic scattering spectroscopy: a study on archival material

Oral squamous cell carcinoma has been shown to infiltrate local bone necessitating either a local or segmental resection for clearance. The current decalcification process takes several weeks before histological examination of the margins is possible. The aim of this study was to determine whether elastic scattering spectroscopy (ESS) could be used to identify bone resection margins positive for tumour. We used an ESS biopsy (optical biopsy) system to assess formalin fixed bone margins resected for squamous cell carcinoma of the oral cavity and compared the results with the histopathological diagnosis. Archival specimens obtained in oral cancer resections over the last 10 years were used, the ESS spectra were obtained from residual resection margins immediately adjacent to the area from which sections were cut and the results correlated with the histopathological diagnosis. Three hundred and forty-one spectra were used in this study taken from the mandibular specimens of 21 patients, of which 231 spectra were taken from histologically positive sites and the rest were of normal tissue. Two different sets of spectra were obtained and using a linear discriminant analysis, a sensitivity of 87% and a specificity of 80% were obtained. These results suggest that ESS may identify tumour involvement of resection margins. This study, on formalin fixed tissue, was shown to be reliable and may significantly reduce pathology workload. If these findings can be applied in vivo, this would be an accurate and instant mechanism for assessment of margins in clinical practice.

Organ procurement organization (OPO), best practices

There are currently 59 organ procurement organizations (OPOs) in the United States which serve their assigned geographic areas with variable productivity. Knowledge of organizational characteristics, programs and practices of more successful OPOs may be useful to increase the productivity of less successful OPOs. A preliminary survey of all OPO executive directors in the United States ascertained the most important beneficial and detrimental factors affecting their success. Site visits were then conducted at OPOs based on a selection process utilizing population size, geographic location, minority population, donors per million population and donors per thousand deaths among potential donors. All OPOs were categorized and the highest ranking OPOs in each of seven categories, based on 4 years of national data, were selected for the site visits. Regression analysis and correlation analysis using Pearson's product-moment correlation were performed. The survey to identify the important factors was returned by 47 (77%) of 61 OPOs existent in 1999. The most important beneficial factors identified by responding OPOs were adequate staffing and experience, allocation of responsibilities, hospital development and leadership. The most important detrimental factors were inadequate staffing and experience, poor donor hospital/transplant center/ OPO relationships and failure in the consent process. Site visits of the highest-ranking OPOs demonstrated all had respected, experienced leadership focused on the donation process; efficient mechanisms for resolving allocation or transplant center conflicts; systems for monitoring activity and tracking outcomes; excellent communication between OPO and transplant centers; open internal communication at all levels of the OPO; immediate, on-site response to vascular donor referrals; and volunteer support of public and/or professional education. Regression and correlation analysis demonstrated that as minority population increases, OPO performance declines (P < 0.03). Moreover, independent OPOs were associated with poorer performance regardless of minority population (P < 0.05). All of the successful OPOs visited had strong leadership, excellent donor hospital and transplant center relationships, well-developed communication and innovative methods to deal with their minority populations. Application of these practices within all OPOs could significantly enhance organ donation.

Plant phenolics as dietary antioxidants for herbivorous insects: a test with genetically modified tobacco

High foliar phenolics are generally assumed to increase resistance to insect herbivores, but recent studies show that tobacco lines modified to over- and underexpress phenolics do not exhibit higher constitutive resistance to caterpillars. This is contrary to the expectation that ingestion of tobacco phenolics, particularly chlorogenic acid, should cause oxidative stress in herbivores. We investigated free radical production and antioxidant capacity of fresh crushed leaves of tobacco lines exhibiting over a sixfold difference in chlorogenic acid content to test whether high phenolic concentrations are associated with increased production of reactive oxygen species (ROS). The effects of in planta phenolic levels on feeding behavior, growth, biochemical markers of oxidative stress, and the antioxidant capacity of midgut fluid and hemolymph were assessed in tobacco budworm, Heliothis virescens. The experiments showed that high phenolic foliage was more prooxidant than low phenolic foliage, but the net balance in crushed tissue was antioxidant in comparison to buffer and the commercial antioxidant standard, Trolox. In H. virescens, the antioxidant capacity of midgut fluid was also powerful, and caterpillars fed high phenolic foliage did not exhibit the expected markers of oxidative stress in midgut tissues (altered ascorbate ratios, disulfides, or total hydroperoxides). Instead, hemolymph of larvae fed high phenolic foliage exhibited improved total Trolox equivalent antioxidant capacity (TEAC). These results suggest that the elevated foliar phenolics in some plants may have beneficial antioxidant properties for herbivorous insects, much as dietary phenolics do in mammals.

Direct ultraviolet spectrophotometric determination of total sulfide and iodide in natural waters

A technique is described that allows the determination of total dissolved sulfide in natural waters using direct ultraviolet detection of the HS- ion. The concentration of bisulfide is determined by measuring absorption from 214 to 300 nm and then deconvolution of the HS- spectra from the complex spectrum of natural fluids. A nonlinear least-squares fitting approach is used for the deconvolution. At a pH near 8, where >95% of total sulfide is present as HS-, the results are indistinguishable from total sulfide measured using the methylene blue method in a wide range of sample types and matrixes including freshwater from groundwater wells, marine hydrothermal vent fluids, and marine sediment porewaters. The method allows simultaneous determination of other UV-absorbing ions, including nitrate, bromide, and iodide, in samples with low total sulfide concentrations. Bisulfide concentrations can be determined in samples with low background absorption, such as well water and hydrothermal fluids, with a detection limit of < 1 microM. The detection limit for bisulfide in sediment porewaters that have a high organic loading, which produces background absorbances of approximately 0.5 A at 260 nm in a 1-cm cuvette, is 5 microM. The only chemical manipulation required is buffering acidic samples to pH > 7 and filtration of particulate-rich samples.

Phylogenetic distribution of cysteine proteinases in beetles: evidence for an evolutionary shift to an alkaline digestive strategy in Cerambycidae

We characterized the digestive proteinases of eight species of beetles to improve our understanding of the phylogenetic distribution of serine and cysteine proteinases. Serine proteinases function optimally under alkaline pH conditions, whereas cysteine proteinases require acidic pH. The phylogenetic distribution of cysteine proteinases suggests that they first appeared in an early cucujiform ancestor, however, data for some groups is patchy, and there has been speculation that they have been lost in at least one group, the long-horned beetles (Cerambycidae). The pattern we found supports the hypothesized origin of the proteinases and extends their distribution to an additional superfamily. In addition, we confirmed the presence of cysteine proteinases in some Curculionoidea. Cysteine proteinases were absent, however, from all three species of cerambycids surveyed, supporting the hypothesis that this group has reverted to the more ancestral serine (alkaline) digestive strategy. In four species we compared the pH optima for total proteolytic activity to the actual pH of the midgut and found the match between optimal and actual pH to be weaker in the cerambycids. These findings suggest that either a close correlation between midgut pH and the proteolytic pH optimum is not needed for adequate digestive efficiency, or that midgut pH is a more constrained digestive feature and there has been insufficient time for it to shift upwards to maximize serine proteinase activity.

Digestive proteinase activity in corn earworm (Helicoverpa zea) after molting and in response to lowered redox potential

Insect digestive proteinases are often strongly influenced by ambient physicochemical conditions, such as pH, ionic strength, and oxidation-reduction potential. Although the effects of the former two parameters are well documented, the influence of redox potential on catalytic rates of digestive enzymes is not well understood. In this study, we manipulated the midgut redox potential of a generalist caterpillar (the corn earworm, Helicoverpa zea) by augmenting artificial diet with dithiothreitol, a powerful thiol reducing agent that lowers the redox potential in the lumen by 40-45 mV. Effects on total proteolytic activity, as well as on elastase, chymotrypsin, trypsin, leucine aminopeptidase, and carboxypeptidase A and B activities were measured using azocasein and nitroanilide model substrates. The profiles of proteinase activities in the epithelium and lumen were also monitored on days 1, 2, and 3 after the molt in penultimate instar larvae. Although the reducing agent strongly inhibited the activity of some proteinases in vitro, ingestion of the reducing diet failed to affect in vivo proteinase activities. There was also no effect on larval relative growth, consumption, or digestive efficiencies. We conclude that dietary reducing agents must lower midgut redox potential to below -40 mV to significantly impact digestive efficiency. Arch.

Oxygen levels in the gut lumens of herbivorous insects

Oxygen levels were measured in the foregut and midgut lumens of ten species of caterpillars and three species of grasshoppers. In most species, the foregut was nearly anoxic, with oxygen levels ranging from 0 to 2.5 mm Hg. However, two caterpillar species with large foreguts (Malacosoma disstria and Lymantria dispar) had elevated oxygen levels (27.9 and 32.1 mm Hg) in this region when they were fed artificial diet. In all of the species surveyed, the anterior and posterior midgut were nearly anoxic, with oxygen levels ranging from 0 to 7.3 mm Hg. Oxygen levels in the midgut lumen of Helicoverpa zea did not differ when caterpillars were fed artificial diet or tomato foliage, suggesting that the insect is capable of reducing the level of ingested oxygen in its gut. An examination of the radial microgradient of oxygen in the gut lumen demonstrated that the midgut epithelium is not a sink for ingested oxygen. However, the midgut contents of larvae fed artificial diet were capable of depleting oxygen. This capacity was reduced by boiling, suggesting that the nearly anoxic state of the midgut lumen in some insects is maintained by endogenous chemical processes. We conclude that low oxygen levels in the gut lumens of most herbivorous insects may greatly reduce the rates of oxidation of ingested plant compounds by oxygen-dependent reactions.

Hydrolyses of alpha- and beta-cellobiosyl fluorides by Cel6A (cellobiohydrolase II) of Trichoderma reesei and Humicola insolens

We have measured the hydrolyses of alpha- and beta-cellobiosyl fluorides by the Cel6A [cellobiohydrolase II (CBHII)] enzymes of Humicola insolens and Trichoderma reesei, which have essentially identical crystal structures [Varrot, Hastrup, Schülein and Davies (1999) Biochem. J. 337, 297-304]. The beta-fluoride is hydrolysed according to Michaelis-Menten kinetics by both enzymes. When the approximately 2.0% of beta-fluoride which is an inevitable contaminant in all preparations of the alpha-fluoride is hydrolysed by Cel7A (CBHI) of T. reesei before initial-rate measurements are made, both Cel6A enzymes show a sigmoidal dependence of rate on substrate concentration, as well as activation by cellobiose. These kinetics are consistent with the classic Hehre resynthesis-hydrolysis mechanism for glycosidase-catalysed hydrolysis of the 'wrong' glycosyl fluoride for both enzymes. The Michaelis-Menten kinetics of alpha-cellobiosyl fluoride hydrolysis by the T. reesei enzyme, and its inhibition by cellobiose, previously reported [Konstantinidis, Marsden and Sinnott (1993) Biochem. J. 291, 883-888] are withdrawn. (1)H NMR monitoring of the hydrolysis of alpha-cellobiosyl fluoride by both enzymes reveals that in neither case is alpha-cellobiosyl fluoride released into solution in detectable quantities, but instead it appears to be hydrolysed in the enzyme active site as soon as it is formed.

CD3X anti-nitrophenyl bispecific diabodies: universal immunotherapeutic tools for retargeting T cells to tumors

We developed a universal recombinant bispecific molecule (BiMol) that is capable of redirecting cytotoxic T cells to tumor cells via tagged anti-tumor ligands such as antibody fragments or cytokines. A recombinant bispecific diabody with binding specificities for the CD3 molecule on T cells as well as for the hapten nitrophenyl (NIP) was produced. This bispecific molecule is capable of redirecting cytotoxic T cells to kill a series of malignant cells, including B cell lymphoma, Hodgkin's lymphoma, and colon carcinoma via NIP-conjugated ligands to tumor-associated antigens. Cytotoxic activity of the diabody was found to be comparable to tetradoma-derived bispecific antibodies with similar specificities. Our findings demonstrate that universal CD3xanti-NIP diabodies could be used for T cell based cellular immunotherapy in a variety of human malignancies. Additionally, these bispecific molecules allow fast and economic testing of tumor-associated antigens on malignant cells for their potential use as immunotherapeutic target structures if corresponding hapten-conjugated antibodies or ligands are available.

A fully human antibody neutralising biologically active human TGFbeta2 for use in therapy

Phage display provides a methodology for obtaining fully human antibodies directed against human transforming growth factor-beta (TGFbeta) suitable for the treatment of fibrotic disorders. The strategy employed was to isolate a human single chain Fv (scFv) fragment that neutralises human TGFbeta2 from a phage display repertoire, convert it into a human IgG4 and then determine its TGFbeta binding and neutralisation properties and its physical characteristics. Several scFv fragments binding to TGFbeta2 were isolated by panning of an antibody phage display repertoire, and subsequent chain shuffling of the selected V(H) domains with a library of V(L) domains. The three most potent neutralising antibodies were chosen for conversion to IgG4 format. The IgG4 antibodies were ranked for their ability to neutralise TGFbeta2 and the most potent, 6B1 IgG4, was chosen for further characterisation. 6B1 IgG4 has a high affinity for TGFbeta2 with a dissociation constant of 0.89 nM as determined using the BIAcore biosensor and only 9% cross-reactivity with TGFbeta3 (dissociation constant, 10 nM). There was no detectable binding to TGFbeta1. 6B1 IgG4 strongly neutralises (IC50 = 2 nM) the anti-proliferative effect of TGFbeta2 in bioassays using TF1 human erythroleukaemia cells. Similarly, there was strong inhibition of binding of TGFbeta2 to cell surface receptors in a radioreceptor assay using A549 cells. 6B1 IgG4 shows no detectable cross-reactivity with related or unrelated antigens by immunocytochemistry or ELISA. The 6B1 V(L) domain has entirely germline framework regions and the V(H) domain has only three non-germline framework amino acids. This, together with its fully human nature, should minimise any potential immunogenicity of 6B1 IgG4 when used in therapy of fibrotic diseases mediated by TGFbeta2.

Directed selection of MIP-1 alpha neutralizing CCR5 antibodies from a phage display human antibody library

The seven trans-membrane chemokine receptor CCR-5 is a coreceptor for macrophage tropic HIV-1 strains. CCR-5 responds to a number of chemokines, including macrophage inflammatory protein (MIP)-1 alpha. We describe the use of MIP-1 alpha in a biotin tyramine-mediated proximity selection to guide the selection of CCR-5-specific phage antibodies from a large phage display human library. Proximity based selections resulted in a population of antibodies recognizing CCR-5 on primary CD4+ lymphocytes, none of which blocked MIP-1 alpha binding to cells. The selected population of phage antibodies were subsequently used as guide molecules for a second phase of selection that was carried out in the absence of MIP-1 alpha. This generated a panel of CCR-5-binding antibodies, of which around 20% inhibited MIP-1 alpha binding to CD4+. The single chain Fvs (scFv) generated by this step-back selection procedure also inhibited MIP-1 alpha-mediated calcium signaling.

Localization of metastable atom beams with optical standing waves: nanolithography at the heisenberg limit

The spatially dependent de-excitation of a beam of metastable argon atoms, traveling through an optical standing wave, produced a periodic array of localized metastable atoms with position and momentum spreads approaching the limit stated by the Heisenberg uncertainty principle. Silicon and silicon dioxide substrates placed in the path of the atom beam were patterned by the metastable atoms. The de-excitation of metastable atoms upon collision with the surface promoted the deposition of a carbonaceous film from a vapor-phase hydrocarbon precursor. The resulting patterns were imaged both directly and after chemical etching. Thus, quantum-mechanical steady-state atom distributions can be used for sub-0.1-micrometer lithography.

Pathfinder selection: in situ isolation of novel antibodies

BACKGROUND

To devise a novel method for targeted recovery of binding molecules from phage libraries.

OBJECTIVES

To assess the potential of the novel technique to the selection of human antibodies to specific cell surface antigens in situ, including carcinoembryonic antigen (CEA), E- and P-selectins, and to the selection of novel antibodies which recognize immobilized purified antigen.

STUDY DESIGN

Recovery of these antibodies from a naive human scFv library was effected using a 'pathfinder' molecule. Monoclonal and polyclonal antibodies, as well as natural ligands can serve as pathfinders when conjugated directly or indirectly to horseradish peroxidase (HRP). In the presence of biotin tyramine these molecules catalyze biotinylation of phage binding in close proximity to the target antigen, allowing specific recovery of 'tagged' phage from the total population using streptavidin. In this way, phage binding to the target itself, or in its immediate proximity, are selectively recovered.

RESULTS

This work demonstrates that an existing binding specificity can be used as a tool to select phage libraries in situ, obviating the need to purify or clone the target.

CONCLUSION

The speed and technical simplicity of this method should find a wide range of applications to phage display libraries, and could be applied to the discovery of new receptors and the elucidation of protein-protein interactions.

Effects of prenatal cocaine exposure on the mesocorticolimbic dopamine system: an in vivo microdialysis study in the rat

Microdialysis studies were conducted on prenatally saline-treated and prenatally cocaine-treated rats, either as pups (10-30 days old) or young adults (40-190 days old), to study the effects of prenatal cocaine exposure on the mesolimbic dopamine (DA) system. In the n. accumbens of saline-treated rats, basal dialysate concentrations of DA were similar in pups and adults; however, the levels of DA metabolites, DOPAC, HVA, and the serotonin metabolite, 5-HIAA, were markedly lower in pups. In pups, prenatal cocaine exposure led to basal dialysate levels of DA in the n. accumbens that were twice control levels; however, there was no difference in response to a period of intermittent tail pinch or an acute injection of cocaine (20 mg/kg). In the adult, basal levels of DA, DOPAC, HVA and 5-HIAA in n. accumbens did not differ across prenatal treatments. However, in prenatally cocaine-treated adults a cocaine injection led to an enhanced rise in extracellular DA compared to controls. In frontal cortex of adult rats, basal levels of DA, DOPAC and HVA did not differ across prenatal treatments; however, basal levels of 5-HIAA in this region were significantly elevated in prenatal-cocaine rats. No group differences were observed in the frontal cortex in response to either tail pinch or cocaine. Thus prenatal cocaine exposure produces an increase in basal extracellular DA in the n. accumbens of pups which returns to normal with aging. While this initial difference normalizes, prenatal cocaine exposure induces other persistent changes in adulthood.

Directing phage selections towards specific epitopes

It is possible to direct selections from antibody repertoires displayed on filamentous phage towards unique epitopes on protein antigens by competing with related molecules. A phage display repertoire of human single chain Fvs (scFvs) was panned three times against foetal haemoglobin (HbF). The selection was dominated by one clone with a Kd of 10 nM but yielded at least 17 others, all of which bound HbF but crossreacted with adult haemoglobin (HbA). To direct selection towards HbF-specific epitopes, the repertoire was preincubated with HbA in solution before each panning. Crossreactive scFvs can form complexes with the soluble HbA and thereby be prevented from binding the immobilized HbF. Four clones with preferential binding to HbF emerged under these conditions. One of these (Hb-1), with a Kd of 6 microM, had exquisite specificity for HbF and could distinguish cells expressing HbF from those expressing HbA by immunocytochemistry and flow cytometry. This antibody has an affinity that is 600-fold lower than the dominant crossreactive clone, and so only emerged under conditions of 'competitive deselection'. Thus, competitive deselection is a viable means for directing selections towards useful epitopes. It permits a more effective 'search' of phage display repertoires and allows the emergence of lower affinity clones with useful specificities. These clones may be useful in themselves or may serve as leads for in vitro affinity maturation.

In vitro selection of a high affinity antibody to oestradiol using a phage display human antibody library

We have isolated a monoclonal antibody binding to oestradiol with high affinity (3.7 nM), and exhibiting a better than 1000-fold selectivity in binding to other steroids. A high affinity antibody with good specificity is essential for the accurate determination of circulating oestradiol levels. To date, conventional hybridoma technology has not yielded a reagent of sufficiently high affinity and specificity for this ligand. The aim of this study was to investigate whether such a reagent was accessible through the engineering of antibodies on the surface of filamentous phage. Antibodies were isolated from a large repertoire of single chain Fv fragments (scFv) derived from non-immunised human donors, with selection and screening procedures biased to favour those binding to free oestradiol. This resulted in an antibody with nanomolar affinity for oestradiol, while affinities for related steroids are in the micromolar range. The relative lack of reactivity for steroids substituted at either end of the molecule suggests that this antibody is unique among anti-steroid monoclonal antibodies in lacking a 'blind-spot'. Our results demonstrate that phage display can provide solutions to problems that have so far proved intractable using conventional hybridoma technology.

Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library

To generate a stable resource from which high affinity human antibodies to any given antigen can be rapidly isolated, functional V-gene segments from 43 non-immunized human donors were used to construct a repertoire of 1.4 x 10(10) single-chain Fv (scFv) fragments displayed on the surface of phage. Fragments were cloned in a phagemid vector, enabling both phage displayed and soluble scFv to be produced without subcloning. A hexahistidine tag has been incorporated to allow rapid purification of scFv by nickel chelate chromatography. This library format reduces the time needed to isolate monoclonal antibody fragments to under two weeks. All of the measured binding affinities show a Kd < 10 nM and off-rates of 10(-3) to 10(-4) s-1, properties usually associated with antibodies from a secondary immune response. The best of these scFvs, an anti-fluorescein antibody (0.3 nM) and an antibody directed against the hapten DTPA (0.8 nM), are the first antibodies with subnanomolar binding affinities to be isolated from a naive library. Antibodies to doxorubicin, which is both immunosuppressive and toxic, as well as a high affinity and high specificity antibody to the steroid hormone oestradiol have been isolated. This work shows that conventional hybridoma technology may be superseded by large phage libraries that are proving to be a stable and reliable source of specific, high affinity human monoclonal antibodies.

Affinity maturation of a high-affinity human monoclonal antibody against the third hypervariable loop of human immunodeficiency virus: use of phage display to improve affinity and broaden strain reactivity

The present study set out to investigate whether phage display could be used to improve the properties of a high-affinity human monoclonal antibody directed against the third hypervariable loop (V3 loop) of human immunodeficiency virus (HIV). The aim was to increase affinity through slowing the dissociation rate (off-rate constant of koff), whilst retaining the ability of this antibody to bind diverse V3 loop sequences. When reformatted as a scFv, the antibody fragment retained the properties of the parental IgG, including the ability to neutralise virus. Heavy and light chains were sequentially replaced with repertoires of variable domains from non-immunised human donors followed by selection on biotinylated synthetic peptide. All selected variants derived from the same germline as the parental antibody. Variants of the light chain provided little if any improvement, whereas two residue changes in VHCDR2 and one in VHFR3 resulted in a reduced koff from gp120 protein of the MN strain (MNgp120) and synthetic V3 loop peptides as measured by surface plasmon resonance using the BIAcore instrument (Pharmacia Biosensor). VHCDR3 was modified using synthetic oligonucleotides and several clones with reduced koff identified, a number of different substitutions occurring at a single residue position. The residues in the heavy chain identified as reducing koff were simultaneously randomised by site-directed mutagenesis, resulting in scFv variants with koff slowed up to sevenfold. Far from compromising recognition of variant loops, binding to these sequences was improved; the koff from synthetic peptides modelled on V3 loop variants being slowed to a degree similar to that observed with MNgp120. All four changes were located towards either extremes of CDRs 2 and 3, suggesting that the mechanism of improvement may be one of alternation of loop conformation. This work illustrates that phage display can be used to tailor the properties of a therapeutic monoclonal antibody in a predefined fashion.

An antibody fragment from a phage display library competes for ligand binding to the low density lipoprotein receptor family and inhibits rhinovirus infection

Recently antibodies with a wide range of binding specificities have been isolated from large repertoires of antibody fragments displayed on filamentous phage, including those that are difficult to raise by immunization. We have used this approach to isolate an antibody fragment against chicken very low density lipoprotein (VLDL) receptor. It binds to the receptor with good affinity (Kaff = 2 x 10(8) M-1) as measured by plasmon surface resonance, and competes for binding of natural ligands (vitellogenin, VLDL, and receptor-associated protein). The antibody also binds to other members of the low density lipoprotein (LDL) receptor family including rat LDL receptor and human and rat low density lipoprotein receptor-related protein (LRP/alpha 2MR), and it competes for binding of receptor-associated protein to LRP/alpha 2MR. Moreover, the antibody fragment inhibits infection of human fibroblasts deficient in LDL-R but expressing LRP/alpha 2MR by human rhinovirus. Binding of the antibody is abolished upon reduction of the receptors and is strictly Ca2+ dependent. The phage antibody thus recognizes the ligand binding site(s) of several members of the LDL receptor family, in contrast to antibodies produced by hybridoma technology.

Demonstration of a nonmagnetic blazed-grating atomic beam splitter

We demonstrate a coherent atomic beam splitter for metastable helium atoms, based on the diffraction of atomic matter waves from a blazed phase grating. The beam splitter is created by driving the two transitions of a three-level V system with differentially detuned standing light waves that have a relative spatial phase shift of pi/2. The light f ields create a potential that is approximately triangular as a function of position in the laser field. Splittings of 38 times the photon momentum have been observed.

Temporal patterns of radiographic infiltration in severely traumatized patients with and without adult respiratory distress syndrome

We prospectively evaluated the patterns of pulmonary structural and functional changes in 100 consecutive surgical intensive care unit trauma patients who had (1) emergent major surgery, (2) a pelvic fracture, or (3) two or more major long bone fractures. For each patient, arterial blood gas measurements (ABGs), central venous pressure (CVP), pulmonary capillary occlusion pressure (PAOP), thoracic compliance, arterial oxygen tension/fraction of inspired oxygen (PAO2/FIO2), pulmonary venous admixture (Qs/Qt), and portable chest roentgenograms were sequentially tracked. The senior staff radiologist interpreted all chest roentgenograms. Pulmonary infiltration was quantitated in each of six fields using a scale ranging from 0 to 4, with 0 being no infiltration and 4 being the maximum. Adult respiratory distress syndrome (ARDS) was defined as follows: Qs/Qt > or = 20%, PAO2/FIO2 < 250 or both; dependence on mechanical ventilation for life support for > or = 24 hours; PAOP or CVP or both < 20 mm Hg; and thoracic compliance < 50 mL/cm H2O. Time zero (T0) the time of onset of ARDS, was defined as the time these criteria were met. Eighty-three of 100 study group patients had penetrating injuries, and 17 were admitted with blunt trauma. Fifty-one of 100 patients developed ARDS: 36 of 51 died. Only 4 of 49 (8%) patients without ARDS died. The injured lungs of patients with and without ARDS had similar amounts of infiltration over most measured time intervals. The noninjured lungs of the ARDS patients, however, had significantly greater infiltration than those without ARDS at T0 and over subsequent time intervals.(ABSTRACT TRUNCATED AT 250 WORDS)

Manganese Flux from Continental Margin Sediments in a Transect Through the Oxygen Minimum

The flux of manganese from continental margin sediments to the ocean was measured with a free-vehicle, benthic flux chamber in a transect across the continental shelf and upper slope of the California margin. The highest fluxes were observed on the shallow continental shelf. Manganese flux decreased linearly with bottom water oxygen concentration, and the lowest fluxes occurred in the oxygen minimum zone (at a depth of 600 to 1000 meters). Although the flux of manganese from continental shelf sediments can account for the elevated concentrations observed in shallow, coastal waters, the flux from sediments that intersect the oxygen minimum cannot produce the subsurface concentration maximum of dissolved manganese that is observed in the Pacific Ocean.

Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains

The display of proteins on the surface of phage offers a powerful means of selecting for rare genes encoding proteins with binding activities. Recently we found that antibody heavy and light chain variable (V) domains fused as a single polypeptide chain to a minor coat protein of filamentous phage fd, could be enriched by successive rounds of phage growth and panning with antigen. This allows the selection of antigen-binding domains directly from diverse libraries of V-genes. Now we show that heterodimeric Fab fragments can be assembled on the surface of the phage by linking one chain to the phage coat protein, and secreting the other into the bacterial periplasm. Furthermore by introducing an amber mutation between the antibody chain and the coat protein, we can either display the antibody on phage using supE strains of bacteria, or produce soluble Fab fragment using non-suppressor strains. The use of Fab fragments may offer advantages over single chain Fv fragments for construction of combinatorial libraries.

Molecular cloning of Taenia taeniaeformis oncosphere antigen genes

Infection of mice with the cestode Taenia taeniaeformis exhibits several important features common to other cestode infections, including the ability to vaccinate with crude antigen mixtures. Partial purification of the protective oncosphere antigens has been reported with a cutout from deoxycholate (DOC) acrylamide gels; this cutout was called fraction II (FII), and comprises approximately 10% of total DOC-soluble oncosphere antigen. Western blots of DOC gels probed with anti-FII antisera revealed a series of 3-5 discrete bands within the FII region. Further fractionation of the FII antigens on DOC gels was impractical due to limitations in supply of oncospheres, so a cDNA library was constructed from 150 ng of oncosphere mRNA and screened with alpha-FII antisera. Two distinct clone families were identified, oncA and oncB. Antibodies affinity-purified on either of two representative members, oncA1 and oncB1, recognised all the FII bands. Individual FII bands excised from a DOC gel resolved into an overlapping series of molecules when re-run on SDS-PAGE, indicating that each FII band consisted of several polypeptides of differing molecular weight. Immunoprecipitates resolved on SDS-PAGE revealed that alpha-FII recognised 3 major oncosphere antigens, of 62, 34 and 25 kDa; antisera against oncB precipitated both the 34- and 25-kDa antigens, whereas alpha-oncA antisera precipitated the 62-kDa antigen. We conclude that oncA and oncB encode the major antigens in the FII complex. The 62-kDa antigen encoded by oncA1 was the only common antigen precipitated by anti-FII and two other antisera raised against different protective extracts, suggesting that it may be a protective component in all three. Southern blot results indicate that oncA and oncB are distinct genes present at low copy number in the genome. Evidence is also presented suggesting that some cestode mRNAs, including oncA, may use variant polyadenylation signals.

Acute effects of single and repeated electroconvulsive therapy on plasma catecholamines and blood pressure in major depressive disorder

The role of activation of adrenergic neurons by electroconvulsive therapy (ECT) in its antidepressant action was studied by examining acute sympathetic nervous system (SNS) responses to ECT during a course of treatment in patients with melancholia. ECT had an acute dose-dependent effect on plasma norepinephrine (NE) level and blood pressure. The postictal increase in plasma NE and blood pressure was independent of electrical seizure duration. Acute levels of NE and epinephrine after ECT correlated positively with ECT dosage. No cumulative effect of repeated ECT was found on the SNS responses. ECT does activate the SNS in a dose-dependent fashion. However, alternative strategies seem necessary for studying the action of ECT on noradrenergic neurons to identify effects that are cumulative, correspond more closely to the time course of its antidepressant action, and correlate with clinical outcome.

Normalization of blunted lymphocyte beta-adrenergic responsivity in melancholic inpatients by a course of electroconvulsive therapy

Electroconvulsive therapy has been reported to desensitize brain beta-adrenergic receptors in rodents, but this effect has not been studied in man. We examined the effect of a course of electroconvulsive therapy on lymphocyte beta-adrenergic responsivity in 19 inpatients with melancholia. Before treatment, beta-adrenergic cyclic adenosine monophosphate response to isoproterenol was significantly blunted in the patients compared with controls. Following a course of electroconvulsive therapy, beta-adrenergic responsivity increased such that patients no longer differed from controls. Thus, blunted lymphocyte beta-adrenergic responsivity is a state-dependent effect of melancholia that can be corrected by a therapeutic course of electroconvulsive therapy. The effect of electroconvulsive therapy on this beta-adrenergic system is in the opposite direction to that reported for rodent forebrain, where electroconvulsive therapy causes desensitization, and may reflect differences between peripheral and central effects, species differences, or disease effects.

Relative efficiency of leukemic cell depletion using anti-murine-IgG1(Fc) or anti-murine-IgG coated immunomagnetic microbeads

Microbeads for immunomagnetic bone marrow purging, to which sheep anti-mouse-IgG1(Fc) antibodies have been linked, and beads linked with antibodies against whole murine immunoglobulin were compared. Competitive binding studies, in which Fc fragments and Fab fragments were titrated onto the microbeads, followed by incubation with 125I-labeled whole mouse Ig, revealed that the beads linked with anti-mouse-IgG1(Fc) specifically bound the Fc region of the murine immunoglobulin molecules. The total amount of antibody of either IgG1 or IgG2 isotype that would adhere to microbeads linked with either type of antibody, as revealed by secondary binding with 125I rabbit antimouse Ig, was identical, suggesting that similar numbers of antibody binding sites were available. In cell depletion studies, it was found that if IgG1 isotype monoclonal antibodies were employed as binding intermediaries between the target cells and the microbeads, the efficiency of target cell depletion was superior with the anti-mouse-IgG1(Fc)-coated beads, even if the amount of MoAb coating the target cells was suboptimal. However, if the intermediary antibodies were of the IgG2 isotype, the efficiency of target cell depletion with these beads was inferior. These findings indicate that the efficiency of immunomagnetic bone marrow purging is dependent upon matching of the targeting MoAb and the secondary antibodies that link to the surface to the microbeads.

The 86-kilodalton antigen from Schistosoma mansoni is a heat-shock protein homologous to yeast HSP-90

We report the sequence of a cDNA clone encoding an 86-kDa polypeptide antigen (p86) from Schistosoma mansoni. Fusion proteins made in Escherichia coli are recognized by human infection sera. The reading frame of this antigen is highly homologous to those of the large heat-shock proteins of Saccharomyces cerevisiae (HSP90) and Drosophila melanogaster (HSP83). mRNA encoding p86 increases in response to heat shock of adult worms, as does HSP70. Comparisons of the sequences of HSP70 and HSP83 homologues show that these two families of heat-shock proteins are not significantly related except for the last four amino acid residues, which are Glu-Glu-Val-Asp in every case. This sequence is not found at the carboxy terminus of any other protein in the current databases.

Vaccination against ovine cysticercosis using a defined recombinant antigen

Cysticercosis caused by larval tapeworms is a major public health problem and a cause of substantial economic losses in the farm-animal industries. Taenia ovis in sheep is a particularly important example. Immunity to reinfection with the larvae has a central role in regulating natural transmission of the parasites, and vaccination with antigens from the early larval oncosphere stage can induce complete protection against infection. As it is impractical to obtain enough oncospheres for a commercial vaccine against these tapeworms, an alternative approach is to use recombinant DNA methods to generate a cheap and plentiful supply of antigens. We report here the expression in Escherichia coli of complementary DNA encoding T. ovis antigens as fusion proteins with the Schistosoma japonicum glutathione S-transferase. Vaccination of sheep with these fusion proteins gave significant, although not complete, immunity against challenge infection with T. ovis eggs. Commercial development of a vaccine is being pursued.

Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase

Plasmid expression vectors have been constructed that direct the synthesis of foreign polypeptides in Escherichia coli as fusions with the C terminus of Sj26, a 26-kDa glutathione S-transferase (GST; EC 2.5.1.18) encoded by the parasitic helminth Schistosoma japonicum. In the majority of cases, fusion proteins are soluble in aqueous solutions and can be purified from crude bacterial lysates under non-denaturing conditions by affinity chromatography on immobilised glutathione. Using batch wash procedures several fusion proteins can be purified in parallel in under 2 h with yields of up to 15 micrograms protein/ml of culture. The vectors have been engineered so that the GST carrier can be cleaved from fusion proteins by digestion with site-specific proteases such as thrombin or blood coagulation factor Xa, following which, the carrier and any uncleaved fusion protein can be removed by absorption on glutathione-agarose. This system has been used successfully for the expression and purification of more than 30 different eukaryotic polypeptides.