Improved immunomatrix methods to detect protein:protein interactions

Immunoprecipitation (IP) and coimmunoprecipitation (co-IP) are key techniques for studying protein-protein interactions. These methods utilize immobilized Protein A or Protein G to isolate antibody-bound target antigens. The main disadvantage of traditional IP and co-IP is that the conditions used to elute the precipitated antigen also release the antibody thus contaminating the antigen and destroying the antibody support. To overcome these problems, we describe two methods to generate a reusable antibody support by cross-linking the antibody to immobilized Protein A or Protein G, or by coupling it directly to the resin (see Scheme 1). Antibody cross-linking can be done in 1 h while antibody coupling requires 4 h. IP or co-IP is accomplished by incubating the antibody resin with the protein sample. Washes and elutions are carried out in a spin column to reduce resin loss and decrease assay time. Target proteins are eluted with 0.1 M glycine (pH 2.8) and the resin-bound antibody is re-equilibrated in phosphate-buffered saline (PBS) for reuse. Our studies have demonstrated that the immobilization efficiency for the antibody coupling method was similar for several species of antibody. Furthermore, we illustrate that using both methods of antibody immobilization yield IP and co-IP results similar to traditional protocols but eliminate the antibody heavy and light chain contamination.     

Towards an e-biology of ageing: integrating theory and data

Ageing is a highly complex process; it involves interactions between numerous biochemical and cellular mechanisms that affect many tissues in an organism. Although work on the biology of ageing is now advancing quickly, this inherent complexity means that information remains highly fragmented. We describe how a new web-based modelling initiative is seeking to integrate data and hypotheses from diverse biological sources.     

Phosphorylation of ATPase subunits of the 26S proteasome

The 26S proteasome complex plays a major role in the non-lysosomal degradation of intracellular proteins. Purified 26S proteasomes give a pattern of more than 40 spots on 2D-PAGE gels. The positions of subunits have been identified by mass spectrometry of tryptic peptides and by immunoblotting with subunit-specific antipeptide antibodies. Two-dimensional polyacrylamide gel electrophoresis of proteasomes immunoprecipitated from [³²P]phosphate-labelled human embryo lung L-132 cells revealed the presence of at least three major phosphorylated polypeptides among the regulatory subunits as well as the C8 and C9 components of the core 20S proteasome. Comparison with the positions of the regulatory polypeptides revealed a minor phosphorylated form to be S7 (MSS1). Antibodies against S4, S6 (TBP7) and S12 (MOV34) all cross-reacted at the position of major phosphorylated polypeptides suggesting that several of the ATPase subunits may be phosphorylated. The phosphorylation of S4 was confirmed by double immunoprecipitation experiments in which 26S proteasomes were immunoprecipitated as above and dissociated and then S4 was immunoprecipitated with subunit-specific antibodies. Antibodies against the non-ATPase subunit S10, which has been suggested by others to be phosphorylated, did not coincide with the position of a phosphorylated polypeptide. Some differences were observed in the 2D-PAGE pattern of proteasomes immunoprecipitated from cultured cells compared to purified rat liver 26S proteasomes suggesting possible differences in subunit compositions of 26S proteasomes.     

Iron-rich particles in embryos of seeds from the family Pinaceae

Summary Iron-rich particles, previously reported in seeds of members of the genus Pinus, were found in radicle-hypocotyl tissues of dry embryos from eight other genera in the family Pinaceae. Thus, these Fe-rich particles are of common occurrence in seeds of this conifer family. These particles were most difficult to locate inPseudolarix amabilis, which has green embryos. Energy-dispersive X-ray analysis was used to determine the elements present in conifer Fe-rich particles and phytoferritin deposits in pea embryo axes. Ferich particles from all species studied contained mainly Fe and P but also contained considerable K and Mg. Abietoideae group I (genera Cedrus andAbies) had lower Fe P ratios compared to all the other combined subfamilies within the Pinaceae. Pea phytoferritin deposits contained markedly lower amounts of P relative to Fe based on peakto-background ratios and quantitative values calculated by using a ferric phosphate standard. We also found, for the first time, that pea phytoferritin contained considerable K. A strong similarity was found between the energy-dispersive X-ray analysis spectra from Ferich particles and portions of a laboratory-synthesized Fe, K, Mg phytate salt. Phytate is a common mineral-nutrient storage compound in seeds. The possibility of these Fe-rich particles being phytoferritin cannot be ruled out, but if they are phytoferritin, they have lower Fe P ratios than almost all other ferritins reported to date.Abbreviations EDX energy-dispersive X-ray     

The American Alligator Detects Food Chemicals in Aquatic and Terrestrial Environments

American alligators (Alligator mississippiensis) were offered raw meat or animal carcasses under water or on land in experiments where only chemoreception could be used to discriminate between these and control materials. Alligators also were presented with aqueous extracts and airborne chemicals from meat. Juvenile alligators, tested in indoor tanks, opened more cheesecloth packets containing meat than control packets when these materials were placed under water and on platforms above the water surface. Adult alligators, tested in outdoor semi-natural enclosures, removed more cheesecloth-wrapped meat presented under water, and more of both meat and raccoon (Procyon lotor) carcasses placed under perforated baskets on land, than control materials. Juvenile alligators, tested in tanks partially filled with water, exhibited more lateral head movements and mouth-openings to an aqueous beef extract than to water alone. Juvenile alligators, tested in an olfactometer, exhibited more gular pumps to airborne chemicals from beef than to distilled water. These experiments indicate that alligators may use chemical cues to locate food both on land and under water, and that they detect both water- and airborne chemicals from meat.     

A Spatiotemporal Database to Track Human Scrub Typhus Using the VectorMap Application

Scrub typhus is a potentially fatal mite-borne febrile illness, primarily of the Asia-Pacific Rim. With an endemic area greater than 13 million km² and millions of people at risk, scrub typhus remains an underreported, often misdiagnosed febrile illness. A comprehensive, updatable map of the true distribution of cases has been lacking, and therefore the true risk of disease within the very large endemic area remains unknown. The purpose of this study was to establish a database and map to track human scrub typhus. An online search using PubMed and the United States Armed Forces Pest Management Board Literature Retrieval System was performed to identify articles describing human scrub typhus cases both within and outside the traditionally accepted endemic regions. Using World Health Organization guidelines, stringent criteria were used to establish diagnoses for inclusion in the database. The preliminary screening of 181 scrub typhus publications yielded 145 publications that met the case criterion, 267 case records, and 13 serosurvey records that could be georeferenced, describing 13,739 probable or confirmed human cases in 28 countries. A map service has been established within VectorMap (www.vectormap.org) to explore the role that relative location of vectors, hosts, and the pathogen play in the transmission of mite-borne scrub typhus. The online display of scrub typhus cases in VectorMap illustrates their presence and provides an up-to-date geographic distribution of proven scrub typhus cases.     

Comprehensive optimization of a single-chain variable domain antibody fragment as a targeting ligand for a cytotoxic nanoparticle

Antibody-targeted nanoparticles have the potential to significantly increase the therapeutic index of cytotoxic anti-cancer therapies by directing them to tumor cells. Using antibodies or their fragments requires careful engineering because multiple parameters, including affinity, internalization rate and stability, all need to be optimized. Here, we present a case study of the iterative engineering of a single chain variable fragment (scFv) for use as a targeting arm of a liposomal cytotoxic nanoparticle. We describe the effect of the orientation of variable domains, the length and composition of the interdomain protein linker that connects VH and VL, and stabilizing mutations in both the framework and complementarity-determining regions (CDRs) on the molecular properties of the scFv. We show that variable domain orientation can alter cross-reactivity to murine antigen while maintaining affinity to the human antigen. We demonstrate that tyrosine residues in the CDRs make diverse contributions to the binding affinity and biophysical properties, and that replacement of non-essential tyrosines can improve the stability and bioactivity of the scFv. Our studies demonstrate that a comprehensive engineering strategy may be required to identify a scFv with optimal characteristics for nanoparticle targeting.     

Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.     

Estimating body size of fossil sirenians

Estimates of fossil sirenian body size are important for understanding niche partitioning among possibly sympatric species. Because of the paucity of complete fossil skeletons, we explored the utility of three morphometric predictors of body size: (condylobasal skull length [BSL]; occipital condyle width [OCW]; and foramen magnum width [FMW]) in extant sirenians—Florida manatees (Trichechus manatus latirostris) and dugongs (Dugong dugon)—and then applied these to obtain estimates of body size in extinct sirenian taxa. Condylobasal length of the skull is a more accurate predictor of body size in extant Florida manatees and dugongs than are width of the occipital condyles or width of the foramen magnum. Body length (BL) is predicted more accurately than is body weight (BW) for all three morphometric predictors. For our sample of fossil sirenians, BSL, OCW, and FMW were used to generate predicted BLs and BWs. Preliminary assessments of fossil sirenian faunas from Florida and India suggest that body mass could have been one of several possible important morphological parameters accounting for feeding niche separation.     

Synthesis and biological activity of a series of tetrasubstituted-imidazoles as P2X7 antagonists

A series of analogues of the pyrazole lead 1 were synthesized in which the heterocyclic core was replaced with an imidazole. A number of potent antagonists were identified and structure–activity relationships (SAR) were investigated both with respect to activity at the P2X₇ receptor and in vitro metabolic stability. Compound 10 was identified as a potent P2X₇ antagonist with reduced in vitro metabolism and high solubility.