Phage display in the study of infectious diseases

Microbial infections are dependent on the panoply of interactions between pathogen and host and identifying the molecular basis of such interactions is necessary to understand and control infection. Phage display is a simple functional genomic methodology for screening and identifying protein-ligand interactions and is widely used in epitope mapping, antibody engineering and screening for receptor agonists or antagonists. Phage display is also used widely in various forms, including the use of fragment libraries of whole microbial genomes, to identify peptide-ligand and protein-ligand interactions that are of importance in infection. In particular, this technique has proved successful in identifying microbial adhesins that are vital for colonization.     

A Small Volume Procedure for Viral Concentration from Water

Small-scale concentration of viruses (sample volumes 1-10 L, here simulated with spiked 100 ml water samples) is an efficient, cost-effective way to identify optimal parameters for virus concentration. Viruses can be concentrated from water using filtration (electropositive, electronegative, glass wool or size exclusion), followed by secondary concentration with beef extract to release viruses from filter surfaces, and finally tertiary concentration resulting in a 5-30 ml volume virus concentrate. In order to identify optimal concentration procedures, two different electropositive filters were evaluated (a glass/cellulose filter [1MDS] and a nano-alumina/glass filter [NanoCeram]), as well as different secondary concentration techniques; the celite technique where three different celite particle sizes were evaluated (fine, medium and large) followed by comparing this technique with that of the established organic flocculation method. Various elution additives were also evaluated for their ability to enhance the release of adenovirus (AdV) particles from filter surfaces. Fine particle celite recovered similar levels of AdV40 and 41 to that of the established organic flocculation method when viral spikes were added during secondary concentration. The glass/cellulose filter recovered higher levels of both, AdV40 and 41, compared to that of a nano-alumina/glass fiber filter. Although not statistically significant, the addition of 0.1% sodium polyphosphate amended beef extract eluant recovered 10% more AdV particles compared to unamended beef extract.     

Transport of groundwater-borne nutrients from watersheds and their effects on coastal waters

Anthropogenic activities on coastal watersheds increase nutrient concentrations of groundwater. As groundwater travels downslope it transports these nutrients toward the adjoining coastal water. The resulting nutrient loading rates can be significant because nutrient concentrations in coastal groundwaters may be several orders of magnitude greater than those of receiving coastal waters. Groundwater-borne nutrients are most subject to active biogeochemical transformations as they course through the upper 1 m or so of bottom sediments. There conditions favor anaerobic processes such as denitrification, as well as other mechanisms that either sequester or release nutrients. The relative importance of advective vs. regenerative pathways of nutrient supply may result in widely different rates of release of nutrients from sediments. The relative activity of denitrifiers also may alter the ratio of N to P released to overlying waters, and hence affect which nutrient limits growth of producers. The consequences of nutrient (particularly nitrate) loading include somewhat elevated nutrient concentrations in the watercolumn, increased growth of macroalgae and phytoplankton, reduction of seagrass beds, and reductions of the associated fauna. The decline in animals occurs because of habitat changes and because of the increased frequency of anoxic events prompted by the characteristically high respiration rates found in enriched waters.     

Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology

Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high‐throughput and multiplexed hybridization‐based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End‐labelled PCR products are hybridized to taxon‐specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37‐day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate.     

The Impact of Seeding Method on Diversity and Plant Distribution in Two Restored Grasslands

Previous studies have compared grassland restoration techniques based on resulting species richness and composition. However, none have determined if different techniques generate different plant distributions in space, which may further impact restoration success. This study tests if there are quadrat‐scale (1 m²) differences between paired drilled and broadcast plantings in diversity, composition, and plant distributions. Higher competition intensity in and more contiguous spaces between rows in drill‐seeded restorations were hypothesized to result in larger patches of native grasses and exotic species. Two paired drill‐ and broadcast‐seeded plantings were sampled in June 2007 in Iowa, U.S.A. Within 10 quadrats in each planting, we measured species abundance with point intercept sampling and plant distributions by dividing the quadrat into 64 cells and recording the most abundant species in each cell. Drilled and broadcast plantings at both sites had similar Simpson’s diversity and evenness. However, the effect of planting type on species richness, composition, and plant distribution was site dependent. Native warm‐season grasses in one site, and exotic species in the second, occupied more space and were distributed in larger patches in drilled plantings. Furthermore, drilled canopies consistently captured more light than broadcast canopies. This suggests that initial differences in seed placement can affect resulting plant distributions, resource use, and potentially long‐term species turnover. Mechanisms structuring vegetation in these communities need to be further investigated to determine if this approach can provide more information on long‐term diversity maintenance in restorations than traditional measures.     

Methods for studying the nematophagous fungus Verticillium chlamydosporium in the root environment

In order to exploit fully the biocontrol potential of the nematophagous fungus Verticillium chlamydosporium, it is important to understand the ecology of the fungus in soil, and interactions with both plant and nematode hosts. Several approaches for studying the fungus in soil and the root environment are compared. These include a semi-selective medium for V. chlamydosporium, PCR primers specific for the fungal -tubulin gene, and monoclonal antibodies. In addition to providing a target for species-specific primers, the -tubulin gene is implicated in resistance to the fungicides used in the semi-selective medium, and the genetic basis for this is investigated. Culture and PCR-based methods were used to screen for the presence of the fungus in field soils known to have been suppressive to cereal cyst nematode and that contained V. chlamydosporium populations. Monoclonal antibodies specific for either hyphae or conidia of the fungus were obtained, and their application as a tool for visualising the infection process on the root was explored.     

An antibody-lectin sandwich assay for quantifying protein glycoforms

We describe an antibody-lectin sandwich assay for quantitation of glycoforms of proteins. The assay uses deglycosylated IgG antibody immobilized on a microtiter plate to capture the protein of interest from the sample. The particular glycoform is then identified by reaction with biotin-labeled lectin, which is measured using streptavidin/alkaline phosphatase. The assay can be adapted to quantitate any protein’s glycoforms by simply substituting the antibody and lectin with specific alternatives,     

Calcified Microspheres as Biological Entities and Their Isolation from Bone

Calcified microspheres, about 1µm in diameter, appear at sites of bone formation where they invest the collagenous matrix, become confluent and disappear. Evidence that the particle boundaries are not lost with compaction but merely deformed is supported in section by the granular histochemical staining of the inorganic phase for bone salt, lipid, fibronectin and acid phosphatase in osteomalacic, acid-etched and normal human bone. Their persistence as discrete objects is confirmed by the application of methods for their isolation from the collagenous matrix of immature mouse calvarium and mature bovine femur. Five methods have been used to extract them and include (i) biochemical, (ii) chemical, (iii) mechanical, (iv) pyrogenous and (v) biological separation. Under the optical microscope, all isolates consisted of similar discrete objects and bridged assemblies, whose birefringence varied with treatment. After decalcification, their organic ghosts remained. Each isolated microsphere had a complex substructure of clusters of non-collagenous calcified filaments surrounding a less dense centre. The filaments were 5nm in diameter with a 5nm periodicity and regular fine interfilamentous connections. It is concluded that the microspheres are independent, complex, pervasive and central to the containment (i.e. packaging) of calcium phosphate in bone. Their extraction will enable further analysis.