Detection and characterization of weak affinity antibody antigen recognition with biomolecular interaction analysis

In biological systems, weak-affinity interactions (association constant, K_a, of less than approximately 10⁴ M ⁻¹) between biomolecules are common and essential to the integrity of such units. However, studies of weak biological interactions are difficult due to the scarcity of analytical methods available for the bioscientist. In this communication, we report on the use of biosensors based on surface plasmon resonance to detect and characterize weak affinity antibody–antigen interactions. Monoclonal antibodies towards carbohydrate antigens were immobilized on sensor surfaces and were used to detect weak binding of the carbohydrate tetraglucose of dissociation constant, K_d, in the millimolar range. Sensorgrams were received in the form of square pulses where the kinetic rate constants were difficult to assess due to the rapid association and dissociation of the antigen to/from the immobilized antibody. © 1997 John Wiley & Sons, Ltd.     

Partial isolation from intact cells of a cell surface-exposed lysophosphatidylinositol-phospholipase C

A novel cell surface phosphoinositide-cleaving phospholipase C (ecto-PLC) activity was isolated from cultured cells by exploiting its presumed external exposure. Biotinylation of intact cells followed by solubilization of the biotinylated proteins from a membrane fraction and recovery onto immobilized-avidin beads, allowed assay of this cell surface enzyme activity apart from the background of the substantial family of intracellular PLCs. Several cell lines of differing ecto-PLC expression were examined as well as cells stably transfected to overexpress the glycosylphosphatidylinositol (GPI)-anchored protein human placental alkaline phosphatase (PLAP) as a cell surface enzyme marker. The resulting bead preparations from ecto-PLC positive cells possessed calcium-dependent PLC activity with preference for lysophosphatidylinositol (lysoPI) rather than phosphatidylinositol (PI). The function of ecto-PLC of intact cells evidently is not to release GPI-anchored proteins at the cell surface, as no detectable Ca²⁺-dependent release of overexpressed PLAP from ecto-PLC-positive cells was observed. To investigate the cell surface linkage of the ecto-PLC itself, intact cells were treated with bacterial PI-PLC to cleave simple GPI anchors, but no decrease in ecto-PLC activity was observed. High ionic strength washes of biotinylated membranes prior to the generation of bead preparations did not substantially reduce the lysoPI-PLC activity. The results verify that the ecto-PLC is truly cell surface-exposed, and unlike other members of the PLC family that are thought to be peripheral membrane proteins, this novel lysoPI-PLC is most likely a true membrane protein. J. Cell. Biochem. 65:550–564. © 1997 Wiley-Liss Inc.     

Medium optimization for spore production of Coniothyrium minitans using statistically‐based experimental designs

Statistically‐based experimental designs were used to optimize a chemically defined solid medium for the spore production of Coniothyrium minitans. In the first optimization step the influence of starch, urea, phosphate, magnesium, calcium, thiamin and trace elements on spore production was evaluated using a fractional factorial design. Starch and trace elements influenced spore production positively while urea affected spore production negatively. The other components had no significant influence on spore production. In the second and third steps the concentrations of starch, urea and trace elements were further optimized using central composite designs and response surface analysis. This optimization strategy allowed the spore production to be increased by a factor 7 from 4 × 10⁹ to almost 3 × 10¹⁰ spores per Petri dish of 9 cm diameter. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 92–100, 1999.     

The use of biosensor technology for the engineering of antibodies and enzymes

Recently developed scientific instrumentation featuring surface plasmon resonance detection allows the detection of biomolecular interactions in real time and without chemical modification of the binding partners. These biosensors are proving invaluable tools in protein engineering, particularly in research aimed at the isolation and improvement of protein binders and catalysts from macromolecular repertoires containing billions of individual members. This article reviews the use of biosensor technology for the isolation and characterization of engineered antibodies and enzymes. Copyright © 1999 John Wiley & Sons, Ltd.     

A multispecific monoclonal antibody G2 recognizes at least three completely different epitope sequences with high affinity

A monoclonal antibody (mAb) G2 possesses an unusual characteristic of reacting with at least three proteins (ATP6V1C1, SEPT3, and C6H10orf76) other than its original antigen, chicken prion protein (ChPrP). The epitopes on ChPrP and ATP6V1C1 have been identified previously. In this study, we identified the epitope in the third protein, SEPT3. Interestingly, there was no amino acid sequence similarity among the epitopes on the three proteins. These epitopes had high binding affinities to G2 (K _D = ～10^?7 M for monovalent binding and K _D = ～10^?9 M for divalent binding), as determined using a SPR biosensor. This is the first report on a three‐in‐one mAb recognizing completely different epitope sequences with high affinity. Additionally, competitive ELISA indicated that the binding sites on G2, specific for the three different epitopes, overlapped, suggesting that the antigen‐binding site may be flexible in the free form and capable of adapting to at least three different conformations to enable interactions with three different antigens.     

Whole‐genome sequencing approaches for conservation biology: Advantages,limitations and practical recommendations

Whole‐genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled‐individual DNA (Pool‐seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.     

Observations and tracking of killer whales (Orcinus orca) with shore‐based X‐band marine radar at a marine energy test site

The Atlantic killer whale (Orcinus orca) is a top‐level marine predator with a global range, being found in all of Earth's oceans. The potential interaction between killer whales and marine renewable energy projects requires surveillance and monitoring efforts that call for new technologies, with marine radar showing promise in the field. Marine radar images recorded at the European Marine Energy Centre (EMEC) were used to track a pair of male killer whales undertaking Surface Active Behavior (SAB) with visual observations used as validation. Using a tidal prediction model, the tide‐adjusted, radar‐derived target speeds between SAB events provide estimates of swim speeds averaging 4 m/s and time between SAB events of 30 s. The similarities between the radar signatures of the animals and sea clutter, combined with their low occurrence compared to other imaged phenomena renders automatic detection with this system difficult. However, the combination of opportunistic radar imagery and independent visual observation has allowed the radar signature of one form of killer whale SAB to be documented. It is hoped that with a greater number of validated observations such as these that automated, radar‐based identification and the benefits it will bring to long‐term observations at MRE sites will be possible.     

Evidence for the functions of surface‐active behaviors in humpback whales (Megaptera novaeangliae)

As part of their social sound repertoire, migrating humpback whales (Megaptera novaeangliae) perform a large variety of surface‐active behaviors, such as breaching and repetitive slapping of the pectoral fins and tail flukes; however, little is known about what factors influence these behaviors and what their functions might be. We investigated the potential functions of surface‐active behaviors in humpback whale groups by examining the social and environmental contexts in which they occurred. Focal observations on 94 different groups of whales were collected in conjunction with continuous acoustic monitoring, and data on the social and environmental context of each group. We propose that breaching may play a role in communication between distant groups as the probability of observing this behavior decreased significantly when the nearest whale group was within 4,000 m compared to beyond 4,000 m. Involvement in group interactions, such as the splitting of a group or a group joining with other whales, was an important factor in predicting the occurrence of pectoral, fluke, and peduncle slapping, and we suggest that they play a role in close‐range or within‐group communication. This study highlights the potentially important and diverse roles of surface‐active behaviors in the communication of migrating humpback whales.