Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls

The last decade has seen a dramatic increase in the use of small‐angle scattering for the study of biological macromolecules in solution. The drive for more complete structural characterization of proteins and their interactions, coupled with the increasing availability of instrumentation and easy‐to‐use software for data analysis and interpretation, is expanding the utility of the technique beyond the domain of the biophysicist and into the realm of the protein scientist. However, the absence of publication standards and the ease with which 3D models can be calculated against the inherently 1D scattering data means that an understanding of sample quality, data quality, and modeling assumptions is essential to have confidence in the results. This review is intended to provide a road map through the small‐angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data. Examples of current best practice are given that also demonstrate the power of the technique to advance our understanding of protein structure and function.     

A Comparative Test of Mechanized and Manual Transplanting of Eelgrass, Zostera marina, in Chesapeake Bay

Abstract The laborious process of manual seagrass transplanting has often limited the size of seagrass restoration efforts. This study tested the efficiency of a mechanized planting boat, previously used for transplanting Halodule wrightii, relative to manual transplanting methods for establishing Zostera marina in Chesapeake Bay. Eelgrass planting was conducted at two sites, one each in the Rappahannock and James rivers, in October 2001. The methods were evaluated by three criteria: (1) initial planting success = proportion of attempted planting units (PUs) initially established (number confirmed in sediment by divers/number attempted); (2) survival = proportion of the initially established PUs persisting over 1, 4, and 24 weeks; and (3) efficiency = labor (in person·seconds) invested in each surviving PU. Initial planting success was significantly lower for the planting boat (24 and 56% at the Rappahannock and James sites, respectively) than for manual transplanting (100% at both sites). At the Rappahannock site, survival of initially established PUs declined over time for both methods, but while mean survival was always higher for manually planted rows, differences in survival between methods were not statistically significant. At the James site, survival to 1 and 4 weeks was significantly lower for the machine than for the manual method, but survival to 24 weeks was not significantly different. While the machine was able to attempt PUs faster than the manual method (2.2 s/PU vs. 5.8 s/PU, respectively), this speed was offset by poorer planting success rates, resulting in a much greater total labor investment for each machine‐planted PU that persisted to 24 weeks than for each similarly persisting manually planted PU (40.6 person·seconds/PU and 22.4 person·seconds/PU, respectively, averaged across sites). In summary, those PUs successfully planted by the machine survived similarly to PUs planted by hand, but as a result of poorer initial planting success, the machine required a greater investment of labor and plant donor stock for each PU surviving to 24 weeks. Therefore, in its tested configuration this planting boat is not a significant improvement over the manual method for transplanting eelgrass.     

Histamine release factor from Dermanyssus gallinae (De Geer): characterization and in vitro assessment as a protective antigen

A cDNA encoding a 174-amino-acid orthologue of a tick histamine release factor (HRF) was identified from the haematophagous poultry red mite Dermanyssus gallinae. The predicted D. gallinae HRF protein (Dg-HRF-1) sequence is highly conserved with the tick HRFs (identity 52-54%) and to a lesser degree with translationally controlled tumour proteins (TCTP) from mammals and other invertebrates (range 38-47%). Phylogenetically, Dg-HRF-1 partitions with the tick HRF clade suggesting a shared linage and potentially similar function(s). A recombinant Dg-HRF-1 protein (rDg-HRF-1) was produced and shown to induce degranulation of rat peritoneal mast cells in vitro, confirming conservation of the histamine-releasing function in D. gallinae. Polyclonal antibodies were generated in rabbits and hens to rDg-HRF-1. Western blotting demonstrated that native Dg-HRF is a soluble protein and immunohistochemical staining of mite sections revealed that the distribution of Dg-HRF, although ubiquitous, is more common in mite reproductive, digestive and synganglion tissues. A survey of hens housed continuously in a mite-infested commercial poultry unit failed to identify IgY specific for recombinant or native Dg-HRF, indicating that Dg-HRF is not exposed to the host during infestation/feeding and may therefore have potential as a vaccine using the concealed antigen approach. To test the protective capability of rDg-HRF-1, fresh heparinised chicken blood was enriched with yolk-derived anti-Dg-HRF IgY antibodies and fed to semi-starved mites using an in vitro feeding system. A statistically significant increase in mortality was shown (P = 0.004) in mites fed with anti-Dg-HRF IgY after just one blood meal. The work presented here demonstrates, to our knowledge for the first time, the feasibility of vaccinating hens with recombinant D. gallinae antigens to control mite infestation and the potential of rDg-HRF-1 as a vaccine antigen.     

Improved abundance prediction from presence–absence data

Aim   Many ecological surveys record only the presence or absence of species in the cells of a rectangular grid. Ecologists have investigated methods for using these data to predict the total abundance of a species from the number of grid cells in which the species is present. Our aim is to improve such predictions by taking account of the spatial pattern of occupied cells, in addition to the number of occupied cells.
Innovation   We extend existing prediction models to include a spatial clustering variable. The extended models can be viewed as combining two macroecological regularities, the abundance–occupancy regularity and a spatial clustering regularity. The models are estimated using data from five tropical forest censuses, including three Panamanian censuses (4, 6 and 50 ha), one Costa Rican census (16 ha) and one Puerto Rican census (16 ha). A serpentine grassland census (8 × 8 m) from northern California is also studied.
Main conclusions   Taking account of the spatial clustering of occupied cells improves abundance prediction from presence–absence data, reducing the mean square error of log-predictions by roughly 54% relative to a benchmark Poisson predictor and by roughly 34% relative to current prediction methods. The results have high statistical significance.     

Dynein is required for polarized dendritic transport and uniform microtubule orientation in axons

Axons and dendrites differ in both microtubule organization and in the organelles and proteins they contain. Here we show that the microtubule motor dynein has a crucial role in polarized transport and in controlling the orientation of axonal microtubules in Drosophila melanogaster dendritic arborization (da) neurons. Changes in organelle distribution within the dendritic arbors of dynein mutant neurons correlate with a proximal shift in dendritic branch position. Dynein is also necessary for the dendrite-specific localization of Golgi outposts and the ion channel Pickpocket. Axonal microtubules are normally oriented uniformly plus-end-distal; however, without dynein, axons contain both plus- and minus-end distal microtubules. These data suggest that dynein is required for the distinguishing properties of the axon and dendrites: without dynein, dendritic organelles and proteins enter the axon and the axonal microtubules are no longer uniform in polarity.     

Apolipoprotein [a] genotype influences isoform dominance pattern differently in African Americans and Caucasians

Plasma lipoprotein [a] (Lp[a]) concentrations are inversely associated with, and largely determined by, apolipoprotein [a] (apo[a]) gene size, a highly polymorphic trait. We studied if, within an individual, the smaller apo[a] isoform always dominated, whether there was interaction between the two alleles, and whether these features differed between Caucasians and African Americans. We determined apo[a] gene sizes, apo[a] protein sizes and relative amounts, and plasma Lp[a] levels in 430 individuals (263 Caucasians and 167 African Americans). Of the 397 heterozygotes with at least one detectable apo[a] isoform (238 Caucasians and 159 African Americans), the larger allele dominated in 28% of Caucasians and 23% of African Americans, while the smaller allele dominated in 56% of Caucasians and 45% of African Americans. In Caucasians, dominance of the smaller allele increased with Lp[a] levels, from 44% at Lp[a] < or = 30 nM to 81% at Lp[a] >100 nM (P < 0.0001). Dominance by the smaller allele increased with increasing size of the larger allele in both groups but with the smaller allele only in African Americans. There was no interaction between apo[a] alleles within genotypes; one apo[a] isoform level was not associated with the other isoform level, and isoform levels were not affected by the difference in size. More of the dominance pattern was explained by Lp[a] level and apo[a] genotype in African Americans than in Caucasians (29% vs. 13%). Thus, genotype influences isoform-specific Lp[a] levels and dominance patterns differently in African Americans and in Caucasians.     

Deletion of the Bax gene disrupts sexual behavior and modestly impairs motor function in mice

Cell death is a nearly ubiquitous feature of the developing nervous system, and differential death in males and females contributes to several well studied sex differences in neuron number. Nonetheless, the functional importance of neuronal cell death has been subjected to few direct tests. Bax, a pro-apoptotic protein, is required for cell death in many neural regions. Deletion of the Bax gene in mice increases neuron number in several areas and eliminates sex differences in cell number in the brain and spinal cord. Here, sexual and motor behaviors were examined in Bax-/- mice and their wild-type siblings to test the functional consequences of preventing Bax-dependent cell death. Animals were gonadectomized in adulthood and provided with ovarian hormones or with testosterone for tests of feminine and masculine sexual behaviors, respectively. Wild-type mice exhibited a sex difference in feminine sexual behavior, with high lordosis scores in females and low scores in males. This sex difference was eliminated by Bax deletion, with very low receptivity exhibited by both male and female Bax-/- mice. Masculine sexual behavior was not sexually dimorphic among wild-type mice, but mounts and pelvic thrusts were nearly eliminated in Bax-/- mice of both sexes. Motor strength and performance at low speeds on a RotaRod apparatus did not differ by sex or Bax gene status. However, Bax-/- animals exhibited impairments on the RotaRod at higher speeds. Thus, developmental cell death may be required for masculine and feminine sexual behaviors and the fine tuning of motor coordination.