Immunocytochemical localization of tubulin with colloidal gold in cilia of rabbit tracheal epithelial cultures

Ciliated tracheal epithelia cell cultures were investigated immunocytochemically with anti-tubulin and colloidal gold. When rabbit tracheal cultures were fixed in paraformaldehyde, treated with acetone, anti-tubulin and a second antibody coupled to FITC, fluorescence was associated with cytoskeletal and axonemal microtubules. Cilia covering the apical surface of the ciliated tracheal cells fluoresced very brightly thus facilitating identification of this cell type. Electron microscopy of tracheal cultures fixed as above, treated with Triton-X 100 and incubated in anti-tubulin and protein A coupled to colloidal gold resulted in the highly specific localization of tubulin in ciliary axonemes and basal bodies. Omission of primary or secondary antibody resulted in extremely low levels of fluorescence while no colloidal gold particles could be detected in cultures at the electron microscopy level when rabbit anti-tubulin was omitted.     

Losing the last feather: feather loss as an antipredator adaptation in birds

Birds often lose feathers during predation attempts, and thisability has evolved as a means of escape. Because predatorsare more likely to grab feathers on the rump and the back thanon the ventral side of an escaping bird, we predicted that theformer feathers would have evolved to be relatively looselyattached as an antipredator strategy in species that frequentlydie from predation. We estimated the force required to removefeathers from the rump, back, and breast by pulling featherswith a spring balance from a range of European bird speciesin an attempt to investigate ecological factors associated withease of feather loss during predation attempts. The force requiredto loosen a feather from the rump was less than that requiredto loosen a feather from back, which in turn was less than thatrequired to loosen a feather from the breast. The relative forceneeded to loosen rump feathers compared with feathers from theback and the breast was smaller for prey species preferred bythe most common predator of small passerine birds, the sparrowhawkAccipiter nisus. Likewise, the relative force was also smallerin species with a high frequency of complete tail loss amongfree-living birds, which we used as an index of the frequencyof failed predation attempts. The relative force required toremove feathers from the rump was smaller in species with ahigh frequency of fear screams, another measure of the relativeimportance of predation as a cause of death. Feather loss requiredparticularly little force among solitarily breeding bird speciesthat suffer the highest degree of predation. Antipredator defensein terms of force required to remove feathers from the rumpwas larger in species with a strong antiparasite defense interms of T-cell–mediated immune response. These findingsare consistent with the hypothesis that different defenses areantagonistic and that they are traded off against each other.     

Selecting high-dimensional mixed graphical models using minimal AIC or BIC forests

Background  

Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems.     

Song and immunological condition in male barn swallows (Hirundo rustica)

Male secondary sexual characters may have evolved as intra-or intersexual signals of male phenotypic or genetic quality.In birds, singing performance may have the function to honestlyreveal health and vigor of individual males. Infectious diseasesand poor body conditions would therefore be expected to negativelyinfluence singing performance. Since bird pathogens are knownto elicit both a humoral and a cell-mediated immune response,it can be predicted that a negative relationship exists betweensinging performance and activity of the immune system. Thisprediction was tested for the first time in this correlationalstudy. The relationships between song rate and features andhematological variables (concentration of leukocytes in peripheralblood, ratio of gamma-globulins to total plasma proteins, bloodcell sedimentation rate, hematocrit) and body condition wereanalyzed in a population of bam swallows (Hirundo rustica).Song rate was negatively correlated with lymphocyte concentrationand with the ratio of gamma-globulins to plasma proteins. Spectrographicanalysis showed that features of song were not significantlycorrelated with hematological variables or body condition. Thelevel of circulating testosterone was not correlated with songrate nor hematological variables. This study is the first toshow a correlation between a bird's singing performance andhematological profile and suggests that song rate of male barnswallows may reflect their health status. Song in this speciesmight thus have evolved because it allows prospecting femalesto assess aspects of phenotypic and/or genetic quality of potentialmates     

The influence of allyl trenbolone (Regumate) on the timing,duration and endocrinology of parturition in sows

A study was undertaken to evaluate the effects of using an oral progestagen for synchronisation of parturition in the sow. Multiparous Landrace X Large White sows were fed 20 mg allyl trenbolone daily from day 110 to 115 of gestation then 15 mg on day 116 (Group R; N = 12); untreated sows of similar background served as controls (Group C; N = 9). Blood samples, taken at 8-h intervals from day 110 of gestation to onset of parturition, then every 4 h until parturition was complete, were assayed for plasma levels of progesterone, unconjugated oestrone, cortisol and prolactin. Duration of farrowing, incidence of stillbirths and individual piglet birth weights were recorded. Five Group R sows farrowed during the period of progestagen administration, while for the remaining 7, the mean interval from last progestagen treatment to emergence of first piglet was 31.6 ±5.5 h. Gestation length, duration of parturition, and mean interval between successive births all were longer in Group R than in Group C (116.5 ± 0.34 compared with 115.0 ± 0.52 days, P < 0.01; 9.73 ± 1.98 compared with 3.08 ± 0.70 h, P < 0.01; and 53.4 ± 10.2 compared with 16.2 ± 2.4 min., P < 0.01, respectively). No significant treatment differences were apparent for litter size at birth, proportion stillborn or piglet birth weights. Profile analysis showed that plasma progesterone levels in Group R were lower (P < 0.05) during the 30 h prefarrowing, suggesting a longer mean interval between functional luteolysis and parturition in these animals. In both Groups plasma levels of unconjugated oestrone rose in the prefarrowing period, the levels being higher (P < 0.05) in Group R Peak oestrone levels occurred at the commencement of, and had declined to low levels by the completion of, farrowing. Cortisol levels exhibited a pattern similar to that of oestrone, although peak levels at parturition were lower in Group R (P < 0.01). Plasma prolactin levels in the 24 h prepartum rose faster and reached higher levels (P < 0.05) in Group C than Group R, but the difference was no longer apparent subsequent to first piglet emergence. It is concluded that the use of this progestagen to delay parturition upset the synchronisation of endocrine events at farrowing, resulting in an increased duration of parturition.     

OpenAWSEM with Open3SPN2: A fast,flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.     

A review of potential techniques for identifying individual stoats (Mustela erminea) visiting control or monitoring stations

Abstract

We review ways of individually identifying stoats (Mustela erminea) and similar small mammals from visits to bait stations or to monitoring devices in the field. Tracking devices are the cheapest and most practical method currently available of measuring the presence of a particular species, but there has been little research on the recognition of individuals. Elongation of tracking tunnels, or using sooty plates rather than ink to record prints, may improve detectability of individual markings. Recording visits to bait stations or tracking tunnels from DNA sequencing of hair or skin samples is likely to be prohibitively expensive for many monitoring programmes. Identification of stoats visiting bait stations or tracking tunnels using electronic devices has great potential, but these techniques are impracticably expensive because stoats move over such large areas that individual receivers and data loggers would be needed for each bait station. Chemical bait markers such as rhodamine B may be the most suitable method for identifying which animals have used a particular bait station.