The Secret Life of Oilbirds: New Insights into the Movement Ecology of a Unique Avian Frugivore

Background: Steatornis caripensis (the oilbird) is a very unusual bird. It supposedly never sees daylight, roosting in huge aggregations in caves during the day and bringing back fruit to the cave at night. As a consequence a large number of the seeds from the fruit they feed upon germinate in the cave and spoil.

Echolocation signal structure in the Megachiropteran bat Rousettus aegyptiacus Geoffroy 1810

Rousettus aegyptiacus Geoffroy 1810 is a member of the only genus of Megachiropteran bats to use vocal echolocation, but the structure of its brief, click-like signal is poorly described. Although thought to have a simple echolocation system compared to that of Microchiroptera, R. aegyptiacus is capable of good obstacle avoidance using its impulse sonar. The energy content of the signal was at least an order of magnitude smaller than in Microchiropteran bats and dolphins (approximately 4 X 10(-8) J m(-2)). Measurement of the duration, amplitude and peak frequency demonstrate that the signals of this animal are broadly similar in structure and duration to those of dolphins. Gabor functions were used to model signals and to estimate signal parameters, and the quality of the Gabor function fit to the early part of the signal demonstrates that the echolocation signals of R. aegyptiacus match the minimum spectral spread for their duration and amplitude and are thus well matched to its best hearing sensitivity. However, the low energy content of the signals and short duration should make returning echoes difficult to detect. The performance of R. aegyptincus in obstacle avoidance experiments using echolocation therefore remains something of a conundrum.

The role of visual landmarks in the avian familiar area map - Commentary

The question of whether homing pigeons use visual landmarks for orientation from distant, familiar sites is an unresolved issue in the field of avian navigation. Where evidence has been found, the question still remains as to whether the landmarks are used independent of the map and compass mechanism for orientation that is so important to birds. Recent research has challenged the extent to which experiments that do not directly manipulate the visual sense can be used as evidence for compass-independent orientation. However, it is proposed that extending a new technique for research on vision in homing to include manipulation of the compasses used by birds might be able to resolve this issue. The effect of the structure of the visual sense of the homing pigeon on its use of visual landmarks is also considered.

Juvenile Songbirds Compensate for Displacement to Oceanic Islands during Autumn Migration

To what degree juvenile migrant birds are able to correct for orientation errors or wind drift is still largely unknown. We studied the orientation of passerines on the Faroe Islands far off the normal migration routes of European migrants. The ability to compensate for displacement was tested in naturally occurring vagrants presumably displaced by wind and in birds experimentally displaced 1100 km from Denmark to the Faroes. The orientation was studied in orientation cages as well as in the free-flying birds after release by tracking departures using small radio transmitters. Both the naturally displaced and the experimentally displaced birds oriented in more easterly directions on the Faroes than was observed in Denmark prior to displacement. This pattern was even more pronounced in departure directions, perhaps because of wind influence. The clear directional compensation found even in experimentally displaced birds indicates that first-year birds can also possess the ability to correct for displacement in some circumstances, possibly involving either some primitive form of true navigation, or 'sign posts', but the cues used for this are highly speculative. We also found some indications of differences between species in the reaction to displacement. Such differences might be involved in the diversity of results reported in displacement studies so far.

Tracking clock-shifted homing pigeons from familiar release sites

Clock-shifted homing pigeons were tracked from familiar sites 17.1km and 23.5 km from the home loft in Pisa, Italy, using an on-board route recorder. At the first release site, north of home, the majority of clock-shifted birds had relatively straight tracks comparable with those of control birds, At the second release site, south of home, the clock-shifted birds deflected in the direction predicted for the degree of clock shift, with many birds travelling some distance in the wrong direction before correcting their course. The possible role of large-scale terrain features in homing pigeon navigation is discussed.

Homing pigeons use olfactory cues for navigation in England

Although the use of olfactory cues in pigeon navigation is well established, the generality of olfactory navigation remains uncertain because of apparent variability in results gained by different researchers in different regions. We report the results of the first experiments investigating the effect of anosmia on homing pigeons reared in a previously uninvestigated region, southern England. In series 1, experienced birds showed little effect of anosmia induced with zinc sulphate at unfamiliar sites 30 km and 39 km from the loft, but treated birds were significantly poorer than controls at homing from an unfamiliar site 66 km distant (and in pooled results). In series 2, naive (untrained) birds, both control and zinc-sulphate-treated, showed poor homing abilities and initial orientation from sites 25 km, 36 km and 39 km from the loft. Nevertheless, in pooled results, controls showed significantly better homeward orientation than anosmic birds and were significantly more likely to home on the day of release. The most likely explanation for our results is that pigeons are able to use olfactory navigation in southern England, but that for some reason the olfactory map is relatively weak.

Loss of functionally unique species may gradually undermine ecosystems

Functionally unique species contribute to the functional diversity of natural systems, often enhancing ecosystem functioning. An abundance of weakly interacting species increases stability in natural systems, suggesting that loss of weakly linked species may reduce stability. Any link between the functional uniqueness of a species and the strength of its interactions in a food web could therefore have simultaneous effects on ecosystem functioning and stability. Here, we analyse patterns in 213 real food webs and show that highly unique species consistently tend to have the weakest mean interaction strength per unit biomass in the system. This relationship is not a simple consequence of the interdependence of both measures on body size and appears to be driven by the empirical pattern of size structuring in aquatic systems and the trophic position of each species in the web. Food web resolution also has an important effect, with aggregation of species into higher taxonomic groups producing a much weaker relationship. Food webs with fewer unique and less weakly interacting species also show significantly greater variability in their levels of primary production. Thus, the loss of highly unique, weakly interacting species may eventually lead to dramatic state changes and unpredictable levels of ecosystem functioning.

Establishing a minimum dataset for prospective registration of systematic reviews: an international consultation

Background: In response to growing recognition of the value of prospective registration of systematic review protocols, we planned to develop a web-based open access international register. In order for the register to fulfil its aims of reducing unplanned duplication, reducing publication bias, and providing greater transparency, it was important to ensure the appropriate data were collected. We therefore undertook a consultation process with experts in the field to identify a minimum dataset for registration. Methods and Findings: A two-round electronic modified Delphi survey design was used. The international panel surveyed included experts from areas relevant to systematic review including commissioners, clinical and academic researchers, methodologists, statisticians, information specialists, journal editors and users of systematic reviews. Direct invitations to participate were sent out to 315 people in the first round and 322 in the second round. Responses to an open invitation to participate were collected separately. There were 194 (143 invited and 51 open) respondents with a 100% completion rate in the first round and 209 (169 invited and 40 open) respondents with a 91% completion rate in the second round. In the second round, 113 (54%) of the participants reported having previously taken part in the first round. Participants were asked to indicate whether a series of potential items should be designated as optional or required registration items, or should not be included in the register. After the second round, a 70% or greater agreement was reached on the designation of 30 of 36 items. Conclusions: The results of the Delphi exercise have established a dataset of 22 required items for the prospective registration of systematic reviews, and 18 optional items. The dataset captures the key attributes of review design as well as the administrative details necessary for registration.

SurfaceSlide: A Multitouch Digital Pathology Platform

Background: Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation.

Methodology: In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer.

Conclusion: SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human–digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

Characterisation of Genome-Wide PLZF/RARA Target Genes

The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear. We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic cell line U937 conditionally expressing PLZF/RARA. By comparing bound regions found in U937 cells expressing endogenous PLZF with PLZF/RARA-induced U937 cells, we isolated specific PLZF/RARA target gene promoters. We next analysed gene expression profiles of our identified target genes in PLZF/RARA APL patients and analysed DNA sequences and epigenetic modification at PLZF/RARA binding sites. We identify 413 specific PLZF/RARA target genes including a number encoding transcription factors involved in the regulation of haematopoiesis. Among these genes, 22 were significantly down regulated in primary PLZF/RARA APL cells. In addition, repressed PLZF/RARA target genes were associated with increased levels of H3K27me3 and decreased levels of H3K9K14ac. Finally, sequence analysis of PLZF/RARA bound sequences reveals the presence of both consensus and degenerated RAREs as well as enrichment for tissue-specific transcription factor motifs, highlighting the complexity of targeting fusion protein to chromatin. Our study suggests that PLZF/RARA directly targets genes important for haematopoietic development and supports the notion that PLZF/RARA acts mainly as an epigenetic regulator of its direct target genes.

Characterisation of a C1qtnf5 Ser163Arg Knock-In Mouse Model of Late-Onset Retinal Macular Degeneration

A single founder mutation resulting in a Ser163Arg substitution in the C1QTNF5 gene product causes autosomal dominant late-onset retinal macular degeneration (L-ORMD) in humans, which has clinical and pathological features resembling age-related macular degeneration. We generated and characterised a mouse

Detection of streptomycin residues in whole milk using an optical immunobiosensor

The development of an assay for the detection of streptomycin residues in pasteurized whole milk using an optical biosensor (Biacore) is reported. Streptomycin-adipic hydrazide coupled to bovine thyroglobulin was used to produce a sheep polyclonal antibody. The antibody displayed excellent cross-reactivity with dihydrostreptomycin (106%). There was no significant cross-reaction with other aminoglycosides or common antibiotics. Streptomycin was also immobilized onto a CM5 sensor chip to provide a stable, reusable surface. The developed assay permitted the direct analysis of whole milk samples (similar to3.5% fat) without prior centrifugation and defatting. Results were available in 5 min. The limit of detection of the assay was determined as 4.1 ng/mL, well below the European maximum residue limit (MRL) of 200 ng/mL. Repeatability (or coefficient of variation) between runs was determined as 3.5% (100 ng/mL; 0.5 x MRL), 5.7% (200 ng/mL; MRL), and 7.6% (400 ng/mL; 2 x MRL).