Migration Routes and Staging Areas of Trans-Saharan Turtle Doves Appraised from Light-Level Geolocators

The identification of migration routes, wintering grounds and stopover sites are crucial issues for the understanding of the Palearctic-African bird migration system as well as for the development of relevant conservation strategies for trans-Saharan migrants. Using miniaturized light-level geolocators we report a comprehensive and detailed year round track of a granivorous trans-Saharan migrant, the European Turtle Dove (Streptopelia turtur). From five recovered loggers, our data provide new insights on migratory journeys and winter destinations of Turtle Doves originating from a breeding population in Western France. Data confirm that Turtle Doves wintered in West Africa. The main wintering area encompassed Western Mali, the Inner Delta Niger and the Malian/Mauritanian border. Some individuals also extended their wintering ranges over North Guinea, North-West of Burkina Faso and the Ivory-Coast. Our results reveal that all individuals did not spend the winter period at a single location; some of them experienced a clear eastward shift of several hundred kilometres. We also found evidence for a loop migration pattern, with a post-breeding migration flyway lying west of the spring route. Finally, we found that on their way back to breeding grounds Turtle Doves needed to refuel after crossing the Sahara desert. Contrary to previous suggestions, our data reveal that birds used stopover sites for several weeks, presumably in Morocco and North Algeria. This later finding is a crucial issue for future conservation strategies because environmental conditions on these staging areas might play a pivotal role in population dynamics of this declining species.     

Three-Dimensional Tracking of Small Aquatic Organisms Using Fluorescent Nanoparticles

Tracking techniques are vital for the understanding of the biology and ecology of organisms. While such techniques have provided important information on the movement and migration of large animals, such as mammals and birds, scientific advances in understanding the individual behaviour and interactions of small (mm-scale) organisms have been hampered by constraints, such as the sizes of existing tracking devices, in existing tracking methods. By combining biology, chemistry and physics we here present a method that allows three-dimensional (3D) tracking of individual mm-sized aquatic organisms. The method is based on in-vivo labelling of the organisms with fluorescent nanoparticles, so-called quantum dots, and tracking of the organisms in 3D via the quantum-dot fluorescence using a synchronized multiple camera system. It allows for the efficient and simultaneous study of the behaviour of one as well as multiple individuals in large volumes of observation, thus enabling the study of behavioural interactions at the community scale. The method is non-perturbing – we demonstrate that the labelling is not affecting the behavioural response of the organisms – and is applicable over a wide range of taxa, including cladocerans as well as insects, suggesting that our methodological concept opens up for new research fields on individual behaviour of small animals. Hence, this offers opportunities to focus on important biological, ecological and behavioural questions never before possible to address.     

Year-Round Schools and the Politics of Time

This ethnographic study explores the politics of time in a multitrack, yearround school in inner-city Los Angeles. We analyze different types and experiences of time within the school and time collisions across institutions in this densely populated immigrant community. Viewing time as a contested commodity, we examine the politics behind the presumed impartiality of the clock and calendar. The school's year-round schedule is especially problematic, involving multiple tracks with lengthened days and a shortened school year. We show how issues of educational equity go to the core of debates over alternative school schedules.     

Tracking Auxin Receptors Using Functional Approaches

Functional approaches toward the identification of auxin receptors developed along two major lines: the isolation and characterization of mutants or transgenic plants affected in their responses to the hormone and the study of early auxin effects at the cell level such as expression of specific genes or modifications of plasma membrane properties. The combination of these approaches with those aiming at the molecular characterization of auxin binding proteins as putative auxin receptors allowed to bring further insight into the mechanisms of auxin perception by plant cells. Studies of membrane responses to auxin clearly demonstrated the existence of elementary response chains to auxin at the plasma membrane, the activation of auxin responsive proteins leading to changes in the membrane potential via the stimulation of the proton pump ATPase or the modulation of ion channels. A two-component model is proposed for the organization of functional auxin perception units at the plasma membrane, comprising an auxin-binding moiety related to the major auxin-binding protein from maize (ZmER-abp1), associated to a transmembrane protein. Current research investigates the relevance of this model and tries to assess whether early responses at the plasma membrane share common perception or transduction steps with gene expression responses and participate in more integrated biological responses to auxin.     

Tracking Protests Using Geotagged Flickr Photographs

Recent years have witnessed waves of protests sweeping across countries and continents, in some cases resulting in political and governmental change. Much media attention has been focused on the increasing usage of social media to coordinate and provide instantly available reports on these protests. Here, we investigate whether it is possible to identify protest outbreaks through quantitative analysis of activity on the photo sharing site Flickr. We analyse 25 million photos uploaded to Flickr in 2013 across 244 countries and regions, and determine for each week in each country and region what proportion of the photographs are tagged with the word “protest” in 34 different languages. We find that higher proportions of “protest”-tagged photographs in a given country and region in a given week correspond to greater numbers of reports of protests in that country and region and week in the newspaper The Guardian. Our findings underline the potential value of photographs uploaded to the Internet as a source of global, cheap and rapidly available measurements of human behaviour in the real world.     

Increased Endoparasite Infection in Late-Arriving Individuals of a Trans-Saharan Passerine Migrant Bird

Earlier migration in males than in females is the commonest pattern in migrating passerines and is positively related to size dimorphism and dichromatism. The early arrival of males is a costly trait that may confer reproductive advantages in terms of better territories and/or mates. Given the physiological cost of migration, early migrants are those in best condition and accordingly the prevalence, load, and/or diversity of parasites is expected to increase in both sexes for late migrants. To test this hypothesis, we sampled 187 trans-Saharan migrant garden warblers Sylvia borin and 64 resident serins Serinus serinus (as a control for potential circannual patterns in parasite load) during spring migration in Spain. We assessed the prevalence of blood parasites (Haemoproteus, Plasmodium, and Leucocytozoon) and the prevalence and load of intestinal parasites (mainly coccidians and spirurids). The relationship between parasite (prevalence, load, and richness) and the timing of passage through a stopover area was tested using generalized linear models. Protandry occurs in the monomorphic garden warbler and males migrated on average 5.5 days before females. Intestinal parasite richness increased with the date of migration. The timing of migration was unrelated to the presence or load of the other parasite groups analyzed. Our results support the idea that the timing of migration is a condition-dependent trait and suggests that multiple intestinal parasite infestations could delay migration in birds. Even in monomorphic species parasites may play a role in sexual selection by delaying the arrival of the most infected individuals at breeding grounds, thereby further increasing the benefits of mating with early-arriving individuals.     

Extended Emitter Target Tracking Using GM-PHD Filter

If equipped with several radar emitters, a target will produce more than one measurement per time step and is denoted as an extended target. However, due to the requirement of all possible measurement set partitions, the exact probability hypothesis density filter for extended target tracking is computationally intractable. To reduce the computational burden, a fast partitioning algorithm based on hierarchy clustering is proposed in this paper. It combines the two most similar cells to obtain new partitions step by step. The pseudo-likelihoods in the Gaussian-mixture probability hypothesis density filter can then be computed iteratively. Furthermore, considering the additional measurement information from the emitter target, the signal feature is also used in partitioning the measurement set to improve the tracking performance. The simulation results show that the proposed method can perform better with lower computational complexity in scenarios with different clutter densities.     

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

The Australasian and South American marsupial mammals, such as kangaroos and opossums, are the closest living relatives to placental mammals, having shared a common ancestor around 130 million years ago. The evolutionary relationships among the seven marsupial orders have, however, so far eluded resolution. In particular, the relationships between the four Australasian and three South American marsupial orders have been intensively debated since the South American order Microbiotheria was taxonomically moved into the group Australidelphia. Australidelphia is significantly supported by both molecular and morphological data and comprises the four Australasian marsupial orders and the South American order Microbiotheria, indicating a complex, ancient, biogeographic history of marsupials. However, the exact phylogenetic position of Microbiotheria within Australidelphia has yet to be resolved using either sequence or morphological data analysis. Here, we provide evidence from newly established and virtually homoplasy-free retroposon insertion markers for the basal relationships among marsupial orders. Fifty-three phylogenetically informative markers were retrieved after in silico and experimental screening of ∼217,000 retroposon-containing loci from opossum and kangaroo. The four Australasian orders share a single origin with Microbiotheria as their closest sister group, supporting a clear divergence between South American and Australasian marsupials. In addition, the new data place the South American opossums (Didelphimorphia) as the first branch of the marsupial tree. The exhaustive computational and experimental evidence provides important insight into the evolution of retroposable elements in the marsupial genome. Placing the retroposon insertion pattern in a paleobiogeographic context indicates a single marsupial migration from South America to Australia. The now firmly established phylogeny can be used to determine the direction of genomic changes and morphological transitions within marsupials.     

Effect of Geolocators on Migration and Subsequent Breeding Performance of a Long-Distance Passerine Migrant

Geolocators are small light-weight data loggers used to track individual migratory routes, and their use has increased exponentially in birds. However, the effects of geolocators on individual performance are still poorly known. We studied geolocator effects on a long-distance migrating passerine bird, the northern wheatear (Oenanthe oenanthe L.). We asked the general question of whether geolocators affect migratory behaviour and subsequent reproductive performance of small passerines by comparing arrival time, breeding time, breeding success and survival of geolocator versus control birds of known identity and breeding history. During two years geolocator birds (n=37) displayed a lower apparent survival (30%) as compared to controls (45%, n=164). Furthermore, returning geolocator birds (n=12) arrived on average 3.5 days later, started laying eggs 6.3 days later, and had lower nest success (25%) than control birds (78%). Our results suggest that geolocators affect migratory performance with carry-over effects to the timing of breeding and reproductive success in the subsequent breeding season. We discuss the implications of such geolocator effects for the study of migratory strategies of small passerines in general and suggest how to identify and investigate such effects in the future.     

Geolocators reveal migration and pre-breeding behaviour of the critically endangered Balearic Shearwater Puffinus mauretanicus

Using combined miniature archival light and salt-water immersion loggers, we characterise the year-round individual at-sea movements of Europe's only critically endangered seabird, the Balearic shearwater Puffinus mauretanicus, for the first time. Focusing on the non-breeding period, we show that all of the 26 breeding birds tracked from their breeding site on Mallorca in the Mediterranean Sea successfully made a 2-4 month migration into the Atlantic Ocean, where they utilised well-defined core areas off Portuguese and French coasts. As well as identifying high-risk areas in the Atlantic, our results confirm that breeding birds spend most of the year concentrated around productive waters of the Iberian shelf in the western Mediterranean. Migration phenology appeared largely unrelated to the subsequent (distinctly synchronous) breeding attempt, suggesting that any carry-over effects were compensated for during a long pre-laying period spent over winter in the Mediterranean. Using the light and salt-water immersion data alone we were also able to characterise the pattern of pre-laying visits to the colony in considerable detail, demonstrating that breeding pairs appear to coordinate their over-day visits using a high frequency of night-time visits throughout the winter. Our study shows that geolocation technology is a valuable tool for assessing the spatial distribution of risks to this critically endangered species, and also provides a low-impact method for remotely observing the detailed behaviour of seabird species that may be sensitive to disturbance from traditional study methods.     

Methods for Generating Year-Round Access to Amphioxus in the Laboratory

Cephalochordates, commonly known as amphioxus, are key to understanding vertebrate origins. However, laboratory work suffers from limited access to adults and embryonic material. Here we report the design and experimental validation of an inland marine facility that allows establishing stable amphioxus colonies in the laboratory and obtaining embryos at any time of day and over almost the entire year, far exceeding natural conditions. This is achieved by mimicking the natural benthic environment, natural day- and moon- light, natural substrate and by providing a strictly controlled and seasonally fluctuating temperature regimen. Moreover, supplemented algae diets allow animals to refill their gonads in consecutive years. Spontaneous spawning, a major problem in previous setups, no longer occurs in our facility; instead, all breeding is induced and fertilization occurs fully in vitro. Our system makes amphioxus a standard laboratory animal model.     

Tracking Cells in GFP-transgenic Zebrafish Using the Photoconvertible PSmOrange System

The rapid development of transparent zebrafish embryos (Danio rerio) in combination with fluorescent labelings of cells and tissues allows visualizing developmental processes as they happen in the living animal. Cells of interest can be labeled by using a tissue specific promoter to drive the expression of a fluorescent protein (FP) for the generation of transgenic lines. Using fluorescent photoconvertible proteins for this purpose additionally allows to precisely follow defined structures within the expression domain. Illuminating the protein in the region of interest, changes its emission spectrum and highlights a particular cell or cell cluster leaving other transgenic cells in their original color. A major limitation is the lack of known promoters for a large number of tissues in the zebrafish. Conversely, gene- and enhancer trap screens have generated enormous transgenic resources discretely labeling literally all embryonic structures mostly with GFP or to a lesser extend red or yellow FPs. An approach to follow defined structures in such transgenic backgrounds would be to additionally introduce a ubiquitous photoconvertible protein, which could be converted in the cell(s) of interest. However, the photoconvertible proteins available involve a green and/or less frequently a red emission state¹ and can therefore often not be used to track cells in the FP-background of existing transgenic lines. To circumvent this problem, we have established the PSmOrange system for the zebrafish^2,3. Simple microinjection of synthetic mRNA encoding a nuclear form of this protein labels all cell nuclei with orange/red fluorescence. Upon targeted photoconversion of the protein, it switches its emission spectrum to far red. The quantum efficiency and stability of the protein makes PSmOrange a superb cell-tracking tool for zebrafish and possibly other teleost species.     

Tracking the Unconscious Generation of Free Decisions Using UItra-High Field fMRI

Recently, we demonstrated using functional magnetic resonance imaging (fMRI) that the outcome of free decisions can be decoded from brain activity several seconds before reaching conscious awareness. Activity patterns in anterior frontopolar cortex (BA 10) were temporally the first to carry intention-related information and thus a candidate region for the unconscious generation of free decisions. In the present study, the original paradigm was replicated and multivariate pattern classification was applied to functional images of frontopolar cortex, acquired using ultra-high field fMRI at 7 Tesla. Here, we show that predictive activity patterns recorded before a decision was made became increasingly stable with increasing temporal proximity to the time point of the conscious decision. Furthermore, detailed questionnaires exploring subjects'' thoughts before and during the decision confirmed that decisions were made spontaneously and subjects were unaware of the evolution of their decision outcomes. These results give further evidence that FPC stands at the top of the prefrontal executive hierarchy in the unconscious generation of free decisions.     

Multiplexed Nanometric 3D Tracking of Microbeads Using an FFT-Phasor Algorithm

Many single-molecule biophysical techniques rely on nanometric tracking of microbeads to obtain quantitative information about the mechanical properties of biomolecules such as chromatin fibers. Their three-dimensional (3D) position can be resolved by holographic analysis of the diffraction pattern in wide-field imaging. Fitting this diffraction pattern to Lorenz-Mie scattering theory yields the bead’s position with nanometer accuracy in three dimensions but is computationally expensive. Real-time multiplexed bead tracking therefore requires a more efficient tracking method, such as comparison with previously measured diffraction patterns, known as look-up tables. Here, we introduce an alternative 3D phasor algorithm that provides robust bead tracking with nanometric localization accuracy in a z range of over 10 μm under nonoptimal imaging conditions. The algorithm is based on a two-dimensional cross correlation using fast Fourier transforms with computer-generated reference images, yielding a processing rate of up to 10,000 regions of interest per second. We implemented the technique in magnetic tweezers and tracked the 3D position of over 100 beads in real time on a generic CPU. The accuracy of 3D phasor tracking was extensively tested and compared to a look-up table approach using Lorenz-Mie simulations, avoiding experimental uncertainties. Its easy implementation, efficiency, and robustness can improve multiplexed biophysical bead-tracking applications, especially when high throughput is required and image artifacts are difficult to avoid.     

Tracking and Predicting Human Somatic Cell Reprogramming Using Nuclear Characteristics

Reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) generates valuable resources for disease modeling, toxicology, cell therapy, and regenerative medicine. However, the reprogramming process can be stochastic and inefficient, creating many partially reprogrammed intermediates and non-reprogrammed cells in addition to fully reprogrammed iPSCs. Much of the work to identify, evaluate, and enrich for iPSCs during reprogramming relies on methods that fix, destroy, or singularize cell cultures, thereby disrupting each cell’s microenvironment. Here, we develop a micropatterned substrate that allows for dynamic live-cell microscopy of hundreds of cell subpopulations undergoing reprogramming while preserving many of the biophysical and biochemical cues within the cells’ microenvironment. On this substrate, we were able to both watch and physically confine cells into discrete islands during the reprogramming of human somatic cells from skin biopsies and blood draws obtained from healthy donors. Using high-content analysis, we identified a combination of eight nuclear characteristics that can be used to generate a computational model to predict the progression of reprogramming and distinguish partially reprogrammed cells from those that are fully reprogrammed. This approach to track reprogramming in situ using micropatterned substrates could aid in biomanufacturing of therapeutically relevant iPSCs and be used to elucidate multiscale cellular changes (cell-cell interactions as well as subcellular changes) that accompany human cell fate transitions.     

DySCo: Quantitating Associations of Membrane Proteins Using Two-Color Single-Molecule Tracking

We present a general method called dynamic single-molecule colocalization for quantitating the associations of single cell surface molecules labeled with distinct autofluorescent proteins. The chief advantages of the new quantitative approach are that, in addition to stable interactions, it is capable of measuring nonconstitutive associations, such as those induced by the cytoskeleton, and it is applicable to situations where the number of molecules is small.     

Europe, Continent of Migrants

Gender and Migration in Southern Europe: Women on the Move. Floya Anthias and Gabriella Lazaridis. eds. New York: Berg, 2000. 263 pp.
Eldorado or Fortress? Migration in Southern Europe. Russell King. Gabriella Lazaridis. and Charalambos G. Tsadanidis. eds. New York: St. Martin's Press, 2000. 368 pp.
Guests and Aliens. Saskia Sassen. New York: The New Press, 1999. 202 pp.