Photography as a research tool

This paper attempts to delineate a research design and method for using the photograph as a research tool. An analysis of the photograph's research suitability will consider its ability to structure “articulated visual statements” of the community and to generate “explanatory models” for analysis and interpretation. A significant aspect of the study is the material it offers for a discussion on an important methodological dimension for acquiring knowledge through visual research data. The question is not whether to use photographs as research tools, but how to fit the photograph into the research design and process.     

Railways as a potential bird census tool in citizen-science projects: a preliminary study

Capsule: Bird surveys carried out during a railway journey capture a significant proportion of the species and individuals recorded through line transects (LT).

Aims: To explore the suitability of railways as a bird census tool in a scenario where bird data massively recorded by passengers of the railway network could be collected through appropriate web portals and cell phone technologies.

Methods: Railway and walked transects were conducted along the 40?km rail line connecting the towns of Valencia and Buñol, Spain. From June 2012 to May 2016, I carried out a weekly survey of birds from the railway line looking through the train window. Additionally, to assess the efficacy of train surveys, a railway section 11?km long was surveyed monthly on foot from December 2014 to November 2015.

Results: Train surveys were unsuitable to detect many woodland birds but were relatively efficient in detecting raptors, open-field and aquatic bird species. About 75% of non-woodland species were detected from the train, and there was a positive correlation between counts obtained through train and LT; mean detection rate per species was between 50% and 80% depending on the season. Overall, larger and numerically more important species were better quantified. Further, detection rates of several medium-large species were greater than one, indicating a superior efficiency of train over LT. Only for nine species were data sufficient to calculate population trends, which in several cases were similar to those obtained through monitoring programmes operating at coarser spatial scales.

Conclusions: The relatively high performance of the method and the fact that broad geographical areas could be easily surveyed (even on a daily basis) by many people in a relatively short time make railway-based bird surveys a candidate to be used in citizen science programmes.     

Functional genomics as a tool in virus research

Genomics is the study of an organism’s entire genome. It started out as a great scientific endeavor in the 1990s which aimed to sequence the complete genomes of certain biological species. However viruses are not new to this field as complete viral genomes have routinely been sequenced since the past thirty years. The ‘genomic era’ has been said to have revolutionized biology. This knowledge of full genomes has created the field of functional genomics in today’s post-genomic era, which, is in most part concerned with the studies on the expression of the organism’s genome under different conditions. This article is an attempt to introduce its readers to the application of functional genomics to address and answer several complex biological issues in virus research.     

Zebrafish as a tool in Alzheimer's disease research

Alzheimer's disease is the most prevalent form of neurodegenerative disease. Despite many years of intensive research our understanding of the molecular events leading to this pathology is far from complete. No effective treatments have been defined and questions surround the validity and utility of existing animal models. The zebrafish (and, in particular, its embryos) is a malleable and accessible model possessing a vertebrate neural structure and genome. Zebrafish genes orthologous to those mutated in human familial Alzheimer's disease have been defined. Work in zebrafish has permitted discovery of unique characteristics of these genes that would have been difficult to observe with other models. In this brief review we give an overview of Alzheimer's disease and transgenic animal models before examining the current contribution of zebrafish to this research area. This article is part of a Special Issue entitled Zebrafish Models of Neurological Diseases.     

Detergent resistance as a tool in membrane research

The biological membrane is a complicated matrix wherein different lipid environments are thought to exist. The more ordered or raft environment has been perceived biochemically accessible via its relative resistance to detergent. This paper outlines the protocols developed in our laboratory for the analysis of such detergent-resistant membranes (DRMs). We stress the fact that DRMs are artifactual in nature and should not be equivocated to lipid rafts, their usefulness being limited to assigning raft-association potential most convincingly when changes in DRM composition are induced by biochemically/physiologically relevant events. These protocols are completed in 1-2 d.     

Zebrafish as a tool in Alzheimer's disease research

Alzheimer's disease is the most prevalent form of neurodegenerative disease. Despite many years of intensive research our understanding of the molecular events leading to this pathology is far from complete. No effective treatments have been defined and questions surround the validity and utility of existing animal models. The zebrafish (and, in particular, its embryos) is a malleable and accessible model possessing a vertebrate neural structure and genome. Zebrafish genes orthologous to those mutated in human familial Alzheimer's disease have been defined. Work in zebrafish has permitted discovery of unique characteristics of these genes that would have been difficult to observe with other models. In this brief review we give an overview of Alzheimer's disease and transgenic animal models before examining the current contribution of zebrafish to this research area. This article is part of a Special Issue entitled Zebrafish Models of Neurological Diseases.     

Detours in bird migration

Bird migration routes often follow detours where passages across ecological barriers are reduced in extent. This occurs in spite of the fact that long barrier crossings are within the birds' potential flight range capacity. Long-distance flights are associated with extra energy costs for transport of the heavy fuel loads required. This paper explores how important the fuel transport costs, estimated on the basis of flight mechanics, may be to explain detours for birds migrating by flapping flight. Maximum detours in relation to expanse of the barrier are predicted for cases where birds travel along the detour by numerous short flights and small fuel reserves, divide the detour into a limited number of flight steps, and where a reduced barrier passage is included in the detour. The principles for determining the optimum route, often involving a shortcut across part of the barrier, are derived. Furthermore, the effects of differences in fuel deposition rates and in transport costs for the profitability of detours are briefly considered. An evaluation of a number of observed and potential detours in relation to the general predictions of maximum detours, indicates that reduction of fuel transport costs may well be a factor of widespread importance for the evolution of detours in bird migration at wide ecological barriers.     

Yeast as a tool for apoptosis research

Apoptosis is a unique cell suicide process that plays important roles in a wide variety of developmental and normal physiological processes in animal species, and causes diseases when inappropriately controlled. Although yeast do not possess the proteases ultimately responsible for the morphological events recognized as apoptosis, these simple unicellular eukaryotes can serve as a powerful tool for apoptosis researchers. Ectopic expression of several human and animal apoptosis proteins in either budding or fission yeast results in phenotypes that create opportunities for genetic screens. Recent exploitation of yeast as tools for studying human apoptosis-regulatory proteins has yielded novel insights into cell death mechanisms, suggesting strategies for identification of genes and drugs that modulate the functions of proteins involved in apoptosis control.     

Storms drive altitudinal migration in a tropical bird

Although migration is a widespread and taxonomically diverse behaviour, the ecological factors shaping migratory behaviour are poorly understood. Like other montane taxa, many birds migrate along elevational gradients in the tropics. Forty years ago, Alexander Skutch postulated that severe storms could drive birds to migrate downhill. Here, we articulate a novel mechanism that could link storms to mortality risks via reductions in foraging time and provide, to our knowledge, the first tests of this hypothesis in the White-ruffed Manakin (Corapipo altera), a small partially migratory frugivore breeding on the Atlantic slope of Costa Rica. As predicted, variation in rainfall was associated with plasma corticosterone levels, fat stores, plasma metabolites and haematocrit. By collecting data at high and low elevation sites simultaneously, we also found that high-elevation residents were more adversely affected by storms than low elevation migrants. These results, together with striking temporal capture patterns of altitudinal migrants relative to storms, provide, to our knowledge, the first evidence that weather-related risks incurred by species requiring high food intake rates can explain altitudinal migrations of tropical animals. These findings resolve conflicting evidence for and against food limitation being important in the evolution of this behaviour, and highlight how endogenous and exogenous processes influence life-history trade-offs made by individuals in the wild. Because seasonal storms are a defining characteristic of most tropical ecosystems and rainfall patterns will probably change in ensuing decades, these results have important implications for understanding the ecology, evolution and conservation of tropical animals.     

Evolution of bird migration in a biogeographical context

We infer from the literature that migratory habits of birds evolved in various phylogenetic lineages and biogeographical contexts, either after gradual range expansion into seasonal habitats, or due to environmental changes within established breeding ranges. Shifts of breeding ranges are the results of interactions between colonization due to dispersal and extinction due to deteriorating conditions. Range expansions provide a platform for the evolution of migration from the newly colonized areas towards seasonally favourable non‐breeding areas. A comparison of palaeoclimatic changes with concurrent evolution and distribution of passerine birds suggests that at least some of the basic genera of the Passerida radiated on the northern continents when quasi‐tropical or subtropical climates prevailed. The Passerida may be a special case, but they suggest that ‘tropical origin’ does not necessarily imply a ‘southern origin’ of migratory species. Climate deterioration required adaptations either towards on‐site survival under harsh conditions or towards escape movements allowing improved non‐breeding survival in less seasonal climates or with reversed seasonality. Taxon‐specific life‐history traits and environmental conditions favoured either sedentary or migratory lines of adaptation. Repeated climate variation induced range shifts and concurrent increases or decreases in the expression of migratory behaviour. Two examples of waders suggest that the principle of range shift, followed by the development of migratory habits, is also applicable for other taxonomic groups.     

Chemiluminescence microscopy as a tool in biomedical research.

Chemiluminescence has become a standard tool in biomedical research. Chemiluminescent probes are used for immunoassays, nucleic acid identification, reporter gene assays, measuring enzyme activity, and the detection of ions and small molecules such as Ca2+, ATP, NO, O2- and H2O2. Along with the development of new chemiluminescent probes, significant progress has been made in techniques to measure chemiluminescence. Ultra-sensitive photometers or luminometers have become widely available and can be obtained with automatic injectors and microplate readers. In addition, imaging photon detectors have been developed that allow the imaging of chemiluminescence from gels, blots, and microplates. Imaging photon detectors have also been attached to microscopes and allow imaging of chemiluminescent probes and reporter genes in cells and tissues. Specific methods of photon collection, storage, and analysis have been developed for microscopic imaging of chemiluminescence. Two of these methods are discussed in detail. The first is a method of data storage that allows days of continuous imaging without creating oversized files. The second is a method for calibrating photon imaging microscopes using a low-light standard. Such calibration will be helpful for comparing the performance of various photon imaging systems and for comparing data obtained in different laboratories.     

Tryptophan-tryptophan energy migration as a tool to follow apoflavodoxin folding

Submolecular details of Azotobacter vinelandii apoflavodoxin (apoFD) (un)folding are revealed by time-resolved fluorescence anisotropy using wild-type protein and variants lacking one or two of apoFD's three tryptophans. ApoFD equilibrium (un)folding by guanidine hydrochloride follows a three-state model: native ↔ unfolded ↔ intermediate. In native protein, W128 is a sink for Förster resonance energy transfer (FRET). Consequently, unidirectional FRET with a 50-ps transfer correlation time occurs from W167 to W128. FRET from W74 to W167 is much slower (6.9 ns). In the intermediate, W128 and W167 have native-like geometry because the 50-ps transfer time is observed. However, non-native structure exists between W74 and W167 because instead of 6.9 ns the transfer correlation time is 2.0 ns. In unfolded apoFD this 2.0-ns transfer correlation time is also detected. This decrease in transfer correlation time is a result of W74 and W167 becoming solvent accessible and randomly oriented toward one another. Apparently W74 and W167 are near-natively separated in the folding intermediate and in unfolded apoFD. Both tryptophans may actually be slightly closer in space than in the native state, even though apoFD's radius increases substantially upon unfolding. In unfolded apoFD the 50-ps transfer time observed for native and intermediate folding states becomes 200 ps as W128 and W167 are marginally further separated than in the native state. Apparently, apoFD's unfolded state is not a featureless statistical coil but contains well-defined substructures. The approach presented is a powerful tool to study protein folding.     

Nocturnal bird migration in the Bay of Biscay as observed by a thermal-imaging camera

Capsule: Bird migration was recorded by an infrared device at three sites in the southeastern Bay of Biscay, indicating seasonal east–west differences in migration flow.

Aims: The main aims of this study were to quantify and describe nocturnal migration dynamics in proximity of a sea barrier, and to assess seasonal and geographical drivers of migration patterns.

Methods: A thermal-imaging camera was used at two coastal study sites (Punta Galea, Cape Higuer) in spring and three study sites (coast: Punta Galea, Cape Higuer; inland: Iregua Valley) in autumn for four hours from sunset over 90 nights in 2014 and 2015.

Results: Migration was strong at both coastal sites in early spring. Autumn migration was weak at the western coast, but strong at the eastern coast and inland. Tailwind had no significant effect on migration intensity, but migration ceased during strong cross- or headwinds despite clear skies. The majority of the targets were passerines.

Conclusions: The patterns observed suggest spring migration occurs on a broader front, potentially involving sea crossing further to the west, while autumn migration concentrates more eastwards over land. In both seasons, there was no significant response to wind conditions.     

The biological race concept as a research tool

In present day research in human biology, the validity of the concept of biological race rests on its utility as a research tool. The methodology of this research into human biological variability is a multidimensional application of the comparative method, utilizing, as one dimension, genetic distance. The body of this paper suggests two generalizing principles for the establishment of genetic distance. Genetic distance may occur due to physical or temporal isolation or in conjunction with environmental differences. A brief analysis of the fifteenth century human populations examines the relationship between these principles and presently used racial taxonomic systems. It is concluded that race may be defined operationally as a rough measure of genetic distance in human populations and as such may function as an informational construct in the multidisciplinary area of research in human biology.