The underestimated role of carrion in vertebrates' diet studies

Aim

Despite the increasing scientific evidence on the importance of carrion in the ecology and evolution of many vertebrates, scavenging is still barely considered in diet studies. Here, we draw attention to how scientific literature has underestimated the role of vertebrates as scavengers, identifying the ecological traits that characterize those species whose role as scavengers could have gone especially unnoticed.

Location

Global.

Time Period

1938–2022.

Major Taxa Studied

Terrestrial vertebrate scavengers.

Methods

We analysed and compared (a) the largest database available on scavenging patterns by carrion-consuming vertebrates, (b) 908 diet studies about 156 scavenger species and (c) one of the most complete databases on bird and mammal diets (Elton Traits database). For each of these 156 species, we calculated their scavenging degree (i.e. proportion of carcases where the species is detected consuming carrion) as a proxy for carrion consumption, and related their ecological traits with the probability of being identified as scavengers in diet studies and in the Elton Traits database.

Results

More than half of the species identified as scavengers at monitored carcasses were not assigned carrion as food source in their diet studies nor in the Elton Traits database. Using a subset of study sites, we found a direct relationship between a species' scavenging degree and its rate of carrion biomass removal. In addition, scavenger species, which were classified as non-predators and mammals had a lower probability of being identified as scavengers in diet studies and in the Elton Traits database, respectively.

Main Conclusions

Our results clearly indicate an underestimation of the role of scavenging in vertebrate food webs. Given that detritus recycling is fundamental to ecosystem functioning, we encourage further recognition and investigation of the role of carrion as a food resource for vertebrates, especially for non-predator species and mammals with higher scavenging degree.     

Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites

Expansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major, which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to the rapidness of image acquisition and three-dimensional reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic and multivesicular tubule-associated microtubules of L. major. We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. Three-dimensional reconstruction of an entire volume of these cells provided details on the morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.     

Condition factor and diet of the catfish Loricariichthys castaneus (Castelnau, 1855): gender differences in three tropical reservoirs

Condition factor and diet of male and female of Loricariichthys castaneus were studied in three tropical reservoirs in which it is the most abundant species of fish. The females had higher condition factors than males in all three environments, but their diet differed from males only in the best-preserved ecosystem (Lajes Reservoir). Loricariichthys castaneus was considered as detritivorous-omnivorous. Starvation during breeding possibly contributes to a decrease of condition factor in males. By studying the gut content, sex-specific foraging and the influence of the diet importance in relation to the available food items in the three reservoirs were analyzed.     

Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy

Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super‐resolution.     

Stable isotope evidence of ontogenetic changes in the diet of gizzard shad Dorosoma cepedianum

Stable sulphur isotopic composition (δ³⁴S) of gizzard shad Dorosoma cepedianum was used to investigate the seasonal and ontogenetic variation in the diet of young and adult fish. This study evaluated fish from a hypereutrophic lake that had recently undergone a 40% reduction of large (>300 mm total length, L _T) D. cepedianum biomass as part of a biomanipulation experiment, which aimed at reducing internal nutrient loading. Dorosoma cepedianum δ³⁴S values showed evidence of ontogenetic changes with young fish (<200 mm L _T) depending more on benthic food sources than adults (>200 mm L _T). The δ³⁴S composition of the adult fish suggested an increasing importance of zooplankton in the diet, although benthic food sources remained part of the diet of all D. cepedianum collected in this study. The results indicated that benthic feeding is used by D. cepedianum of all sizes, suggesting that biomanipulation efforts may need to target all sizes of fish to realize benefits.     

High-resolution single-shot phase-shifting interference microscopy using deep neural network for quantitative phase imaging of biological samples

White light phase-shifting interference microscopy (WL-PSIM) is a prominent technique for high-resolution quantitative phase imaging (QPI) of industrial and biological specimens. However, multiple interferograms with accurate phase-shifts are essentially required in WL-PSIM for measuring the accurate phase of the object. Here, we present single-shot phase-shifting interferometric techniques for accurate phase measurement using filtered white light (520±36 nm) phase-shifting interference microscopy (F-WL-PSIM) and deep neural network (DNN). The methods are incorporated by training the DNN to generate (a) four phase-shifted frames and (b) direct phase from a single interferogram. The training of network is performed on two different samples i.e., optical waveguide and MG63 osteosarcoma cells. Further, performance of F-WL-PSIM+DNN framework is validated by comparing the phase map extracted from network generated and experimentally recorded interferograms. The current approach can further strengthen QPI techniques for high-resolution phase recovery using a single frame for different biomedical applications.     

Fluorescence microscopy techniques for quantitative evaluation of organic biocide distribution in antifouling paint coatings: application to model antifouling coatings

A test matrix of antifouling (AF) coatings including pMMA, an erodible binder and a novel trityl copolymer incorporating Cu₂O and a furan derivative (FD) natural product, were subjected to pontoon immersion and accelerated rotor tests. Fluorescence and optical microscopy techniques were applied to these coatings for quantification of organic biocide and pigment distribution. Total leaching of the biocide from the novel copolymer binder was observed within 6 months of rotor immersion, compared to 35% from the pMMA coating. In pontoon immersions, 61% of the additive was lost from the pMMA coating, and 53% from the erodible binder. Profiles of FD content in the binders revealed an accelerated loss of additive from the surface of the CDP resulting from rosin degradation, compared to even depletion from pMMA. In all samples, release of the biocide was inhibited beyond the Cu₂O front, corresponding to the leached layer in samples where Cu₂O release occurred.     

Cannibalism prevents evolutionary suicide of ontogenetic omnivores in life‐history intraguild predation systems

The majority of animal species are ontogenetic omnivores, that is, individuals of these species change or expand their diet during life. If small ontogenetic omnivores compete for a shared resource with their future prey, ecological persistence of ontogenetic omnivores can be hindered, although predation by large omnivores facilitates persistence. The coupling of developmental processes between different life stages might lead to a trade‐off between competition early in life and predation later in life, especially for ontogenetic omnivores that lack metamorphosis. By using bioenergetic modeling, we study how such an ontogenetic trade‐off affects ecological and evolutionary dynamics of ontogenetic omnivores. We find that selection toward increasing specialization of one life stage leads to evolutionary suicide of noncannibalistic ontogenetic omnivores, because it leads to a shift toward an alternative community state. Ontogenetic omnivores fail to re‐invade this new state due to the maladaptiveness of the other life stage. Cannibalism stabilizes selection on the ontogenetic trade‐off, prevents evolutionary suicide of ontogenetic omnivores, and promotes coexistence of omnivores with their prey. We outline how ecological and evolutionary persistence of ontogenetic omnivores depends on the type of diet change, cannibalism, and competitive hierarchy between omnivores and their prey.     

Polarization-resolved SHG imaging as a fast screening method for collagen alterations during aging: Comparison with light and electron microscopy

Our previous study on rat skin showed that cumulative oxidative pressure induces profound structural and ultrastructural alterations in both rat skin epidermis and dermis during aging. Here, we aimed to investigate the biophotonic properties of collagen as a main dermal component in the function of chronological aging. We used second harmonic generation (SHG) and two-photon excited fluorescence (TPEF) on 5 μm thick skin paraffin sections from 15-day-, 1-month- and 21-month-old rats, respectively, to analyze collagen alterations, in comparison to conventional light and electron microscopy methods. Obtained results show that polarization-resolved SHG (PSHG) images can detect collagen fiber alterations in line with chronological aging and that this method is consistent with light and electron microscopy. Moreover, the β coefficient calculated from PSHG images points out that delicate alterations lead to a more ordered structure of collagen molecules due to oxidative damage. The results of this study also open the possibility of successfully applying this fast and label-free method to previously fixed samples.     

Effects of diet and heavy metals on growth rate and fertility in the deposit-feeding snail Potamopyrgus jenkinsi (Smith) (Gastropoda: Hydrobiidae)

Evidence for the influence of food type and heavy metals on shell growth and fertility is presented for a freshwater population of the snail P. jenkinsi. When fed an excess of lettuce or lamb heart (protein source), growth rates were higher for lettuce. Highest growth rates occurred at a diet of lettuce plus lamb heart. Fertility was favoured by a diet of lamb heart. When fed an excess of lettuce, the EC₅₀ growth values were 16 µg Cd l^–1, 13 µg Cu l^–1, and 103 µg Zn l^–1 in lake water; snail fertility was inhibited at 25 µg Cd l^–1 and 30 µg Cu l^–1. A diet of lake detritus spiked with Cd or Cu resulted in a decrease of approximately 50% in growth rates, when compared with growth on non-spiked detritus. Spiked detritus lost metals into lake water. Food type positively interacted with metal stress, both for growth rate and fertility. The assessment of inhibitory effects of detritus contaminated either in the field or, notably, by spiking, and serving as food source for deposit feeders is hampered by sampling problems in the field and by redistribution processes of pollutants between particles and water in laboratory-scale experiments.     

Use of polarized light microscopy in porcine reproductive technologies

The meiotic spindle in the oocyte is composed of microtubules and plays an important role during chromosome alignment and separation at meiosis. Polarized light microscopy (PLM) could be useful for a non-invasive evaluation of the meiotic spindle and may allow removal of nuclear structures without fluorochrome staining and ultraviolet exposure. In this study, PLM was used to assess its potential application in porcine reproductive technologies. The objectives of the present study were to assess the efficiency of PLM to detect microtubule-polymerized protein in in vitro-matured porcine oocytes; to examine its effects on the oocyte developmental competence; to select oocytes based on the presence of the meiotic spindle detected by PLM; and to assess the efficiency oocyte enucleation assisted with PLM. In the first experiment, the presence of microtubule-polymerized protein was assessed and confirmed in oocytes (n = 117) by immunostaining and chromatin detection. In the second experiment, oocytes (n = 160) were exposed or not (controls) to PLM for 10 minutes, and then parthenogenetically activated and cultured in vitro. In the third experiment, development competence of oocytes with a positive or negative signal to PLM was analyzed after in vitro fertilization. Finally, oocytes (n = 54) were enucleated using PLM as a tool to remove the meiotic spindle. A positive PLM signal was detected in 98.2 % of the oocytes, which strongly correlated (r = 1; p < 0.0001) with the presence of microtubule-polymerized protein as confirmed by immunostaining. Oocytes exposed to PLM did not differ significantly from controls on cleavage, total blastocyst, expanded blastocyst rates and total cell numbers. The percentage of oocytes at the MII stage and blastocyst formation rate in the negative PLM group significantly differed from control and PLM positive groups. Overall efficiency of spindle removal using the PLM-Oosight system was 92.6%. These results suggest that polarized light microscopy is an efficient system to detect microtubule-polymerized protein in in vitro-matured porcine oocytes and does not exert detrimental effects on porcine oocyte developmental competence. Selecting oocytes by the presence of a PLM signal provides limited improvement on IVF results. Finally, PLM appears as an efficient method to enucleate porcine oocytes.     

To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era

Digital fluorescence microscopy is now a standard technology for assaying molecular localisation in cells and tissues. The choice of laser scanning (LSM) and wide-field microscopes (WFM) largely depends on the type of sample, with LSMs performing best on thick samples and WFMs performing best on thin ones. These systems are increasingly used to collect large multidimensional datasets. We propose a unified image structure that considers space, time, and fluorescence wavelength as integral parts of the image. Moreover, the application of fluorescence imaging to large-scale screening means that large datasets are now routinely acquired. We propose that analysis of these data requires querying tools based on relational databases and describe one such system.     

Comparing lipid remodeling of brown adipose tissue,white adipose tissue,and liver after one-week high fat diet intervention with quantitative Raman microscopy

Brown adipose tissue (BAT) consists of highly metabolically active adipocytes that catabolize nutrients to produce heat. Playing an active role in triacylglycerol (TAG) clearance, research has shown that dietary fatty acids can modulate the TAG chemistry deposition in BAT after weeks-long dietary intervention, similar to what has been shown in white adipose tissue (WAT). Our objective was to compare the influence of sustained, nonchronic dietary intervention (a 1-week interval) on WAT and interscapular BAT lipid metabolism and deposition in situ. We use quantitative, label-free chemical microscopy to show that 1 week of high fat diet (HFD) intervention results in dramatically larger lipid droplet (LD) growth in BAT (and liver) compared to LD growth in inguinal WAT (IWAT). Moreover, BAT showed lipid remodeling as increased unsaturated TAGs in LDs, resembling the dietary lipid composition, while WAT (and liver) did not show lipid remodeling on this time scale. Concurrently, expression of genes involved in lipid metabolism, particularly desaturases, was reduced in BAT and liver from HFD-fed mice after 1 week. Our data show that BAT lipid chemistry remodels exceptionally fast to dietary lipid intervention compared WAT, which further points towards a role in TAG clearance.     

Advances in nonlinear optical microscopy techniques for in vivo and in vitro neuroimaging

Understanding the mechanism of the brain via optical microscopy is one of the challenges in neuroimaging, considering the complex structures. Advanced neuroimaging techniques provide a more comprehensive insight into patho-mechanisms of brain disorders, which is useful in the early diagnosis of the pathological and physiological changes associated with various neurodegenerative diseases. Recent advances in optical microscopy techniques have evolved powerful tools to overcome scattering of light and provide improved in vivo neuroimaging with sub-cellular resolution, endogenous contrast specificity, pinhole less optical sectioning capability, high penetration depth, and so on. The following article reviews the developments in various optical imaging techniques including two-photon and three-photon fluorescence, second-harmonic generation, third-harmonic generation, coherent anti-Stokes Raman scattering, and stimulated Raman scattering in neuroimaging. We have outlined the potentials and drawbacks of these techniques and their possible applications in the investigation of neurodegenerative diseases.     

Differences in black pigmentation in lepidopteran cuticles as revealed by light and electron microscopy

Summary Black cuticles of larvae and pupae from various Lepidoptera were studied by light and electron microscopy. There are striking differences in the representation of black pigmentation, especially at the ultrastructural level. Two types may be described: 1. With the light microscope black melanin-like grana, electron-dense electron microscopically, are found in the distal parts of the exocuticle. This type is demonstrated in larvae of Celerio euphorbiae, Papilio machaon, and Phalera bucephala. 2. With the light microscope a dark homogeneous layer in the distal exocuticle can be recognized, however, electron microscopically no structures correlated with this dark pigment layer. This type of pigmentation was present in pupae of Pieris brassicae and Aglais urticae; in Pieris larvae the dark pigmented layer appeared to be limited to the epicuticle. In Celerio processes of the epidermal cells are involved in transporting precursors to the exocuticle. The conclusion was reached that black pigmentation in cuticles is based on different mechanisms as proposed by structural features. The two likely mechanisms are melanization and sclerotization.This work was supported by the Deutsche Forschungsgemeinschaft (SFB 87, project A1, granted to Prof. Bückmann)     

Transmission electron microscopy studies of Moraxella (Branhamella) catarrhalis

A trypsin-sensitive 200-kDa protein has been reported to be exclusively associated with haemagglutinating isolates of Moraxella (Branhamella) catarrhalis. Transmission electron microscopy studies revealed that haemagglutination by M. catarrhalis to both human and rabbit erythrocytes was mediated by a trypsin-sensitive outer fibrillar coat. This fibrillar layer was absent on non-haemagglutinating isolates examined. Immuno-electron microscopy, using a polyclonal antiserum containing antibodies to the 200-kDa protein as a probe, showed that the 200-kDa protein is present on the outer fibrillar layer of the bacterium. These findings suggest that the haemagglutinin of M. catarrhalis is a 200-kDa protein present on the outer fibrillar coat.     

Challenges in quantitative single molecule localization microscopy

Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.     

What do tadpoles really eat? Assessing the trophic status of an understudied and imperiled group of consumers in freshwater habitats

1. Understanding the trophic status of consumers in freshwater habitats is central to understanding their ecological roles and significance. Tadpoles are a diverse and abundant component of many freshwater habitats, yet we know relatively little about their feeding ecology and true trophic status compared with many other consumer groups. While many tadpole species are labelled herbivores or detritivores, there is surprisingly little evidence to support these trophic assignments. 2. Here we discuss shortcomings in our knowledge of the feeding ecology and trophic status of tadpoles and provide suggestions and examples of how we can more accurately quantify their trophic status and ecological significance. 3. Given the catastrophic amphibian declines that are ongoing in many regions of the planet, there is a sense of urgency regarding this information. Understanding the varied ecological roles of tadpoles will allow for more effective conservation of remaining populations, benefit captive breeding programmes, and allow for more accurate predictions of the ecological consequences of their losses.