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1,079 results for “source data”
Data from: More than skin and bones: comparing extraction methods and alternative sources of DNA from avian museum specimens
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch, and bone) from ten historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, likely a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
Data from: Social information from immigrants: multiple immigrant based sources of information for dispersal decisions in a ciliate
1. Dispersal is increasingly recognized as being an informed process, based on information organisms obtain about the landscape. While local conditions are often found to drive dispersal decisions, local context is not always a reliable predictor of conditions in neighbouring patches, making the use of local information potentially useless or even maladaptive. In this case, using social information gathered by immigrants might allow adjusting dispersal decisions without paying the costs of prospecting. However, this hypothesis has been largely neglected despite its major importance for ecological and evolutionary processes. 2. We investigated three fundamental questions about immigrant-informed dispersal: Do immigrants convey information that influences dispersal, do organisms use multiple cues from immigrants, and is immigrant-informed dispersal genotype dependent? 3. Using Tetrahymena thermophila ciliates in microcosms, we manipulated the number of immigrants arriving, the density of congeners, the resource quality in neighbouring patches, matrix characteristics and the level of cooperation of individuals in the neighbouring populations. 4. We provide the first experimental evidence that immigrants convey a number of different cues about neighbouring patches and matrix (patch quality, matrix characteristics and cooperation in neighbouring populations) in this relatively simple organism. Furthermore, we demonstrate genotype-dependent immigrant-informed dispersal decisions about patch quality and matrix characteristics. 5. Multiple cues from immigrants and genotype-dependent use of cues have major implications for theoretical metapopulation dynamics and the potential for local adaptation.
Data from: Integrated population modelling reveals a perceived source to be a cryptic sink
Demographic links among fragmented populations are commonly studied as source-sink dynamics, whereby source populations exhibit net recruitment and net emigration, while sinks suffer net mortality but enjoy net immigration. It is commonly assumed that large, persistent aggregations of individuals must be sources, but this ignores the possibility that they are sinks instead, buoyed demographically by immigration. We tested this assumption using Bayesian integrated population modelling of Greenland white-fronted geese (Anser albifrons flavirostris) at their largest wintering site (Wexford, Ireland), combining capture–mark–recapture, census and recruitment data collected from 1982 to 2010. Management for this subspecies occurs largely on wintering areas; thus, study of source-sink dynamics of discrete regular wintering units provides unprecedented insights into population regulation and enables identification of likely processes influencing population dynamics at Wexford and among 70 other Greenland white-fronted goose wintering subpopulations. Using results from integrated population modelling, we parameterized an age-structured population projection matrix to determine the contribution of movement rates (emigration and immigration), recruitment and mortality to the dynamics of the Wexford subpopulation. Survival estimates for juvenile and adult birds at Wexford and adult birds elsewhere fluctuated over the 29-year study period, but were not identifiably different. However, per capita recruitment rates at Wexford in later years (post-1995) were identifiably lower than in earlier years (pre-1995). The observed persistence of the Wexford subpopulation was only possible with high rates of immigration, which exceeded emigration in each year. Thus, despite its apparent stability, Wexford has functioned as a sink over the entire study period. These results demonstrate that even large subpopulations can potentially be sinks, and that movement dynamics (e.g. immigration) among winters can dramatically obscure key processes driving subpopulation size. Further, novel population models which integrate capture–mark–recapture, census and recruitment data are essential to correctly ascribing source-sink status and accurately informing development of site-safeguard networks.
Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and/or tree inference, the alignment software PRANK was used, and/or detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa.
Data from: Gaps, an elusive source of phylogenetic information
Morrison (2009) raises a very fundamental question, "Why would phylogeneticists ignore computerized sequence alignment?" While well aware of the difficulties, he considers the whole issue is a 'gaping hole that needs to be filled'. Particularly with the expansion of genomic-scale data there are many advantages to using automated alignment for phylogenetic analyses, the most obvious being that it is much more efficient and potentially less prone to experimenter bias. So yes, it is obviously desirable to automate data preparation as far as possible, but the question remains whether we are yet at the stage that automated sequence alignment can obtain the full and correct phylogenetic information in the data. In this paper we use an example shorebird dataset to explore three related questions regarding the interplay between alignment and phylogeny estimation: 1) are gap-rich alignments reliable for phylogenetic inference? 2) How much phylogenetic information is contained in gaps as compared to sequences? 3) Are models of the insertion/deletion process essential, and if so at what phylogenetic depths? We report that there is considerable information created by the indel (insertion/deletion) process that is potentially available for phylogenetic inference. Ideally, we should be able to independently obtain the same tree from both sequences and from gaps; however there is still considerable variability in the alignments produced by different programs. We predict that better and more computationally tractable models of the indel process will be required before the information in gaps can be fully exploited for phylogenetic inference.
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1601 individuals from 18 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
Data from: Random sequences are an abundant source of bioactive RNAs or peptides
It is generally assumed that new genes arise through duplication and/or recombination of existing genes. The probability that a new functional gene could arise out of random non-coding DNA is so far considered to be negligible, as it seems unlikely that such an RNA or protein sequence could have an initial function that influences the fitness of an organism. Here, we have tested this question systematically, by expressing clones with random sequences in Escherichia coli and subjecting them to competitive growth. Contrary to expectations, we find that random sequences with bioactivity are not rare. In our experiments we find that up to 25% of the evaluated clones enhance the growth rate of their cells and up to 52% inhibit growth. Testing of individual clones in competition assays confirms their activity and provides an indication that their activity could be exerted by either the transcribed RNA or the translated peptide. This suggests that transcribed and translated random parts of the genome could indeed have a high potential to become functional. The results also suggest that random sequences may become an effective new source of molecules for studying cellular functions, as well as for pharmacological activity screening.
Data from: Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid-based plumage colouration
Many color ornaments are composite traits consisting of at least four components, which themselves may be more complex, determined by independent evolutionary pathways, and potentially being under different environmental control. To date, little evidence exists that several different components of color elaboration are condition-dependent and no direct evidence exists that different ornamental components are affected by different sources of variation. For example, in carotenoid-based plumage coloration, one of the best-known condition-dependent ornaments, color elaboration stems from both condition-dependent pigment concentration and structural components. Some environmental flexibility of these components has been suggested, but specifically which and how they are affected remains unknown. Here we tested whether multiple color components may be condition-dependent, by using a comprehensive 3 x 2 experimental design, in which we carotenoid supplemented and immune challenged great tit nestlings (Parus major) and quantified effects on different components of coloration. Plumage coloration was affected by an interaction between carotenoid availability and immune challenge. Path analyses showed that carotenoid supplementation increased plumage saturation via feather carotenoid concentration and via mechanisms unrelated to carotenoid-deposition, while immune challenge affected feather length, but not carotenoid concentration. Thus, independent condition-dependent pathways, affected by different sources of variation, determine color elaboration. This provides opportunities for the evolution of multiple signals within components of ornamental traits. This finding indicates that the selective forces shaping the evolution of different components of a composite trait and the trait's signal content may be more complex than believed so far, and that holistic approaches are required for drawing comprehensive evolutionary conclusions.
Data from: Inferences on population history of a seed chalcid wasp: invasion success despite a severe founder effect from an unexpected source population
Most invasive species established in Europe originate from either Asia or North America, but little is currently known about the potential of the Anatolian Peninsula (Asia Minor) and/or the Near East to constitute invasion sources. Mediterranean forests are generally fragile ecosystems that can be threatened by invasive organisms coming from different regions of the Mediterranean Basin, but for which historical data are difficult to gather and the phylogeographic patterns are still poorly understood for most terrestrial organisms. In this study, we characterized the genetic structure of Megastigmus schimitscheki, an invasive seed-feeding insect species originating from the Near East, and elucidated its invasion route in Southeastern France in the mid 1990's. To disentangle the evolutionary history of this introduction, we gathered samples from the main native regions (Taurus Mountains in Turkey, Lebanon and Cyprus) and from the invaded region, that we genotyped using five microsatellite markers and for which we sequenced the mitochondrial Cytochrome Oxidase I gene. We applied a set of population genetic statistics and methods, including approximate Bayesian computation. We proposed a detailed phylogeographic pattern for the Near East populations, and we unambiguously showed that the French invasive populations originated from Cyprus, although the available historical data strongly suggested that Turkey could be the most plausible source area. Interestingly, we could show that the introduced populations were founded from an extremely restricted number of individuals that realized a host switch from Cedrus brevifolia to C. atlantica. Evolutionary hypotheses are discussed to account for this unlikely scenario.
Data from: Testing for multiple invasion routes and source populations for the invasive brown treesnake (Boiga irregularis) on Guam: implications for pest management
The brown treesnake (Boiga irregularis) population on the Pacific island of Guam has reached iconic status as one of the most destructive invasive species of modern times, yet no published works have used genetic data to identify a source population. We used DNA sequence data from multiple genetic markers and coalescent-based phylogenetic methods to place the Guam population within the broader phylogeographic context of B. irregularis across its native range and tested whether patterns of genetic variation on the island are consistent with one or multiple introductions from different source populations. We also modeled a series of demographic scenarios that differed in the effective size and duration of a population bottleneck immediately following the invasion on Guam, and measured the fit of these simulations to the observed data using approximate Bayesian computation. Our results exclude the possibility of serial introductions from different source populations, and instead verify a single origin from the Admiralty Archipelago off the north coast of Papua New Guinea. This finding is consistent with the hypothesis that B. irregularis was accidentally transported to Guam during military relocation efforts at the end of World War II. Demographic model comparisons suggest that multiple snakes were transported to Guam from the source locality, but that fewer than 10 individuals could be responsible for establishing the population. Our results also provide evidence that low genetic diversity stemming from the founder event has not been a hindrance to the ecological success of B. irregularis on Guam, and at the same time offers a unique 'genetic opening' to manage snake density using classical biological approaches.
Data from: Fog as a source of nitrogen for redwood trees: evidence from fluxes and stable isotopes
A defining feature of the redwood forest in coastal California is the presence of fog in the summer months, a time when there is typically little rainfall. Our goal was to determine the role of summer fog in canopy transformation of nitrogen, nitrogen uptake by trees and photosynthesis within a coastal redwood forest ecosystem. We measured horizontal and vertical inputs of nitrogen, the isotopic composition of nitrogen in a variety of atmospheric sources (summer fog, winter rain and throughfall throughout the year), nitrogen pools (soil solution) and plant tissue (roots and foliage), as well as rates of photosynthesis and nitrogen uptake by trees. Throughfall nitrogen fluxes were greater at the forest edge compared to the interior both within the canopy (sampled 10 m above-ground) and onto the forest floor (sampled 1 m above-ground; P < 0.05). Similarly, soil solution inline image and total inorganic nitrogen were greater at the forest edge compared to the interior (P = 0.0014 and 0.009, respectively). Whereas natural abundance δ15NO3 values were not significantly different between winter rain (measured as bulk precipitation) and summer fog water (average δ15N = −1.2 ± 0.680/00), δ15NH4 values were significantly greater in fog water (11.4 ± 2.70/00) compared to rain (1.2 ± 0.90/00). We found no difference in δ15N in roots from forest edge trees compared to interior trees. In contrast, nitrogen concentrations and δ15N in foliage from forest edge trees were significantly greater compared to interior trees (P < 0.0001), suggesting that the leaves of forest edge trees may be obtaining a greater proportion of their nitrogen from fog compared to those of the interior trees. Natural abundance 13C of leaf sugars and rates of photosynthesis were significantly higher at the forest edge compared to the interior during the fog season (P < 0.05), but not different between locations in the rain season (P > 0.05). Nitrification in the forest floor, rather than the canopy, is the primary source of inline image in these soils throughout the year. Synthesis. Summer fog provides nitrogen directly and indirectly to redwood trees, especially those at the forest edge, and affects the physiologic function of redwood trees.
Supplementary data for: Mosquito phytophagy – sources exploited, ecological function, and evolutionary transition to haematophagy
<p>This dataset consists of two files:</p> <p><strong>Floral visitation records of mosquitoes</strong><br> Plant sugar, primarily in the form of floral nectar, is the ubiquitous basic food of adult mosquitoes. However, records of mosquito floral visitation are not usually the focus of research publications and, as such, are often reported as secondary parts of larger studies and are scattered throughout more than a century of scientific literature. Here we provide a summary of more than 500 recorded literature and field instances of floral and extra-floral nectary visitation by mosquitoes, including the plant and mosquito species involved as well as known pollination records.<br> <em>file name: Summary_of_Field_Mosquito_Floral_Visitation_Instances.xlsx</em></p> <p><strong>Summary of floral semiochemical blends that are attractive to mosquitoes</strong><br> Floral nectar is the primary food source of adult mosquitoes and mosquitoes, along with many other pollinators, use floral semiochemicals to locate this resource. Here we provide a summary of floral semiochemical blends attractive to mosquitoes that have been reported in the literature. The mosquito species involved have also been listed.<br> <em>file name: Summary_of_Floral_Semiochemical_Blends_Attractive_to_Mosquitoes.xlsx</em></p>
Data from: Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys
Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.
Data from: Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine.
Cross-fostering experiments are widely used by quantitative geneticists to study genetics and by behavioral ecologists to study the effects of prenatal in- vestment. Generally, the effects of genes and prenatal investment are confounded and the interpretation given to such experiments is largely dependent on the in- terests of the researcher. Using a large-scale well controlled experiment on a wild population of blue tits (Cyanistes caeruleus) we are able to partition variation in body mass across ontogeny into the effects of genes and the effects of between- clutch variation in egg characteristics. We show that although egg effects are important early in ontogeny they quickly dissipate, suggesting that the genetic interpretation of cross-fostering experiments may be preferable for many types of trait. However, the heritability of body mass is smaller than has previously been reported. Our results suggest that this is due to a combination of control- ling postnatal environmental effects more carefully and accounting for viability selection operating early in ontogeny.
Data from: Personality and gonadal development as sources of individual variation in response to GnRH challenge in female great tits
Seasonal timing of reproduction is a key life-history trait, but we know little about the mechanisms underlying individual variation in female endocrine profiles associated with reproduction. In birds, 17β-estradiol is a key reproductive hormone that links brain neuroendocrine mechanisms, involved in information processing and decision making, to downstream mechanisms in the liver, where egg-yolk is produced. Here we test, using a simulated induction of the reproductive system through a GnRH-challenge, whether the ovary of pre-breeding female great tits responds to a brain stimulation by increasing estradiol. We also assess how this response is modified by individual-specific traits like age, ovarian follicle size and personality, using females from lines artificially selected for divergent levels of exploratory behaviour. We show that a GnRH injection leads to a rapid increase in circulating concentrations of estradiol but responses varied among individuals. Females with more developed ovarian follicles showed stronger responses and females from lines selected for fast exploratory behaviour showed stronger increases compared to females from the slow line, indicating a heritable component. This study shows that the response of the ovary to a reproductive stimulation from the brain greatly varies among individuals and that this variation can be attributed to several commonly measured individual traits, which sheds light on the mechanisms shaping heritable endocrine phenotypes.
Data from: Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers
Epithelial tissue structure is the emergent outcome of the interactions between large numbers of individual cells. Experimental cell biology offers an important tool to unravel these complex interactions, but current methods of analysis tend to be limited to mean field approaches or representation by selected subsets of cells. This may result in bias towards cells that respond in a particular way and/or neglect local, context-specific cell responses. Here, an automated algorithm was applied to examine in detail the individual calcium transients evoked in genetically homogeneous, but asynchronous populations of cultured non-immortalized normal human urothelial cells when subjected to either the global application of an external agonist or a localized scratch wound. The recorded calcium transients were classified automatically according to a set of defined metrics and distinct sub-populations of cells that responded in qualitatively different ways were observed. The nature of this variability in the homogeneous cell population was apportioned to two sources: intrinsic variation in individual cell responses and extrinsic variability due to context-specific factors of the environment, such as spatial heterogeneity. Statistically significant variation in the features of the calcium transients evoked by scratch wounding according to proximity to the wound edge was identified. The manifestation of distinct sub-populations of cells is considered central to the coordination of population-level response resulting in wound closure.
Data from: Intrinsic and extrinsic drivers of source-sink dynamics
Many factors affect the presence and exchange of individuals among subpopulations and influence not only the emergence, but the strength of ensuing source–sink dynamics within metapopulations. Yet their relative contributions remain largely unexplored. To help identify the characteristics of empirical systems that are likely to exhibit strong versus weak source–sink dynamics and inform their differential management, we compared the relative roles of influential factors in strengthening source–sink dynamics. In a series of controlled experiments within a spatially explicit individual-based model framework, we varied patch quality, patch size, the dispersion of high- and low-quality patches, population growth rates, dispersal distances, and environmental stochasticity in a factorial design. We then recorded source–sink dynamics that emerged from the simulated habitat and population factors. Long-term differences in births and deaths were quantified for sources and sinks in each system and used in a statistical model to rank the influences of key factors. Our results suggest that systems with species capable of rapid growth, occupying habitat patches with more disparate qualities, with interspersed higher- and lower-quality habitats, and that experience relatively stable environments (i.e., fewer negative perturbations) are more likely to exhibit strong source–sink dynamics. Strong source–sink dynamics emerged under diverse combinations of factors, suggesting that simple inferences of process from pattern will likely be inadequate to predict and assess the strength of source–sink dynamics. Our results also suggest that it may be more difficult to detect and accurately measure source–sink dynamics in slow-growing populations, highly variable environments, and where a subtle gradient of habitat quality exists.
Data from: Experimental demonstration of accelerated extinction in source-sink metapopulations
Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source-sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source-sink effects in laboratory populations of Daphnia magna. Time-to-extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source-sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.
Data from: Growth mode and carbon source impact the surfaceome dynamics of Lactobacillus rhamnosus GG
Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.
Data from: Sources of intraspecific variation in the collective tempo and synchrony of ant societies
<p>Populations of independently oscillating agents can sometimes synchronize. In the context of animal societies, conspicuous synchronization of activity is known in some social insects. However, the causes of variation in synchrony within and between species have received little attention. We repeatedly assessed the short-term activity cycle of ant colonies (<em>Temnothorax rugatulus</em>) and monitored the movements of individual workers and queens within nests. We detected persistent differences between colonies in the waveform properties of their collective activity oscillations, with some colonies consistently oscillating much more erratically than others. We further demonstrate that colony crowding reduces the rhythmicity (i.e., the consistent timing) of oscillations. Workers in both erratic and rhythmic colonies spend less time active than completely isolated workers, but workers in erratic colonies oscillate out of phase with one another. We further show that the queen's absence can impair the ability of colonies to synchronize worker activity and that behavioral differences between queens are linked with the waveform properties of their societies.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.