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opencc-by-4.0Sep 2023View details →

Data and code for: "Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities."

Data and code for "Foraging rates from metabarcoding: Predators have reduced functional responses in wild, diverse prey communities."

opencc-by-4.0Dec 2023View details →

Data on mitochondrial respiratory function in skeletal muscle of adult male mice in response to 3-weeks heat stress

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opencc-zeroNov 2021View details →

On this side of the fence: Functional responses to linear landscape features shape the home range of large herbivores

1. Understanding the consequences of global change for animal movement is a major issue for conservation and management. In particular, habitat fragmentation generates increased densities of linear landscape features that can impede movements. 2. While the influence of these features on animal movements has been intensively investigated, they may also play a key role at broader spatial scales (e.g. the home range scale) as resources, cover from predators/humans, corridors/barriers, or landmarks. How space use respond to varying densities of linear features has been mostly overlooked in large herbivores, in contrast to studies done on predators. Focusing on large herbivores should provide additional insights to understand how animals solve the trade-off between energy acquisition and mortality risk. 3. Here, we investigated the role of anthropogenic (roads and tracks) and natural (ridges, valley bottoms and forest edges) linear features on home range features in five large herbivores. We analysed an extensive GPS monitoring data base of 696 individuals across nine populations, ranging from mountain areas mostly divided by natural features to lowlands that were highly fragmented by anthropogenic features. 4. Nearly all of the linear features studied were found at the home range periphery, suggesting that large herbivores primarily use them as landmarks to delimit their home range. In contrast, for mountain species, ridges often occurred in the core range, probably related to their functional role in terms of resources and refuge. When the density of linear features was high, they no longer occurred predominantly at the home range periphery, but instead were found across much of the home range. We suggest that, in highly fragmented landscapes, large herbivores are constrained by the costs of memorising the spatial location of key features, and by the requirement for a minimum area to satisfy their vital needs. 5. These patterns were mostly consistent in both males and females and across species, suggesting that linear features have a preponderant influence on how large herbivores perceive and use the landscape.

opencc-zeroDec 2021View details →

The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator

Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether (1) ease-of-travel or (2) access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features. We highlight the importance of considering landscape heterogeneity and habitat characteristics, and the functional response in habitat selection when investigating seasonal behaviour-based selection patterns. Our results support behaviour in line with search for primary prey during summer and fall, and ease-of-travel during spring, while patterns of selection during winter aligned best with ease-of-travel for the less-industrialized foothills landscape, and with search for primary prey in the more-industrialized boreal landscape. These results highlight that time-sensitive restoration actions on anthropogenic features can affect the probability of overlap between predators and threatened prey within different landscapes.

opencc-zeroFeb 2022View details →

Discovery of thermostable fluorescently responsive glucose biosensors by structure-assisted function extrapolation

Accurate assignment of protein function from sequence remains a fascinating and difficult challenge. The periplasmic binding protein (PBP) superfamily present an interesting case of function prediction, because they are both ubiquitous in prokaryotes, and they tend to diversify through gene duplication "explosions" that can lead to large numbers of paralogs in a genome. An engineered version of the moderately thermostable glucose-binding PBP from Escherichia coli has been used successfully as a reagentless fluorescent biosensor both in vitro and in vivo. To develop more robust sensors that meet the challenges of real-world applications, we report the discovery of thermostable homologs that retain a glucose-mediated conformationally coupled fluorescence response. Accurately identifying a glucose-binding PBP homolog among closely related paralogs is challenging. We demonstrate that a structure-based method that filters sequences by residues that bind glucose in an archetype structure is highly effective. Using fully sequenced bacterial genomes we found that this filter reduced high paralog numbers to single hits in a genome, consistent with accurate separation of glucose binding from other functions. We expressed engineered proteins for eight homologs, chosen to represent different degrees of sequence identity and tested their glucose-mediated fluorescence responses. We accurately predicted the presence of glucose binding down to 31% sequence identity. We also have successfully identified suitable candidates for next-generation robust, fluorescent glucose sensors.

opencc-zeroApr 2022View details →

Restoring function: positive responses of carbon and nitrogen to 20 years of hydrologic restoration in montane meadows

Montane meadows are highly productive ecosystems that contain high densities of soil carbon (C) and nitrogen (N). However, anthropogenic disturbances that lead to channel incision and disconnected floodplain hydrology have altered the C balance of many meadows, converting them from net C sinks to net sources of C to the atmosphere. Restoration efforts designed to reconnect floodplain hydrology may slow rates of soil C loss from degraded meadows and restore conditions for C sequestration and N immobilization, yet questions remain about the long-term impact of such efforts. Here, we used a 22-year meadow restoration chronosequence to measure the decadal impact of hydrologic restoration on above- and belowground C and N stocks and concentrations. Increases in herbaceous vegetation biomass preceded changes in soil C stocks, with the largest gains occurring belowground. Root biomass (0-15 cm) increased at a rate of 270.3 g m-2 y-1 and soil C stocks (0-15 cm) increased by 232.9 g C m-2 y-1 across the chronosequence. Increases in soil C concentration (2.99 g C kg-1 y-1) were tightly coupled with increases in soil N concentration (0.21 g N kg-1 y-1) and soil C:N did not vary with time since restoration. Fourier Transformed Infrared Spectroscopy results show that the fraction of labile aliphatic C-H and carboxylate C-O (COO) compounds in the soil increased with age of restoration and were positively correlated with soil C and N concentration. Our results demonstrate that restoration of floodplain hydrology in montane meadows has significant impacts on belowground C and N stocks, soil C and N concentration, and soil C chemistry within the first two decades following restoration.

opencc-by-4.0May 2022View details →

Generation-dependent functional and numerical responses of Neoseiulus californicus (Phytoseiidae) long-term reared on thorn apple pollen

Raw data of Functional and numerical response of N. califrnicus on T. urticae in different generaaations

opencc-zeroJun 2022View details →

Data from: Predation probabilities and functional responses: How piscivorous waterbirds respond to pulses in fish abundance

How predators respond to changes in prey abundance (i.e. functional responses) is foundational to consumer-resource interactions, predator-prey dynamics, and the stability of predator-prey systems. Predation by piscivorous waterbirds on out-migrating juvenile steelhead trout (Oncorhynchus mykiss) is considered a factor affecting the recovery of multiple Endangered Species Act-listed steelhead populations in the Columbia River basin. Waterbird functional responses, however, may vary by predator species and location, with important implications to predator management strategies. We used a 13-year dataset on waterbird abundance across seven breeding colonies (three Caspian tern [Hydroprogne caspia], two double-crested cormorant [Nannopterum auritum], and two California and ring-billed gull [Larus californicus and L. delawarensis] colonies) and steelhead tag-recovery data (>645,000 tagged and >32,000 recovered steelhead) to quantify weekly predation probabilities and functional responses across waterbird species, colonies, and years. Weekly predation probabilities were highly variable, ranging from 0.01–0.30 at tern colonies, 0.01–0.20 at cormorant colonies, and 0.03–0.13 at gull colonies. Per capita predation probabilities were an order of magnitude higher at inland tern and cormorant colonies relative to estuary colonies of the same species. Terns displayed Type II functional responses across colonies and years, where predation probabilities peaked at low steelhead abundances and declined as steelhead abundance increased (i.e., predator swamping). Cormorants nesting at the large estuary colony (several thousand birds) displayed a Type III functional response, but cormorants nesting at the smaller inland colony (several hundred birds) displayed a Type II response. Consumption probabilities of steelhead by gulls remained consistent across a large range of steelhead availability, suggesting a Type I or a Type III functional response, but a lack of colony abundance data prevented quantifying functional responses. The level of tern predation combined with Type II functional responses indicate possible population-level impacts that could destabilize small or declining prey populations. Conversely, the apparent Type III functional responses of gulls and estuary nesting cormorants are indicative of prey switching behaviors targeted at periods of high steelhead abundance. Our results illustrate the complexity of predator-prey interactions and the importance of quantifying predator- and location-specific functional responses when predicting the efficacy of management strategies to enhance prey populations.

opencc-by-4.0Jul 2022View details →

Responses of a semiarid grassland to recurrent drought is linked to community functional composition

Climate change-driven increases in the frequency of extreme droughts could negatively impact the functioning of grassland ecosystems. While several studies have documented the impact of individual droughts on grassland function, less is known about how grasslands will respond to recurrent drought. We conducted a repeated extreme drought experiment in a semiarid grassland that consisted of three stages: (1) initial drought, (2) recovery, and (3) subsequent drought. We measured aboveground net primary productivity (ANPP), species richness, plant functional traits, and functional diversity. Using structural equation modeling (SEM), we investigated the causal mechanisms of ANPP response to recurrent drought. The initial drought led to reduced ANPP, although this was driven by a differential reduction in the growth of grasses and forbs. Total ANPP completely recovered as the rapid recovery of grass productivity compensated for the slow recovery of forb productivity. The magnitude of ANPP responses to the subsequent drought was greater than the initial drought. The SEMs revealed that soil moisture influenced ANPP responses directly during the initial drought, and indirectly during the subsequent drought by altering community functional trait means and diversity during the subsequent drought. These differential mechanisms alter our fundamental understanding of ecosystem drought sensitivity, which is primarily based on single drought studies.

opencc-by-4.0May 2024View details →

Normal Saline versus Lactated Ringer's Solution: Effects on Organ Function and Inflammatory Responses in Heat Stroke in Rat

The data set includes the data generated during the experiment, including vital signs, test indicators, etc. The image file includes the expression of inflammasome proteins measured using WB.

opencc-zeroJun 2024View details →

Data from: Functional modularity and mechanical stress shape plastic responses during fish development

The adaptive potential of plastic phenotypes relies on combined developmental responses. Here, we investigated how manipulation of developmental conditions related to foraging mode in Megaleporinus macrocephalus fish induces plastic responses at different levels: 1) functional modularity of skull bones, 2) biomechanical properties of the chondrocranium using Finite Element Models, 3) bmp4 expression levels, used as a proxy for molecular pathways involved in bone responses to mechanical load. We identified new modules in the experimental groups, suggesting increased integration in head bone elements associated with the development of subterminal and upturned mouths, which are major features of Megaleporinus plastic morphotypes released in the lab. Plastic responses in head shape involved differences in the magnitude of mechanical stress, which seem restricted to certain chondrocranium regions. Three bones represent a 'mechanical unit' related to changes in mouth position induced by foraging mode, suggesting that functional modularity might be enhanced by specific regions responding to load. Differences in bmp4 expression levels between plastic morphotypes indicate associations between molecular signaling pathways and biomechanical responses to load. Our results offer a multilevel perspective of epigenetic factors involved in plastic responses, expanding our knowledge about mechanisms of developmental plasticity that originate novel complex phenotypes.

Trajectories and thresholds of multi-diversities and multi-functions in response to nitrogen enrichment

An ecosystem is composed by multiple biota across several trophic levels, which interactively perform multiple ecosystem functions. Anthropogenic reactive nitrogen is expected to alter these ecosystem attributes including biota diversities and ecosystem functions. Here, we find that five biota diversities differ substantially in response trajectory and threshold with increasing nitrogen amount, and so do the four examined functions. Our study provides a vivid picture of how multi-biota diversities and multiple functions concurrently respond to nitrogen enrichment and suggests that the attribute-specific response trajectories and thresholds should be taken into account in models predicting ecosystem feedbacks to nitrogen deposition.

Transcriptome analysis and functional study of phospholipase A2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae

The file is the raw data of "Transcriptome analysis and functional study of phospholipase A2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae".

Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-Function ATP13A2 Variant and Response to Antipsychotic Therapy

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ASO-mediated knockdown of GPNMB in mutant-GRN and Grn-deficient peripheral myeloid cells disrupts lysosomal function and immune responses

Background: Increases in GPNMB are detectable in FTD-GRN cerebrospinal fluid (CSF) and post-mortem brain, and brains of aged Grn-deficient mice. Although no upregulation of GPNMB is observed in the brains of young Grn-deficient mice, peripheral immune cells of these mice do exhibit this increase in GPNMB. Importantly, the functional significance of GPNMB upregulation in progranulin-deficient states is currently unknown. Given that GPNMB has been discussed as a potential therapeutic target in GRN-mediated neurodegeneration, it is vital for the field to determine what the normal function of GPNMB is in the immune system, and whether targeting GPNMB will elicit beneficial or deleterious effects. Methods: The effects of GPNMB knock-down via antisense oligonucleotide (ASO) were assessed in peripheral blood mononuclear cells (PBMCs) from 25 neurologically healthy controls (NHCs) and age- and sex-matched FTD-GRN patients, as well as peritoneal macrophages (pMacs) from progranulin-deficient (Grn-/-) and B6 mice. Lysosomal function, antigen presentation and MHC-II processing and recycling were assessed, as well as cytokine release and transcription. Results: We demonstrate here that ASO-mediated knockdown of GPNMB increases lysosomal burden and cytokine secretion in FTD-GRN carrier and neurologically healthy controls (NHCs) monocytes. ASO-mediated knockdown of GPNMB in Grn-deficient macrophages decreased lysosomal pan-cathepsin activity and protein degradation. In addition, ASO-mediated knockdown of GPNMB increased MHC-II surface expression, which was driven by decreased MHC-II uptake and recycling, in macrophages from Grn-deficient females. Finally, ASO-mediated knockdown of GPNMB dysregulated IFNg-stimulated cytokine transcription and secretion by mouse macrophages due to the absence of regulatory actions of the GPNMB extracellular fragment (ECF). Conclusions: Our data herein reveals that GPNMB has a regulatory effect on multiple immune effector functions, including capping inflammation and immune responses in myeloid cells via secretion of its ECF. Therefore, in progranulin-deficient states, the drastic upregulation in GPNMB transcript and protein may represent a compensatory mechanism to preserve lysosomal function in myeloid cells. These novel findings indicate that targeted depletion in FTD-GRN would not be a rational therapeutic strategy because it is likely to dysregulate important immune cell effector functions.

Fig. 3 in Structure and Composition of Dung Beetle Assemblages (Coleoptera: Scarabaeidae) in a Livestock Ranch in Central Uruguay: Responses of Functional Groups and Species to Local Habitats and Trophic Resources

Fig. 3. Dominance/diversity curves based on a) abundance and b) biomass of the dung beetle species of Scarabaeidae in three habitats in Puntas de Sauce Maciel, Florida, Uruguay. PHS = pasture on humid soil; PDS = pasture on dry soil; EP = Eucalyptus plantation.

Fig. 1. a in Structure and Composition of Dung Beetle Assemblages (Coleoptera: Scarabaeidae) in a Livestock Ranch in Central Uruguay: Responses of Functional Groups and Species to Local Habitats and Trophic Resources

Fig. 1. a) Sample completeness curves as a function of dung beetle abundance in three study habitats in Puntas de Sauce Maciel, Florida, Uruguay, b) Coverage-based rarefaction (solid lines) and extrapolation (dash above endpoint for PHS) sampling curves for species richness of the dung beetle data from the three habitats. PHS = pasture on humid soil; PDS = pasture on dry soil; EP = Eucalyptus plantation.

Fig. 2 in Structure and Composition of Dung Beetle Assemblages (Coleoptera: Scarabaeidae) in a Livestock Ranch in Central Uruguay: Responses of Functional Groups and Species to Local Habitats and Trophic Resources

Fig. 2. Diversity profiles for dung beetle assemblages in three habitats in Puntas de Sauce Maciel, Florida, Uruguay as a function of Hill numbers (q) with 95% confidence intervals (shaded areas). PHS = pasture on humid soil; PDS = pasture on dry soil; EP = Eucalyptus plantation.

Fig. 4 in Structure and Composition of Dung Beetle Assemblages (Coleoptera: Scarabaeidae) in a Livestock Ranch in Central Uruguay: Responses of Functional Groups and Species to Local Habitats and Trophic Resources

Fig. 4. Detrended correspondence analysis ordination of dung beetle species sampled with baited pitfall traps in three different habitats in Puntas de Sauce Maciel, Florida, Uruguay. PHS = pasture on humid soil; PDS = pasture on dry soil; EP = Eucalyptus plantation.