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opencc-by-4.0Jan 2020View details →

Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor

Data for the figures in the manuscript  <a href="https://pubs.acs.org/doi/10.1021/acssynbio.9b00166">https://pubs.acs.org/doi/10.1021/acssynbio.9b00166</a> Abstract: Caenorhabditis elegans has become a key model organism within biology. In particular, the transparent gut, rapid growing time, and ability to create a defined gut microbiota make it an ideal candidate organism for understanding and engineering the host microbiota. Here we present the development of an experimental model that can be used to characterize whole-cell bacterial biosensors in vivo. A dual-plasmid sensor system responding to isopropyl β-d-1-thiogalactopyranoside was developed and fully characterized in vitro. Subsequently, we show that the sensor was capable of detecting and reporting on changes in the intestinal environment of C. elegans after introducing an exogenous inducer into the environment. The protocols presented here may be used to aid the rational design of engineered bacterial circuits, primarily for diagnostic applications. In addition, the model system may serve to reduce the use of current animal models and aid in the exploration of complex questions within general nematode and host–microbe biology.

opencc-by-4.0May 2020View details →

Wind turbine blade simulations under changing environment for benchmarking SHM algorithms

This data set contains the flapwise vibration response simulation of a wind turbine blade under Environmental and Operational Variability (EOV) as well as increasing damage. The blade’s dynamics are represented by means of a 4 element FEM of a cantilever beam, while dynamic loading corresponds to a discretized turbulent wind field calculated with the help of the software TurbSim for prescribed 10-minute average wind speed and turbulence. Rotation effects are ignored. The wind loading is coupled with the structural dynamics considering aeroelastic interactions, based on lift and drag forces calculated from a NACA 64-618 airfoil. Ambient temperature (10-minute average) is used to set the elasticity (Young’s) modulus of the blade material. While on the healthy state, the vibration response of the blade is simulated over a year of temperature and wind speed variations according to the average values measured in an area of north-central Switzerland. In addition, a week of extreme weather (abnormally high temperature in summer) and a month where the blade is subject to increasing damage are also simulated. Damage is represented as a decrement of the stiffness on a single FEM element located on the blade’s root. Damage increments linearly from 0 to 25% decrease of the total stiffness during a period of two weeks, while on the remaining two weeks a 25% stiffness decrement is sustained. The main aim of this data set is to be used as a benchmark of vibration based SHM methods, particularly on damage detection and localization under EOV. To this end, both the blade’s vibration response and the environmental and operational parameters (temperature and wind) used to simulate each response are provided. Further details can be found in the publication attached.

opencc-by-4.0Nov 2023View details →

Human auditory ecology : Extending hearing research to the perception of natural soundscapes by humans in rapidly-changing environments

The audiomaterial corresponding to boreal, tropical and temperate forests, desert, savannah, sub-alpine meadow, and the construction site in New York is copyrighted (license from Wild Sanctuary) and cannot be used without explicit agreement of Bernie Krause. Additional audiomaterial (urban park and street traffic in Paris, France; fast street traffic in Marseille, France; English and French speech material) may only be used with the explicit agreement of the following authors: Jérôme Sueur and Sylvain Haupert (Museum National d'Histoire Naturelle in Paris, France); Sabine Meunier (LMA/CNRS in Marseille, France); Franck Ramus (CNRS in Paris, France) (see Figure legends).

opencc-by-4.0Dec 2021View details →

Accelerated change in the glaciated environments of western Canada revealed through trend analysis of optical satellite imagery (Polygons)

Automatically generated dataset of glacier outlines from the journal article: "Accelerated change in the glaciated environments of western Canada revealed through trend analysis of optical satellite imagery" Research paper: https://www.sciencedirect.com/science/article/pii/S0034425721005824 More information can be found here: https://github.com/bevingtona/glacier_change_western_canada

Figs 41–50 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 41–50. Discostella gabinii Paillès & Sylvestre sp. nov., Lake Petén-Itzá (Guatemala); LM valve views. 41–42. Modern specimens of D. gabinii sp. nov. from Cenote Juarez. 43–44. Modern specimens of D. gabinii sp. nov. from Lake Amatitlan. 45–50. Type material of fossil lacustrine diatom D. gabinii sp. nov. 45. Holotype (MNHN, slide PC060873). 48–50. A shadow line is visible in large specimens. Scale bar = 10 µm.

Figs 25–32 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 25–32. Type material of fossil lacustrine diatom Cyclocostis rolfii Paillès gen. et sp. nov.; SEM external valve views. 25. Valve view of concentrically undulated marginal area and tangentially undulated central area; punctuated striae become in the central area rows of larger areolae arranged in a stellate pattern. 26. Valve surface with scattered papillae; the external opening of the single valve face fultoportula is located on the raised part (white arrowhead). 27. Marginal area showing the external openings of marginal fultoportulae, collared but with no projections (white arrowheads). 28. Side view of marginal area showing striation, papillae, external openings of marginal fultoportulae (mfp – two white arrows), and the cingulum consisting of an open valvocopula and several copulae (white arrow). 29. Detail of the central area with large areolae; external areolae are bigger and occluded by volae in places where ribs are fusing. 30. Broken valve view showing the different striation between the margins and the center, the steep transversal undulation and the valve thickness. 31. Marginal area with the external openings of marginal fultoportulae (white arrowheads), papillae, and the cingulum. 32. Broken valve view showing the simple structure of anastomosing ribs covered by a finely perforated silica layer. Scale bars: 25 = 5 µm; 26, 28–32 =2 µm; 27 = 1 µm (27).

Fig. 59 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Fig. 59. Diagram showing the succession of Stephanodiscaceae Glezer & Makarova in Pleistocene sediments (0–84 ka) from Lake Petén-Itzá (Guatemala).

Figs 1–24 in New fossil genus and new extant species of diatoms (Stephanodiscaceae, Bacillariophyceae) from Pleistocene sediments in the Neotropics (Guatemala, Central America): adaptation to a changing environment?

Figs 1–24. Type material of fossil lacustrine diatom Cyclocostis rolfii Paillès gen. et sp. nov., Lake PeténItzá (Guatemala); LM girdle view (1) and valve views (2–24). 4. Holotype (MNHN, slide PC0608731). 7–8. Valve surface strongly tangentially undulated, forming an S shape. Scale bar = 10 µm.

opencc-by-4.0Oct 2020View details →

Exploring Rapid Changes in the Arctic Marine Environment - First ECOTIP Expedition to the Kongsfjorden on Svalbard

Video of flash talk (5 min) given by Claudia Elena Schmidt during the YOUMARES 11 conference in Session 4: Fjord systems: Ecology, bentho-pelagic coupling, and anthropogenic impacts on 15.10.2020 in Hamburg. The Arctic Ocean and its adjacent seas are especially vulnerable to climate change. Its ecosystem is rapidly changing in response to temperature increase, loss of sea ice, and the combined effects of additional stressors such as invasive species and pollution. However, the scientific community currently lacks sufficient information on the mechanisms, drivers and thresholds of these environmental changes on the Arctic ecosystem and the consequences that may arise for many Arctic communities. The recently launched ECOTIP project aims at closing these knowledge gaps by investigating the impacts of climate change on the Arctic marine environment in order to identify tipping points that can induce an abrupt and sometimes irreversible change in the ecosystem. In a joint sampling campaign between the Helmholtz-Zentrum Hereon and the Alfred Wegener Institute (AWI) water and sediment samples from key marine and terrestrial locations in the Kongsfjorden area on the west coast of the Svalbard archipelago were collected in July 2020. The aim of the ongoing study will be to understand the mechanism of carbon cycling in a polar fjord system that is influenced by profound environmental changes by measuring alkalinity and dissolved inorganic carbon (DIC). Furthermore, the biogeochemical cycle of metals, trace metals and other elements in coastal and shelf waters influenced by melt water streams, draining from land terminating glaciers, will be investigated by multi-element analyses. The collected data will provide scientific insight into biogeochemical processes in high-latitude fjord and coastal regions affected by climate change and thus help to predict future changes in Arctic ecosystems.

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Data from: Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments

Regulating transcription allows organisms to respond to their environment, both within a single generation (plasticity) and across generations (adaptation). We examined transcriptional differences in gill tissues of fishes in the Poecilia mexicana species complex (family Poeciliidae), which have colonized toxic springs rich in hydrogen sulfide (H2S) in southern Mexico. There are gene expression differences between sulfidic and non-sulfidic populations, yet regulatory mechanisms mediating this gene expression variation remain poorly studied. We combined capped-small RNA sequencing (csRNA-seq), which captures actively transcribed (i.e., nascent) transcripts, and traditional messenger RNA sequencing (mRNA-seq) to examine how variation in transcription, enhancer activity, and associated transcription factor binding sites may facilitate adaptation to extreme environments. csRNA-seq revealed thousands of differentially initiated transcripts between sulfidic and non-sulfidic populations, many of which are involved in H2S detoxification and response. Analyses of transcription factor binding sites in promoter and putative enhancer csRNA-seq peaks identify a suite of transcription factors likely involved in regulating H2S-specific shifts in gene expression, including several key transcription factors known to respond to hypoxia. Our findings uncover a complex interplay of regulatory processes that reflect the divergence of extremophile populations of P. mexicana from their non-sulfidic ancestors and suggest shared responses among evolutionarily independent lineages.

opencc-zeroMay 2024View details →

opencc-by-4.0Jun 2024View details →

Behavioural changes in the city: the common black garden ant defends aphids more aggressively in urban environments

Data and R code to analyse changes in aphid and ant populations and behaviour along a gradient of urbanisation in Berlin, Germany. This release is associated to a publication in preparation and includes the updated R code used for publication: Gaber, H., Ruland, F, Jeschke, J. & Bernard-Verdier, M. (2024) Behavioural changes in the city: the common black garden ant defends aphids more aggressively in urban environments. Ecology & Evolution (publication details will soon be added)

opencc-by-4.0Jul 2024View details →

Data for: Environment-dependent relationships between corticosterone and energy expenditure during reproduction: insights from seabirds in the context of climate change

We studied the relationship between baseline levels of the steroid hormone corticosterone and daily energy expenditure (DEE) in the little auk (Alle alle), an Arctic sea bird that is experiencing mounting energetic challenges due to climate change. We specifically investigated the hypothesis that there might be environment-dependent relationships between baseline corticosterone, DEE, time activity budgets, diving behavior and fitness-related traits (chick provisioning rate, adult body condition). Furthermore, we also examined whether mercury (Hg) contamination might interfere with corticosterone production, and hence potentially the capacity to upregulate DEE.  In addition, we performed a phylogenetically controlled analysis across breeding seabird species to assess the relationship between baseline corticosterone and DEE, which we estimated via a model derived from a phylogenetically controlled meta-analysis, available within a web-based app (‘Seabird FMR Calculator’, <a href="https://ruthedunn.shinyapps.io/seabird_fmr_calculator/">https://ruthedunn.shinyapps.io/seabird_fmr_calculator/</a>) (Dunn et al. 2018).  These datasets contain information on corticosterone levels, DEE, TABs and Hg in little auks, and the data used in our phylogenetically controlled analysis. Please see the READ me file for details.

opencc-by-4.0Feb 2021View details →

Figure 5 in Hundred years of Botany at the NWU: contributions towards understanding plant and algae function, diversity and restoration in a changing environment

Figure 5: Mr Sello D. Phalatse, first Botanist at Mahikeng Campus (1983–2008), founder and curator of the University of NorthWest Herbarium (Source: NWU Records, Archives and Museum) (Source: NWU Corporate Relations and Marketing).

opencc-by-4.0Feb 2021View details →

Figure 4 in Hundred years of Botany at the NWU: contributions towards understanding plant and algae function, diversity and restoration in a changing environment

Figure 4. Botanical Garden – Waterfall on Prof. Daan Botha's koppie. (Photo: Chris van Niekerk from NWU Botanical Garden collection).

opencc-by-4.0Feb 2021View details →

Figure 3. Prof. A.P in Hundred years of Botany at the NWU: contributions towards understanding plant and algae function, diversity and restoration in a changing environment

Figure 3. Prof. A.P Goossens, first Professor and Head of Department of Botany (Source: NWU Records, Archives and Museum).

opencc-by-4.0Dec 2013View details →

Fig. 1 in Benthic and Planktic Foraminifera as Indicators of Late Glacial to Holocene Paleoclimatic Changes in a Marginal Environment: An Example from the Southeastern Bay of Biscay

Fig. 1. Study area bathymetry (Liu and Dittert 2010), surface circulation patterns (Koutsikopoulos et al. 1996), and location of the study Site WH (44°33′N, 2°45′W; 2,000 m water depth). The position of Site KS10b (Mojtahid et al. 2013) is marked by a white square. IPC – Iberian Poleward Current, ENACW – Eastern North Atlantic Central Waters.

opencc-by-4.0Dec 2013View details →

Fig. 5. a in Benthic and Planktic Foraminifera as Indicators of Late Glacial to Holocene Paleoclimatic Changes in a Marginal Environment: An Example from the Southeastern Bay of Biscay

Fig. 5. a – oxygen stable isotope ratios (δ18O) performed on G. bulloides and G. inflata; b – Δδ 18O between δ18O and δ18O; G. inflata G. bulloides c – carbon stable isotope ratios (δ13C) performed on G. bulloides and G. inflata; d – Δδ 13C between δ13C and δ13C. The grey G. inflata G. bulloides lines represent FC WH and the black colour represents CADIAC WH. The horizontal dotted lines delimitate the major changes (see text for all the details).

opencc-by-4.0Dec 2013View details →

Fig. 4. a in Benthic and Planktic Foraminifera as Indicators of Late Glacial to Holocene Paleoclimatic Changes in a Marginal Environment: An Example from the Southeastern Bay of Biscay

Fig. 4. a – time records in Cores CADIAC WH (black color) and FC WH (grey color) of benthic foraminiferal abundances (ind. g–1 of dry sediment), benthic foraminiferal accumulation rates (ind. cm–2 ka–1), relative abundances of the main benthic species present with ≥ 5% in at least one sample (after removing the non-fossilizing taxa), and species richness; b – time records in Cores CADIAC WH (black color) and FC WH (grey color) of planktic foraminiferal abundances (ind. g–1 of dry sediment), same indications as for benthic faunas. The horizontal dotted lines delimitate the major foraminiferal changes (see text for all the details).