cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10277458
title: Quantification of phosphorylated metabolites, organic acids, and intermediates of the TCA cycle using capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) following treatment of Escherichia coli with ciprofloxacin

description: Data for the following article published in Frontiers in Microbiology:

Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer M-P, Rye MB, Droit A, Bruheim P and Otterlei M (2024) SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front. Microbiol. 15:1373344. doi: 10.3389/fmicb.2024.1373344

Capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) was used to quantify phosphorylated metabolites, organic acids, and intermediates of the TCA cycle of Escherichia coli treated with ciprofloxacin, BTP-001 (a novel antimicrobial peptide), and a combination of the two . Metabolite extracts were analyzed with a Xevo TQ-XS triple quadrupole mass spectrometer (Waters, USA).

Samples were gathered from E. coli cultures grown in batch cultivations using 1 liter bioreactors. Briefly, intracellular metabolites were extracted by cycling samples between −20 °C EtOH and N2 (l) in three consecutive freeze–thaw cycles, with vortexing every 10 min during the thawing phase. Filters were removed and the cell debris was pelleted (4500 rcf, 10 min, -9 °C). The supernatants were transferred to a new tube, snap frozen in N2 (l), and lyophilized. Lyophilized extracts were reconstituted in 500 µL cold Milli-Q H2O and cleared by spin-filtration with a 10 kDa molecular cutoff (20817 rcf, 10 min, 0 °C). A mix of 80 µL centrifuged sample and 20 µL 13C-labeled ISTD extract from yeast was sent to analysis. 

Data processing and absolute quantification was performed as earlier described using the TargetLynx application manager of MassLynx v 4.1 (Waters) to interpolate calibration curves made with appropriate dilutions of analytical grade standards (Sigma-Aldrich). The response factor of the corresponding U13C-isotopologues were used to correct the standard and sample extract response factors. Extract concentrations were normalized to the CDW, which was calculated from interpolation of the OD600 vs. CDW (g/L) curve. 

Further statistical analysis in MetaboAnalyst v 5.0 replaced missing values with 1/5 of the minimum value of the respective metabolite. An unpaired T-test with unequal variance determined differential enriched metabolites with a false discovery rate (FDR) < 0.05 which are presented as log2 fold-change compared to control.
DOI: 10.5281/zenodo.10277459
title: Quantification of phosphorylated metabolites, organic acids, and intermediates of the TCA cycle using capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) following treatment of Escherichia coli with ciprofloxacin

description: Data for the following article published in Frontiers in Microbiology:

Bergum OET, Singleton AH, Røst LM, Bodein A, Scott-Boyer M-P, Rye MB, Droit A, Bruheim P and Otterlei M (2024) SOS genes are rapidly induced while translesion synthesis polymerase activity is temporally regulated. Front. Microbiol. 15:1373344. doi: 10.3389/fmicb.2024.1373344

Capillary ion chromatography tandem mass spectrometry (capIC-MS/MS) was used to quantify phosphorylated metabolites, organic acids, and intermediates of the TCA cycle of Escherichia coli treated with ciprofloxacin, BTP-001 (a novel antimicrobial peptide), and a combination of the two . Metabolite extracts were analyzed with a Xevo TQ-XS triple quadrupole mass spectrometer (Waters, USA).

Samples were gathered from E. coli cultures grown in batch cultivations using 1 liter bioreactors. Briefly, intracellular metabolites were extracted by cycling samples between −20 °C EtOH and N2 (l) in three consecutive freeze–thaw cycles, with vortexing every 10 min during the thawing phase. Filters were removed and the cell debris was pelleted (4500 rcf, 10 min, -9 °C). The supernatants were transferred to a new tube, snap frozen in N2 (l), and lyophilized. Lyophilized extracts were reconstituted in 500 µL cold Milli-Q H2O and cleared by spin-filtration with a 10 kDa molecular cutoff (20817 rcf, 10 min, 0 °C). A mix of 80 µL centrifuged sample and 20 µL 13C-labeled ISTD extract from yeast was sent to analysis. 

Data processing and absolute quantification was performed as earlier described using the TargetLynx application manager of MassLynx v 4.1 (Waters) to interpolate calibration curves made with appropriate dilutions of analytical grade standards (Sigma-Aldrich). The response factor of the corresponding U13C-isotopologues were used to correct the standard and sample extract response factors. Extract concentrations were normalized to the CDW, which was calculated from interpolation of the OD600 vs. CDW (g/L) curve. 

Further statistical analysis in MetaboAnalyst v 5.0 replaced missing values with 1/5 of the minimum value of the respective metabolite. An unpaired T-test with unequal variance determined differential enriched metabolites with a false discovery rate (FDR) < 0.05 which are presented as log2 fold-change compared to control.
DOI: 10.5061/dryad.fqz612jvd
title: Statistics and quantification dataset of Haspin and its related proteins analysis in mouse spermatocytes

description: Chromosome segregation requires that centromeres properly attach to
 spindle microtubules. This essential step regulates the accuracy of cell
 division and therefore must be precisely regulated. One of the main
 centromeric regulatory signaling pathways is the Haspin-H3T3ph-chromosomal
 passenger complex (CPC) cascade, which is responsible for the recruitment
 of the CPC to the centromeres. In mitosis, Haspin kinase phosphorylates
 histone H3 at threonine 3 (H3T3ph), an essential epigenetic mark that
 recruits the CPC, whose catalytic component is Aurora B kinase. However,
 the centromeric Haspin-H3T3ph-CPC pathway remains largely uncharacterized
 in mammalian male meiosis. We have analyzed Haspin functions by either its
 chemical inhibition in cultured spermatocytes using LDN-192960, or the
 ablation of Haspin gene in Haspin-/-. Our studies suggest that Haspin
 kinase activity is required for proper chromosome congression during both
 meiotic divisions and for the recruitment of Aurora B and kinesin MCAK to
 meiotic centromeres. However, the absence of H3T3ph histone mark does not
 alter Borealin and SGO2 centromeric localization. These results add new
 and relevant information regarding the regulation of the Haspin-H3T3ph-CPC
 pathway and centromere function during meiosis.
description: Quantification of the
 immunofluorescence intensity was estimated by measuring the integrated
 fluorescence density in individual nuclei using ImageJ by creating a
 binary mask with the DAPI staining. The acquisition time was fixed for all
 acquired images, and the quantification was only performed using the
 original unmodified images. A minimum of 10 metaphase spermatocytes per
 condition were analyzed in each experiment. All graphics and statistical
 tests were performed with GraphPad Prism 9.0 software. Mean differences
 for each group were evaluated by an independent sample unpaired t-test.
 Values were expressed as mean ± SEM and p-values below 0.05 were
 considered statistically significant.
DOI: 10.26165/juelich-data/nycpxe
title: ETHOS.BUILDA: Building Footprint and Height Dataset Germany

description: Zenodo
DOI: 10.5061/dryad.gtht76hpg
title: Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens

description: Morphological evolution in mosses has long been hypothesized to accompany
 shifts in microhabitats and can be tested using comparative phylogenetics.
 These lines of inquiry have developed substantially, in part, by target
 capture sequencing allowing for phylogenomic scale data generated from
 herbarium specimens. In the present study, we test the relationship
 between taxonomically important morphological characters in the moss genus
 Fissidens, using both a 400-locus dataset generated using a target-capture
 approach as well as a three-locus phylogeny generated using sanger
 sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian
 Inference and used to test the monophyly of subgenera/sections and
 provided the basis for ancestral character reconstruction and phylogenetic
 correlation analyses among five morphological characters as well as
 habitat moisture scored from literature. The characters axillary hyaline
 nodules, limbidium, costa, and peristome morphology as well as sexual
 system, minimum habitat moisture, average habitat moisture, maximum
 habitat moisture, and habitat moisture niche breadth each exhibit
 statistically significant phylogenetic signal. Significant correlations
 were found between the limbidium (phyllid/leaf border) and habitat
 moisture niche breadth, which could be interpreted as a more extensive
 limbidium enabling species to survive across a wider variety of habitats.
 Correlations were also found between costa anatomy and the limbidum of the
 gametophyte and sporophyte peristome morphology, as well as average
 habitat moisture and sexual system. Continued exploration of the
 relationships between morphological evolution, life history, and habitat
 will enable us to expand our understanding of functional morphology in
 mosses.
description: The three-gene dataset was generated by Sanger sequencing. Each
 locus was analyzed individually using maximum likelihood implemented in
 RAxML. These three genes were concatenated and analyzed using Bayesian
 inference implemented in Mr.Bayes.  The ASTRAL dataset
 was generated by target capture methods using the GoFlag 451 and 408 loci
 probe sets. 404 loci were analyzed. We conducted phylogenetic analyses
 using two sets of data: (1) the probe dataset that includes only the
 conserved exon regions targeted by the sequencing probes, which are each,
 on average, 200 bp long and (2) the full dataset that included both the
 conserved exon regions from the probe dataset as well as the flanking
 intron regions. For both the probe and full dataset we conducted analyses
 of the concatenated supermatrix of all the loci using maximum likelihood
 implemented in RAxML. Additionally, each locus was analyzed individually
 using maximum likelihood implemented in RAxML. These individual gene trees
 were used to build a species tree using ASTRAL.
description: Descriptions of all files are listed in the file entitled
 README_FileExplanations.txt
DOI: 10.6084/m9.figshare.31167985.v1
title: Characterisation of gas-liquid two-phase flow transition in horizontal-to- upward vertical pipe systems

description: The research focused on experimental investigation of behaviour of gas-liquid two-phase flow as it transitions from horizontal to vertical section of pipe.
DOI: 10.5061/dryad.wwpzgmsmn
title: Strong migratory connectivity indicates Willets need subspecies-specific conservation strategies

description: By combining all available banding and tracking data, we found that
 Willets (Tringa semipalmata) have strong migratory connectivity between
 breeding and nonbreeding locations at the range-wide and subspecies
 levels, exposing the two subspecies to varying threats such as hunting for
 the eastern subspecies (T. s. semipalmata) and climatically-altered
 coastal habitats for both subspecies. We found that Western Willets (T. s.
 inornata) primarily used nonbreeding habitats along the Pacific Coast of
 the United States, although their reported nonbreeding range extends to
 the U.S. Atlantic and Gulf Coasts and the Pacific Coast of Central and
 South America. Eastern Willets wintered in Central and South America,
 which covers much of the subspecies’ known nonbreeding range. By
 quantifying migratory connectivity within and between two subspecies, we
 could suggest subspecies-specific threats and potential limiting factors
 in the breeding and nonbreeding periods of the annual cycle of a declining
 migratory shorebird. Effective management of the species will likely
 require a range of conservation strategies across the diverse nonbreeding
 regions the two subspecies occupy within the United States, Central
 America, and South America. However, more data are needed from Willets
 breeding in mid-continent North America to understand the complete extent
 of overlap of the two subspecies throughout the annual cycle. The strong
 migratory connectivity documented here highlights the need to manage
 Willets by subspecies and protect a diversity of breeding and nonbreeding
 habitats, which will benefit the conservation of other shorebird species
 that overlap with Willets throughout the annual cycle.
DOI: 10.5061/dryad.02v6wwq5k
title: Effects of phenological mismatch under warming are modified by community context

description: Climate change is altering the relative timing of species interactions by
 shifting when species first appear in communities and modifying the
 duration organisms spend in each developmental stage. However, community
 contexts, such as intraspecific competition and alternative resource
 species, can prolong shortened windows of availability and may mitigate
 the effects of phenological shifts on species interactions. Using a
 combination of laboratory experiments and dynamic simulations, we
 quantified how the effects of phenological shifts in Drosophila-parasitoid
 interactions differed with concurrent changes in temperature,
 intraspecific competition, and the presence of alternative host species.
 Our study confirmed that warming shortens the window of host
 susceptibility. However, the presence of alternative host species
 sustained interaction persistence across a broader range of phenological
 shifts than pairwise interactions by increasing the degree of temporal
 overlap with suitable development stages between hosts and parasitoids.
 Irrespective of phenological shifts, parasitism rates declined under
 warming due to reduced parasitoid performance, which limited the ability
 of community context to manage temporally mismatched interactions. These
 results demonstrate that the ongoing decline in insect diversity may
 exacerbate the effects of phenological shifts in ecological communities
 under future global warming temperatures.
description: We experimentally manipulated the timing of host-parasitoid
 interactions in current and expected warming temperatures. We did this in
 high and low levels of resource competition and in simple and complex
 communities. We also used this data to parameterize a multigenerational
 dynamic model to investigate the long-term consequences of phenological
 shifts.
DOI: 10.5061/dryad.c2fqz61b6
title: Carbohydrates complement high protein diets to maximize the growth of an actively hunting predator

description: In nature, food is often variable in composition and availability. As a
 consequence, predators may need to seek non-prey food sources. Some
 predators are known to feed on nectar when food is limited. Nectar and
 other carbohydrate resources could also be beneficial when prey are more
 abundant if it helps predators balance protein-biased diets. We tested if
 an actively hunting predator, the jumping spider, Phidippus audax,
 benefited from liquid carbohydrates when prey were not limited. We also
 tested if the benefit of carbohydrates varied with the nutrient content of
 prey (i.e., from protein to lipid-biased). Spiders were reared on one of
 six live prey, Drosophila melanogaster, treatments that ranged from high
 protein to high lipid. Half of the spiders were given access to a 20%
 sucrose solution. After two months, we measured spider mass, cephalothorax
 width, instar duration, percent body fat, survival, and estimated number
 of prey eaten. Spiders reared on high protein diets with carbohydrates
 were larger and heavier than spiders on other treatments. Access to
 carbohydrates also increased percent body fat and survival across prey
 treatments. Our results suggest that carbohydrates may be a valuable
 component of spider diets, especially when prey have high protein and low
 lipid content as is commonly observed in prey in the field. Our results
 highlight the importance of diet balancing for predators, and that liquid
 carbohydrates can be an important nutrient to supplement a diet of prey
 rather than just being an energy supplement during periods of starvation.
DOI: 10.5061/dryad.8931zcrsq
title: Finding what you don’t know: testing SDMs methods for poorly-known species

description: Aim: A limitation of species distribution models (SDMs) is that species
 with low sample sizes are difficult to model. Yet it is often important to
 know the habitat associations of poorly known species to guide
 conservation efforts. Techniques have been proposed for modeling species’
 distributions from few records, but their performance relative to one
 another has not been compared. Because these models are built and
 evaluated with small datasets, sampling error could cause severely biased
 sampling in environmental space. As a result, SDMs are likely to
 underpredict geographic distributions given small sample sizes. We perform
 the first comparison of methods explicitly promoted or developed for
 predicting the geographic ranges of species with very low sample sizes.
 Location: North Carolina, USA Taxon: South Mountains Gray-cheeked
 Salamander (Plethodon meridianus) Methods: Using the sparse, existing
 georeferenced records of P. meridianus, we built SDMs using a range of
 methods that previous researchers have argued should work for low sample
 sizes. We then tested each SDM’s ability to accurately predict independent
 survey data that were not georeferenced prior to our study. We compared
 SDMs using omission error and AUC. Results: Roughly half of the models
 successfully predicted survey records in the range center, and all models
 had high omission error rates in the range exterior. In the range interior
 or exterior, the ‘ensemble of small models’ technique produced SDMs with
 high omission error rates. Spatial filtering had negligible impact on
 model performance. Most, but not all, models outperformed predictions
 using distance from known populations. Using one of the best-performing
 methods, we developed an improved range map of P. meridianus. Main
 Conclusions: Geographically peripheral populations were difficult to
 predict for all SDMs, though some methods were clearly inferior for our
 dataset. We recommend that when sample sizes are low, researchers use
 Maxent with species-specific model settings.
DOI: 10.5061/dryad.fxpnvx0v1
title: Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

description: Post-divergence gene flow can trigger a number of creative evolutionary
 outcomes, ranging from the transfer of beneficial alleles across species
 boundaries (i.e., adaptive introgression) to the formation of new species
 (i.e., hybrid speciation). While neutral and adaptive introgression has
 been broadly documented in nature, hybrid speciation is assumed to be rare
 and the evolutionary and ecological context facilitating this phenomenon
 still remains controversial. Through combining genomic and phenotypic
 data, we evaluate the hypothesis that the dual feeding regime (based on
 both scrub legumes and gramineous herbs) of the
 taxonomically controversial grasshopper Chorthippus saulcyi
 algoaldensis resulted from hybridization between the sister
 taxa C. binotatus (that exclusively feeds on scrub
 legumes) and C. saulcyi (that only feeds
 on gramineous herbs). Genetic clustering analyses and inferences
 from coalescent-based demographic simulations confirm that C. s.
 algoaldensis represents an independently evolving lineage and
 support the ancient hybrid origin of this taxon (ca. 1.4 Ma), which sheds
 light on its uncertain phylogenetic position and might explain its broader
 trophic niche. We propose a Pleistocene hybrid speciation model where
 range shifts resulting from climatic oscillations can promote the
 formation of hybrid swarms and facilitate its long-term persistence
 through geographic isolation from parental forms in topographically
 complex landscapes.
description: Refer to README file.
DOI: 10.15468/dl.hrpcyd
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus evansi"
 ]
}

 The dataset includes 29 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003104-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t76hdr837
title: Data from: Tracking population genetic signatures of local extinction with herbarium specimens

description: Background and Aims  Habitat degradation and landscape
 fragmentation dramatically lower population sizes of rare plant species.
 Decreasing population sizes may, in turn, negatively affect genetic
 diversity and reproductive fitness which can ultimately lead to local
 extinction of populations. Although such extinction vortex dynamics have
 been postulated in theory and modelling for decades, empirical evidence
 from local extinctions of plant populations is scarce. In particular,
 comparisons between current vs. historical genetic diversity and
 differentiation are lacking despite their potential to guide conservation
 management. Methods  We studied the population genetic signatures
 of the local extinction of Biscutella laevigata subsp. gracilis
 populations in Central Germany. We used microsatellites to genotype
 individuals from 15 current populations, one ex-situ population, and 81
 herbarium samples from five extant and 22 extinct populations. In the
 current populations, we recorded population size and fitness proxies,
 collected seeds for a germination trial and conducted a vegetation survey.
 The latter served as surrogate for habitat conditions to study how habitat
 dissimilarity affects functional connectivity among the current
 populations. Key Results  Bayesian clustering revealed similar
 gene pool distribution in current and historical samples but also
 indicated that a distinct genetic cluster was significantly associated
 with extinction probability. Gene flow was affected by both spatial
 distance and floristic composition of population sites, highlighting the
 potential of floristic composition as powerful predictor of functional
 connectivity which may promote decision making for reintroduction
 measures. For an extinct population, we found a negative relationship
 between sampling year and heterozygosity. Inbreeding negatively affected
 germination. Conclusions  Our study illustrates the usefulness of
 historical DNA to study extinction vortices in threatened species. Our
 novel combination of classical population genetics together with data from
 herbarium specimens, an ex-situ population and a germination trial
 underscores the need for genetic rescue measures to prevent extinction of
 B. laevigata in Central Germany.