cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.18150/ryqosy
title: Aged polyethylene microplastics modulate herbicide and antibiotic bioavailability and plant responses: a case study with glyphosate and tetracycline

description: The dataset contains raw and processed results obtained during hydroponic exposure experiments with Brassica napus L., conducted to assess the effects of aged polyethylene microplastics (MP PE) and co-occurring xenobiotics (tetracycline and [C₁₂TMA][Glyph]) on plant physiology, biochemical stress responses, and pollutant sorption behavior.The dataset consists exclusively of Excel (XLSX) files containing primary experimental measurements used for statistical analysis and data visualization. The files are organized according to analytical endpoints, as outlined below:Sorption experimentsHydroponic_sorption_Tetracycline.xlsx – concentrations of tetracycline in hydroponic medium over time (0 h, 1 h, 1 day, 7 days, 10 days) in systems with and without microplastics.Hydroponic_sorption_ILs.xlsx – concentrations of the ionic liquid [C₁₂TMA][Glyph] in hydroponic medium over time under analogous experimental conditions.Photosynthetic pigmentsHydroponic_chlorophyll.xlsx – chlorophyll a, chlorophyll b, and carotenoid contents in shoots of Brassica napus exposed to different treatments (control, microplastics, xenobiotics, humic acids, and their mixtures), used to calculate pigment ratios.Antioxidant enzymes and stress markersHydroponic_enzymes_CAT.xlsx – catalase (CAT) activity.Hydroponic_enzymes_APx.xlsx – ascorbate peroxidase (APx) activity.Hydroponic_enzymes_GST.xlsx – glutathione S-transferase (GST) activity.Hydroponic_enzymes_POx.xlsx – peroxidase (POx) activity.Hydroponic_enzymes_TBARS.xlsx – TBARS values representing lipid peroxidation and membrane damage.Secondary metabolites and osmotic stress indicatorsHydroponic_phenolic_compounds.xlsx – total phenolic content (TPC) in roots and shoots.Hydroponic_proline_content.xlsx – proline content as an indicator of osmotic and oxidative stress.Hydroponic_protein_content.xlsx – total soluble protein content in plant tissues.Toxicity screeningHydroponic_EC50.xlsx – EC₅₀ values derived from preliminary toxicity assays for tetracycline and [C₁₂TMA][Glyph], based on root and shoot length inhibition.
DOI: 10.5061/dryad.qr818
title: Data from: Appraisal of the fossil record of Homarus (nephropid lobster), with description of a new species from the upper Oligocene of Hungary and remarks on the status of Hoploparia

description: The fossil record of the clawed lobster genus, Homarus, is appraised. The
 taxonomic history of Homarus and Hoploparia is summarized, and a list of
 species recognized for each is provided. A tabulation of all fossil
 species of the family Nephropidae permits assessment of nephropid species
 diversity through time. A new species of Homarus, H. hungaricus, is
 recorded from the upper Oligocene (Chattian) Mány Formation at Mány,
 northern Hungary. The species is known by a single specimen consisting of
 a partial cephalothorax, a pleon minus telson, and partial chelipeds.
 Homarus is now known by two extant species (H. americanus and H. gammarus)
 and six fossil taxa, one of Early Cretaceous (Albian; H. benedeni) and
 five of Cenozoic age (H. hungaricus n. sp., H. klebsi, H. lehmanni, H.
 morrisi, and H. percyi). The new fossil Homarus differs from modern
 congeners in aspects of carapace and pleon ornamentation and, especially,
 cutter claw shape. This is the fourth Oligocene occurrence of a nephropid
 species; all are Homarus and all are from Western Europe. Homarus makes
 its appearance in the fossil record in the Early Cretaceous (Albian) and
 then is not known again until the Paleogene, despite the fact that
 nephropid lobsters in general are well known from the Late Cretaceous.
 Nephropid lobsters are better known from the Cretaceous than from the
 Cenozoic. Both raw species numbers and numbers corrected (normalized) for
 epicontinental sea coverage show that shelf-dwelling nephropid lobsters
 were most diverse during the Late Cretaceous.
description: APPENDIX 2 - species of
 Nephropidae - Tshudy et al.Pre-Holocene
 stratigraphic distribution of species of the family Nephropidae (sensu De
 Grave et al., 2009), inclusive of the former
 Thaumastochelidae.APPENDIX 2 revised 2-2-17
 DRYAD.docxAPPENDIX 3 - data for
 Vail Curve method - Tshudy et al.Data and calculations
 for Figure 6; “*” indicates standard for normalizing as per the Vail Curve
 method of Tshudy (2003).APPENDIX 3 DSp
 DRYAD.docx
DOI: 10.5061/dryad.9f63r
title: Data from: Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis

description: During sampling of several Coffea arabica plantations in Tanzania severe
 root galling, caused by a root-knot nematode was observed. From pure
 cultures, morphology and morphometrics of juveniles and females matched
 perfectly with Meloidogyne africana, whereas morphology of the males
 matched identically with those of Meloidogyne decalineata. Based on their
 Cox1 sequence, however, the recovered juveniles, females and males were
 confirmed to belong to the same species, creating a taxonomic conundrum.
 Adding further to this puzzle, re-examination of M. oteifae type material
 showed insufficient morphological evidence to maintain its status as a
 separate species. Consequently, M. decalineata and M. oteifae are
 synonymized with M. africana, which is herewith redescribed based on
 results of light and scanning electron microscopy, ribosomal and
 mitochondrial DNA sequences, isozyme electrophoresis, along with bionomic
 and cytogenetic features. Multi-gene phylogenetic analysis placed M.
 africana outside of the three major clades, together with M. coffeicola,
 M. ichinohei and M. camelliae. This phylogenetic position was confirmed by
 several morphological features, including cellular structure of the
 spermatheca, egg mass position, perineal pattern and head shape. Moreover,
 M. africana was found to be a polyphagous species, demonstrating that
 “early-branching” Meloidogyne spp. are not as oligophagous as had
 previously been assumed. Cytogenetic information indicates M. africana (2n
 = 21) and M. ardenensis (2n = 51–54) to be a triploid mitotic
 parthenogenetic species, revealing at least four independent origins of
 mitotic parthenogenesis within the genus Meloidogyne. Furthermore, M. mali
 (n = 12) was found to reproduce by amphimixis, indicating that amphimictic
 species with a limited number of chromosomes are widespread in the genus,
 potentially reflecting the ancestral state of the genus. The wide
 variation in chromosome numbers and associated changes in reproduction
 modes indicate that cytogenetic evolution played a crucial role in the
 speciation of root-knot nematodes and plant-parasitic nematodes in
 general.
description: Karyology Meloidogyne
 africanaKaryology Meloidogyne
 africanaKaryology Meloidogyne
 ardenensisKaryology Meloidogyne
 ardenensisKaryology Meloidogne
 ardenensis.zipKaryology Meloidogyne
 javanicaKaryology Meloidogyne
 javanicaKaryology Meloidogyne
 maliKaryology Meloidogyne
 maliMeloidogyne africana
 female reproducive systemMeloidogyne africana
 female reproducive systemMeloidogyne mali female
 reproducive systemMeloidogyne mali female
 reproducive systemMultiple sequence
 alignmentsMultiple sequence
 alignments
DOI: 10.5061/dryad.0ps2f
title: Data from: Parasitism and the expression of sexual dimorphism

description: Although a negative covariance between parasite load and sexually selected
 trait expression is a requirement of few sexual selection models, such a
 covariance may be a general result of life-history allocation trade-offs.
 If both allocation to sexually selected traits and to somatic maintenance
 (immunocompetence) are condition dependent, then in populations where
 individuals vary in condition, a positive covariance between trait
 expression and immunocompetence, and thus a negative covariance between
 trait and parasite load, is expected. We test the prediction that parasite
 load is generally related to the expression of sexual dimorphism across
 two breeding seasons in a wild salamander population and show that males
 have higher trematode parasite loads for their body size than females and
 that a key sexually selected trait covaries negatively with parasite load
 in males. We found evidence of a weaker negative relationship between the
 analogous female trait and parasite infection. These results underscore
 that parasite infection may covary with expression of sexually selected
 traits, both within and among species, regardless of the model of sexual
 selection, and also suggest that the evolution of condition dependence in
 males may affect the evolution of female trait expression.
description: DeLisle&Rowe_parasitedataParasite loads of wild-caught male and female newts, from two years in a single population.
DOI: 10.5061/dryad.k7cr5
title: Data from: Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies

description: Migration of hosts and parasites can have a profound impact on
 host–parasite ecological and evolutionary interactions. Using the
 bacterium Pseudomonas aeruginosa UCBPP-PA14 and its phage DMS3vir, we here
 show that immigration of naive hosts into coevolving populations of hosts
 and parasites can influence the mechanistic basis underlying host defence
 evolution. Specifically, we found that at high levels of bacterial
 immigration, bacteria switched from clustered regularly interspaced short
 palindromic repeats (CRISPR-Cas) to surface modification-mediated defence.
 This effect emerges from an increase in the force of infection, which tips
 the balance from CRISPR to surface modification-based defence owing to the
 induced and fixed fitness costs associated with these mechanisms,
 respectively.
description: Chabas et al Proc B 2016
 - raw dataraw data Chabas et al
 Proc B 2016
DOI: 10.5061/dryad.b2j3405
title: Data from: Simple parameterization of aerodynamic roughness lengths and the turbulent heat fluxes at the top of midlatitude August‐one glacier, Qilian Mountains, China

description: The fluxes of sensible heat (H) and latent heat (LE), which are generally
 the important parts of the energy and mass balances over glacier surfaces,
 are widely quantified by the bulk method. However, due to the difficulty
 of determining the aerodynamic roughness length z0m in this method, H and
 LE values may still have large uncertainties with significant inaccuracy.
 To acquire reliable varying and intrinsic z0m values, new simpler
 parameterizations for z0m values at different ranges of the friction
 velocity u*b were fitted in this study. The method was implemented using
 the related meteorological data and glacial sublimation/condensation
 measured at the top of the August‐one glacier (4817 m a.s.l.) in the
 Qilian Mountains from 1 July 2016 to 15 August 2017. The parameterization
 shows that z0m increased sharply when u*b exceeded 0.43 m/s (the
 approximate threshold value) and that the effect of snowdrift was slight
 for the hourly z0m values in the range 0.15 ≤ u*b ≤ 0.43 m/s, which could
 thus be used to calculate the daily z0m. During the wet period (1 July to
 24 September 2016 and 5 May to 15 August 2017), the turbulent fluxes
 calculated by the bulk method showed that net radiation Rnet was the
 primary source of surface energy (60.7 w/m2), whereas during the dry
 period (25 September 2016 to 4 May 2017), the main heat sink was the
 positive H (28.5 w/m2) rather than the negative Rnet (–10.0 w/m2).
description: Meteorological data at
 the August-one glacierThe meteorological data
 at the August-one glacier
DOI: 10.5061/dryad.gh221
title: Data from: Three-dimensional preservation of cellular and subcellular structures reveal 1.6 billion-year-old probable crown-group red algae

description: The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India
 contains phosphatized stromatolitic microbialites. We report from there
 uniquely well-preserved fossils interpreted as crown-group rhodophytes
 (red algae). The filamentous form Rafatazmia chitrakootensis n.gen, n.sp.
 has uniserial rows of large cells and grows through diffusely distributed
 septation. Each cell has a centrally suspended, conspicuous rhomboidal
 disk interpreted as a pyrenoid. The septa between the cells have central
 structures that may represent pit connections and pit plugs. Another
 filamentous form, Denaricion mendax n.gen., n.sp., has coin-like cells
 reminiscent of those in large sulfur-oxidizing bacteria, but much more
 recalcitrant than the liquid-vacuole-filled cells of the latter. Its wider
 affinities are uncertain. Ramathallus lobatus n.gen., n.sp. is a lobate
 sessile alga with pseudoparenchymatous thallus and apparent tetraspore
 formation, suggesting florideophycean affinity. Rafatazmia and Ramathallus
 are interpreted as crown-group multicellular rhodophytes, antedating the
 oldest previously accepted red alga in the fossil record by about 400
 million years.
description: Tomograms of Vindhyan
 algaeThe file is a ZIP
 archive of 28 tomograms in 3D-TIFF format. Details about the imaged
 specimens are in the associated ReadMe file.Bengtson_et_al_Red_Algae_Data_Files.zip
DOI: 10.5061/dryad.f01t1
title: Data from: Repeated evolution of exaggerated dewlaps and other throat morphology in lizards

description: The existence of elaborate ornamental structures in males is often assumed
 to reflect the outcome of female mate choice for showy males. However,
 female mate choice appears weak in many iguanian lizards, but males still
 exhibit an array of ornament-like structures around the throat. We
 performed a phylogenetic comparative study to assess whether these
 structures have originated in response to male-male competition or the
 need for improved signal efficiency in visually difficult environments. We
 found little evidence for the influence of male-male competition. Instead,
 forest species were more likely to exhibit colourful throat appendages
 than species living in open habitats, suggesting selection for signal
 efficiency. On at least three independent occasions, throat ornamentation
 has become further elaborated into a large, conspicuously coloured moving
 dewlap. Although the function of the dewlap is convergent, the underlying
 hyoid apparatus has evolved very differently, revealing the same adaptive
 outcome has been achieved through multiple evolutionary trajectories. More
 generally, our findings highlight that extravagant, ornament-like
 morphology can evolve in males without the direct influence of female mate
 choice, and that failure to consider alternative hypotheses for the
 evolution of these structures can obscure the true origins of signal
 diversity among closely related taxa.
description: ORD_TJ-JEB-2015-00382R1_agamid_dataORD_TJ-JEB-2015-00382R1_hyoid_data
DOI: 10.5061/dryad.mh981
title: Data from: Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA

description: We compared DNA, pollen and macrofossil data obtained from Weichselian
 interstadial and Holocene (maximum age 8400 cal yr BP) peat sediments from
 northern Europe and used them to reconstruct contemporary floristic
 compositions at two sites. The majority of the samples provided plant DNA
 sequences of good quality with success amplification rates depending on
 age. DNA and sequencing analysis provided five plant taxa from the older
 site and nine taxa from the younger site, corresponding to 7% and 15% of
 the total number of taxa identified by the three proxies together. At both
 sites, pollen analysis detected the largest (54) and DNA the lowest (10)
 number of taxa, but five of the DNA taxa were not detected by pollen and
 macrofossils. The finding of a larger overlap between DNA and pollen than
 between DNA and macrofossils proxies seems to go against our previous
 suggestion based on lacustrine sediments that DNA originates principally
 from plant tissues and less from pollen. At both sites, we also detected
 Quercus spp. DNA, but few pollen grains were found in the record, and
 these are normally interpreted as long-distance dispersal. We confirm that
 in palaeoecological investigations, sedimentaryDNA analysis is less
 comprehensive than classical morphological analysis, but is a
 complementary and important tool to obtain a more complete picture of past
 flora.
description: trnL
 sequencesThe file include trnL
 sequences obtained using Sanger/cloning technique at Uppsala University
 from sedimentary (bulk) DNA samples from peat layers located on in
 Northern Finland (NEF)and in Northern Russia (NER)
DOI: 10.5061/dryad.0j2k7
title: Data from: Enhanced B-cell receptor recognition of the autoantigen transglutaminase 2 by efficient catalytic self-multimerization

description: A hallmark of the gluten-driven enteropathy celiac disease is autoantibody
 production towards the enzyme transglutaminase 2 (TG2) that catalyzes the
 formation of covalent protein-protein cross-links. Activation of
 TG2-specific B cells likely involves gluten-specific CD4 T cells as
 production of the antibodies is dependent on disease-associated HLA-DQ
 allotypes and dietary intake of gluten. IgA plasma cells producing TG2
 antibodies with few mutations are abundant in the celiac gut lesion. These
 plasma cells and serum antibodies to TG2 drop rapidly after initiation of
 a gluten-free diet, suggestive of extrafollicular responses or germinal
 center reactions of short duration. High antigen avidity is known to
 promote such responses, and is also important for breakage of
 self-tolerance. We here inquired whether TG2 avidity could be a feature
 relevant to celiac disease. Using recombinant enzyme we show by dynamic
 light scattering and gel electrophoresis that TG2 efficiently utilizes
 itself as a substrate due to conformation-dependent homotypic association,
 which involves the C-terminal domains of the enzyme. This leads to the
 formation of covalently linked TG2 multimers. The presence of exogenous
 substrate such as gluten peptide does not inhibit TG2 self-cross-linking,
 but rather results in formation of TG2-TG2-gluten complexes. The celiac
 disease autoantibody epitopes, clustered in the N-terminal part of TG2,
 are conserved in the TG2-multimers as determined by mass spectrometry and
 immunoprecipitation analysis. TG2 multimers are superior to TG2 monomer in
 activating A20 B cells transduced with TG2-specific B-cell receptor, and
 uptake of TG2-TG2-gluten multimers leads to efficient activation of
 gluten-specific T cells. Efficient catalytic self-multimerization of TG2
 and generation of multivalent TG2 antigen decorated with gluten peptides
 suggest a mechanism by which self-reactive B cells are activated to give
 abundant numbers of plasma cells in celiac disease. Importantly, high
 avidity of the antigen could explain why TG2-specific plasma cells show
 signs of an extrafollicular generation pathway.
description: CTR
 (4032)Mass spectrometry
 QExactive RAW data file; tryptic digest of non-crosslinked
 TG2CTR_4032.rawMonomer (I) (4036)Mass spectrometry QExactive RAW data file; tryptic digest of self-crosslinked TG2 (monomer, size exclusion fraction I)Monomer_I_4036.rawDimer (II) (4040)Mass spectrometry QExactive RAW data file; tryptic digest of self-crosslinked TG2 (dimer, size exclusion fraction II)Dimer_II_4040.rawTrimer (III) (4044)Mass spectrometry QExactive RAW data file; tryptic digest of self-crosslinked TG2 (trimer, size exclusion fraction III)Trimer_III_4044.rawTrimer plus (III+) (4048)Mass spectrometry QExactive RAW data file; tryptic digest of self-crosslinked TG2 (trimer +, size exclusion fraction III+)Trimer_plus_IIIplus_4048.raw
DOI: 10.5061/dryad.0s0h7
title: Data from: A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle

description: Glycolytic potential (GP) in skeletal muscle is economically important in
 the pig industry because of its effect on pork processing yield. We have
 previously mapped a major quantitative trait loci (QTL) for GP on
 chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein
 performed a systems genetic analysis to identify the causal variant
 underlying the phenotype QTL (pQTL). We first conducted genome-wide
 association analyses in the F2 intercross and an F19 Sutai pig population.
 The QTL was then refined to an 180-kb interval based on the 2-LOD drop
 method. We then performed expression QTL (eQTL) mapping using muscle
 transcriptome data from 497 F2 animals. Within the QTL interval, only one
 gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the
 same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase
 kinase (PhK), which functions in the cascade activation of glycogen
 breakdown. Deep sequencing of PHKG1 revealed a point mutation (C&gt;A)
 in a splice acceptor site of intron 9, resulting in a 32-bp deletion in
 the open reading frame and generating a premature stop codon. The aberrant
 transcript induces nonsense-mediated decay, leading to lower protein level
 and weaker enzymatic activity in affected animals. The mutation causes an
 increase of 43% in GP and a decrease of&gt;20% in water-holding
 capacity of pork. These effects were consistent across the F2 and Sutai
 populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The
 unfavorable allele exists predominantly in Duroc-derived pigs. The
 findings provide new insights into understanding risk factors affecting
 glucose metabolism, and would greatly contribute to the genetic
 improvement of meat quality in Duroc related pigs.
description: Openarray SNPs and
 GenotypesGlycogen
 contentPHKG1 gene
 expression
DOI: 10.5061/dryad.8j5j72t
title: Data from: Changes in melanocyte RNA and DNA methylation favor pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds

description: Cysteine plays essential biological roles, but excessive amounts produce
 cellular oxidative stress. Cysteine metabolism is mainly mediated by the
 enzymes cysteine dioxygenase and γ-glutamylcysteine synthetase,
 respectively coded by the genes CDO1 and GCLC. Here we test a new
 hypothesis posing that the synthesis of the pigment pheomelanin also
 contributes to cysteine homeostasis in melanocytes, where cysteine can
 enter the pheomelanogenesis pathway. We conducted a experiment in the
 Eurasian nuthatch Sitta europaea, a bird producing large amounts of
 pheomelanin for feather pigmentation, to investigate if melanocytes show
 epigenetic lability under exposure to excess cysteine. We increased
 systemic cysteine levels in nuthatches by supplementing them with dietary
 cysteine during growth. This caused in feather melanocytes the
 downregulation of genes involved in intracellular cysteine metabolism
 (GCLC), cysteine transport to the cytosol from the extracellular medium
 (Slc7a11) and from melanosomes (CTNS), and regulation of tyrosinase
 activity (MC1R and ASIP). These changes were mediated by increases in DNA
 m5C in all genes excepting Slc7a11, which experienced RNA m6A depletion.
 Birds supplemented with cysteine synthesized more pheomelanin than
 controls, but did not suffer higher systemic oxidative stress. These
 results suggest that excess cysteine activates an epigenetic mechanism
 that favors pheomelanin synthesis and may protect from oxidative stress.
description: Cysteine supplementation
 - Dryad