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FIGURE. Microscopic structures of Gliophorus roseus (PAN612, holotype). a. Upper part of pileipellis, gelatinous matrix not indicated. b. Basidiospores. c. Ixo-cheilocystidia in a gelatinous matrix (not indicated). d. Basidia at different developmental stages. Bars = 10 µm. Drawings by K. Reschke. in New and interesting species of Agaricomycetes from Panama

FIGURE. Microscopic structures of Gliophorus roseus (PAN612, holotype). a. Upper part of pileipellis, gelatinous matrix not indicated. b. Basidiospores. c. Ixo-cheilocystidia in a gelatinous matrix (not indicated). d. Basidia at different developmental stages. Bars = 10 µm. Drawings by K. Reschke.

FIGURE. Basidiocarps of Gliophorus roseus. a. KaiR619. b. PAN612, holotype. Bars a, b = 1 cm. a Photo by K. Reschke. b Photo by H. Lotz-Winter. in New and interesting species of Agaricomycetes from Panama

FIGURE. Basidiocarps of Gliophorus roseus. a. KaiR619. b. PAN612, holotype. Bars a, b = 1 cm. a Photo by K. Reschke. b Photo by H. Lotz-Winter.

FIGURE. Bayesian MCMC phylogram of Gliophorus spp. based on ITS sequences. Rooted to Hygrophorus pudorinus. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap. in New and interesting species of Agaricomycetes from Panama

FIGURE. Bayesian MCMC phylogram of Gliophorus spp. based on ITS sequences. Rooted to Hygrophorus pudorinus. Bar = estimated changes/nucleotide. Support values above or below branches: Bayesian posterior probability/maximum likelihood bootstrap.

FIGURE. Macro- and microscopic structures of Multiclavula caput-serpentis (KaiR699, holotype). a. Thallus with basidiocarps. b. Basidiospores. c. Hymenium with basidia at different developmental stages and subhymenial hyphae. d. Bulbils of green algae wrapped in hyphae, different developmental stages. Bars a = 2 mm, b, c and d = 10 µm. Drawings by H. Lotz-Winter. in New and interesting species of Agaricomycetes from Panama

FIGURE. Macro- and microscopic structures of Multiclavula caput-serpentis (KaiR699, holotype). a. Thallus with basidiocarps. b. Basidiospores. c. Hymenium with basidia at different developmental stages and subhymenial hyphae. d. Bulbils of green algae wrapped in hyphae, different developmental stages. Bars a = 2 mm, b, c and d = 10 µm. Drawings by H. Lotz-Winter.

opennotspecifiedJan 2022View details →

FIGURES 12–15 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus

FIGURES 12–15. Grunowia mannii Kociolek & Danz sp. nov. SEM. Valve interior. 12–14. Entire valves, showing differences in valve shape relative to length. Large fibulae and large portules over the raphe canal are evident. 15. View of central nodule showing small, helictoglossa-like center and discontinuous raphe branch. Scale bars = 5 µm (Fig. 12), 4 µm (Fig. 13), 3 µm (Fig. 14), 1 µm (Fig. 15).

opennotspecifiedJan 2022View details →

FIGURES 1–7 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus

FIGURES 1–7. Grunowia mannii Kociolek & Danz sp. nov. LM. Size diminution series. Fig. 1 represents an initial valve. The holotype is presented in fig. 4. Scale bar = 10 µm.

opennotspecifiedJan 2022View details →

FIGURES 8–11 in Taxonomy and valve ultrastructure of new and interesting freshwater fossil diatoms (Bacillariophyta) of Miocene age from the Espanola Formation of New Mexico, U.S.A. II. Description of a New Grunowia species with comments on the genus

FIGURES 8–11. Grunowia mannii Kociolek & Danz sp. nov. SEM of valve exterior. 8, 9. Valve view showing characteristic shape and distinctly-elevated, raphe-bearing keel. 10. Apex of the valve showing raphe end extending onto the mantle. 11. Central portion of the valve, with raphe branches interrupted. Scale bars = 5 µm (Figs 8, 9), 3 µm (Fig. 10), 2 µm (Fig. 11).

opencc-by-4.0Dec 2021View details →

Lipidomics and metabolomics datasets for "Adverse effects of arsenic uptake in rice metabolome and lipidome revealed by untargeted liquid chromatography coupled to mass spectrometry (LC-MS) and regions of interest multivariate curve resolution"

Files description Raw files for lipidomics and metabolics studies on the impact of arsenic exposure on rice growth. File details on the worksheets lipids_files.xlsx and metabolomics_files.xlsx Files have been organized as follows: Lipidomics <blockquote> 1) Control samples: lip_controls.rar 2) Watering low As exposure: lip_water_1.rar 3) Watering high As exposure: lip_water_1000.rar 4) Soil low As exposure: lip_soil_5.rar 5) Soil high As exposure: lip_soil_50.rar 6) QC samples: lip_qcs.rar </blockquote> Metabolomics (positive ionization mode) <blockquote> 1) Control samples: met_pos_controls.rar 2) Watering low As exposure: met_pos_water_1.rar 3) Watering high As exposure: met_pos_water_1000.rar 4) Soil low As exposure: met_pos_soil_5.rar 5) Soil high As exposure: met_pos_soil_50.rar 6) QC samples: met_pos_qcs.rar </blockquote> Metabolomics (negative ionization mode) <blockquote> 1) Control samples: met_neg_controls.rar 2) Watering low As exposure: met_neg_water_1.rar 3) Watering high As exposure: met_neg_water_1000.rar 4) Soil low As exposure: met_neg_soil_5.rar 5) Soil high As exposure: met_neg_soil_50.rar 6) QC samples: met_neg_qcs.rar   </blockquote>   Experimental details <blockquote> Arsenic Exposure Arsenic was supplied through two main routes: watering with contaminated water or soil containing arsenic. In addition, this new study includes metabolomic as well as lipidomic analysis, in order to have a more global overview of arsenic exposure. For the watering treatment, during the first 11 days, rice was irrigated with Milli-Q water. From that day until harvesting, plants were watered with 1 and 1000 μM of As (V) for the two concentration levels of exposure, and with Milli-Q water for control samples. The lowest concentration was established at 1 μM as it is the limit of the acceptable arsenic concentration in water by European legislation. The upper concentration was set at 1000 μM, a threshold established to ensure that the experiment was performed under sub-lethal arsenic concentration for the plant, based on previous studies. For the soil treatment, two containers were prepared with 1 kg of soil two days before planting. Soil from the container was exposed to two arsenic concentration levels (5 and 50 mg L-1). Once sowing, rice was irrigated the whole growth period with a solution containing 0.001 μM of As (V). The lowest arsenic limit in this treatment was set at 5 mg L-1 as a maximum value of common arsenic leaches without toxic characteristics, although background soil content of arsenic varies between one and 40 ppm according to the US food and drug administration (FDA) report. The highest arsenic limit was established to 50 mg L-1, as a considerably high arsenic content in the soil, slightly above the maximum frequently encountered levels. Lipidomic Analysis The lipidomic analysis was performed using a Waters Acquity UPLC system (Waters Corporation, MA, USA), connected to a Waters LCT Premier orthogonal accelerated time of flight mass spectrometer (Waters), operated in both positive and negative electrospray (ESI) ionization modes. Full scan spectra were acquired from 50 to 1500 Da. The chromatographic column employed was a Kinetex C8 (100 x 2.1 mm, 1.7 μm) (Phenomenex) under the following conditions (already used in [47]): temperature at 30˚C, injection volume at 10 μL, and flow rate at 0.3 mL min-1. Mobile phases selected were (A) MeOH 1mM ammonium formate, and (B) H2O 2mM ammonium formate, both at 0.2% formic acid. The gradient started at 80% A, increased to 90% A in 3 min, from 3 to 6 min remained at 90% A, changed to 99 % A until minute 15, remained constant 1 min, and returned to initial conditions until minute 20. Metabolomic analysis The metabolomic analysis was performed using a Waters Acquity UPLC system connected to a Q-Exactive (Thermo Fisher Scientific, Hemel Hempstead, UK) equipped with a quadrupole-Orbitrap mass analyzer. Electrospray (ESI) was used as an ionization source in both positive and negative ion modes. Full scan mass range was set from m/z 90 to 1000, and all ion fragmentation (AIF) was performed with normalized collision energy (NCE) of 35 eV. The column employed was an HILIC TSK gel amide-80 column (250 x 2.0 mm i.d., 5 μm) provided by Tosoh Bioscience (Tokyo, Japan), under the following experimental conditions (already employed in [45]): flow rate at 0.15 mL min-1, at room temperature, and 5 μL injection volume. Mobile phases were (A) AcN, and (B) 5 mM ammonium acetate, adjusted at pH 5.5 with acetic acid. The gradient employed was: starting conditions at 25% B, then increased until 30% B in 8 min; a 60% B was reached at 10 min, held for 2 min more and then back to 25% B until minute 14 min; lastly, a re-equilibration step was added and from 14 to 20 min at 25% B. </blockquote>   Funding: This research was funded by the Spanish Ministry of Science and Innovation (MCI, Grant CTQ2017-82598-P) and Severo Ochoa Project CEX2018-000794-S (funded by MCIN/AEI/ 10.13039/501100011033), and supported from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). MPC was funded by a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP).

opencc-by-4.0Feb 2022View details →

Community Meeting of the Sensitive Data Interest Group: February 2022

This is the recording from the RDA Sensitive Data Interest Group community meeting held February 23, 20:00 UTC, 2022. More information about the series can be found here: https://www.rd-alliance.org/group/sensitive-data-interest-group/post/2022-sensitive-data-community-meeting-series-register-now

FIGURE 6 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 6. Chamobates callipygis, dissected adult, microscope images: A—mediodistal part of lamella; B—bothridial seta; C—tutorial cusp; D—posteromedian protuberance in male; E—part of subcapitular mentum; F—part of epimeral region; G— part of podosomal region; H—prodorsal and humeral porose areas; I—mediodistal part of pedotectum I; J—part of genital plate; K—leg genu I; L—leg femur I.

FIGURE 5 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 5. Chamobates callipygis, adult, SEM micrographs: A—dorsoanterior view (female); B—dorsoposterior view (male); C—posteromedian protuberance, dorsoanterior view (male); D—right lateral view (male); E—partially subcapitulum, epimeral and podosomal regions, right lateral view; F—partially epimeral and genital regions, lateral view; G—right bothridial seta, antiaxial view; H—right bothridium, dorsal view; I—partially aggenital region. Scale bar 100 μm (A, B, D), 20 μm (C, E), 10 μm (F–I).

FIGURE 4 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 4. Chamobates callipygis, adult (A, C—females; B, D—males), SEM micrographs: A, B —dorsal view, male with transverse striations on notogaster indicated by arrow; C, D —ventral view. Scale bar 100 μm.

FIGURE 3 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 3. Chamobates callipygis, adult: A—subcapitulum, ventral view; B—palp, left, antiaxial view; C—chelicera, right, antiaxial view; D—leg I, right, antiaxial view; E—leg II, without tarsus, right, antiaxial view; F—leg III, without tarsus, left, antiaxial view; G—leg IV, left, antiaxial view. Scale bar 20 μm (A, C–G), 10 μm (B).

FIGURE 1 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 1. Chamobates callipygis, adult: A—dorsal view of female (legs not shown); B—posterior part of body in male, dorsal view; C—ventral view of female (gnathosoma and legs except trochanters not shown); D—posterior part of body in male, ventral view. Scale bar 50 μm.

FIGURE 2 in An interesting sexually dimorphic species, Chamobates callipygis Pavlichenko, 1991 (Acari, Oribatida, Chamobatidae), with remarks on sexual dimorphism in Ceratozetoidea

FIGURE 2. Chamobates callipygis, adult: A—variations of bothridial setae; B—right lateral view of female; C—posterior part of body in male, right lateral view; D—rostrum, anterior view; E—posterior view of female; F—posterior view of male (porose areas A3 not visible due to posteromedian protuberance). Scale bar 20 μm (A, D), 50 μm (B, C, E, F).

opencc-by-4.0Apr 2022View details →

Community Meeting of the Sensitive Data Interest Group: April 2022

This is the recording from the RDA Sensitive Data Interest Group community meeting held April 27, 20:00 UTC, 2022. More information about the series can be found here: https://www.rd-alliance.org/group/sensitive-data-interest-group/post/2022-sensitive-data-community-meeting-series-register-now

FIGURE 7 in Three interesting fungal species associated with the Asian House Gecko in Kunming, China

FIGURE 7. Colletotrichum jiangxiense (KUMCC 21-0466). a, b Colonies on PDA. c Hyphae. d Hyphae stained by cotton blue reagent. e, f Conidophores connected with conidia (f: stained by congo red reagent). g–i Conidia (g: stained by cotton blue reagent). Scale bars: c, d = 20 μm, e–i = 10 μm.

FIGURE 6 in Three interesting fungal species associated with the Asian House Gecko in Kunming, China

FIGURE 6. Phylogram generated from maximum likelihood analysis based on a combined ITS, HIS, CAL, ACT, tub2 and GPDH sequence datasets. Related sequences were taken from Diao et al. (2017) and Chaiwan et al. (2021). The 52 strains are included in the combined gene analyses, 2882 total characters including gaps (ITS: 1–579 bp, HIS: 580–874 bp, CAL: 875–1610 bp, ACT: 1611–1888 bp, tub2: 1889–2602 bp, GPDH: 2603–2882). Tree topology of the ML analysis was similar to the BI. The matrix had distinct alignment patterns, with the final ML optimization likelihood value of -14018.222367 (ln). All free model parameters were estimated using the RAxML model, with 1867 distinct alignment patterns and 15.05% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.227166, C = 0.283924, G = 0.257262, T = 0.216566, with substitution rates AC = 1.035930, AG = 0.298823, AT = 0.248992, CG = 0.225019, CT = 4.115498, GT = 1.000000. The gamma distribution shape parameter alpha = 0.904631 and the Tree-Length = 0.821909. The final average standard deviation of split frequencies at the end of total MCMC generations calculated as 0.009613 in BI analysis. The species determined in this study are indicated in red. Bootstrap values equal to or greater than 70% (ML, left) and Bayesian posterior probabilities (BI, right) equal to or greater than 0.95 are given at the nodes. Hyphens (-) represent support values less than 70% in ML/0.95 in BI.

FIGURE 5 in Three interesting fungal species associated with the Asian House Gecko in Kunming, China

FIGURE 5. Beauveria bassiana (KUMCC 21-0468). a Appearance of fungal colonies on PDA. b Close-up of fungal colonies. c Mycelium with conidia. d Mycelium mass stained by cotton blue reagent. e Conidia connected with conidiogenous cells and stained by cotton blue reagent. f A conidophore. g A branched mycelium stained by congo red reagent. h Minus and plus mycelium stained by congo red reagent. i Conidia stained by congo red reagent. j Conidia stained by cotton blue reagent. Scale bars: d = 50 μm, c, e = 30 μm, g, h = 10 μm, f, i, j = 5 μm.

FIGURE 4 in Three interesting fungal species associated with the Asian House Gecko in Kunming, China

FIGURE 4. Phylogram generated from maximum likelihood analysis based on a combined ITS, rpb1, rpb2, tef1-α and Bloc sequence datasets. Related sequences were taken from Chen et al. (2018) and Khonsanit et al. (2020). A total of 81 strains are included in the combined gene analyses; 5090 total characters including gaps (ITS: 1–566 bp, rpb1: 567–1307 bp, rpb2: 1308–2430 bp, tef1-α: 2431–3429 bp, Bloc: 3430-5090 bp). Tree topology of the ML analysis was similar to the BI. The matrix had distinct alignment patterns, with the final ML optimization likelihood value of -29154.321884 (ln). All free model parameters were estimated using the RAxML model, with 1867 distinct alignment patterns and 15.05% of undetermined characters or gaps. Estimated base frequencies were as follows: A = 0.242248, C = 0.283924, G = 0.257262, T = 0.216566, with substitution rates AC = 0.928484, AG = 3.845624, AT = 0.649405, CG = 0.874887, CT = 4.792288, GT = 1.000000. The gamma distribution shape parameter alpha = 0.712530 and the Tree-Length = 1.618181. The final average standard deviation of split frequencies at the end of total MCMC generations calculated as 0.009746 in BI analysis. The species determined in this study are indicated in red. Bootstrap values equal to or greater than 70% (ML, left) and Bayesian posterior probabilities (BI, right) equal to or greater than 0.95 are given at the nodes. Hyphens (-) represent support values less than 70% in ML/0.95 in BI.