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opennotspecifiedNov 2017View details →

Distribution. Recorded from montane localities isolated by intervening areas of lowland habitat in New Guinea, including Foja Mts, Adelbert Range, Huon Peninsula (Finisterre and Saruwaged ranges), and E Central Cordillera, including both N (Jimi and Ramu rivers) and S catchments (Purari and Aroa rivers). in Muridae

Distribution. Recorded from montane localities isolated by intervening areas of lowland habitat in New Guinea, including Foja Mts, Adelbert Range, Huon Peninsula (Finisterre and Saruwaged ranges), and E Central Cordillera, including both N (Jimi and Ramu rivers) and S catchments (Purari and Aroa rivers).

opennotspecifiedJul 2022View details →

FIGURE 2 in Fusarium citri-sinensis sp. nov. (Ascomycota: Nectriaceae) isolated from fruit of Citrus sinensis in China

FIGURE 2. Morphological characteristics of Fusarium citri-sinensis (YZU 191316). A–B. colonies on PDA; C–D. conidium formed on the carnation leaf; E. microconidia; F–G. chlamydospores; H. macroconidia.—Scale bars: C–G = 10 μm, H = 25 μm.

opennotspecifiedJul 2022View details →

FIGURE 1 in Fusarium citri-sinensis sp. nov. (Ascomycota: Nectriaceae) isolated from fruit of Citrus sinensis in China

FIGURE 1. Phylogenetic tree of Fusarium citri-sinensis and its related species based on the combined dataset of the ITS, EF-1α and RPB2 gene sequences. The maximum likelihood, maximum parsimony bootstrap support values>60% (BS), and Bayesian posterior probabilities>0.7 (PP) are given at the nodes (BS/PP). Type strains are marked 'T' or 'NT'.

opencc-by-4.0Aug 2022View details →

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of Dunaliella tertiolecta and Phaeodactylum tricornutum. Effect of Triton X-100 and temperature

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of microalgae Dunaliella tertiolecta (D. tertiolecta) and Phaeodactylum tricurnutum (P. tricornutum) by dynamic light scattering are presented. The project contains spreadsheet files with the measured dependencies of g2 function on time. We collected several g2 functions for each setting (3 for D. tertiolecta samples, 5 for D. tertiolecta with added TX100, 3 for P. tricornutum samples, 3 for P. tricornutum with added TX100). Curves were analyzed independently and compared with the respective averaged curve fitted by the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). The correlation curves were fitted with up to 50 exponents. For analysis of stability of small cellular particles with respect to temperature change, we have overall reports for each microalgae type and reports on the size distribution function, data for the g2 function and dependence of scattered light intensity on time for each temperature measured. There were 14 temperatures chosen for each type of microalgae. The files are marked with respective temperatures. The samples were prepared as described below: Cultivation of the algae: Cultures of D. tertiolecta CCAP 19/22 and P. tricornutum CCAP 1052/1A from the Culture Collection of Algae and Protozoa (CCAP) of SAMS (Oban, Scotland) were grown in artificial seawater (Reef Crystals, Aquarium Systems, France). 22 g of salt was dissolved in one litre of distilled water, sterile filtered (0.2-micron cellulose filters, ref. 11107-47-CAN, Sartorius Stedim Biotech GmbH, Germany), autoclaved, and supplemented with Guillard’s (F/2) Marine Water Enrichment Solution (ref. G0154, Sigma Aldrich, USA). Cultures were grown in a respirometer (Echo, Slovenia) in 0.5-L borosilicate bottles, at 20 °C and 20 % illumination (approximately 250 μmol/m2s) with a 14-hour light / 10-hour dark cycle, with aeration of 0.2 L/min. Isolation of small cellular nanoparticles: Small cellular particles were isolated by differential centrifugation, using a protocol widely used for the isolation of extracellular vesicles (Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. Current Protocols in Cell Biology. 2006;30(1). doi:10.1002/0471143030.cb0322s30). Microalgal cells were removed by low-speed centrifugation (300 g, 10 min, 4°C, centrifuge Centric 260R with rotor RA 6/50 (Domel, Slovenia)), using 50 mL conical centrifuge tubes (ref. S.078.02.008.050, Isolab Laborgeräte GmbH, Germany); and 2000 g, 10 min, 4°C (Centric 400R centrifuge with rotor RS4/100 (Domel, Slovenia)), using 15 mL conical centrifuge tubes (ref. S.078.02.001.050, Isolab Laborgeräte GmbH, Germany). Each step was repeated twice. Then, the cell-depleted medium was centrifuged twice at 10 000g and 4°C for 30 min (Beckman L8-70M ultracentrifuge, rotor SW55Ti (Beckman Coulter, USA)), using thin-wall polypropylene centrifuge tubes (ref. 326819, Beckman Coulter, USA) to remove larger cell debris. Finally, small cellular particles were pelleted by centrifugation at 118 000 g and 4°C, for 70 min in the same type of ultracentrifuge and ultracentrifuge tubes. The isolate obtained from about 30 mL of conditioned media was not visible to the eye. For treatment with Triton X-100, the sample was incubated with Triton X-100 at concentration of 0.1%. Dynamic light scattering (DLS): The average hydrodynamic radius (Rh) of NPs and the average intensity of scattered light (I) were assessed for characterization of small cellular particles by DLS. The value of I was interpreted as a measure of small cellular particles concentration (in the case of preserved particle size distribution) or as a topological change (in the case of altered particle size distribution)(Paterna A, Rao E, Adamo G, et al. Isolation of Extracellular Vesicles From Microalgae: A Renewable and Scalable Bioprocess. Front Bioeng Biotechnol. 2022;10:836747. doi:10.3389/fbioe.2022.836747; Brown W, ed. Dynamic Light Scattering: The Method and Some Applications. Clarendon Press ; Oxford University Press; 1993). For analysis of the samples we used Instrument 3D-DLS-SLS cross-correlation spectrometer from LS Instruments GmbH (Fribourg, Switzerla nd) with a 100 mW DPSS laser (Cobolt Flamenco, Cobolt AB, Sweden) having a wavelength λ0 = 660 nm. Before measurements, samples were equilibrated in a decalin bath at 25 °C for 15 min. The scattered light was measured at an angle θ = 90° for 120 s. The correlation functions and integral time-averaged intensities I(θ)&equiv; I(q) (where q is the scattering vector, defined as q =(4πn0/λ0)sin(θ/2), with n0  the refractive index of the medium, in our case estimated by the corresponding value for water, i.e. n0 = 1.33 at 25°C), were recorded simultaneously. The Rh values of small cellular particles were obtained from the diffusion coefficients (D) that were assessed from the correlation function of the scattered electric field (g1(t)). The g1(t) function was calculated from the measured correlation function of the scattered light intensity g2(t) by applying Siegert’s relation (Schärtl W. Light Scattering from Polymer Solutions and Nanoparticle Dispersions. Springer; 2007; Shurer CR, Kuo JCH, Roberts LM, et al. Physical Principles of Membrane Shape Regulation by the Glycocalyx. Cell. 2019;177(7):1757-1770.e21. doi:10.1016/j.cell.2019.04.017). To convert D to Rh, the Stokes-Einstein equation was used (Rh = kT6πηD, where k is the Boltzmann constant, T is the absolute temperature, and η is the viscosity of the medium in which the particles diffuse). It was assumed that particles have a spherical shape. The viscosity of the medium was not known. We approximated the viscosity value to that of of water at 25°C.To test the effect of Triton X-100 on the samples, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TX100) was determined. The analysis was made with an in-house created software based on the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). We collected several intensity correlation functions for each setting. Curves were analyzed independently and compared with the averaged curve. The correlation curves were fitted with up to 50 exponents. To test the effect of Triton X-100 on NPs, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TritonX-100) was determined. Thermal stability analysis was performed using the LitesizerTM 500 instrument (Anton Paar GmbH). Samples were heated from 15 °C to 80 °C in 5 °C steps. When the target temperature was reached, the samples were equilibrated for another 5 minutes before 10 measurements of 20 s duration were performed. The size distributions were determined from the mean correlation function using the Anton Paar Kalliope Professional; Version 2.16.0. (Anton Paar GmbH), <a href="https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/">https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/</a>,  applying the CONTIN approach. A new version of KalliopeTM 4.12.0 <a href="https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en">https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en</a> is freely available online.

FIGURE. Petalidium parvifolium, flower and leaf morphology. A. Branchlet showing leaves that are not succulent; blade ± flat and margins without long, robust, multi-cellular trichomes and isolated, robust, stalked glandular trichomes. B. Flower in front view. C. Flower in lateral view. Scale bar = 5 mm. Photographs by W. Swanepoel. in Petalidium mannheimerae (Acanthaceae), a new species from Namibia and South Africa, with notes on the taxonomic identity of P. parvifolium

FIGURE. Petalidium parvifolium, flower and leaf morphology. A. Branchlet showing leaves that are not succulent; blade ± flat and margins without long, robust, multi-cellular trichomes and isolated, robust, stalked glandular trichomes. B. Flower in front view. C. Flower in lateral view. Scale bar = 5 mm. Photographs by W. Swanepoel.

FIGURE. Petalidium mannheimerae, morphology of flowers from different localities in the Richtersveld, Northern Cape, South Africa (A–D), and leaf morphology (E). A. Flower in lateral view (Sun Valley). B. Flower in front view (Sun Valley). C. Flower in front view (Kosies). D. Flowers (Umdaus). E. Branchlet showing leaves being semi-succulent, the blade subconduplicate to conduplicate, recurved towards apex, the margins with isolated, robust, stalked glandular trichomes. Scale bar = 5 mm. Photographs by M. Koekemoer (A–C), N. Jürgens (D), & W. Swanepoel (E). in Petalidium mannheimerae (Acanthaceae), a new species from Namibia and South Africa, with notes on the taxonomic identity of P. parvifolium

FIGURE. Petalidium mannheimerae, morphology of flowers from different localities in the Richtersveld, Northern Cape, South Africa (A–D), and leaf morphology (E). A. Flower in lateral view (Sun Valley). B. Flower in front view (Sun Valley). C. Flower in front view (Kosies). D. Flowers (Umdaus). E. Branchlet showing leaves being semi-succulent, the blade subconduplicate to conduplicate, recurved towards apex, the margins with isolated, robust, stalked glandular trichomes. Scale bar = 5 mm. Photographs by M. Koekemoer (A–C), N. Jürgens (D), & W. Swanepoel (E).

FIGURE 5 in Two novel Oidiodendron species isolated from roots of Vaccinium boninense in the Bonin Islands, Japan

FIGURE 5. Line drawings of microscopic morphology of Oidiodendron tokumasui sp. nov. A‒B. Conidia. C‒D. Conidiophores, fertile hyphae, and conidia. Scale bar: A‒B = 5 µm, C‒D = 10 µm.

FIGURE 2 in Two novel Oidiodendron species isolated from roots of Vaccinium boninense in the Bonin Islands, Japan

FIGURE 2. Morphology of Oidiodendron boniense sp. nov. A. 28 day old colony on CMA. B. 28 day old colony on PDA. C. 28 day old colony on MEA. D. 28 day old colony on OA. E. Conidia. F. Scanning electron micrograph of conidia. G‒H. Conidiophores, fertile hyphae, and conidia. I. Hyphal coils within hair roots of Vaccinium virgatum. Hyphae are stained brown. Scale bar: E, G‒I = 10 µm, F = 5 µm.

FIGURE 4 in Two novel Oidiodendron species isolated from roots of Vaccinium boninense in the Bonin Islands, Japan

FIGURE 4. Morphology of Oidiodendron tokumasui sp. nov. A. 28 day old colony on CMA. B. 28 day old colony on PDA. C. 28 day old colony on MEA. D. 28 day old colony on OA. E. Conidia. F. Scanning electron micrograph of conidia. G‒H. Conidiophores, fertile hyphae, and conidia. I. Hyphal coils within hair roots of Vaccinium virgatum. Hyphae are stained brown. Scale bar: E, G‒I = 10 µm, F = 5 µm.

FIGURE 3 in Two novel Oidiodendron species isolated from roots of Vaccinium boninense in the Bonin Islands, Japan

FIGURE 3. Line drawings of the microscopic morphology of Oidiodendron boniense sp. nov. A‒B. Conidia. C‒E. Conidiophores, fertile hyphae, and conidia. Scale bar: A‒B = 5 µm, C‒E = 10 µm.

FIGURE 1. A in Two novel Oidiodendron species isolated from roots of Vaccinium boninense in the Bonin Islands, Japan

FIGURE 1. A maximum-likelihood phylogenetic tree of Oidiodendron boniense sp. nov., Oidiodendron tokumasui sp. nov. and other taxa of the family Myxotrichaceae based on a combined dataset with ITS, LSU, MCM7, and RPB1 sequences. Bootstrap support values (>60%) are presented at the nodes. Hyphodiscus hyaloscyphoides and Venturiocistella japonica were selected as outgroups.

opencc-by-4.0Sep 2023View details →

Highly contiguous genomes of Giardia duodenalis isolates

<pre>High-quality genome data sets for Giardia duodenalis are scarce. Here, we generated highly contiguous genomes by a hybrid PacBio/Illumina sequencing approach of four assemblage A (one AI from a cat, and three AII from humans) and five assemblage B isolates (from humans) derived by axenic culture from clinical samples.</pre> Raw data available under PRJNA879307.

opennotspecifiedOct 2022View details →

FIGURE 3 in Mucor tofus, a new species isolated from Mao-tofu (a fermented soybean food) in China

FIGURE 3. Morphology of Mucor tofus sp. nov. a, b. Front and reverse of colony on PDA. c, d. Front and reverse of colony on SMA. e. Lateral view of tall sporangiophores. f‒l. Tall and lateral sporangiophores with sporangia. Note that tall sporangiophores are irregular swollen when young. m‒o. Details of lateral sporangia. p‒r. Columellae with or without collars. s. Sporangiospores. Scale bars: e‒i = 500 µm, j‒l = 200 µm, m‒r = 50 µm, s =20 µm.

opennotspecifiedOct 2022View details →

FIGURE 2 in Mucor tofus, a new species isolated from Mao-tofu (a fermented soybean food) in China

FIGURE 2. Phylogenetic tree depicting the relationships of Mucor tofus sp. nov. and related species based on maximum likelihood (ML) analysis of LSU rDNA. Backusella grandis and B. lamprospota were used as outgroups. Support values of maximum likelihood bootstrap proportion (MLBP), maximum parsimony bootstrap support (MPBS) and Bayesian inference posterior probability (BPP) are shown along the branches. Dash (-) indicates nodes with MLBP<70%, MPBS<70% or BPP<0.95. New taxa are in red and ex-type isolates are in bold.

opennotspecifiedOct 2022View details →

FIGURE 1 in Mucor tofus, a new species isolated from Mao-tofu (a fermented soybean food) in China

FIGURE 1. Phylogenetic tree depicting the relationships of Mucor tofus sp. nov. and related species based on the maximum likelihood (ML) analysis of rDNA ITS sequences. Backusella grandis and B. lamprospota were used as the outgroups. Support values of maximum likelihood bootstrap proportion (MLBP), maximum parsimony bootstrap support (MPBS) and Bayesian inference posterior probability (BPP) are shown along the branches. Dash (-) indicates nodes with MLBP<70%, MPBS<70% or BPP<0.95. New taxa are in red and extype isolates are in bold.

dryad32/100

Dataset for Xia et al.: Reproductive isolation via divergent genital morphology due to cascade reinforcement in Ohomopterus ground beetles

Secondary contact between incipient species and selection against maladaptive hybridization can drive reinforcement between populations in contact and result in reproductive character displacement (RCD). Resultant divergence in mating traits within a species may generate downstream reproductive isolation between populations with displaced and non-displaced traits, referred to as the cascade reinforcement hypothesis. We examined this hypothesis using three allopatric populations of the ground beetle Carabus maiyasanus with a genital lock-and-key system. This species shows RCD in male and female genital morphologies in populations in contact with the sister species C. iwawakianus. In a reciprocal mating experiment using three allopatric populations with differences in male and female genital sizes, inseminationfailure increased as the difference in genital size increased. Based on the reproductive isolation index, insemination failure was the major postmating-prezygotic isolation barrier, at least in one population pair with comparable total isolation to those of other species pairs. By contrast, there was only incomplete premating isolation among populations. These results suggest that RCD in genital morphologies drives incipient allopatric speciation, supporting the cascade reinforcement hypothesis. These findings provide insight into the roles of interspecific interactions and subsequent trait diversification in speciation processes.

opencc-zeroOct 2022View details →

Estimating belowground carbon stocks in isolated wetlands of the Northern Everglades Watershed, central Florida, using ground penetrating radar (GPR) and aerial imagery

This data set includes raw GPR profiles for isolated wetlands in the Disney Wilderness Preserve (Kissimmee, FL) for the purpose of below ground soil C stock estimations.

Supplementary material 7 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688

Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of cmdA gene sequences : Data type: molecular data

Supplementary material 3 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688

Phylogenetic tree of Calonectria species in the Prolate group based on maximum likelihood (ML) analysis of cmdA gene sequences : Data type: molecular data

Supplementary material 6 from: Liu QL, Chen SF (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26: 25-60. https://doi.org/10.3897/mycokeys.26.14688

Phylogenetic tree of Calonectria species in the Sphaero-Naviculate group based on maximum likelihood (ML) analysis of his3 gene sequences : Data type: molecular data