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56 protocols using illustrator cs2

1

Phylogenetic Analysis of Sequenced Taxa

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The generated sequences were blasted against the National Center for Biotechnology Information (NCBI) GenBank sequence database using MegaBLAST to identify related taxa at the genus level. To identification at the species level sequences were subjected to maximum parsimony (MP) phylogenetic analyses using PAUP v. 4.0b1032 .
Generated sequences and authentic sequences retrieved from GenBank together with the outgroup species were aligned using ClustalX v. 1.8333 (link). Alignments were edited manually where necessary. For phylogenetic analysis a maximum parsimony analysis was performed in PAUP v. 4.0b1032 . The heuristic search option with 1000 random taxa additions and tree bisection and reconnection (TBR) branch-swapping algorithm were used. All characters were unordered and of equal weight. Gaps were treated as missing data. Branches of zero length were collapsed and all multiple, equally parsimonious trees were saved. The robustness of the most parsimonious trees was evaluated by 1000 bootstrap replications34 (link). Other measures used were consistency index (CI), homoplasy index (HI), retention index (RI) and tree length (TL).The generated equally most parsimonious phylogenetic trees were visualized in FigTree v. 1.4.3 (http://tree.bio.ed.ac.uk/software/figtree) and edited in Adobe Illustrator CS2 v. 12.0.0.
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2

Consensus Mapping of Maternal Genome

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Development of the maternal (MN1264) consensus map was conducted using LPmerge (Endelman and Plomion 2014 (link)). Contrary to the approach of minimizing an objective function based on the observed recombination frequencies between markers, this software employs a linear programming algorithm to minimize the mean absolute error between the consensus map and the genetic maps from each family. This minimization step results in preservation of marker order in linkage maps. At instances where marker order is inconsistent between maps, LPmerge implements an additional algorithm to resolve ordinal conflicts.
The LPmerge software contains two key parameters that are set by the user: (1) maximum interval size between bins and (2) weights applicable to each map. In our analysis, the maximum interval parameter was set at K = 8, while weights were adjusted based on family sizes due to more progeny providing better resolution. At each LG, the best consensus map was selected using two criteria: (1) minimization of the average root-mean-squared error (RMSE), and (2) map length comparable to the mean of the linkage maps. Final images of LGs were generated using MapChart 2.2 (Voorrips 2002 (link)) before they were exported to Adobe Illustrator CS2 for alignment and vector transformation.
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3

Confocal Microscopy of Organelle Markers

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Confocal microscopy was performed as described previously22 (link) using the following primary antibodies: β-tubulin (IgG1, clone D66; Sigma-Aldrich), Ki67 (ab15580; Abcam), LAMP-1 (Abcam), SNX1 (BD Biosciences), EEA1 (BD Biosciences), FAM21 (Millipore), calreticulin (Abcam), and LC3 (L8918; Sigma-Aldrich). Cells were counterstained with 4′,6-diamidino-2-phenylindole (DAPI; 0.1 mg/ml) where indicated. For labeling of acidic organelles, LysoSensor Green DND-189 (1 μM) was added to cells in growth medium and incubated at 37°C for 30 min before imaging. A Zeiss LSM710 confocal microscope with a 63× 1.4 NA Plan-Apochromatic oil differential interference contrast objective was used, and image acquisition was performed using LSM710 version 3.2SP2 software. Images were analyzed with ImageJ (NIH) and edited using Adobe Photoshop 7.0 and Illustrator CS2 software.
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4

Jurassic Insect Lagerstätten at Daohugou

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The two type specimens, both with part and counterpart, were collected from a finely laminated tuff in the latest Middle Jurassic Jiulongshan Formation at Daohugou Village, Ningcheng County, Inner Mongolia, China. The Daohugou locality is now considered to be one of the most important insect Lagerstätten31 32 . Because of new calibrations for the Jurassic System, this deposit should be now considered as latest Middle Jurassic (late Callovian) in age9 , approximately 165 Mya - 164 Mya.
The specimens studied in this paper were examined and then photographed, either dry or wetted with 95% ethanol, with a Leica DFC450 digital camera attached to a Leica M250 C dissecting microscope (Leica, Wetzlar, Germany). The line drawings were prepared using Adobe Illustrator CS2 and Adobe Photoshop CS5 software. The wing venation nomenclature used in this article is modified after Rasnitsyn1 2 . The type materials described are deposited in the Key Lab of Insect Evolution and Environmental Changes, College of Life Sciences, Capital Normal University, in Beijing, China (CNUB; Dong Ren, Curator). Recent species were examined under the dissecting microscopes and kept in the Museum of Forest Biodiversity, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, in Beijing, China (CAF).
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5

Stylet Outline Reconstruction Protocol

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The head capsule and stylets of all individuals were outlined through vector-drawing programs (Inkscape 1.1, Adobe Illustrator CS2). The outline of the better-accessible half was drawn. The stylet was artificially rotated to be straight; the innermost distal point and the innermost proximal point were oriented to form a line parallel to the anterior–posterior midline [79 (link)]. Then, the half object was mirrored.
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6

Comprehensive Imaging Techniques for Specimen Documentation

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The specimen was documented with composite imaging under different white light conditions, as well as under autofluorescence. The white-light microscopic images were recorded with a Keyence VHX-6000 equipped with a 20–2000 × objective, either under ring illumination or under coaxial cross-polarised illumination. Black and white background colour was used. To achieve an optimal result, every image was recorded with different exposure times (HDR) [18 (link), 21 (link)]. For autofluorescence images, a Keyence BZ-9000 was used [22 , 23 (link)].
Each image detail was documented as a stack, with the single images of the stack (frames) being recorded in different focal levels in z-axis to overcome limitations in depth of field. The frames of each stack were fused to achieve an entirely sharp image. Several adjacent stacks were recorded in x-y axis to overcome limitations in field of view. All image details were stitched to a final panorama image [24 , 25 (link)].
Additionally, based on the stacks the three-dimensional relief information was extracted (virtual surface). This information is presented as red-cyan stereo anaglyphs [26 (link)].
Drawings of the specimen and of comparative material were prepared in Adobe Illustrator CS2.
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7

Imaging Meiosis I Oocyte Centromeres

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Meiosis I oocytes, at 5 h after release from IBMX, unless otherwise stated, were fixed and permeabilized in PHEM buffer (60 mM Pipes, 25 mM Hepes, 10 mM EGTA, and 2 mM MgCl2) containing 4% paraformaldehyde and 0.5% Triton X-100 and then labeled with calcinosis, Raynaud’s phenomenon, esophageal dysmotility, sclerodactyly, and telangiectasia (CREST) serum, a human centromere antiserum, (1:300; a gift from G. Fitzharris, University College London, London, England, UK), rabbit anti-Mad2 (PRB-452C; 1:300; Covance), mouse anti–β-tubulin (T4026; 1:1,000; Sigma-Aldrich), and 10 µg/ml Hoechst 33342 (Sigma-Aldrich). Serial z sections of fixed oocytes in PBS were acquired at room temperature using a Plan Apochromat 63×, 1.4 NA oil differential interference contrast objective and a laser-scanning confocal microscope imaging system (LSM 510 META; Carl Zeiss) with the following band pass emission filters in nm 385–470 (Hoechst 33342), 505–530 (Alexa Fluor 488), and 585–615 (Alexa Fluor 546). Z sections were analyzed and projected into one picture using the LSM image browser (Carl Zeiss). The images were then assembled by Illustrator CS2 (Adobe).
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8

Imaging Salivary Glands, Embryos, and Ovaries

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Salivary gland images were taken with a Multiphoton Zeiss LSM780 upright confocal microscope using a 10× objective lens with Zeiss Zen software. Fluorescent images of whole-mount larvae or multiple salivary glands were taken on the Zeiss SteREO Discovery V.12 microscope using the 1.50× lens with AxioVision software. Embryo images were taken with a Multiphoton Zeiss LSM780 upright confocal microscope using a 20× objective lens with Zeiss Zen software. Ovary images were taken with a Multiphoton Zeiss LSM780 upright confocal microscope using a 40W× objective lens with Zeiss Zen software. Antibody staining image comparisons between wild-type, p53, and all other indicated genotypes were done with the same laser image intensities and master gain settings. Z-stacks were taken at 0.5-μm sections. Z-stacks of images were projected using ImageJ software (National Institutes of Health). The Z-stacks were projected using the maximum fluorescence intensity and the total area of the GFP signal was normalized to Hoechst signal (normalized Fluorescence intensity) of each respective salivary gland or embryo. Ratios were graphed on Prism software and statistical analysis was performed using one-way ANOVA. Figures were prepared using Adobe Photoshop and Illustrator CS2 (Adobe Systems).
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9

Comparative Larval Morphometric Analysis

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We re-used parts of data of the head and stylet shape from Haug et al.19 (link). Specimens included are extant larvae of the groups Berothidae and Dilaridae as well as fossil larvae potentially representing the same two groups. Additionally, of two specimens depicted in Badano et al.58 (link) the outlines of the head capsule and stylets were redrawn in Adobe Illustrator CS2. Finally, of one of the newly reported larvae the outline of head capsule and stylets were also redrawn and included into the data set. All these outline drawings were transformed into bitmap files and included into an Elliptic Fourier Analysis (EFA) performed with the software SHAPE81 (link), followed by a principal component analysis (PCA) (for details, see19 (link),82 (link)).
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10

Live Cell Imaging of GFP-VDR Dynamics

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Live cell imaging was performed as described before (77 (link)) using an inverted Axiovert 200 fluorescence microscope (Zeiss), equipped with 100×/1.4 Plan-Apochromat oil-immersion objective (Zeiss), pulsed excitation module (470 nm, 390 nm LEDs), bandpass filters 510–560 nm (EGFP) and 417–477 nm (Hoechst 33342) and gated CCD camera (LaVision BioTec). Briefly, HeLa cells were seeded onto 8-well chambers precoated with a mixture of collagen IV and poly-d-lysine (Ibidi), allowed to attach (24 h) and forward transfected for 24 h with plasmids encoding GFP-VDR fusions as indicated. Prior to live imaging, cells were counterstained with Hoecsht 33342 (1 μm, 30 min). Fluorescence images were collected before (resting) and after stimulation with calcitriol (10−7m, 10 min, 37 °C). Images were exported using ImSpector software (LaVision BioTec) and combined in Adobe Illustrator CS2.
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