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3 protocols using ec plan neofluar 40x 0.75 objective

1

Microscopic Phototrophic Organism Enumeration

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Fixed samples were sub-sampled three times and were diluted 1:10 in tap water. One ml was transferred to an Uthermol's chamber for microscopic analysis. An inverted microscope (Zeiss Axiovert 135) was used to identify and count (Zeiss EC Plan-Neofluar 40x/0.75 objective, Zeiss EC Plan-Neofluar 100 × 1.3 Oil objective, if necessary) phototrophic organisms at the level of genera and, if possible, species within three fields of vision. For samples obtained from laboratory experiments, semi-quantitative abundance was described as dominant (‘5', >30 of the cell number counted), frequent (‘4', 10–30%), regular (‘3', 3–10%), scarce (‘2', 1–3%) and sporadic (‘1', <1%) based on two taxonomic references and the recommendations by the Swiss Federal Office for the Environment33 34 35 . For field samples, presence-absence data were documented.
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2

Immunofluorescence Analysis of Nucleolar Proteins

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HeLa cells grown on glass coverslips were fixed with 3.7% paraformadehyde and permeabilized with 0.5% NP40. The following primary antibodies were used: Rabbit anti-FBL (ab5821, Abcam), rabbit anti-Drosha (ab12286, Abcam) and rabbit anti-DGCR8 (ab36865, Abcam). Antibodies were detected with secondary antibodies conjugated to Alexa 488 or 594 (Molecular Probes, Invitrogen) and nuclei were counterstained with Hoechst 33258. Images were captured using Axioplan2 fluorescence microscope (Zeiss) equipped with AxioCam HRc CCD-camera and AxioVision 4.5 software using EC Plan-Neofluar 40x/0.75 objective (Zeiss). Image quantification was carried out according to refs. [34] , [35] (link).
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3

Immunofluorescent Staining of Phospho-Histone H2A.X

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Cells harvested at specific time points were fixed in 10% formalin. After fixation, cells were embedded first in HistoGel (Thermo Fisher Scientific Inc., Rockville, MD) according to the manufacturer’s instruction, then in paraffin, and sectioned transversely. Unstained paraffin sections were used for immunofluorescent staining. Paraffin sections on slides were treated with Target Retrieval Solution and Protein Block Serum-Free (Dako North America, Inc., Carpinteria, CA) according to the manufacturer’s instruction, and stained with anti-phospho-Histone H2A.X antibody (Cell Signaling Technology®, Danvers, MA) followed by Alexa Fluor® 647 Goat Anti-Rabbit IgG (Life Technologies Corporation, Grand Island, NY) antibody with washing between and after in phosphate-buffered saline (PBS) with 0.1% Tween® 20. Resulting slides were briefly rinsed with PBS, desalted by dipping in distilled-deionized water, and sealed with coverslips in mounting medium with 4′,6-diamidino-2-phenylindole (DAPI, Life Technologies Corporation, Grand Island, NY). A Zeiss LSM710 laser scanning confocal microscope (Carl Zeiss MicroImaging, Thornwood, NY) with an EC Plan-Neofluar 40x/0.75 objective was used to scan the signals.
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