The slides were deparaffinized in xylene and transferred to 100% alcohol for 30 min before hybridisation. The hybridisation was carried out at 45°C with 40 ml of hybridisation buffer (100 mM Tris [pH 7.2], 0.9 M NaCl, 0.1% sodium dodecyl sulfate) and 200 ng of each probe for 16 hours in a Sequenza Slide Rack (Thermo Shandon, Cheshire, UK). The samples were then washed three LY2157299 datasheet times in prewarmed (45°C) hybridisation buffer for 15 min and subsequently three times in prewarmed (45°C) washing solution (100 mM Tris [pH 7.2], 0.9 M NaCl). The samples were rinsed in water, air dried and mounted in Vectashield (Vector Laboratories Inc., Burlingame, CA, USA) for

epifluorescence microscopy. An Axioimager M1 epifluorescence microscope equipped for epifluorescence with a 100-W HBO lamp and filter sets 43 and 38 were used to visualize Cy3 and fluorescein, respectively. Images were obtained using an AxioCam MRm version 3 FireWiremonocrome camera and the software AxioVision version 4.5 (Carl Zeiss, Oberkochen, Germany). Evaluation of the epifluorescence microscopy was performed by description of the subjective amount, morphologic

appearance and location of fluorescing cells apparent in each tissue sample. In addition, all tissue sections were stained by H&E and evaluated histopathologically. 16S rDNA amplification and cloning LY2606368 in vivo After the detection of bacteria using FISH, sub samples from horses demonstrating bacteria of various morphologies were chosen for 16S rRNA gene cloning. The DNA was isolated from 4 tissue samples by using the Easy-DNA kit (Invitrogen, Tåstrup, Denmark) according to the manufacturer’s instructions. The 16S rRNA gene was amplified using primers S-D-Bact-0008-a-S-20 (5′-AGAGTTTGATCMTGGCTCAG-3′) [37]

and S-*-Univ-1492-a-A-19 (5′-GGTTACCTTGTTACGACTT-3′) [38]. PCR cycling consisted of an initial denaturation at 94°C for 6 min; followed by 30 cycles of denaturation at 94°C for 30 s, annealing at 55°C for 45 s and extension at 72°C for 2 min; and a final extension at 72°C for 3 min. Amplified DNA was verified by electrophoresis on agarose gels. The PCR products were purified using the QIAquick PCR purification kit columns (Qiagen GmbH, Hilden, Germany). To create Chlormezanone blunt-ended DNA the following was mixed in a 0.5-ml microcentrifuge tube, 4 μl of 5 × T4 DNA polymerase buffer, 14.7 μl of purified PCR product 0.8 μl of dNTP (2.5 mmol l-1 each) and 0.5 μl (1.2 U) of T4 DNA polymerase (Invitrogen) and incubated at 12°C for 15 min. The T4 DNA polymerase was heat-inactivated, and the blunt-ended DNA was purified using the QIAquick PCR purification kit columns (Qiagen GmbH) and eluted in a final volume of 10 μl of double-distilled water. Following the manufacturer’s descriptions the cloning was performed by using a Zero blunt TOPO cloning kit (Invitrogen).