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6 protocols using sorvall st 40r centrifuge

1

Semen Preparation for Artificial Insemination

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Only ejaculates meeting the quality standard limits for the preparation of semen AI-doses were used in this study (Supplementary Table S1). Ejaculates were collected using the gloved-hand method, allowing separate collection of three different ejaculate portions as follows: the first 10 mL-SRF (sperm-peak portion), the remaining SRF and the post-SRF. These 3 portions correspond with the 3 analysed samples. A fourth sample, mimicking the EE, was generated by the proportional mixture of the other three portions 10 mL-SRF, rest of SRF and post-SRF as described previously by Perez-Patiño et al.45 . Each one of four samples were separately centrifuged at 800 × g for 8 min (Eba 20, Hettich Zentrifugen, Germany) immediately after collection to separate spermatozoa from the SP. Both, spermatozoa and SP samples were placed in sterile tubes and transported in cooled box (4 °C) to the Veterinary Andrology Laboratory of the University of Murcia. Once in the laboratory, each sperm sample was split into two aliquots and whereas one was stored at − 80 °C until use for WB analysis, the other was immediately processed for ICC as described below. The SP samples were twice centrifuged at 1,500 × g for 10 min (Sorvall ST 40R Centrifuge, Thermo Scientific, MA, USA) to remove any remaining spermatozoa or cell debris and, then, were stored at − 80 °C until use for WB analysis.
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2

Enzyme-Mediated eATP Degradation in Bladder

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Samples from ELS of nondistended and distended bladder preparations were prepared as described previously [9 (link)]. Briefly, the 2.9 mL ELS collected at the end of time equivalent to the time for bladder filling (nondistended condition) or at the end of filling (distended condition) were placed in 4 mL Amicon Ultra centrifugal filter units with 10 kDa molecular weight cut-off (MWCO) pore size (Millipore Sigma, Burlington, MA, USA) to be concentrated by centrifugation. The ELS samples were concentrated to approximately 80–100 µL volume at 4000× g for 25 min using SorvallST 40R centrifuge (Thermofisher, Langenselbold, Germany). The concentrated ELS (cELS) were used to detect the degradation of eATP substrate by enzymes that were released in the ELS at rest or during bladder filling.
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3

Metabolite Profiling of Biological Samples

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Mass spectrometric grade formicacid (98%), ammonium formate (≥98%), bilirubin, L-tryptophan, and Intralipid® were obtained from Sigma- Aldrich, along with HPLC-grade acetonitrile and methanol (VWR), BSA (IgG, fatty acid, and protease-free) (GenDEPOT), PBS (Fisher Scientific), β-pseudouridine and acetyl-L-threonine (Santa Cruz Biotechnology), phenylacetyl-L-glutamine, β-pseudouridine-13C,15N2, and L-tryptophan-d5 (Toronto Research Chemicals), Nα-(phenyl-d5-acetyl)-L-glutamine and N-acetyl-d3-L- threonine-2,3-day2 (C/D/N Isotopes), and human serum (Bioreclamation). Deionized water (18 mol/LΏ) was purified using a Hydro water purification system. Centrifugation was done with a Sorvall ST-40R centrifuge (Thermo Scientific).
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4

HIV-1 JRFL Clone Production

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The HIV-1 JRFL clone is a full-length molecular clone of HIV-1 based on NL4-3 (57 (link), 88 (link)) that expresses the JRFL envelope. Cre is inserted in place of the nef gene, and Nef expression is restored by a downstream internal ribosome entry site (IRES) (81 (link)). Plasmid was amplified in Stbl2 electrocompetent E. coli and isolated using a Qiagen Midi-kit. The human epithelial 293T cell line was used to produce HIV-1 virions. 293T cells were maintained in Dulbecco’s modified Eagle medium (DMEM; Sigma) containing 10% heat-inactivated fetal bovine serum (Sigma), 100 U/mL of penicillin (Gibco), 10 U/mL of streptomycin (Gibco), and 2 mM glutamine (Gibco) (complete DMEM). Cell-free virus particles were produced by transfection of 293T cells in a 10 cm dish using Polyjet (Signajen) per the manufacturer’s protocol. Virus supernatant was harvested 48 h post-transfection, filtered with a 0.45-µm filter and concentrated by high-speed centrifugation (Sorvall ST 40R centrifuge; ThermoFisher Scientific) at 100,000g for 2 h at 4°C. The pelleted virus was resuspended in DPBS, aliquoted, and stored at −80°C.
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5

Taqman Array Microfluidic Card Gene Expression Analysis

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Taqman Array Microfluidic Cards (Thermo Fisher) were custom-made with the probes described in Additional file 1: Table S2 and the manufacturer's protocol was followed. Briefly, we loaded 100 μL of each sample-specific PCR reaction mix, composed of Taqman mastermix (Thermo Scientific) (2x), and cDNA at 10 ng/μl. Eight samples per card, balanced for Braak stage, were run simultaneously. We vertically centrifuged the plate at 1200 rpm for 2 min on a Sorvall ST40R centrifuge (Thermo Scientific). After sealing, the plate was read in the ViiATM 7 Real-Time PCR System (Applied Biosystems). Similarly to real-time RT-PCR, the Ct comparison method was used to quantify cDNA levels. In this case, the amount of cDNA was normalized by the geometric mean of the four housekeeping genes (see Additional file 1: Table S2). The expression of the different genes was referred to the average expression of the Braak II group (n = 16 different individuals).
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6

Production of HIV-1 JRFL Clone Virions

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The HIV-1 JRFL clone is a full-length molecular clone of HIV-1 based on NL4–3 (57 (link), 88 (link)) that expresses the JRFL envelope. Cre is inserted in place of the nef gene, and Nef expression is restored by a downstream internal ribosome entry site (IRES) (81 (link)). Plasmid was amplified in Stbl2 electrocompetent E. coli (NEB) and isolated using Qiagen Midi-kit. The human epithelial 293T cell line was used to produce HIV-1 virions. 293T cells were maintained in Dulbecco’s modified Eagle medium (DMEM; Sigma) containing 10% heat-inactivated fetal bovine serum (Sigma), 100 U/ml of penicillin (Gibco), 10 U/ml of streptomycin (Gibco), and two mM glutamine (Gibco) (complete DMEM). Cell-free virus particles were produced by transfection of 293T cells in a 10 cm dish using polyjet (Signajen) per the manufacturer’s protocol. Virus supernatant was harvested 48h post-transfection and filtered with 0.45 μm filter, concentrated by high-speed centrifugation (Sorvall ST 40R centrifuge; Thermo Fisher Scientific) at 100,000g for two h at 4°C. The pelleted virus was resuspended in DPBS, aliquoted, and stored at −80°C.
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