Zirconium silica beads

Manufactured by Biospec

Sourced in United States

Zirconium silica beads are a type of laboratory equipment used in various applications. They are spherical particles composed of zirconium and silica, with a high surface area and chemical inertness. These beads are commonly used in chromatography, solid-phase extraction, and other separation techniques.

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Lab products found in correlation

Nanodrop 200c, by Thermo Fisher Scientific (2 mentions) 4 bromanisole, by Molecular Research Center (2 mentions) Iscript cdna synthesis kit, by Bio-Rad (2 mentions) Rnaeasy mini kit, by Qiagen (2 mentions) Rnalater solution, by Qiagen (2 mentions) Bullet blender tissue homogenizer, by Next Advance (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Mini beadbeater 8, by Biospec (2 mentions) Iscript reverse transcriptase, by Bio-Rad (2 mentions) Kapa sybr fast, by Roche (2 mentions) Turbo dnase, by Thermo Fisher Scientific (2 mentions) Precellys 24 high throughput tissue homogenizer, by Bertin Technologies (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Turbo dna free kit, by Thermo Fisher Scientific (1 mentions) Ultrapure dnase rnase free distilled water, by Thermo Fisher Scientific (1 mentions) Trizol reagent, by Molecular Research Center (1 mentions) Vortex mixer, by Labnet (1 mentions) Precellys evolution, by Bertin Technologies (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Qiaamp dna stool mini kit, by Qiagen (1 mentions)

17 protocols using zirconium silica beads

Quantifying Gut Pathogen Colonization in Mice

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Mouse fecal pellets (2–3 pellets/mouse) were collected on day 1, 2, 3, and 4 p.i. Pellets were immediately weighed and homogenized using 1.0 mm diameter zirconium/silica beads (Biospec Products, United States) with a bead-beating machine. Then, ST-W77 and SE-W109 numbers (PFU/gm fecal pellet or tissue) were calculated by a double-layer agar assay.
Mouse tissues (colon content, cecal content, colon, cecum, ileum, liver, and spleen) were collected on day four p.i. when the most prominent gut inflammation occurred (Tsolis et al., 2011 (link)). Tissues were immediately weighed and homogenized using 1.0 mm diameter zirconium/silica beads (Biospec Products, Bartesville, United States) with a bead-beating machine. S. Tm colony-forming unit (CFU)/gm tissues were determined by a serial diluting technique on the LB agar with nalidixic acid (0.05 mg/ml).

Sukjoi C., Buddhasiri S., Tantibhadrasapa A., Kaewsakhorn T., Phothaworn P., Nale J.Y., Lopez-Garcia A.V., AbuOun M., Anjum M.F., Malik D.J., Galyov E.E., Clokie M.R., Korbsrisate S, & Thiennimitr P. (2022). Therapeutic effects of oral administration of lytic Salmonella phages in a mouse model of non-typhoidal salmonellosis. Frontiers in Microbiology, 13, 955136.

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Bacterial DNA Extraction from Fecal Samples

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We used a modification of Repeated Bead Beating (RBB) method that efficiently extracts bacterial community DNA based on comparative analysis of human fecal samples [23 (link)]. All frozen samples were thawed on ice and 1 ml of sterile ice-cold PBS was added, except for the left fornix flocked swabs that were stored in saline. Before the removal of the sampling device with sterile forceps the samples were vortexed for 30 secs to dislodge the bacteria and briefly spun down to avoid spills when opening the tube. An aliquot of the clarified supernatant was taken for the measurement of soluble protein content. The rest of the sample, including both the mucous pellet and the supernatant, was moved to 2 ml screw-cap tube and an equal volume of lysis buffer (500 mM NaCl, 50 mM Tris-HCl (pH 8.0), 50 mM EDTA, 4% SDS) was added. To break to cells, samples were bead beaten using a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, France) with 0.1 mm zirconium-silica beads (Biospec Products, Bartlesville, OK, USA) for 2 x 30 sec at 5500 rpm. DNA from the lysates was purified using QIAamp DNA Minikit (Qiagen, Hilden, Germany) without the lysis step according to the manufacturer’s instructions. The samples were eluted in 200 μl of kit elution buffer.

Virtanen S., Kalliala I., Nieminen P, & Salonen A. (2017). Comparative analysis of vaginal microbiota sampling using 16S rRNA gene analysis. PLoS ONE, 12(7), e0181477.

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Caecum Tissue RNA Extraction Protocol

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Tissue samples from the caudal part of the caecum were cut into 20 mg pieces, placed immediately into RNA Later solution (Qiagen, UK), and stored at −70°C prior to RNA purification. Single tissue fragments were transferred into 1 ml of TRIzol Reagent (Molecular Research Center, USA), and homogenized with zirconium silica beads (BioSpec Products, USA) in a vortex mixer (Labnet, USA). To separate the phases, 50 μl of 4-bromanisole (Molecular Research Center, USA) was added. The whole content of the tube was centrifuged and the upper aqueous phase was collected for total RNA purification with the RNAeasy mini kit (Qiagen, UK), according to the manufacturer's instructions. Turbo DNA-free kit (Ambion, USA) was used for the treatment of RNA samples to remove genomic DNA. Both the purity and concentration of RNA were determined spectrophotometrically on NanoDrop 200c (Thermo Scientific, USA) and 1 μg of the total RNA immediately underwent reverse transcription with iScript cDNA Synthesis Kit (Bio-Rad, USA). The resulting cDNA was diluted 10-fold in UltraPure DNase/RNase-Free distilled water (Invitrogen, USA) and used as a template for real-time PCR, or stored at −20°C until used.

Mudroňová D., Karaffová V., Koščová J., Bartkovský M., Marcinčáková D., Popelka P., Klempová T., Čertík M., Mačanga J, & Marcinčák S. (2018). Effect of fungal gamma-linolenic acid and beta-carotene containing prefermented feed on immunity and gut of broiler chicken. Poultry Science, 97(12), 4211-4218.

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Bacterial Profiling of Fecal Samples

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DNA was extracted from faecal samples using QIAamp DNA Stool Minikit (Qiagen, Hilden, Germany). The DNA isolation followed the instructions of the manufacturer, but with an extra mechanical lysis step, using 0.1 mm Zirconium/Silica beads (Biospec products, Bartlesville, USA), 2 × 1 min at 6000 rpm with a Precellys evolution (Bertin Instruments, Montigny-le-Bretonneux, France). The isolated DNA was stored at − 20 °C until analysis. 16S rRNA gene amplicons were generated from the V3 and V4 region using the primers (341F 5′-CCTACGGGAGGCAGCAG-3′ and 806R 5′-GGACTACNNGGGTATCTAAT-3′). Sequencing libraries were generated using NEB Next^® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) and the amplicon library was sequenced on an Illumina HiSeq 2500 platform at Novogene. The generated paired-end reads were merged with FLASH (V1.2.7, http://ccb.jhu.edu/software/FLASH/)⁴¹ and assigned to each sample according to the sample specific barcodes. Quality filtering of sequence data was performed with QIIME (V1.7.0)^{42 (link)} and UCHIME^{43 (link)} was used to detect and remove chimeric sequences^{44 (link)}. The reads were clustered using Uparse software (Uparse v7.0.1001)^{45 (link)} and OTUs (Operational Taxonomic Units) were generated based on 97% sequence homology.

Verbeek E., Keeling L., Landberg R., Lindberg J.E, & Dicksved J. (2021). The gut microbiota and microbial metabolites are associated with tail biting in pigs. Scientific Reports, 11, 20547.

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RNA Extraction and cDNA Synthesis

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Tissue samples (jejunum, ileum and cecum) were cut into 20-mg pieces, immediately placed into RNA Later solution (Qiagen, Manchester, UK) and stored at −70 °C prior to RNA purification. A single tissue fragment was transferred into 1 mL of TRI Reagent (Molecular Research Center, Cincinnati, OH, USA), and homogenized using 2.7 mm of zirconium silica beads (BioSpec Products, Bartlesville, OK, USA) in a Magnalyser (Roche, Indianapolis, IN, USA). To separate the phases, 50 μL of 4-bromanisole (Molecular Research Center, USA) was added. The whole content of the tube was centrifuged and the upper aqueous phase was collected for total RNA purification using the RNAeasy mini kit (Qiagen, UK) following the manufacturer’s instructions. An Ambion^® Turbo DNA-free kit (Life Technologies, Carlsbad, CA, USA) was used for the treatment of RNA samples to remove genomic DNA. Both the purity and concentration of RNA were detected spectrophotometrically on a NanoDrop 200c (Thermo Scientific, Madison, WI, USA) and 1 μg of the total RNA was immediately reverse transcribed using the iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). The resulting cDNA was 10× diluted in nuclease-free water (Qiagen, UK) and used as a template in a quantitative real-time PCR.

Karaffová V., Mudroňová D., Mad’ar M., Hrčková G., Faixová D., Gancarčíková S., Ševčíková Z, & Nemcová R. (2021). Differences in Immune Response and Biochemical Parameters of Mice Fed by Kefir Milk and Lacticaseibacillus paracasei Isolated from the Kefir Grains. Microorganisms, 9(4), 831.

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Immunoprecipitation and Quantitative PCR

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Meiotic cells were processed as described [65 (link)], with the following modifications: Lysis was performed in Lysis buffer plus 1 mM PMSF, 50 μg/mL Aprotinin and 1X Complete Mini EDTA-Free (Roche), using 0.5 mm zirconium/silica beads (Biospec Products, Bartlesville, OK). 2 μg of the mouse monoclonal anti-FLAG antibody M2 (Sigma) and 30 μL Protein G magnetic beads (New England Biolabs) were used. Quantitative PCR was performed from the immunoprecipitated DNA or the whole-cell extract using a 7900HT Fast Real-Time PCR System (Applied Biosystems, Thermo Scientific) and SYBR Green PCR master mix (Applied Biosystems) as described [65 (link)]. Results were expressed as % of DNA in the total input present in the immunoprecipitated sample. Primers for GAT1, BUD23, ERG1, Axis and NFT1 loci have been described [50 (link), 51 (link), 66 (link)].

Voelkel-Meiman K., Cheng S.Y., Parziale M., Morehouse S.J., Feil A., Davies O.R., de Muyt A., Borde V, & MacQueen A.J. (2019). Crossover recombination and synapsis are linked by adjacent regions within the N terminus of the Zip1 synaptonemal complex protein. PLoS Genetics, 15(6), e1008201.

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Quantitative E. coli Strain Identification

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Spleen, MLN, liver, or stool were homogenized in PBS by 0.1 mm diameter zirconium silica beads (BioSpec) and homogenized Bullet Blender Tissue Homogenizer (Next Advance). The obtained homogenate was quantified for E. coli strain by MLST identification.^[⁵³^]

Cai J., Peng J., Zang X., Feng J., Li R., Ren P., Zheng B., Wang J., Wang J., Yan M., Liu J., Deng R, & Wang D. (2022). Mammary Leukocyte‐Assisted Nanoparticle Transport Enhances Targeted Milk Trace Mineral Delivery. Advanced Science, 9(26), 2200841.

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Isolation of Intestinal Immune Cells and E. coli

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Small intestines or colons were harvested, rinsed with PBS, and Peyer’s patches or colonic patches were removed and discarded. Epithelial cell populations were released by incubating the intestines for 15 min in a 37 °C rotating incubator in 20 mL Hank’s balanced salt solution (HBSS) media (BioWhittaker) containing 5 mM EDTA and gentamicin (50 μg/mL) as previously described (50 (link)). Following removal of epithelium, isolated lamina propria was cut into pieces. We recovered splenic, MLN, and lamina propria cells as previously described (50 (link)). Lamina propria pieces, spleen, MLN, liver, or stool were homogenized in 500 μL PBS with 200 mg 0.1 mm diameter zirconium silica beads (BioSpec), and homogenized Bullet Blender Tissue Homogenizer (Next Advance) vortexed on bead beater. Supernatant was plated on MacConkey agar containing 20 ng/mL nalidixic acid to identify nalidixic acid-resistant E. coli, and identity of E. coli strain was confirmed through MLST identification.

Knoop K.A., Coughlin P.E., Floyd A.N., Ndao I.M., Hall-Moore C., Shaikh N., Gasparrini A.J., Rusconi B., Escobedo M., Good M., Warner B.B., Tarr P.I, & Newberry R.D. (2020). Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. Proceedings of the National Academy of Sciences of the United States of America, 117(14), 7941-7949.

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Extraction of T. trichiura Adult Worm RNA

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Adult T. trichiura worms were obtained by treatment of infected children from the province of Esmeraldas-Ecuador with pyrantel pamoate and collection of worms from stool samples for 1-2 days after treatment, as described (Meekums et al., 2015) . Ethical approval was provided by the Ethical Committee of the Universidad San Francisco de Quito-Ecuador and written informed consent was provided by parents or guardians. Adult worms were washed carefully in 0.15 M phosphate-buffered saline (pH 7.4) and total RNA was extracted using a standard Trizol (Life technologies) protocol with the aid of zirconium/silica beads (BioSpec Products, Inc.). RNA quality was verified spectrophotometrically (260 nm/280 nm ratio = 1.95) and quantitation was done fluorometrically using the Qubit ® RNA Assay kit (Life Technologies).

Santos L.N., Silva E.S., Santos A.S., De Sá P.H., Ramos R.T., Silva A., Cooper P.J., Barreto M.L., Loureiro S., Pinheiro C.S., Alcantara-Neves N.M, & Pacheco L.G. (2016). De novo assembly and characterization of the Trichuris trichiura adult worm transcriptome using Ion Torrent sequencing. Acta tropica, 159.

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Quantitative RT-PCR for Fungal RNA Analysis

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Total RNA isolation and quantitative RT-PCR (qRT-PCR) assays were conducted as previously described [14 (link)]. Briefly, conidia (5 × 10⁵ conidia/mL) of the WT and mutant strains were inoculated into MMY medium and incubated at 37 °C for 3 days or 4 days (for gliZ). Individual colonies were then collected and squeeze-dried. Each sample was homogenized using a Mini Bead beater in the presence of the TRIzol^® reagent (Invitrogen, Carlsbad, CA, USA) and silica/zirconium beads (BioSpec Products, Bartlesville, OK, USA). QRT-PCR assays were performed according to the manufacturer’s instructions using a Rotor-Gene Q device (Qiagen, Germantown, MD, USA). For the qRT-PCR process, the One Step RT-PCR SYBR Mix (MGmed, Seoul, Korea) was used. The primers used in this experiment are listed in Table S1. The PCR conditions were 95℃ for 5 min followed by 95 and 55℃/30 s for 40 cycles. Amplification of one single specific target DNA was checked by a melting curve analysis. The expression ratios were normalized to the ef1α expression level and calculated according to the ΔΔCt method [29 (link)].

Choi Y.H., Lee N.Y., Kim S.S., Park H.S, & Shin K.S. (2020). Comparative Characterization of G Protein α Subunits in Aspergillus fumigatus. Pathogens, 9(4), 272.

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