Colibri microvolume spectrophotometer

Manufactured by Berthold Technologies

Sourced in Germany

The Colibri Microvolume spectrophotometer is a compact and precise instrument designed for measuring the absorbance of small sample volumes. It utilizes advanced optical technology to accurately determine the concentration and purity of biomolecules such as DNA, RNA, and proteins.

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Lab products found in correlation

Cdna synthesis kit, by Takara Bio (2 mentions) Vacutainer, by BD (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Dneasy powerbiofilm kit, by Qiagen (1 mentions) Miseq platform, by Illumina (1 mentions) Deme medium, by Thermo Fisher Scientific (1 mentions) Cell free dna blood collection tube, by Streck (1 mentions) Qiaamp circulating nucleic acid kit, by Qiagen (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Lightcycler 96 instrument, by Roche (1 mentions) Lightcycler 96 sw 1, by Roche (1 mentions) Lightcycler 96, by Roche (1 mentions) Phosphate buffered saline (pbs), by Merck Group (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions) Magna lyser, by Roche (1 mentions) Miseq sequencer, by Illumina (1 mentions)

Close spelling variants of this product

Colibri (12 citations) Colibri spectrophotometer (4 citations)

13 protocols using colibri microvolume spectrophotometer

Field Blood Sampling and Molecular Analysis

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A total of 80 field blood samples were collected on four farms in the Mayabeque Province of Cuba from March to May, 2014 (Fig. 1). The studied farms were small, low-income and family-owned operations that functioned as dairy farms.
For all the animals, blood samples were collected by jugular venopuncture using 10 ml vacutainer collecting tubes containing EDTA (BD Vacutainer®, Becton Dickinson Vacutainer Systems, Franklin Lakes, NJ, USA). The hematocrit was assessed by microcentrifugation from each blood sample in a Jouan Hema-C microhematocrit centrifuge (Hawksley and Sons, Ltd, Sussex, UK; 18,600× g, 5 min); the value was determined with a DAMON/IEC hematocrit reader (Damon/IEC Division, Needham Heights, MA, USA). The remaining EDTA blood samples were stored at -20 °C prior to nucleic acid extraction. TNA was extracted from 100 μl of blood using a DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. The concentration and purity of the TNA was determined by measuring absorbance at 260 and 230 nm using a Colibri Microvolume Spectrophotometer (Titertek-Berthold, Pforzheim, Germany), and TNA was stored at -20 °C until use for qPCR analysis.

Díaz-Sánchez A.A., Corona-González B., Meli M.L., Álvarez D.O., Cañizares E.V., Rodríguez O.F., Rivero E.L, & Hofmann-Lehmann R. (2019). First molecular evidence of bovine hemoplasma species (Mycoplasma spp.) in water buffalo and dairy cattle herds in Cuba. Parasites & Vectors, 12, 78.

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Fecal DNA Extraction and Characterization

Cited 2 times

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Fecal samples were collected on the same day of blood collection as in our previous studies [11 (link),22 (link)]. In brief, the fecal samples were collected and stored at −80 °C for up to three days before processing. A stool DNA Extraction kit (Topgen Biotechnology Co., Ltd., Kaohsiung, Taiwan) was used to extract bacterial DNA. The fecal samples weighted to 50 to 100 mg were supplemented using a preceding bead beating (45 s; 3450 oscillations/min). The subsequent steps of DNA extraction were performed according to the manufacturer’s protocol. DNA concentration and quality were assessed using the Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). Extracted DNA samples were immediately stored at −20 °C before use.

Pai C.S., Wang C.Y., Hung W.W., Hung W.C., Tsai H.J., Chang C.C., Hwang S.J., Dai C.Y., Ho W.Y, & Tsai Y.C. (2022). Interrelationship of Gut Microbiota, Obesity, Body Composition and Insulin Resistance in Asians with Type 2 Diabetes Mellitus. Journal of Personalized Medicine, 12(4), 617.

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Metagenomic Analysis of Subgingival Microbiome

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The subgingival microbial DNA in a 500 µL transport medium was extracted by using the DNeasy PowerBiofilm kit (Qiagen, Hilden, Germany) with a preceding bead beating (45 s; speed: 3450 oscillations/min) and stored at −20 °C. Then, the DNA concentration was determined by a Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). The 16S rRNA gene of each sample was amplified using the primer pairs 341F (5′-CCTACGGGNGGCWGCAG-3′) and 805R (5′-GACTACHVGGGTATCTAATCC-3′) targeting the V3–V4 region. Library preparation was achieved by the Illumina MiSeq platform generating 300 bp paired-end reads. The raw sequence data were imported into QIIME2 [51 (link)], in which paired-end reads were merged and denoised into amplicon sequence variants (ASVs) using the DADA2 plugin [52 (link)]. The reads were filtered based on exact matches to the barcode/primer and an average quality score of 30. Due to the issue of sample bleeding between the Illumina MiSeq runs [53 (link)], the low-abundance filters (a cutoff threshold of 0.1% of mean frequency 70,651) were applied to reduce the number of spurious ASVs in the data set.

Chen Y.J., Hung W.C., Chou Y.H., Lai C.H., Peng P., Jhou P.S., Tsai M.R., Sheu J.J, & Yen J.H. (2022). Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis. International Journal of Molecular Sciences, 23(17), 9883.

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Fecal Sample Collection and DNA Extraction

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The patients were asked to collect fecal samples at home, immediately place them in their household freezer, and then bring them to the hospital within 12 h. All fecal samples were collected either on the evening before or the morning of the biochemical tests. After the patients brought the samples to the hospital, they were stored at −80 °C for up to 3 days before being processed. A Stool DNA Extraction kit (Topgen Biotechnology Co., Ltd., Kaohsiung, Taiwan) was used to extract bacterial DNA. In brief, 50–100 mg of the fecal samples were subjected to bead-beating (45 s; speed: 3450 oscillations/min). DNA was then extracted according to the manufacturer’s instructions. The purified DNA was eluted in a volume of 35 μL. The concentration and quality of the DNA were evaluated using a Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). The DNA samples were then immediately frozen at −20 °C until use.

Tsai H.J., Tsai W.C., Hung W.C., Hung W.W., Chang C.C., Dai C.Y, & Tsai Y.C. (2021). Gut Microbiota and Subclinical Cardiovascular Disease in Patients with Type 2 Diabetes Mellitus. Nutrients, 13(8), 2679.

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Non-Small Cell Lung Cancer Cell Culturing and Circulating DNA Extraction

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Human non-small cell lung cancer cell A549 was cultured in DEME medium (ThermoFisher, CA, US) with 10% fetal bovine serum (FBS) at 37 °C in 5% CO₂ atmosphere. 5 mL of blood samples from patients with non-small cell lung cancer were collected in a Cell-Free DNA Blood Collection Tube (Streck, La Vista, USA) in the department of thoracic surgery at Hebei Chest Hospital before surgery, according to a protocol approved by the Ethics Committee of these institutions. All patients provided written informed consent. This study was approved by the ethics board of the institute of Hebei Chest Hospital and complied with the Declaration of Helsinki. Within 1 hour, all whole blood samples were centrifuged at 820 g for 10 min. Plasma was collected and subjected to a second centrifugation at 16 000 g for 10 min. The supernatant was then transferred to fresh tubes and stored at −80 °C. Genomic DNA was extracted from the cells using a DNA Extraction Kit (Apexbio, Beijing, China) according to the user manual. Circulating DNA from plasma was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. DNA quantification was performed in a Colibri microvolume spectrophotometer (Titertek-Berthold, Pforzheim, Germany).

Gong J., Li Y., Lin T., Feng X, & Chu L. (2018). Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC Advances, 8(48), 27375-27381.

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Quantitative Real-Time PCR Protocol

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Total RNA was isolated from tissues using TRIzol™ reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer’s instructions. The concentration of total RNA was determined by a Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). Reverse transcription of total RNA was performed using a cDNA Synthesis Kit (Takara Bio, Shiga, Japan). Quantitative real-time PCR analysis was performed using SYBR Green I and a Lightcycler ^® 96 instrument (Roche, Basel, Switzerland). The PCR conditions were 95 °C for 10 min, followed by 45 cycles of amplification (95 °C for 10 s, 55 °C for 10 s, and 72 °C for 10 s). The Cq value for each reaction was determined by the software (the LightCycler 96 SW1.1, Roche, Basel, Switzerland). The expression levels of genes were normalized to GAPDH. The primers used are presented in Table 1.

Hwang D., Lee H., Lee J., Lee M., Cho S., Kim T, & Kim H. (2021). Micro-Current Stimulation Has Potential Effects of Hair Growth-Promotion on Human Hair Follicle-Derived Papilla Cells and Animal Model. International Journal of Molecular Sciences, 22(9), 4361.

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RNA Extraction and qPCR Analysis Protocol

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RNA preparation, qPCR, and primer sequencing were performed as previously described [41 (link)]. Total RNA was isolated from tissues extracted from the dorsal lesions of mice using TRI-reagent. The total RNA concentration was determined using a Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). Further, total RNA was used as a template for cDNA synthesis using a cDNA synthesis kit (Takara Bio, Shiga, Japan). qPCR was performed using SYBR Green I and a LightCycler 96 instrument (Roche, Basel, Switzerland). The cycling conditions were as follows: one cycle of denaturation at 95 °C for 10 min, followed by 45 cycles of denaturation at 95 °C for 10 s, annealing at 55 °C for 10 s, and extension at 72 °C for 10 s. The Cq value for each reaction was determined using LightCycler 96 SW1.1 software. The expression levels of the analyzed genes were normalized to that of GAPDH. The primers used are presented in Table 1.

Baek Y.H., Lee J.H., Chang S.J., Chae Y., Lee M.H., Kim S.H., Han K.I, & Kim T.J. (2022). Heat-Killed Enterococcus faecalis EF-2001 Induces Human Dermal Papilla Cell Proliferation and Hair Regrowth in C57BL/6 Mice. International Journal of Molecular Sciences, 23(10), 5413.

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Fecal Microbiome Collection and DNA Extraction

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Fecal samples were collected by patients at home, immediately frozen in the household freezer, and brought to the hospital within 12 hours. The time of fecal sample collection was either the evening one day before or the morning on the same day of obtaining biochemical data. Then, fecal samples were transferred to the laboratory and stored at -80 °C for up to three days before processing. Bacterial DNA was extracted using the Stool DNA Extraction kit (Topgen Biotechnology Co., Ltd, Kaohsiung, Taiwan). In brief, the fecal samples were weighed to 50-100 mg and were supplemented with a preceding bead beating (45 seconds; speed: 3450 oscillations/min). The subsequent steps of DNA extraction were performed according to the manufacturer's protocol. DNA concentration and quality was assessed by Colibri Microvolume spectrophotometer (Titertek Berthold, Pforzheim, Germany). Extracted DNA samples were immediately stored at -20 °C before use.

Hung W.C., Hung W.W., Tsai H.J., Chang C.C., Chiu Y.W., Hwang S.J., Kuo M.C., Chen S.C., Dai C.Y, & Tsai Y.C. (2021). The Association of Targeted Gut Microbiota with Body Composition in Type 2 Diabetes Mellitus. International Journal of Medical Sciences, 18(2), 511-519.

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RNA Extraction and Purification Protocol

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RNA extraction was performed using RNeasy Mini Kit (Cat. No. 74004, QIAGEN, Hilden, Germany) as previously described by Rattanachak et al. (2022) [31 (link)]. Total RNA samples were also isolated using RNase-Free DNase Set (Cat. No. 79254, QIAGEN, Hilden, Germany) to remove genomic DNA contamination. For all downstream applications, total RNA samples extracted were quantified and analyzed for purity using a Colibri Microvolume Spectrophotometer (Titertek Berthold, Pforzheim, Germany). The purity of total RNA (A₂₆₀/A₂₈₀) was around 2.0. All RNA extracts were kept at −80 °C for further analysis.

Rattanachak N., Weawsiangsang S., Daowtak K., Thongsri Y., Ross S., Ross G., Nilsri N., Baldock R.A., Pongcharoen S., Jongjitvimol T, & Jongjitwimol J. (2022). High-Throughput Transcriptomic Profiling Reveals the Inhibitory Effect of Hydroquinine on Virulence Factors in Pseudomonas aeruginosa. Antibiotics, 11(10), 1436.

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DNA Extraction from Blood and Ticks

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DNA extraction from blood samples was conducted within 24 h of collection using the Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA) following the manufacturer’s instructions. The DNA samples were eluted in 100 µL of DNA Rehydration Solution and stored at −80 °C until they were used as templates for polymerase chain reaction (PCR) assays.
For tick samples, one female tick per animal was selected from the total collected during the last three sampling sessions for total DNA extraction. Ticks were homogenized using a MagNA Lyser instrument (Roche Molecular Diagnostics, Rotkreuz, Switzerland) at a speed of 5000 rpm for 5 cycles of 60 s each. During homogenization, 50 μL of PBS (Sigma, St. Louis, MO, USA) were added to a MagNA Lyser tube containing ceramic beads. The tick homogenates were then subjected to total DNA extraction using the Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA) according to the manufacturer’s instructions. The DNA samples were eluted in 60 µL of DNA Rehydration Solution. The quantitative and qualitative assessment of DNA extraction was performed using a Colibri Microvolume Spectrophotometer (Titertek-Berthold, Pforzheim, Germany). All extracted DNA samples were stored at −80 °C until they were used.

Piloto-Sardiñas E., Foucault-Simonin A., Wu-Chuang A., Mateos-Hernández L., Marrero-Perera R., Abuin-Denis L., Roblejo-Arias L., Díaz-Corona C., Zając Z., Kulisz J., Woźniak A., Moutailler S., Corona-González B, & Cabezas-Cruz A. (2023). Dynamics of Infections in Cattle and Rhipicephalus microplus: A Preliminary Study. Pathogens, 12(8), 998.

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