Millennium software

Manufactured by Waters Corporation

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Millennium software is a data management and analysis platform developed by Waters Corporation. It provides a comprehensive solution for collecting, processing, and managing data from various analytical instruments used in scientific laboratories. The software's core function is to enable users to efficiently acquire, store, and analyze data generated during laboratory experiments and analyses.

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Millennium chromatography software (3 citations) Waters millennium chromatography software (2 citations)

15 protocols using millennium software

Extraction and Analysis of Ester-Bound Phenolics

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Following exhaustive extraction of soluble phenolics with aqueous methanol, ester bound phenolics were extracted from the cell walls of freeze dried powdered cell cultures (50 mg), with 1 M NaOH (5 ml) followed by incubation at 25 °C for 24 h, in the dark under N₂. After centrifugation, acidification and precipitation of solubilised carbohydrates with MeOH at 4 °C, the extracted phenolics in the aqueous phase were loaded onto an activated reverse phase C₁₈ µNova Sep-Pak column and eluted with 100% MeOH, and analysed by HPLC.
HPLC was carried out on a µNova Pak C18 8 × 10 Radial Compression Module (Waters) with MeOH: 5% acetic acid either with a 35–65% linear MeOH gradient in 15 min (for FAE assay) or with a 30–70% linear MeOH gradient in 25 min (for monomer and dimer cell wall components) at 2 ml/min. Hydroxycinnamic acids were monitored and quantified at 340 nm, with a Waters 996 photo-diode array detector with UV /visible spectra collected at 240–400 nm, and analysed with Millennium software (Waters Inc) against authentic monomer standards, or using response factors for the various dehydrodiferulate dimers reported by Waldron et al. (1996 (link)).

Morris P., Dalton S., Langdon T., Hauck B, & de Buanafina M.M. (2017). Expression of a fungal ferulic acid esterase in suspension cultures of tall fescue (Festuca arundinacea) decreases cell wall feruloylation and increases rates of cell wall digestion. Plant Cell, Tissue and Organ Culture, 129(2), 181-193.

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Determining ParB Dimerization in Solution

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To examine whether ParB forms dimers in solution, we performed a size exclusion chromatography (SEC) coupled with UV, on-line laser light scattering (LS) and refractive index (RI) detectors (SEC-UV/LS/RI). Specifically, purified His6-ParB (pre-filtered through a 0.22 µm filter) was applied on a Superose 6, 10/30, HR SEC column (GE Healthcare Life Sciences) equilibrated in 100 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM DTT buffer and chromatographed at a flow rate of 0.3 ml/min. Elution from SEC was monitored by a photodiode array (PDA) UV/VIS detector (996 PDA, Waters Corp., Milford, MA), differential refractometer (OPTI-Lab, or OPTI-rEx Wyatt Corp., Santa Barbara, CA), and static, multi-angle laser light scattering detector (DAWN-EOS, Wyatt Corp.). The Millennium software (Waters Corp.) controlled the HPLC Alliance 2965 (Waters Corp.) system, to which the column was connected to, and data collection from the multi-wavelength UV/VIS detector, while the ASTRA software (Wyatt Corp.) collected data from the refractive index detector, the light scattering detectors, and recorded the UV trace at 280 nm sent from the PDA detector. Data collection and analyses were carried out at the Keck Foundation Biotechnology Resource Laboratory, Yale University.

Lim H.C., Surovtsev I.V., Beltran B.G., Huang F., Bewersdorf J, & Jacobs-Wagner C. (2014). Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation. eLife, 3, e02758.

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Bioactive Compound Isolation and Identification

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Microfractionation of the DCM extract was performed on a Waters chromatographic system (Waters 600 controller, Waters Corporation, Milford, MA, USA). All separation was done on a Luna Phenomenex reverse phase column (250 × 4.60 mm, 5 μm). The mobile phase consisted of H₂O (0.05% trifluoroacetic acid) as solvent A and acetonitrile (ACN) (0.05% trifluoroacetic acid) as solvent B. A gradient elution of 5–95% solvent B was carried out for 30 min at a flow rate of 1 mL/min. An injection volume of 30 µL corresponding to 300 µg of sample was used. Data were collected using Millennium^® software (Waters Corporation, Milford, MA, USA). A total of 30 fractions were collected in a 96 deep-well plate, corresponding to approximately 10 µg of the fractions in each well of the plate. This was repeated three times before evaporating until dry in a Genevac EZ-2 centrifugal evaporator (Genevac Ltd., Ipswich, UK). The 30 microfractions were dissolved in dimethyl sulfoxide (DMSO) and subjected to anti-HIV screening using the deCIPhR assay as previously described [17 (link)]. Five bio-active microfractions were combined and subjected to UPLC-QTOF-MS/MS analysis to tentatively identify the compounds in the fractions.

Tembeni B., Sciorillo A., Invernizzi L., Klimkait T., Urda L., Moyo P., Naidoo-Maharaj D., Levitties N., Gyampoh K., Zu G., Yuan Z., Mounzer K., Nkabinde S., Nkabinde M., Gqaleni N., Tietjen I., Montaner L.J, & Maharaj V. (2022). HPLC-Based Purification and Isolation of Potent Anti-HIV and Latency Reversing Daphnane Diterpenes from the Medicinal Plant Gnidia sericocephala (Thymelaeaceae). Viruses, 14(7), 1437.

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Reversed Phase HPLC Analysis of Casein and Whey

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Casein fractions and whey proteins were determined by the Reversed Phase -High Performance Liquid Chromatography (RP-HPLC) method [21 (link)] on a HPLC system consisting of a pump capable of mixing four solvents (Waters 600E, Waters, Milford, MA, USA), a photodiode array detector (Waters 996), a helium degasser, a Rheodyne 7125 injector (Rheodyne Inc., Cotati, CA, USA) and Millennium software (v.3.05.01, Waters, Milford, MA, USA).

Panopoulos G., Moatsou G., Psychogyiopoulou C, & Moschopoulou E. (2020). Microfiltration of Ovine and Bovine Milk: Effect on Microbial Counts and Biochemical Characteristics. Foods, 9(3), 284.

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CYP3A4 Enzymatic Assay with NADPH

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CYP3A4 incorporated Nanodiscs with CPR as described (48 (link)) with added substrates were preincubated for 5 minutes at 37˚C, in a 1 ml reaction volume in 100 mM HEPES buffer (pH 7.4), 10 mM MgCl₂, 0.1 mM dithiothreitol. The concentration of CYP3A4 was in the range from 60 to 100 nM. The reaction was initiated with the addition of 200 nmol of NADPH. NADPH consumption was monitored for 5 min and calculated from the absorption changes at 340 nm using the extinction coefficient 6.22 mM⁻¹ cm⁻¹.
Reactions for product analysis were performed under similar conditions. At the end of the incubation period, 0.2 ml aliquots were quenched with 1.6 ml of 2:1 mixture of acetonitrile/methanol supplemented with the internal standard mevastatine, and dried. The samples were dissolved in 100 μl of methanol and 30 ul was injected onto Ace 3 C18 HPLC column, 2.1 × 150 mm (MAC-MOD Analytical, Chadds Ford, PA). The mobile phase contained 15% acetonitrile and 15% methanol in water; products were separated in linear gradient of acetonitrile and methanol rising from 15% to 37% each over 35 min at flow rate 0.2 ml/min. The calibration and method validation was performed using commercially available metabolites of DND and ARVS. The chromatograms were processed with Millennium software (Waters).

Denisov I.G., Baylon J.L., Grinkova Y.V., Tajkhorshid E, & Sligar S.G. (2017). Drug-drug interactions between Atorvastatin and Dronedarone mediated by monomeric CYP3A4. Biochemistry, 57(5), 805-816.

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Quantification of Sphingolipid Levels

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Samples were lysed in a homogenization buffer containing 50 mM HEPES (Gibco), 150 mM NaCl (Sigma-Aldrich), 0.2% Igepal (Sigma-Aldrich) and protease inhibitors (Calbiochem). To quantify sphingosine and sphingomyelin levels, the dried lipid extract was resuspended in 0.2% Igepal CA-630. Four microliters of the lipid extract was added to 20 μl of a naphthalene-2, 3-dicarboxyaldehyde (NDA) derivatization reaction mixture (25 mM borate buffer, pH 9.0, containing 2.5 mM each of NDA and NaCN). The reaction mixture was diluted with ethanol in a 1:3 ratio, incubated at 50°C for 10 min, and centrifuged (13,000 g for 5 min). An aliquot (30 μl) of the supernatant was then transferred to a sampling glass vial and 5 μl was applied to an ultra performance liquid chromatography (UPLC) system for analysis. The ﬂuorescence was measured using a model 474 scanning ﬂuorescence detector (Waters). Quantiﬁcation of sphingosine and sphingomyelin peaks was carried out by calculation against the sphingosine and sphingomyelin standard calibration curves using Waters Millennium software.

Jeong M.S., Bae J.S, & Jin H.K. (2019). Vascular endothelial growth factor improves the therapeutic effects of cyclodextrin in Niemann-Pick type C mice. Animal Cells and Systems, 23(5), 346-354.

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HPLC Analysis of Iohexol in Plasma

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Iohexol was determined using a Waters 626 HPLC system with a 996 photodiode array detector (Waters, Milford, Massachusetts) (1 spectrum/second; wavelength 200‐320 nm, extracting the chromatogram at 254 nm). Iohexol was separated in a Simmetry100 C18 column, 3.5 μm, 2.1 x 150 mm (Waters) using a mixture of CH₃CN and 0.1% orthophosphoric acid in water (3:97, vol/vol) at a flow rate of 0.3 mL/min. During separation, the column was held at 30°C. Standard iohexol (Omnipaque 350; 755 mg/mL iohexol) was added to untreated dog plasma to obtain the following standard solutions: 5, 20, 50, 200, and 500 μg iohexol/mL. Plasma samples were deproteinized with 5% perchloric acid (1:1, vol/vol), centrifuged at 11000 g for 10 minutes at 5°C, and 10 μL of supernatants were injected into the HPLC column. Data was processed using Millennium software (Waters). The peak areas of both iohexol isomers were used to calculate the iohexol concentrations and plasma clearance. The long‐term stability of iohexol in plasma was tested by reanalysis after 36 months in a freezer at −30°C, on 60 samples collected during the GFR₅ test of 12 dogs.

Pocar P., Scarpa P., Berrini A., Cagnardi P., Rizzi R, & Borromeo V. (2019). Diagnostic potential of simplified methods for measuring glomerular filtration rate to detect chronic kidney disease in dogs. Journal of Veterinary Internal Medicine, 33(5), 2105-2116.

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Quantification of Enzymatic Activity in Biological Samples

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We performed the enzymatic activity measurements as previously described^{17 (link),21 (link)} using a UPLC system (Waters). Briefly, the brain was lysed in homogenization buffer containing 50 mM HEPES (Sigma-Aldrich, H3375), 150 mM NaCl (Sigma-Aldrich, S3014), 0.2% Igepal CA-630 (Sigma-Aldrich, I8896), and protease inhibitor (Calbiochem, 539131). Three microliters of the samples (plasma, serum, or brain) were mixed with 3 µl of 200 µM Bodipy-C12-sphingomyelin (Invitrogen, D7711) diluted in 0.2 M of sodium acetate buffer, pH 5.0, 0.2 mM ZnCl₂, and 0.2% Igepal CA-630 and incubated at 37 °C for 1 h. The hydrolysis reactions were stopped by adding 114 µl of ethanol, and centrifuged at 15,493 × g for 5 min. Thirty microliters of the supernatant was then transferred to a sampling glass vial and 5 µl was applied onto a UPLC system for analysis. Quantification was achieved by comparison to Bodipy-C12-ceramide using the Waters Millennium software.

Choi B.J., Park M.H., Park K.H., Han W.H., Yoon H.J., Jung H.Y., Hong J.Y., Chowdhury M.R., Kim K.Y., Lee J., Song I.S., Pang M., Choi M.K., Gulbins E., Reichel M., Kornhuber J., Hong C.W., Kim C., Kim S.H., Schuchman E.H., Jin H.K, & Bae J.S. (2023). Immunotherapy targeting plasma ASM is protective in a mouse model of Alzheimer’s disease. Nature Communications, 14, 1631.

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PLGA Molecular Weight Characterization via GPC

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Using gel permeation chromatography (GPC), the average molecular weight of the PLGA in the collected freeze-dried microspheres was measured (at 1 d, 1 w, 2 w, 4 w, 6 w, 8 w, 12 w, 16 w, 20 w and 24 w). A Waters 2515 HPLC pump, a Waters 2707 Plus Autosampler, a Waters 2414 refractive index detector and two Waters Styragel high-resolution columns (HT3 and HT4; effective molecular weight ranges: 500–30,00 and 5000–600,000, respectively) were installed on the instrument. The mobile phase was tetrahydrofuran (THF, HPLC grade) at a flow rate of 1.0 mL/min at 35 °C. Samples were dissolved in THF at a concentration of 1 mg/mL and filtered through a 0.45 μm filter before detection. Monodispersed polystyrene standards obtained from Waters Co. with a molecular weight range of 1000 to 2.0 × 10⁵ g/mol were used to generate the calibration curve. The weight-average molecular weight (Mw) and the number-weight molecular weight (Mn) were evaluated using Waters Millennium software [46 (link),47 (link)].

Zhang H., Yang Z., Wu D., Hao B., Liu Y., Wang X., Pu W., Yi Y., Shang R, & Wang S. (2023). The Effect of Polymer Blends on the In Vitro Release/Degradation and Pharmacokinetics of Moxidectin-Loaded PLGA Microspheres. International Journal of Molecular Sciences, 24(19), 14729.

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Enzymatic Activity Quantification of Sphingomyelin

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Enzymatic activity was measured as previously described (15 (link), 31 (link)) using a UPLC system (Waters). Briefly, the spinal cord was lysed in a homogenization buffer containing 50 mM HEPES (Sigma-Aldrich, H3375), 150 mM NaCl (Sigma-Aldrich, S3014), 0.2% Igepal CA-630 (Sigma-Aldrich, I8896), and protease inhibitors (Calbiochem, 539131). Three microliters of the samples (plasma or spinal cord) were mixed with 3 μl of 200 μm BODIPY-C12-sphingomyelin (Invitrogen, D7711) diluted in 0.2 M of sodium acetate buffer, pH 5.0, 0.2 mM ZnCl₂, and 0.2% Igepal CA-630, and incubated at 37°C for 1 h. Hydrolysis reactions were stopped by adding 114 μl and centrifuged at 13,000 rpm for 5 min. Thirty microliters of the supernatant was then transferred to a sampling glass vial, and 5 μl was applied to a UPLC system for analysis. Quantification was achieved by comparison with BODIPY-C12-ceramide using the Waters Millennium software.

Choi B.J., Park K.H., Park M.H., Huang E.J., Kim S.H., Bae J.S, & Jin H.K. (2022). Acid sphingomyelinase inhibition improves motor behavioral deficits and neuronal loss in an amyotrophic lateral sclerosis mouse model. BMB Reports, 55(12), 621-626.

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