nanodrop nd 1000 spectrometer  (Thermo Fisher)


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    Thermo Fisher nanodrop nd 1000 spectrometer
    Nanodrop Nd 1000 Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nanodrop nd 1000 spectrometer/product/Thermo Fisher
    Average 99 stars, based on 100 article reviews
    Price from $9.99 to $1999.99
    nanodrop nd 1000 spectrometer - by Bioz Stars, 2020-02
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    Centrifugation:

    Article Title: Metabolic reprogramming during neuronal differentiation
    Article Snippet: After centrifugation, the DNA pellet was washed with 70% EtOH, air dried and dissolved in sterile water. .. DNA concentrations were measured using a Nanodrop 1000 spectrometer (Thermo Scientific).

    Amplification:

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: Paragraph title: Total RNA extraction, RNA quality analysis, amplification and labeling ... Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity.

    Synthesized:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. With primer/probe sets from TaqMan® Gene Expression Assays, the forward and reverse primers were specific to each gene and synthesized by Applied Biosystems from the following mRNA reference sequences: Il-1α ( ); Tnf-α ( ); Mip-2 ( ); and Ccl2 ( ).

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Quantification of RNA was done using Nanodrop (ND-1000) spectrometer. .. The samples were then given DNase I treatment to remove DNA contamination and RNA quality was checked by running a 1.5% agarose gel. cDNA was synthesized using High Capacity kit (ABI) as per manufacture's protocol. cDNA quality was checked by performing PCR with respective primers and observing the desired band for PCR product.

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: The first and second strands of cDNA were synthesized by adding reverse transcriptase to the mix. .. Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity.

    Quantitative RT-PCR:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: Paragraph title: Quantitative RT-PCR ... The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE).

    Article Title: Condition-dependent virulence of slow bee paralysis virus in Bombus terrestris: are the impacts of honeybee viruses in wild pollinators underestimated?
    Article Snippet: .. Real-time quantitative RT-PCR RNA extractions from all bee guts in the infection time course were measured on a Nanodrop 1000 spectrometer. ..

    Article Title: Retinoic Acid Availability Drives the Asynchronous Initiation of Spermatogonial Differentiation in the Mouse 1
    Article Snippet: Paragraph title: RNA Isolation and Real-Time RT-PCR ... Total RNA was extracted using a PicoPure RNA Isolation Kit (Molecular Devices, Sunnyvale, CA) and quantified in an ND-1000 Spectrometer (Thermo Scientific, Wilmington, DE).

    Article Title: Metabolic reprogramming during neuronal differentiation
    Article Snippet: DNA concentrations were measured using a Nanodrop 1000 spectrometer (Thermo Scientific). .. The relative amount of mtDNA was valued by qRT-PCR performed in an ABI PRISM 7000 Sequence Detection System (Applied Biosystem) with SYBR green ready mix (Applied Biosystem) with the following primers: SDHA Fwd 5′-AGACCTTGAATGAGGCTGACTGTG-3′, SDHA Rev 5′-GAGACAAAGTCTGGCGCAACTC-3′, ND5 Fwd 5′-TGATGGTACGGACGAACAGACG-3′, and ND5 Rev 5′-CTGATGGTAGTCATGGGTGGAG-3′

    SYBR Green Assay:

    Article Title: Retinoic Acid Availability Drives the Asynchronous Initiation of Spermatogonial Differentiation in the Mouse 1
    Article Snippet: Total RNA was extracted using a PicoPure RNA Isolation Kit (Molecular Devices, Sunnyvale, CA) and quantified in an ND-1000 Spectrometer (Thermo Scientific, Wilmington, DE). .. Real-time RT-PCR used a 7500 Fast Real-Time PCR System and Fast SYBR GREEN Mastermix (Applied Biosystems).

    Article Title: Metabolic reprogramming during neuronal differentiation
    Article Snippet: DNA concentrations were measured using a Nanodrop 1000 spectrometer (Thermo Scientific). .. The relative amount of mtDNA was valued by qRT-PCR performed in an ABI PRISM 7000 Sequence Detection System (Applied Biosystem) with SYBR green ready mix (Applied Biosystem) with the following primers: SDHA Fwd 5′-AGACCTTGAATGAGGCTGACTGTG-3′, SDHA Rev 5′-GAGACAAAGTCTGGCGCAACTC-3′, ND5 Fwd 5′-TGATGGTACGGACGAACAGACG-3′, and ND5 Rev 5′-CTGATGGTAGTCATGGGTGGAG-3′

    Microarray:

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: The results are intended to provide expected versus observed log ratios for monitoring microarray hybridization linearity, sensitivity, and accuracy. .. Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity.

    Article Title: Prefrontal cortical and striatal transcriptional responses to the reinforcing effect of repeated methylphenidate treatment in the spontaneously hypertensive rat, animal model of attention-deficit/hyperactivity disorder (ADHD)
    Article Snippet: Tissue collection and RNA preparation One day after the final self-administration session, we removed the brains of 3 rats from cohort 2 (i.e., those which showed the most robust self-administration) as well as 3 rats from the control group for microarray analyses. .. The total RNA concentration was determined using NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Incubation:

    Article Title: Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora
    Article Snippet: Extraction buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 1.5 mM MgCl2 , 0.1% NP-40, 1 mM phenylmethylsulfonyl fluoride (PMSF), 1 μg/ml leupeptin, 1 μg/ml pepstatin A) was mixed with 500 μl ground mycelia and incubated on ice for approximately 30 minutes with frequent vortexing. .. Protein concentration was determined by NanoDrop 1000 spectrometer.

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Isopropanol (500 µl) was added in the samples and these were incubated at −20°C for 60 min. .. Quantification of RNA was done using Nanodrop (ND-1000) spectrometer.

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: Mixtures were incubated in a thermocycler with 16 thermal cycles at 95 °C for 30 s and 50 °C for 1 h. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulfonation and purification. .. The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer.

    Article Title: Metabolic reprogramming during neuronal differentiation
    Article Snippet: Then samples were incubated for 10 min at 95 °C to inhibit the Proteinase K and centrifuged at 8000 r.p.m. for 15 min at 4 °C. .. DNA concentrations were measured using a Nanodrop 1000 spectrometer (Thermo Scientific).

    Activity Assay:

    Article Title: Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora
    Article Snippet: Protein concentration was determined by NanoDrop 1000 spectrometer. .. Cellulase activity was calculated by using Azo-CM-Cellulose (Megazyme, Bray, Ireland) according to the manufacturer's protocol with minor modifications.

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: .. Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity. .. The yield for the rice RNA was in the range expected for plant products, with an average specific activity of cyanine 3- and cyanine 5-labeled cRNA targets of 14.6 (±3.3) pmol dye/μg cRNA.

    Infection:

    Article Title: Condition-dependent virulence of slow bee paralysis virus in Bombus terrestris: are the impacts of honeybee viruses in wild pollinators underestimated?
    Article Snippet: .. Real-time quantitative RT-PCR RNA extractions from all bee guts in the infection time course were measured on a Nanodrop 1000 spectrometer. ..

    Article Title: Deciphering the nature of the coral–Chromera association
    Article Snippet: Paragraph title: Coral larvae and Chromera infection experiment ... RNA was quantitated and its integrity assessed using a NanoDrop ND-1000 spectrometer (Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

    Expressing:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. With primer/probe sets from TaqMan® Gene Expression Assays, the forward and reverse primers were specific to each gene and synthesized by Applied Biosystems from the following mRNA reference sequences: Il-1α ( ); Tnf-α ( ); Mip-2 ( ); and Ccl2 ( ).

    Article Title: Binding of NAD+-Glycohydrolase to Streptolysin O Stabilizes Both Toxins and Promotes Virulence of Group A Streptococcus
    Article Snippet: Paragraph title: Protein expression and purification. ... Protein concentration was determined by measuring A 280 on a NanoDrop ND-1000 spectrometer (Thermo Fisher Scientific).

    Hybridization:

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: The results are intended to provide expected versus observed log ratios for monitoring microarray hybridization linearity, sensitivity, and accuracy. .. Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity.

    Dissection:

    Article Title: Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs
    Article Snippet: The dissection procedure was performed as previously described [ ]. .. The total RNA concentration was measured using a ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Cell Culture:

    Article Title: Deciphering the nature of the coral–Chromera association
    Article Snippet: Cultured Chromera were washed three times in 0.2 μm FSW and added at a density of 5 × 103 cells/ml. .. RNA was quantitated and its integrity assessed using a NanoDrop ND-1000 spectrometer (Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

    Protein Concentration:

    Article Title: Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora
    Article Snippet: .. Protein concentration was determined by NanoDrop 1000 spectrometer. .. Cellulase activity was calculated by using Azo-CM-Cellulose (Megazyme, Bray, Ireland) according to the manufacturer's protocol with minor modifications.

    Article Title: Binding of NAD+-Glycohydrolase to Streptolysin O Stabilizes Both Toxins and Promotes Virulence of Group A Streptococcus
    Article Snippet: .. Protein concentration was determined by measuring A 280 on a NanoDrop ND-1000 spectrometer (Thermo Fisher Scientific). .. Analytical gel filtration and size exclusion chromatography-multiangle light scattering (SEC-MALS).

    Polymerase Chain Reaction:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. To quantify relative mRNA levels of selected genes: macrophage inflammatory protein-2 (Mip-2), Ccl2, interleukin 1-alpha (Il-1α), and tumor necrosis factor-alpha (Tnf-α), real-time polymerase chain reaction (PCR) was performed on an Applied Biosystems 7300 Real-Time PCR instrument (Applied Biosystems, Foster City, CA), under the following conditions: 10 min at 95°C followed by 40 cycles at 95°C and 60°C (15 sec and 1 min, respectively).

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Paragraph title: RNA isolation and real time Polymerase Chain Reaction (PCR) ... Quantification of RNA was done using Nanodrop (ND-1000) spectrometer.

    Methylation:

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer. .. Sequencing was conducted using Pyromark Q24, and percent methylation was computed using the Pyromark Q24 Software v.2 in CpG mode.

    Isolation:

    Article Title: Retinoic Acid Availability Drives the Asynchronous Initiation of Spermatogonial Differentiation in the Mouse 1
    Article Snippet: .. Total RNA was extracted using a PicoPure RNA Isolation Kit (Molecular Devices, Sunnyvale, CA) and quantified in an ND-1000 Spectrometer (Thermo Scientific, Wilmington, DE). .. For real-time RT-PCR, forward and reverse primers (Supplemental Table S1; all Supplemental Data are available at ) were designed using Primer Express 2.0 (Applied Biosystems, Foster City, CA).

    Article Title: Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs
    Article Snippet: Paragraph title: Tissue collection and RNA isolation ... The total RNA concentration was measured using a ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Paragraph title: RNA isolation and real time Polymerase Chain Reaction (PCR) ... Quantification of RNA was done using Nanodrop (ND-1000) spectrometer.

    Article Title: Deciphering the nature of the coral–Chromera association
    Article Snippet: Total RNA from these larvae was isolated as described by Mohamed et al. [ ] using TRIzol® reagent (Ambion Life Technologies, Austin, TX, USA) according to manufacturer’s instructions. .. RNA was quantitated and its integrity assessed using a NanoDrop ND-1000 spectrometer (Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

    Article Title: Prefrontal cortical and striatal transcriptional responses to the reinforcing effect of repeated methylphenidate treatment in the spontaneously hypertensive rat, animal model of attention-deficit/hyperactivity disorder (ADHD)
    Article Snippet: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. .. The total RNA concentration was determined using NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Size-exclusion Chromatography:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. To quantify relative mRNA levels of selected genes: macrophage inflammatory protein-2 (Mip-2), Ccl2, interleukin 1-alpha (Il-1α), and tumor necrosis factor-alpha (Tnf-α), real-time polymerase chain reaction (PCR) was performed on an Applied Biosystems 7300 Real-Time PCR instrument (Applied Biosystems, Foster City, CA), under the following conditions: 10 min at 95°C followed by 40 cycles at 95°C and 60°C (15 sec and 1 min, respectively).

    Labeling:

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: .. Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity. .. The yield for the rice RNA was in the range expected for plant products, with an average specific activity of cyanine 3- and cyanine 5-labeled cRNA targets of 14.6 (±3.3) pmol dye/μg cRNA.

    Purification:

    Article Title: Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs
    Article Snippet: RNA was isolated following the manufacturer’s protocol and further purified using the RNeasy Mini Kit (Qiagen Inc.). .. The total RNA concentration was measured using a ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Article Title: Binding of NAD+-Glycohydrolase to Streptolysin O Stabilizes Both Toxins and Promotes Virulence of Group A Streptococcus
    Article Snippet: Paragraph title: Protein expression and purification. ... Protein concentration was determined by measuring A 280 on a NanoDrop ND-1000 spectrometer (Thermo Fisher Scientific).

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: Mixtures were incubated in a thermocycler with 16 thermal cycles at 95 °C for 30 s and 50 °C for 1 h. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulfonation and purification. .. The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer.

    Article Title: Prefrontal cortical and striatal transcriptional responses to the reinforcing effect of repeated methylphenidate treatment in the spontaneously hypertensive rat, animal model of attention-deficit/hyperactivity disorder (ADHD)
    Article Snippet: The RNA was further purified using the RNEasy mini kit (Qiagen Inc.). .. The total RNA concentration was determined using NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA).

    Sequencing:

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer. .. Sequencing was conducted using Pyromark Q24, and percent methylation was computed using the Pyromark Q24 Software v.2 in CpG mode.

    Article Title: Metabolic reprogramming during neuronal differentiation
    Article Snippet: DNA concentrations were measured using a Nanodrop 1000 spectrometer (Thermo Scientific). .. The relative amount of mtDNA was valued by qRT-PCR performed in an ABI PRISM 7000 Sequence Detection System (Applied Biosystem) with SYBR green ready mix (Applied Biosystem) with the following primers: SDHA Fwd 5′-AGACCTTGAATGAGGCTGACTGTG-3′, SDHA Rev 5′-GAGACAAAGTCTGGCGCAACTC-3′, ND5 Fwd 5′-TGATGGTACGGACGAACAGACG-3′, and ND5 Rev 5′-CTGATGGTAGTCATGGGTGGAG-3′

    SDS Page:

    Article Title: Binding of NAD+-Glycohydrolase to Streptolysin O Stabilizes Both Toxins and Promotes Virulence of Group A Streptococcus
    Article Snippet: The protein was then passed over a new 4-ml resin bed of Ni-NTA agarose, and the flowthrough along with 10 ml of wash with the same composition as the dialysis buffer was collected and analyzed for purity by SDS-PAGE. .. Protein concentration was determined by measuring A 280 on a NanoDrop ND-1000 spectrometer (Thermo Fisher Scientific).

    Software:

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer. .. Sequencing was conducted using Pyromark Q24, and percent methylation was computed using the Pyromark Q24 Software v.2 in CpG mode.

    Real-time Polymerase Chain Reaction:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. To quantify relative mRNA levels of selected genes: macrophage inflammatory protein-2 (Mip-2), Ccl2, interleukin 1-alpha (Il-1α), and tumor necrosis factor-alpha (Tnf-α), real-time polymerase chain reaction (PCR) was performed on an Applied Biosystems 7300 Real-Time PCR instrument (Applied Biosystems, Foster City, CA), under the following conditions: 10 min at 95°C followed by 40 cycles at 95°C and 60°C (15 sec and 1 min, respectively).

    Article Title: Condition-dependent virulence of slow bee paralysis virus in Bombus terrestris: are the impacts of honeybee viruses in wild pollinators underestimated?
    Article Snippet: Real-time quantitative RT-PCR RNA extractions from all bee guts in the infection time course were measured on a Nanodrop 1000 spectrometer. .. Two samples fell below 1.8 and were excluded from qPCR analysis.

    Article Title: Retinoic Acid Availability Drives the Asynchronous Initiation of Spermatogonial Differentiation in the Mouse 1
    Article Snippet: Total RNA was extracted using a PicoPure RNA Isolation Kit (Molecular Devices, Sunnyvale, CA) and quantified in an ND-1000 Spectrometer (Thermo Scientific, Wilmington, DE). .. Real-time RT-PCR used a 7500 Fast Real-Time PCR System and Fast SYBR GREEN Mastermix (Applied Biosystems).

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Paragraph title: RNA isolation and real time Polymerase Chain Reaction (PCR) ... Quantification of RNA was done using Nanodrop (ND-1000) spectrometer.

    RNA Extraction:

    Article Title: Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients
    Article Snippet: Paragraph title: RNA extraction ... RNA quantity and quality were measured with a NanoDrop ND-1000 spectrometer and RNA integrity was assessed by standard denaturing agarosegel electrophoresis.

    Article Title: Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
    Article Snippet: Paragraph title: Total RNA extraction, RNA quality analysis, amplification and labeling ... Fluorescently labeled cRNAs were analyzed on a ND-1000 Spectrometer (NanoDropTechnologies, Rockland, DE) for determining yield and specific activity.

    Agarose Gel Electrophoresis:

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: Quantification of RNA was done using Nanodrop (ND-1000) spectrometer. .. The samples were then given DNase I treatment to remove DNA contamination and RNA quality was checked by running a 1.5% agarose gel. cDNA was synthesized using High Capacity kit (ABI) as per manufacture's protocol. cDNA quality was checked by performing PCR with respective primers and observing the desired band for PCR product.

    Electrophoresis:

    Article Title: Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients
    Article Snippet: .. RNA quantity and quality were measured with a NanoDrop ND-1000 spectrometer and RNA integrity was assessed by standard denaturing agarosegel electrophoresis. .. Sample labeling and array hybridization were performed according to the Agilent one-color microarray-based gene expression analysis protocol (Agilent Technology) with minor modifications.

    Homogenization:

    Article Title: Elevated polyamines induce c-MYC overexpression by perturbing quadruplex-WC duplex equilibrium
    Article Snippet: The Trizol reagent (1 ml) was added in a six-well plate and continuous pipetting was done for 5 min. After homogenization, 200 µl of chloroform was added to the samples followed by vortexing for 30 s and incubation at room temperature for 5 min. .. Quantification of RNA was done using Nanodrop (ND-1000) spectrometer.

    DNA Methylation Assay:

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: DNA bisulfite conversion was accomplished using EZ DNA Methylation Kits (Zymo Research) by following the manufacturer’s manual. .. The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer.

    Concentration Assay:

    Article Title: Pulmonary response after exposure to inhaled nickel hydroxide nanoparticles: short and long-term studies in mice
    Article Snippet: .. The quality and concentration was determined using a Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). .. Using High Capacity cDNA Reverse Transcription Kits (Applied Biosystems, Foster City, CA) and following the provided manufacturer’s protocol, total RNA was reverse transcribed into cDNA.

    Article Title: Novel drug-regulated transcriptional networks in brain reveal pharmacological properties of psychotropic drugs
    Article Snippet: .. The total RNA concentration was measured using a ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA). .. RNA quality was determined using an Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA).

    Article Title: Associations of LEP, CRH, ICAM-1, and LINE-1 methylation, measured in saliva, with waist circumference, body mass index, and percent body fat in mid-childhood
    Article Snippet: .. The concentration of eluted DNA was measured using a NanoDrop 1000 spectrometer. .. DNA methylation was quantitated using bisulfite-PCR and pyrosequencing using the following kits from Qiagen: ICAM1_02 for ICAM-1 , CRH_01 for CRH , LEP_01 for LEP , and NOS3_02 for LINE-1.

    Article Title: Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program
    Article Snippet: .. The concentration and purity of each RNA sample was assessed using a Nanodrop 1000 spectrometer (Nanodrop Inc—Thermo Fisher Scientific, Wilmington, DE). .. The RNA yield from each sample was calculated as ng/mg of tissue (wet weight).

    Article Title: Prefrontal cortical and striatal transcriptional responses to the reinforcing effect of repeated methylphenidate treatment in the spontaneously hypertensive rat, animal model of attention-deficit/hyperactivity disorder (ADHD)
    Article Snippet: .. The total RNA concentration was determined using NanoDrop ND-1000 Spectrometer (NanoDrop Technologies Inc., Montchanin, DE, USA). .. The RNA integrity was assessed using a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    UV-Vis Spectroscopy:

    Article Title: Siderocalin/Lcn2/NGAL/24p3 Does Not Drive Apoptosis Through Gentisic Acid Mediated Iron Withdrawal in Hematopoietic Cell Lines
    Article Snippet: Paragraph title: UV/Vis Spectroscopy ... Absorbance data ( ) were collected immediately at ambient temperature using a Nanodrop ND-1000 spectrometer (Thermo Scientific).

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  • 90
    Thermo Fisher mouse anti gfap
    <t>IL-1β</t> signal is colocalized with <t>GFAP,</t> and not with Iba-1 or NeuN, in the dorsal hippocampus in stressed and non-stressed animals A. Representative images of IL-1β, NeuN, Iba-1, and GFAP immunoreactivity in the dentate gyrus of the DH (AP −3.36 mm from bregma) acquired at 20X are shown. Because we did not detect any differences in colocalization between stressed and non-stressed rats, all images here are taken from animals that received stress exposure. Bitplane Imaris was used for background subtraction to better visualize individual cells presented. B. Bitplane Imaris software was used to calculate the colocalization of the IL-1β signal with GFAP, Iba-1, and NeuN. Colocalization analyses revealed that the percent of the IL-1β signal colocalized with GFAP was significantly greater than the percent of the IL-1β signal colocalized with either Iba-1 or NeuN. * p
    Mouse Anti Gfap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mouse anti gfap/product/Thermo Fisher
    Average 90 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
    mouse anti gfap - by Bioz Stars, 2020-02
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    Thermo Fisher acarbose
    Schematic overview of the effect of repurposed drugs on biofilm and its outcome on tuberculosis treatment: Under stress like conditions Mycobacteria secrete exogenous layer of matrix that forms a physical barrier for entry of drugs. The cells within the matrix continuously secrete to develop a biomass of biofilm that enables the cells to withstand high minimum inhibitory concentration (MIC) of drugs. As a result, higher dosage of drugs is required to kill the cells. Cells at the core of the biofilm matrix are least affected by drugs and evolve in due time so as to withstand even higher concentration of drugs. This confers drug tolerance and leads to drug toxicity, increased treatment cost and mortality. Cyclosporine-A, <t>acarbose</t> and GaNP inhibit the activity of PpiB that play crucial role in biofilm formation. Treatment with these drugs suppresses formation of biofilm and the bacterium is exposed directly to the drugs. As a result the drug is effective at low MIC values. Treatment with these drugs also reduces the MIC of existing anti-tubercular drugs resulting in decreased toxicity. The end result is that patient mortality and treatment cost may be reduced significantly. Regular and dotted arrows in the figure denote confirmed and putative roles respectively
    Acarbose, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/acarbose/product/Thermo Fisher
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    Price from $9.99 to $1999.99
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    <t>BCL9</t> regulates mRNA levels of calcium wave-associated genes through paraspeckle proteins. a Network of BCL9-interacting proteins identified by Co-IP MS. Each node represents a group of BCL9-interacting proteins with functional relationships. Lines between different nodes represent the “weight” of the protein-protein interaction according to String database (colored) or total peptides in Co-IP assay (black). Groups were clustered by k-means unsupervised classification according to the interacting “weight” among different nodes. b Representative IF showing co-localization of BCL9, NONO, and ILF2 in CRC but not in normal colon epithelial cells. Scale bars: 20 µm (top, left), and 2 µm (inset). c , d <t>SFPQ</t> binding motif in the 3′UTR region of indicated mRNA-encoding genes down-regulated in BCL9- knock out RKO cells. High fold change: Genes whose mRNA levels decreased more than 1.5-fold in BCL9 knockout cells. Low-fold change: others. P values were calculated using χ 2 test, ** P
    Sfpq, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sfpq/product/Thermo Fisher
    Average 80 stars, based on 1 article reviews
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    IL-1β signal is colocalized with GFAP, and not with Iba-1 or NeuN, in the dorsal hippocampus in stressed and non-stressed animals A. Representative images of IL-1β, NeuN, Iba-1, and GFAP immunoreactivity in the dentate gyrus of the DH (AP −3.36 mm from bregma) acquired at 20X are shown. Because we did not detect any differences in colocalization between stressed and non-stressed rats, all images here are taken from animals that received stress exposure. Bitplane Imaris was used for background subtraction to better visualize individual cells presented. B. Bitplane Imaris software was used to calculate the colocalization of the IL-1β signal with GFAP, Iba-1, and NeuN. Colocalization analyses revealed that the percent of the IL-1β signal colocalized with GFAP was significantly greater than the percent of the IL-1β signal colocalized with either Iba-1 or NeuN. * p

    Journal: Brain, behavior, and immunity

    Article Title: Hippocampal interleukin-1 mediates stress-enhanced fear learning: A potential role for astrocyte-derived interleukin-1β

    doi: 10.1016/j.bbi.2017.09.016

    Figure Lengend Snippet: IL-1β signal is colocalized with GFAP, and not with Iba-1 or NeuN, in the dorsal hippocampus in stressed and non-stressed animals A. Representative images of IL-1β, NeuN, Iba-1, and GFAP immunoreactivity in the dentate gyrus of the DH (AP −3.36 mm from bregma) acquired at 20X are shown. Because we did not detect any differences in colocalization between stressed and non-stressed rats, all images here are taken from animals that received stress exposure. Bitplane Imaris was used for background subtraction to better visualize individual cells presented. B. Bitplane Imaris software was used to calculate the colocalization of the IL-1β signal with GFAP, Iba-1, and NeuN. Colocalization analyses revealed that the percent of the IL-1β signal colocalized with GFAP was significantly greater than the percent of the IL-1β signal colocalized with either Iba-1 or NeuN. * p

    Article Snippet: The following primary antibodies were used: rabbit anti-IL-1β (1:500, Abcam, Cambridge, MA, Cat# Ab9722), mouse anti-GFAP (1:1000, ThermoFisher Scientific, Waltham, MA, Cat #MS-1376P), mouse anti-NeuN-Alexa 568 (1:1000, Abcam Cambridge, MA, ), and rabbit anti-Iba-1-biotinylated (1:500, Wako, Richmond, VA, Cat#016-26461).

    Techniques: Software

    Schematic overview of the effect of repurposed drugs on biofilm and its outcome on tuberculosis treatment: Under stress like conditions Mycobacteria secrete exogenous layer of matrix that forms a physical barrier for entry of drugs. The cells within the matrix continuously secrete to develop a biomass of biofilm that enables the cells to withstand high minimum inhibitory concentration (MIC) of drugs. As a result, higher dosage of drugs is required to kill the cells. Cells at the core of the biofilm matrix are least affected by drugs and evolve in due time so as to withstand even higher concentration of drugs. This confers drug tolerance and leads to drug toxicity, increased treatment cost and mortality. Cyclosporine-A, acarbose and GaNP inhibit the activity of PpiB that play crucial role in biofilm formation. Treatment with these drugs suppresses formation of biofilm and the bacterium is exposed directly to the drugs. As a result the drug is effective at low MIC values. Treatment with these drugs also reduces the MIC of existing anti-tubercular drugs resulting in decreased toxicity. The end result is that patient mortality and treatment cost may be reduced significantly. Regular and dotted arrows in the figure denote confirmed and putative roles respectively

    Journal: NPJ Biofilms and Microbiomes

    Article Title: Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention

    doi: 10.1038/s41522-018-0075-0

    Figure Lengend Snippet: Schematic overview of the effect of repurposed drugs on biofilm and its outcome on tuberculosis treatment: Under stress like conditions Mycobacteria secrete exogenous layer of matrix that forms a physical barrier for entry of drugs. The cells within the matrix continuously secrete to develop a biomass of biofilm that enables the cells to withstand high minimum inhibitory concentration (MIC) of drugs. As a result, higher dosage of drugs is required to kill the cells. Cells at the core of the biofilm matrix are least affected by drugs and evolve in due time so as to withstand even higher concentration of drugs. This confers drug tolerance and leads to drug toxicity, increased treatment cost and mortality. Cyclosporine-A, acarbose and GaNP inhibit the activity of PpiB that play crucial role in biofilm formation. Treatment with these drugs suppresses formation of biofilm and the bacterium is exposed directly to the drugs. As a result the drug is effective at low MIC values. Treatment with these drugs also reduces the MIC of existing anti-tubercular drugs resulting in decreased toxicity. The end result is that patient mortality and treatment cost may be reduced significantly. Regular and dotted arrows in the figure denote confirmed and putative roles respectively

    Article Snippet: Anhydrotetracycline induced Ms_PpiB and Ms_VC cells were cultured in the presence of various concentrations of cyclosporine-A (0, 10, 100, and 1000 µg/ml), acarbose (0, 1, 10, 100, 500, 1000 µg/ml) or GaNP (0, 10, 50, 100, 1000 µg/ml) in sterile flat bottom 96-well microtiter plate (Thermo Scientific, India).

    Techniques: Concentration Assay, Activity Assay

    Multiple sequence alignment of M.tb PpiB in biofilm forming bacteria and interaction of PpiB with cyclosporine-A, acarbose and GaNP. a M.tb similarly binds to Gly residue (highlighted in black box), which is conserved within the PpiB binding site of all biofilm-forming bacteria. b , d , f Interaction of cyclosporine-A, acarbose and dimer of atomic gallium with PpiB was tested by molecular docking analysis. b The docked complex of cyclosporine-A and PpiB. The protein (pink) is shown in surface view whereas interacting residues (grey) and ligand (green) is represented in stick model. Hydrogen bond (yellow) is shown in dotted lines. d Interactions of PpiB with acarbose showing various hydrogen and hydrophobic interactions. f The docked complex of dimer of atomic gallium and PpiB. The protein (pink) is shown in surface view whereas interacting residues (green) and ligand (red) is represented in stick model. Hydrogen bond (black) is shown in dotted lines. c , e , g SPR analysis was performed as described in methods. Response units (RU) of the interaction of PpiB with cyclosporine-A ( c ) or acrabose e , or GaNP g from representative experiment are shown

    Journal: NPJ Biofilms and Microbiomes

    Article Title: Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention

    doi: 10.1038/s41522-018-0075-0

    Figure Lengend Snippet: Multiple sequence alignment of M.tb PpiB in biofilm forming bacteria and interaction of PpiB with cyclosporine-A, acarbose and GaNP. a M.tb similarly binds to Gly residue (highlighted in black box), which is conserved within the PpiB binding site of all biofilm-forming bacteria. b , d , f Interaction of cyclosporine-A, acarbose and dimer of atomic gallium with PpiB was tested by molecular docking analysis. b The docked complex of cyclosporine-A and PpiB. The protein (pink) is shown in surface view whereas interacting residues (grey) and ligand (green) is represented in stick model. Hydrogen bond (yellow) is shown in dotted lines. d Interactions of PpiB with acarbose showing various hydrogen and hydrophobic interactions. f The docked complex of dimer of atomic gallium and PpiB. The protein (pink) is shown in surface view whereas interacting residues (green) and ligand (red) is represented in stick model. Hydrogen bond (black) is shown in dotted lines. c , e , g SPR analysis was performed as described in methods. Response units (RU) of the interaction of PpiB with cyclosporine-A ( c ) or acrabose e , or GaNP g from representative experiment are shown

    Article Snippet: Anhydrotetracycline induced Ms_PpiB and Ms_VC cells were cultured in the presence of various concentrations of cyclosporine-A (0, 10, 100, and 1000 µg/ml), acarbose (0, 1, 10, 100, 500, 1000 µg/ml) or GaNP (0, 10, 50, 100, 1000 µg/ml) in sterile flat bottom 96-well microtiter plate (Thermo Scientific, India).

    Techniques: Sequencing, Binding Assay, SPR Assay

    Effect of anti-TB drugs on the survival of M. smegmatis in the presence and absence of cyclosporine-A or acarbose or GaNP. Ms_VC and Ms_PpiB cells were induced with anhydrotetracycline to express ppiase in absence and presence of cyclosporine-A (100 μg/ml) a , d or acarbose (1000 μg/ml) b or GaNP (50 μg/ml) c , e . Cells were incubated in static culture to allow biofilm formation. At the end of 7 days Ms _ VC and Ms_PpiB, cultured in absence of anhydrotetracycline [( )VC tet-, ( ) PpiB tet-] or presence of anhydrotetracycline [( ) VC tet+, ( ) PpiB tet+], were treated either with isoniazid (0, 8, 16, 32, 64 μg/ml) or ethambutol (0, 0.25, 1, 4, 16 μg/ml) and further incubated for 68 h. Susceptibility of M. smegmatis to isoniazid in absence and presence of biofilm was scored by assessing the viability of cells in a 4 h alamar blue assay. Values shown from a representative experiment are means [±s.e.m] of percent cell viability

    Journal: NPJ Biofilms and Microbiomes

    Article Title: Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention

    doi: 10.1038/s41522-018-0075-0

    Figure Lengend Snippet: Effect of anti-TB drugs on the survival of M. smegmatis in the presence and absence of cyclosporine-A or acarbose or GaNP. Ms_VC and Ms_PpiB cells were induced with anhydrotetracycline to express ppiase in absence and presence of cyclosporine-A (100 μg/ml) a , d or acarbose (1000 μg/ml) b or GaNP (50 μg/ml) c , e . Cells were incubated in static culture to allow biofilm formation. At the end of 7 days Ms _ VC and Ms_PpiB, cultured in absence of anhydrotetracycline [( )VC tet-, ( ) PpiB tet-] or presence of anhydrotetracycline [( ) VC tet+, ( ) PpiB tet+], were treated either with isoniazid (0, 8, 16, 32, 64 μg/ml) or ethambutol (0, 0.25, 1, 4, 16 μg/ml) and further incubated for 68 h. Susceptibility of M. smegmatis to isoniazid in absence and presence of biofilm was scored by assessing the viability of cells in a 4 h alamar blue assay. Values shown from a representative experiment are means [±s.e.m] of percent cell viability

    Article Snippet: Anhydrotetracycline induced Ms_PpiB and Ms_VC cells were cultured in the presence of various concentrations of cyclosporine-A (0, 10, 100, and 1000 µg/ml), acarbose (0, 1, 10, 100, 500, 1000 µg/ml) or GaNP (0, 10, 50, 100, 1000 µg/ml) in sterile flat bottom 96-well microtiter plate (Thermo Scientific, India).

    Techniques: Mass Spectrometry, Incubation, Cell Culture, Alamar Blue Assay

    Effect of cyclosporine-A, acarbose or GaNP on induction of biofilm in M. smegmatis (Crystal violet assay). Ms_VC and Ms_PpiB cells were cultured in absence [( )VC tet-, ( ) PpiB tet-] or presence [( ) VC tet+, ( ) PpiB tet+] of anhydrotetracycline, as described in methods. Cells were treated with cyclosporine-A (0, 10, 100, 1000 μg/ml) a or acarbose (0, 1, 10, 100, 500, 1000 μg/ml) b or GaNP (0, 10, 50, 100, 1000 μg/ml) c and incubated for 7 days. At the end point, biofilm was quantified as described in methods. Values shown from a representative experiment are means [±s.e.m] of biofilm formed.* p

    Journal: NPJ Biofilms and Microbiomes

    Article Title: Peptidyl-prolyl isomerase-B is involved in Mycobacterium tuberculosis biofilm formation and a generic target for drug repurposing-based intervention

    doi: 10.1038/s41522-018-0075-0

    Figure Lengend Snippet: Effect of cyclosporine-A, acarbose or GaNP on induction of biofilm in M. smegmatis (Crystal violet assay). Ms_VC and Ms_PpiB cells were cultured in absence [( )VC tet-, ( ) PpiB tet-] or presence [( ) VC tet+, ( ) PpiB tet+] of anhydrotetracycline, as described in methods. Cells were treated with cyclosporine-A (0, 10, 100, 1000 μg/ml) a or acarbose (0, 1, 10, 100, 500, 1000 μg/ml) b or GaNP (0, 10, 50, 100, 1000 μg/ml) c and incubated for 7 days. At the end point, biofilm was quantified as described in methods. Values shown from a representative experiment are means [±s.e.m] of biofilm formed.* p

    Article Snippet: Anhydrotetracycline induced Ms_PpiB and Ms_VC cells were cultured in the presence of various concentrations of cyclosporine-A (0, 10, 100, and 1000 µg/ml), acarbose (0, 1, 10, 100, 500, 1000 µg/ml) or GaNP (0, 10, 50, 100, 1000 µg/ml) in sterile flat bottom 96-well microtiter plate (Thermo Scientific, India).

    Techniques: Crystal Violet Assay, Mass Spectrometry, Cell Culture, Incubation

    BCL9 regulates mRNA levels of calcium wave-associated genes through paraspeckle proteins. a Network of BCL9-interacting proteins identified by Co-IP MS. Each node represents a group of BCL9-interacting proteins with functional relationships. Lines between different nodes represent the “weight” of the protein-protein interaction according to String database (colored) or total peptides in Co-IP assay (black). Groups were clustered by k-means unsupervised classification according to the interacting “weight” among different nodes. b Representative IF showing co-localization of BCL9, NONO, and ILF2 in CRC but not in normal colon epithelial cells. Scale bars: 20 µm (top, left), and 2 µm (inset). c , d SFPQ binding motif in the 3′UTR region of indicated mRNA-encoding genes down-regulated in BCL9- knock out RKO cells. High fold change: Genes whose mRNA levels decreased more than 1.5-fold in BCL9 knockout cells. Low-fold change: others. P values were calculated using χ 2 test, ** P

    Journal: Nature Communications

    Article Title: BCL9 provides multi-cellular communication properties in colorectal cancer by interacting with paraspeckle proteins

    doi: 10.1038/s41467-019-13842-7

    Figure Lengend Snippet: BCL9 regulates mRNA levels of calcium wave-associated genes through paraspeckle proteins. a Network of BCL9-interacting proteins identified by Co-IP MS. Each node represents a group of BCL9-interacting proteins with functional relationships. Lines between different nodes represent the “weight” of the protein-protein interaction according to String database (colored) or total peptides in Co-IP assay (black). Groups were clustered by k-means unsupervised classification according to the interacting “weight” among different nodes. b Representative IF showing co-localization of BCL9, NONO, and ILF2 in CRC but not in normal colon epithelial cells. Scale bars: 20 µm (top, left), and 2 µm (inset). c , d SFPQ binding motif in the 3′UTR region of indicated mRNA-encoding genes down-regulated in BCL9- knock out RKO cells. High fold change: Genes whose mRNA levels decreased more than 1.5-fold in BCL9 knockout cells. Low-fold change: others. P values were calculated using χ 2 test, ** P

    Article Snippet: The membrane was subsequently probed using anti-BCL9 (1:1000 dilution, H00000607-M01, Abnova), NONO (1:1000 dilution, TA504777, Origene), SFPQ (1:1000 dilution, MA1-25325, ThermoFisher), ILF2 (1:5000 dilution, PA5-18718, ThermoFisher), or β-catenin (1:1000 dilution, 610154, BD Transduction Laboratories) antibodies.

    Techniques: Co-Immunoprecipitation Assay, Mass Spectrometry, Functional Assay, Binding Assay, Knock-Out