Journal: ACS applied materials & interfaces

Article Title: Electrochemical quantification of glycated and non-glycated human serum albumin in synthetic urine

doi: 10.1021/acsami.8b16071

Figure Lengend Snippet: Preparation of the biosensor for measurements. (a) Electrical contacts to the prepared devices are made with copper tape, platinum foil (as the counter electrode) and alligator pins. (b) Measurements were performed using a PalmSens3 analyzer controlled by PS-Trace 4.8. Data was processed with GNU Octave, Igor Pro, and OriginLab Pro 8.

Article Snippet: The potential was scanned in PBS (pH 7.4) from −0.6 to −0.8 V with a step potential of 5 mV, an amplitude of 25 mV, and a frequency of 20 Hz, and a baseline correction of the obtained voltammograms was performed using OriginLab Pro 8 software ( ).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Overcoming Antimicrobial Resistance in Bacteria Using Bioactive Magnetic Nanoparticles and Pulsed Electromagnetic Fields

doi: 10.3389/fmicb.2017.02678

Figure Lengend Snippet: Applied magnetic field protocols. The pulses have been measured using a calibrated loop sensor (VGTU, Vilnius, Lithuania), a DPO4034 oscilloscope (Tektronix, Beaverton, OR, United States), and a Gaussmeter 475DSP (Lakeshore, Carson, CA, United States), post-processed in OriginPro Software (OriginLab, Northampton, MA, United States).

Article Snippet: The data were post-processed in OriginPro Software (OriginLab, Northampton, MA, United States).

Techniques: Software

Journal: PLoS ONE

Article Title: Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains

doi: 10.1371/journal.pone.0131142

Figure Lengend Snippet: Effect of the PDZ domain upon ΔN-HtrA3 proteolytic activity. (A) Rates of cleavage of the peptide Ala(Mca)IRRVSYSF-ANB-NH 2 (5 μM) by ΔN-HtrA3, ΔN-HtrA3-ΔPDZ, and ΔN-HtrA3S at increasing enzyme concentrations at 30°C. (B) Concentration dependence of the rate of peptide cleavage by ΔN-HtrA3, ΔN-HtrA3-ΔPDZ and ΔN-HtrA3S (50 nM) at 30°C. The data were fitted to the Michaelis-Menten equation using GraphPad Prism 5. (C) The temperature dependence of ΔN-HtrA3 activity, assayed with saturating amount of peptide (5 μM). (D) Temperature dependence of ΔN-HtrA3 activity, assayed with β-casein. The insets in C and D show Arrhenius plots of the same data. The data were fitted by linear regression using OriginPro 9.1 software. ΔN-HtrA3 concentrations were calculated for monomers. Error bars are averages +/ SD ( n = 3).

Article Snippet: The data were fitted by linear regression using OriginPro 9.1 software (OriginLab Corp., USA, www.originlab.com ).

Techniques: Activity Assay, Concentration Assay, Software

Journal: The Journal of Biological Chemistry

Article Title: Structure and Function of the Bacterial Heterodimeric ABC Transporter CydDC

doi: 10.1074/jbc.M114.590414

Figure Lengend Snippet: ATPase activity of purified CydDC (peak 2). a , reaction time courses for the ATPase reaction catalyzed by the peak 2 gel filtration fraction measured in the presence of 5 m m GSH or various non-thiol reductants (fitted lines for the non-thiol reductants (except sodium dithionite) not shown for clarity). Dose-response curves for the ATPase activity of C-His 6 -CydDC ( Fig. 3 a , peak 2 ) in 0.02% DDM with cysteine/GSH ( b ), hemin (in the presence or absence of 5 m m GSH) ( c ), and hemin/PPIX (in the presence or absence of 5 m m GSH) ( d ). The response curves shown for hemin in d are derived from the full dose-response curves in c to facilitate the comparison with PPIX datasets. Curve fitting through the thiol/hemin datasets in b , c , and d used the logistic dose-response function of the OriginPro 7 software. c , the fitting to each response curve dataset was performed separately against two subdatasets, each encompassing data points in the rising ( solid line ) and the falling ( dashed line ) parts of the response curve. Each of the data points represents the mean ± S.E. of multiple ( n ≥ 3) protein preparations produced from independent membrane preparations. TCEP , tris(2-carboxyethyl)phosphine.

Article Snippet: Non-linear curve fitting was performed using either SigmaPlot (Systat Software Inc., San Jose, CA) or OriginPro 7 (OriginLab, Northampton, MA).

Techniques: Activity Assay, Purification, Filtration, Derivative Assay, Software, Produced

Journal: PLoS ONE

Article Title: High-Throughput Screening (HTS) and Hit Validation to Identify Small Molecule Inhibitors with Activity against NS3/4A proteases from Multiple Hepatitis C Virus Genotypes

doi: 10.1371/journal.pone.0075144

Figure Lengend Snippet: IC 50 value comparisons of two confirmed hit compounds. Bar graphs are shown with IC 50 values of two identified compounds against NS3/4As from four HCV genotypes, genotypes 1a (GT1a), 1b (GT1b), 2a (GT2a), and 4d (GT4d), and five mutants from genotype 1b. IC 50 determination was done in triplicate with a total of 32 positive and 32 negative controls in a plate. IC 50 values were calculated by fitting the data to the three parameter Hill equation with OriginPro 8.5 (See Methods). Bars that reached the top represent IC 50 values of over 100 µM (no inhibitory effect).

Article Snippet: The IC50 values were calculated by fitting with the Hill ), with OriginPro 8.5 (OriginLab, Inc.) where y is percent inhibition, x is inhibitor concentration, n is the slope of the concentration–response curve (Hill slope), and Vmax (1) The enzyme omission assay was done by exactly the same method as IC50 determination, but without the NS3/4A enzyme in order to test for fluorescence signal interference by tested compounds.

Techniques:

Journal: Toxins

Article Title: Peptide Mimics of the Ribosomal P Stalk Inhibit the Activity of Ricin A Chain by Preventing Ribosome Binding

doi: 10.3390/toxins10090371

Figure Lengend Snippet: Inhibition of depurination activity of RTA by P11. The depurination levels were determined by qRT-PCR. ( a ) Yeast ribosomes were used at 60 nM and RTA was used at 1.0 nM. ( b ) Rat liver ribosomes were used at 60 nM and RTA was used at 0.2 nM. Different concentrations of P11 and RTA were mixed first and the reaction was started by adding ribosomes. The reaction was incubated at the room temperature for 5 min and was stopped by adding 2×RNA extraction buffer. The RNA was purified and the depurination levels were determined by qRT-PCR. The depurination level of the reaction without toxin was set as 100%. The depurination levels were calculated and plotted as percent of no toxin control. Experiments were conducted four to six times and the data were fit with the Michaelis–Menten equation using Origin Pro 9.1. IC 50 : the half maximal inhibitory concentration. I max : maximal inhibition.

Article Snippet: The IC50 values were obtained by fitting the inhibition curves with the Michaelis–Menten equation using the Origin Pro 9.1 software (OriginLab, Northampton, MA, USA).

Techniques: Inhibition, Activity Assay, Quantitative RT-PCR, Incubation, Purification, Concentration Assay

Journal: Pigment cell & melanoma research

Article Title: Oculocutaneous Albinism Type 1: Link between Mutations, Tyrosinase Conformational Stability, and Enzymatic Activity

doi: 10.1111/pcmr.12546

Figure Lengend Snippet: Urea-induced equilibrium unfolding/refolding of hTyrC tr and OCA1B-related mutants Intrinsic tryptophan fluorescence was measured using an excitation wavelength of 285 nm. Emission spectra were recorded in the range between 300 and 400 nm. Proteins (10 μM) were in 10 mM phosphate buffer, pH 7.4 with 0–8 M urea. For refolding, proteins were dialyzed against 10 mM phosphate buffer, pH 7.4 at 4°C for 24 h. Unfolding and refolding curves were measured as a 360/320 nm ratio and indicated by black and green points, respectively. To visualize the unfolding/refolding the experimental points were fitted with a Boltzmann function using OriginPro 2015 as indicated by black and green lines for unfolding and refolding, respectively.

Article Snippet: The experimental curves were fitted with a Boltzmann function using OriginPro 2015 (Origin Lab Corporation, MA).

Techniques: Fluorescence

Journal: Scientific Reports

Article Title: Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions

doi: 10.1038/s41598-020-69197-3

Figure Lengend Snippet: Cysteine-rich D2L5 extracellular loops in LCa v 3 T-type channels regulate the Ca 2+ block of the Na + current and relative Ca 2+ current passage through the physiological range of Ca 2+ concentrations. Data are represented as mean ± SEM, with statistical comparisons shown in Supplementary Tables S8 and S9 . Sample replicate current tracings are shown in Fig. 5 . ( A ) Increasing extracellular [Ca 2+ ] in presence of 60 mM extracellular [Na + ] illustrates typical U-shape dependence as Ca 2+ effectively competes with Na + ions in the pore and passes effectively at physiological mM levels in human Ca v 3 channels. ( B ) Snail D2L5 extracellular loops regulate an intermediate (LCa V 3–12b/12bΔcys) to steep (LCa V 3–12a/12aΔcys) monotonic decline of peak currents with increasing Ca 2+ concentrations, reflecting the D2L5 extracellular loop’s role in the regulation of the relative size of contributing Na + and Ca 2+ currents. ( C ) Graph illustrating the weakened capacity of 10 µM external Ca 2+ to block the inward Na + current through snail LCa v 3 channels especially in its Δ cys D2L5 extracellular loop mutants. ( D ) Graph illustrating the weakened capacity of snail LCa v 3 channels, especially its Δ cys D2L5 extracellular loop mutants to pass Ca 2+ currents at physiological levels of [Ca 2+ ] (from 10 µM to 10 mM). Graphs illustrated in ( C , D ) contain mean ± SEM with replicates indicated as grey diamonds. Data contained in this figure were analyzed and illustrated using OriginPro 2018 (64-bit) SR1 b9.5.1.195. Data to generate graphs were compared in a parametric one-way ANOVA with statistical significance evaluated in a Turkey post hoc analyses. Data are significant (p

Article Snippet: Statistical analysesNumerical values in electrophysiological experiments were compared using a parametric one-way ANOVA within OriginPro 2018 (64-bit) SR1 b9.5.1.195. (OriginLabs).

Techniques: Blocking Assay

Journal: Scientific Reports

Article Title: Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions

doi: 10.1038/s41598-020-69197-3

Figure Lengend Snippet: Neutralization of the negatively-charged “calcium beacon” residue in Cav3.2 channels generates high Na + current passing T-type channels. ( A ) Side view and ( B ) top view of human Ca v 3.1 channel (PDB: 6kzp , 3.1 Å resolution (Zhao et al. 18 ), illustrating the opposing DI–DIII and DII–DIV pore loops alone (s5-P-s6), plus DI s1–s2 loop which contains a cysteine bonded to a cysteine in DII L5 (s5-P) loop in Ca v 3.1. Unique extracellular loops (purple colored lines, sequence above) in DII L5 (s5-P) between F891–D902 and DIV L6 (P-s6) between D1791–Y1798 of Cav3.1 are positioned in invertebrate Cav3 channels. Regions F891–D902 and D1791–Y1798 in Cav3.1 are unresolved in the Cav3.1 structure, indicating that these extracellular loop regions are likely highly flexible in Cav3.1. F891 and D902 are within one amino acid of pore selectivity filter residues (E923 and D924) critical for calcium selectivity. It is modelled that the extracellular loop between cysteines (C1054–C1075) in exon 12a of LCa v 3 in position between F891–D902 in Ca v 3.1, brings positively-charged amino acids in proximity of D924, a key aspartate residue omni-present in identified calcium (Ca v 1, Ca v 2 and Ca v 3) channels to date. ( C ) Charge neutralization (D975N) of the “calcium beacon” in Cav3.2T-type channels generates high sodium current passing channels ( D , sample currents; E , graph), revealed as the 6.48 ± 0.98, n = 11 fold increase in peak currents when 135 mM external Na + replacing equimolar impermeant NMDG + in the presence of 2 mM external Ca 2+ . Graph includes mean ± SEM with replicates (n) illustrated with grey diamonds. Large fold increases in sodium current passing channels can similarly be generated in Cav3.2 channels in replacement of D2L5 extracellular loops (Cav3.2-12a) or D2L5/D4L6 extracellular loop pairs (Cav3.2-12a/D4L6) (see Fig. 10 ). A potential mechanism for the greater Na in LCav3 channels is in the charge neutralization of the calcium beacon, by the juxta-positioning of positively-charged residues within the D2L5 extracellular loop contained within exon 12a. PDB files in Fig. 7a,b are illustrated using PyMOL Molecular Graphics System, Version 2.3, Schrödinger, LLC, https://pymol.org/2/ . Data in Fig. 8 c,d were analyzed and illustrated using OriginPro 2018 (64-bit) SR1 b9.5.1.195.

Article Snippet: Statistical analysesNumerical values in electrophysiological experiments were compared using a parametric one-way ANOVA within OriginPro 2018 (64-bit) SR1 b9.5.1.195. (OriginLabs).

Techniques: Neutralization, Sequencing, Generated

Journal: Scientific Reports

Article Title: Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions

doi: 10.1038/s41598-020-69197-3

Figure Lengend Snippet: Bi-ionic reversal potentials experiments quantifying the relative monovalent and divalent ion permeation through Ca v 3 T-type channels by means of measuring the monovalent ion efflux (with 100 mM internal Li + or Na + or K + or Cs + solutions) relative to Ca 2+ influx (with 4 mM Ca 2+ external solution). Comparisons are made for human Ca v 3 channels, snail LCa v 3 with exons 12a or 12b and LCa V 3–Δcys mutants where cysteines replace alanines in exon 12. Graphs in ( B ) and ( C ) contain mean ± SEM. with replicates illustrated as grey diamonds. ( A ) Current voltage relationships, with highlights of the currents crossing near the reversal potential (inset). Note the scale of the Y-axis is extended for snail LCa v 3 channels reflecting the greater monovalent ion permeation compared to human Ca v 3 channels. ( B ) Shifts in reversal potential reflect a relative permeability (P) change reflected in a PCa/Px ratio, where x is the monovalent ion, Li + or Na + or K + or Cs + . Data to generate bar graphs were compared in a parametric one-way ANOVA with statistical significance evaluated in a Turkey post hoc test. Data contained in this figure were analyzed and illustrated using OriginPro 2018 (64-bit) SR1 b9.5.1.195. See Supplementary Tables S2 and S3 for table of mean ± SEM and results of ANOVA analyses, respectively. Data are significant (p

Article Snippet: Statistical analysesNumerical values in electrophysiological experiments were compared using a parametric one-way ANOVA within OriginPro 2018 (64-bit) SR1 b9.5.1.195. (OriginLabs).

Techniques: Permeability

Journal: Scientific Reports

Article Title: Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions

doi: 10.1038/s41598-020-69197-3

Figure Lengend Snippet: Cysteine replacements with alanines in D2L5 extracellular loops of LCa v 3 channels alter the relative passage of differing divalent cations, Ba 2+ or Sr 2+ relative to Ca 2+ . ( A ) Representative current traces of peak barium (Ba 2+ ) and calcium (Ca 2+ ) currents normalized to the size of peak Ca 2+ currents. Current–voltage relationships of the fold change in peak ( B ) Ba 2+ and ( C ) Sr 2+ current size normalized to peak Ca 2+ current levels. Graphs of the fold change in peak current sizes for ( B ) Ba 2+ and ( C ) Sr 2+ compared to Ca 2+ currents. Graphs in ( B , C ) are illustrated with mean ± SEM with replicates (n) indicated by grey diamonds. Fold change in LCa V 3–12a and LCa V 3–12b T-type channel currents are inverted when cysteines replaces alanines in D2L5 extracellular loops (LCa v 3 Δcys), where Ca 2+ currents are larger instead of smaller than Ba 2+ or Sr 2+ currents. Data contained in this figure were analyzed and illustrated using OriginPro 2018 (64-bit) SR1 b9.5.1.195.

Article Snippet: Statistical analysesNumerical values in electrophysiological experiments were compared using a parametric one-way ANOVA within OriginPro 2018 (64-bit) SR1 b9.5.1.195. (OriginLabs).

Techniques:

Journal: Scientific Reports

Article Title: Unique cysteine-enriched, D2L5 and D4L6 extracellular loops in CaV3 T-type channels alter the passage and block of monovalent and divalent ions

doi: 10.1038/s41598-020-69197-3

Figure Lengend Snippet: High potency of Zn 2+ and Ni 2+ block of Ca v 3.2 channels is conferred onto LCa v 3 channels by replacement of cysteines in D2L5 extracellular loops. ( A , B ) Representative current traces of LCa v 3b channels with and without D2L5 extracellular loop cysteine replacements with alanines, in response to Zn 2+ doses. T-type currents were generated by step depolarizations from − 110 mV to peak voltage (− 40 mV) (left panel). Peak currents per sweep (middle panel) in Ca 2+ containing external solution (Table 1 ). Tau mono-exponential fits of mean inactivation kinetics (right panel). Normalized, overlapping currents illustrating kinetic rate differences (right panel, inset). ( C ) Zn 2+ and ( D ) Ni 2+ blocking effects. Dose response curves (left panel) and box plot of 50% inhibitory concentrations (IC50) (right panel), with human Ca v 3.1, Ca v 3.2 and Ca v 3.3 shown for comparison. Human Ca v 3.x channel response to Zn 2+ taken from 17,18 and human Ca v 3.x response to Ni 2+ taken from 15 , 16 . The graphs in ( C , D ) represent mean ± s.e.m. with replicates illustrated in grey diamonds. IC50 block with Zn 2+ dose16s of wild type channels (LCa V 3–12b/LCa V 3–12a), as well as cysteine mutant pairs (LCa V 3–12b ΔCys/LCa V 3–12b ΔCys) are not statistically significant from each other. Snail LCa v 3 channels possess the weak Zn 2+ and Ni 2+ block of Ca v 3.1 and Ca v 3.3 channels, but are conferred the high potency of Zn 2+ and Ni 2+ block of Ca v 3.2 channels as well as the characteristic Ca v 3.2 behavior with a loss of the property where inactivation kinetics slows with increasing Zn 2+ doses, after alanine replacement of cysteines in D2L5 extracellular loops. Color coding of differing Ca v 3 channels: Ca v 3.1 (light blue), Ca v 3.2 (dark blue), Ca v 3.3 (green), LCa V 3–12b (orange), LCa V 3–12a (red), LCa v 3 Δcys mutants (striped orange or red bars or dotted lines). Data contained in this figure were analyzed and illustrated using OriginPro 2018 (64-bit) SR1 b9.5.1.195.

Article Snippet: Statistical analysesNumerical values in electrophysiological experiments were compared using a parametric one-way ANOVA within OriginPro 2018 (64-bit) SR1 b9.5.1.195. (OriginLabs).

Techniques: Blocking Assay, Generated, Mutagenesis

Journal: Neurobiology of aging

Article Title: Amyloid beta and the longest-lived rodent: the naked mole-rat as a model for natural protection from Alzheimer’s disease

doi: 10.1016/j.neurobiolaging.2013.03.032

Figure Lengend Snippet: Grain analysis data reveal that aggregation properties depend on sequence and incubation conditions. Grain analysis data extracted from 3 fields for both human and NMR Aβ 1–42 examined with AFM OriginPro 8.6 (OriginLab Corp., Northampton,

Article Snippet: Grain analysis data collected from 3 0.49 µm2 or 1 µm2 fields in each case was further examined with OriginPro 8.6 (OriginLab Corp, Northampton, MA).

Techniques: Sequencing, Incubation, Nuclear Magnetic Resonance

Journal: Nature Communications

Article Title: Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

doi: 10.1038/s41467-020-15839-z

Figure Lengend Snippet: Development of highly efficient Ms MDH G11Q variant based on structural comparison between Ms MDH and Cg MDH. a The OAA/malate binding site and b NADH/NAD + binding site of the two crystal structures; Ms MDH (left, green model) and Cg MDH (right, magenta model). The conformation of OAA is obtained from a superimposed structure of Methylobacterium extorquens MDH (PDB code 4ROS). The mobile loop is distinguished by different color schemes of light blue ( Ms MDH) and gray ( Cg MDH). The observed residual differences are indicated by red color. c Site-directed mutagenesis and the relative activities of the Ms MDH and Cg MDH variants in comparison with the activity of Ms MDH ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. Each of the corresponding variants are indicated by the same color scheme and arrow. The Ms MDH A224S variant, which is labeled as ‘Inclusion body’, was expressed insoluble. The Ms MDH G11Q variant is indicated by a green star. d Optimal pH of the Ms MDH G11Q variant ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. The specific activity at pH 10.0 was determined from a single data. e Catalytic performance of the Ms MDH G11Q variant at different pH ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. f kcat , g km , h kcat/km , and i ki values of the Ms MDH G11Q variant at different pH. The ki value of the Ms MDH G11Q variant at pH 9.0 is shown in number because its value is significantly higher than the rest of the ki values. Data f – i are presented as parameters ± standard error. The standard errors from determining the kinetic parameters using OriginPro 2019 software ( n = the number of mean velocity data at specific pH) are shown as bars.

Article Snippet: Based on the plotted kinetic data, the kinetic parameters were determined from non-linear regression analyses based on the modified Briggs-Haldane equation , using OriginPro 2019 software (OriginLab, Northampton, MA, USA).

Techniques: Variant Assay, Binding Assay, Mutagenesis, Activity Assay, Standard Deviation, Labeling, Software

Journal: Nature Communications

Article Title: Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

doi: 10.1038/s41467-020-15839-z

Figure Lengend Snippet: Comparison of MDH activities. a SA biosynthetic pathway in the M. succiniciproducens PALK strain. Deleted genes are indicated as green thunder symbol. Key enzymes in SA production are indicated as red arrows. GLC glucose, PEP phosphoenolpyruvate, GOL glycerol, PYR pyruvate, LAC lactate, ACO acetyl-CoA, ACP acetyl-phosphate, ACT acetate, OAA oxaloacetate, MAL malate, FUM fumarate, SUC succinate, SCO succinyl-CoA, AKG alpha-ketoglutarate, CIT citrate, PCKA phosphoenolpyruvate carboxylase, LDHA lactate dehydrogenase, PTA phosphate acetyltransferase, ACKA acetate kinase, MDH malate dehydrogenase, FUMC fumarate hydratase, FRD fumarate reductase, MQ red menaquinol. b The relative activities of four MDHs from various SA producers, including M. succiniciproducens , C. glutamicum , E. coli , and Y. lipolytica , in comparison with the activity of Ms MDH ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. c Optimal pH of Ms MDH and Cg MDH ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. The specific activities at pH 10.0 were determined from a single data. d Catalytic performances of Ms MDH and Cg MDH at different pH ( n = 3 independent experiments). Data are presented as mean values ± standard deviation. e kcat , f km , g kcat/km , and h ki values of Ms MDH and Cg MDH at different pH. Red and blue lines represent Ms MDH and Cg MDH, respectively. The ki value of Cg MDH at pH 9.0 is shown in number because its value is significantly higher than the rest of the ki values. Data e – h are presented as parameters ± standard error. The standard errors from determining the kinetic parameters using OriginPro 2019 software ( n = the number of mean velocity data at specific pH) are shown as bars.

Article Snippet: Based on the plotted kinetic data, the kinetic parameters were determined from non-linear regression analyses based on the modified Briggs-Haldane equation , using OriginPro 2019 software (OriginLab, Northampton, MA, USA).

Techniques: Activity Assay, Standard Deviation, Software