scholarly journals Immunological Off-Target Effects of microRNA Control Sequences.

2021 ◽  
Author(s):  
Rua Al-Modawi ◽  
Jan Brinchmann ◽  
Tommy Karlsen
Keyword(s):  
Mirna Precursor ◽  
Negative Control ◽  
Correct Interpretation ◽  
Thermo Fisher Scientific ◽  
Target Effect ◽  
Donor Variation ◽  
Negative Controls ◽  
Fisher Scientific ◽  
Target Effects ◽  
Control Sequences

Abstract Immunological off-target effects of RNA and RNAi therapy are a considerable challenge in research and the future of RNA-therapy. Here we investigated some of the hurdles we previously encountered when transfecting mircroRNA (miRNA) control sequences into chondrocytes in an inflammatory model simulating osteoarthritis (OA). We investigated different negative control sequences of different technologies; Pre-miR miRNA Precursor and mirVana from Thermo Fisher Scientific. We used RT-qPCR, western blot analysis and mass spectrometry to asses for the effects of the transfected control sequences.The data did not show a global immunological off-target effect, however a specific off-target effect on IL6 and IL8 was observed. IL6 and IL8 were both upregulated by the negative control from the Pre-miR miRNA Precursor technology (Pre-neg #1), and downregulated by the negative control from the mirVana technology (mirVana-neg). Moreover, the results suggested that the effect on IL6 and IL8 was dependent on both sequence and type of chemical modifications in addition to donor variation. We conclude that negative controls should be selected wisely, and suggest that scientists need to test several controls to ensure correct interpretation of data before drawing any conclusions.

scholarly journals POS0009 THE RELATIONSHIP BETWEEN DIFFERENT IGG AND IGA ANTI-MODIFIED PROTEIN AUTOANTIBODIES IN RHEUMATOID ARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 206.1-207
Author(s):  
C. Grönwall ◽  
L. Liljefors ◽  
H. Bang ◽  
A. Hensvold ◽  
M. Hansson ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Disease Activity ◽  
Comprehensive Evaluation ◽  
Patient Characteristics ◽  
Post Translational Modifications ◽  
Cell Clones ◽  
Thermo Fisher Scientific ◽  
History Of ◽  
The Relationship ◽  
Fisher Scientific

Background:Seropositive rheumatoid arthritis (RA) is characterized by the presence of rheumatoid factor (RF) and anti-citrullinated protein autoantibodies (ACPA) with different fine-specificities. Yet, other serum anti-modified protein autoantibodies (AMPA), e.g. anti-carbamylated (Carb), anti-acetylated (KAc), and anti-malondialdehyde acetaldehyde (MAA) modified protein antibodies, have been described. By using RA patient single-cell derived monoclonal antibodies we have previously shown that individual ACPA clones recognize small distinct citrulline-containing epitopes giving them extensive multireactivity when these epitopes are found in many peptides and proteins. Moreover, certain CCP2+ multireactive ACPA clones bind also to cabamylated and acetylated autoantigens [1].Objectives:To provide a comprehensive evaluation of serum IgG and IgA autoreactivity to different post-translational modifications in RA.Methods:We analyzed 30 different IgG and IgA AMPA reactivities to modified antigens by ELISA and autoantigen arrays, in N=1985 newly diagnosed RA patients and population controls. The study utilized both previously established (i.e IgG and IgA CCP2; IgG ACPA fine-specificities; IgG anti-Carb fibrinogen and Carb FCS; IgG and IgA Cit/Carb/KAc/Orn(Ac)-vimentin), and novel assays (e.g. IgG anti-MAA and IgG anti-acetylated histones). Association with patient characteristics such as smoking and disease activity were explored. The newly developed assays were also evaluated in SLE disease controls and CCP2+ RA-risk individuals without arthritis.Results:Carb and KAc reactivities by different assays were primarily seen in patients also positive for citrulline-reactivity. Modified vimentin (mod-Vim) peptides were used for direct comparison of different AMPA reactivities, revealing that IgA AMPA recognizing mod-Vim was mainly detected in subsets of patients with high IgG anti-Cit-Vim levels and a history of smoking. IgG acetylation reactivity was mainly detected in a subset of patients with Cit and Carb reactivity. Anti-acetylated histone 2B reactivity was RA-specific and associated with high anti-CCP2 IgG levels, multiple ACPA fine-specificities, and smoking. This reactivity was also found to be present in CCP2+ RA-risk individuals without arthritis. Our data further demonstrate that IgG autoreactivity to MAA was increased in RA compared to controls with highest levels in CCP2+ RA, but was not RA-specific, and showed low correlation with other AMPA. Anti-MAA was instead associated with disease activity and was not significantly increased in CCP2+ individuals at risk of RA. Notably, RA patients could be subdivided into four different subsets based on their AMPA IgG and IgA reactivity profiles.Conclusion:We conclude that autoantibodies exhibiting different patterns of ACPA fine-specificities as well as Carb and KAc reactivity are present in RA and may be derived from multireactive B-cell clones. Anti-Carb and anti-KAc could be considered reactivities within the “Cit-umbrella” similar to ACPA fine-specificities, while MAA is distinctly different.References:[1]Sahlström P, Hansson M, Steen J, Amara K, Titcombe PJ, Forsström B, Stålesen R, Israelsson L, Piccoli L, Lundberg K, Klareskog L, Mueller DL, Catrina AI, Skriner K, Malmström V, Grönwall C. Different Hierarchies of Anti-Modified Protein Autoantibody Reactivities in Rheumatoid Arthritis. Arthritis Rheumatol. 2020 Oct;72(10):1643-1657. PMID: 32501655Caroline Grönwall: None declared, Lisa Liljefors: None declared, Holger Bang Employee of: Employee at ORGENTEC Diagnostika GmbH, Aase Hensvold: None declared, Monika Hansson: None declared, Linda Mathsson-Alm Employee of: Employee at Thermo Fisher Scientific, Lena Israelsson: None declared, Anna Svärd: None declared, Cyril CLAVEL: None declared, Elisabet Svenungsson: None declared, Iva Gunnarsson: None declared, Guy Serre: None declared, Saedis Saevarsdottir: None declared, Alf Kastbom: None declared, Lars Alfredsson: None declared, Vivianne Malmström: None declared, Johan Rönnelid: None declared, Anca Catrina: None declared, Karin Lundberg: None declared, Lars Klareskog: None declared

Évaluation du CDx90® (Microgenics Thermo Fisher Scientific) pour le dosage urinaire des drogues

2010 ◽  
Vol 25 (2) ◽  
pp. 118-122
Author(s):  
K. Barrial ◽  
T. Le Bricon ◽  
F. Courtier ◽  
M.-H. Tourvieille ◽  
S. Hilaire ◽  
...  
Keyword(s):  
Thermo Fisher Scientific ◽  
Fisher Scientific

scholarly journals Evaluation of ionic degradation and slot corrosion of metallic brackets by the action of different dentifrices

2013 ◽  
Vol 18 (1) ◽  
pp. 86-93
Author(s):  
Gustavo Antônio Martins Brandão ◽  
Rafael Menezes Simas ◽  
Leandro Moreira de Almeida ◽  
Juliana Melo da Silva ◽  
Marcelo de Castro Meneghim ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Artificial Saliva ◽  
Positive Control ◽  
Negative Control ◽  
Sem Analysis ◽  
Wilcoxon Test ◽  
Surface Polishing ◽  
Aluminium Ion ◽  
Negative Controls

OBJECTIVE: To evaluate the in vitro ionic degradation and slot base corrosion of metallic brackets subjected to brushing with dentifrices, through analysis of chemical composition by Energy Dispersive Spectroscopy (EDS) and qualitative analysis by Scanning Electron Microscopy (SEM). METHODS: Thirty eight brackets were selected and randomly divided into four experimental groups (n = 7). Two groups (n = 5) worked as positive and negative controls. Simulated orthodontic braces were assembled using 0.019 x 0.025-in stainless steel wires and elastomeric rings. The groups were divided according to surface treatment: G1 (Máxima Proteção Anticáries®); G2 (Total 12®); G3 (Sensitive®); G4 (Branqueador®); Positive control (artificial saliva) and Negative control (no treatment). Twenty eight brushing cycles were performed and evaluations were made before (T0) and after (T1) experiment. RESULTS: The Wilcoxon test showed no difference in ionic concentrations of titanium (Ti), chromium (Cr), iron (Fe) and nickel (Ni) between groups. G2 presented significant reduction (p < 0.05) in the concentration of aluminium ion (Al). Groups G3 and G4 presented significant increase (p < 0.05) in the concentration of aluminium ion. The SEM analysis showed increased characteristics indicative of corrosion on groups G2, G3 and G4. CONCLUSION: The EDS analysis revealed that control groups and G1 did not suffer alterations on the chemical composition. G2 presented degradation in the amount of Al ion. G3 and G4 suffered increase in the concentration of Al. The immersion in artificial saliva and the dentifrice Máxima Proteção Anticáries® did not alter the surface polishing. The dentifrices Total 12®, Sensitive® and Branqueador® altered the surface polishing.

slowly growing natural populations. Various approaches have been adopted in order to improve the sensitivity. These have included the use of multiple probes labelled with a single fluor (Lee et al. 1993); or labelled with multiple fluors (Trebesius et al. 1994) and enzyme-linked probes or detection systems that allow signal amplification (Lebaron et al. 1997, Schonhuber et al. 1999). The latter indirect approach not only has the potential for signal amplification, but may also be used in natural samples showing high levels of autofluorescence. Any thorough identification method has to include positive and negative controls. False-positive results may either be caused by cells emitting autofluorescence upon excitation or by nonspecific binding of the probe to nontarget cells. Samples should therefore be checked for autofluorescence before hybridization and a negative control with a fluorescent oligonucleotide not complementary to rRNA has to be applied to check for sequence-independent nonspecific binding. Such non-specific binding may be due to interaction of the dye compound of the probe with hydrophobic cell components. Failures to detect cells containing target sequences (false-negatives) may originate from cells with either low cellular ribosome content or limited permeability of the cell periphery for the fluorescent probe (Manz et al. 1992). With the rapidly expanding database of 16S rRNA sequences, the problem of probe specificity has become more apparent and the design of probes is becoming increasingly difficult. These problems are also applicable to PCR and other oligonucleotide-dependent techniques. The problem of probe specificity may be overcome by using multiple specific oligonucleotide probes targeting different sites on the rRNA molecule and labelled with different fluorochromes. While a single oligonucleotide target sequence may be found in a number of related taxa, the probability that target sites for three designed oligonucleotides are found in a nontarget organism is, however, much reduced.

2003 ◽  
pp. 232-232
Keyword(s):  
Signal Amplification ◽  
Specific Binding ◽  
Natural Populations ◽  
Negative Control ◽  
Target Sequence ◽  
Cell Periphery ◽  
Nonspecific Binding ◽  
Detection Systems ◽  
Cell Components ◽  
Negative Controls

scholarly journals Immune Repertoire Analysis of Multiple Myeloma Research Samples Using NGS Characterization of Multiple B Cell Receptors in a Single Reaction

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1881-1881
Author(s):  
Geoffrey Lowman ◽  
Landon Pastushok ◽  
Karen Mochoruk ◽  
Wayne Hill ◽  
Michelle Toro ◽  
...  
Keyword(s):  
B Cell ◽  
Light Chain ◽  
Somatic Hypermutation ◽  
Cell Receptor ◽  
Clonal Lineage ◽  
Repertoire Analysis ◽  
Targeted Ngs ◽  
Thermo Fisher Scientific ◽  
Fisher Scientific ◽  
Single Reaction

Abstract Introduction B cell repertoire analysis by next-generation sequencing (NGS) is at the forefront of leukemia and lymphoma research. Some advantages provided by NGS-based techniques include a lower limit-of-detection and simpler paths to standardization compared to other methods. Importantly, in research of post-germinal B cell disorders, such as multiple myeloma (MM), NGS methods allow for the study of clonal lineage based on somatic hypermuation patterns. Current targeted NGS assays require multiple libraries to survey each B cell receptor chain (IGH, IgK, IgL), and this fact is highlighted when initial clonality detection fails due to mutations under primer binding sites. This issue can be especially true in MM which has a high rate of SHM. To address these issues, we have developed an assay for B cell analysis, based on Ion AmpliSeq™ technology, which enables efficient detection of IGH, IgK, and IgL chain rearrangements in a single reaction. Methods The B cell pan-clonality panel (Oncomine™ BCR Pan-Clonality Assay) targets the framework 3 (FR3) portion of the variable gene and the joining gene region of heavy- and light-chain loci (IGH, IgK, IgL) for all alleles found within the IMGT database, enabling readout of the complementary-determining region 3 (CDR3) sequence of each immunoglobulin chain. To maximize sensitivity, we included primers to amplify IgK loci rearrangements involving Kappa deletion element and the constant region intron. To evaluate assay performance, we conducted reproducibility studies and clonality assessment using gDNA from a total of 45 MM research samples. All MM cases examined in this work were confirmed clonal previously by light chain restriction via flow cytometry or IHC/ISH in tissue sections - 16 of the 45 MM samples were identified as lambda light chain restricted. For comparison, a small cohort of 12 B-ALL samples were also included in the study. Sequencing and repertoire analyses were performed using the Ion GeneStudio S5 System and Ion Reporter 5.16 analysis software. Results Clonality assessment of MM clinical research samples show an 93% overall positive detection rate by an assay which combines the IGH, IgK, and IgL chains in a single reaction using published guidelines for clonality assignment. Thirty-four of 45 samples show positive detection of an IGH rearrangement, while 41 of 45 showed positive detection of at least one light chain receptor. In total, 42 of 45 samples were deemed clonal by the single tube assay based on detection for one or more receptor. Clonality results for this sample set are well correlated with orthogonal data from flow, IHC/ISH, or alternate NGS assays. A clonal lambda light chain was identified in 14 of 16 samples determined to be lambda restricted by flow cytometry. In two of the lambda restricted samples only a clonal lambda rearrangement was identified, showing the benefit of including primers targeting both the kappa and lambda light chains in a pan-clonality NGS assay. Both the MM and B-ALL cohorts were evaluated for biased IGHV gene usage. IGHV3-11 was observed in 5 of 45 MM and 5 of 12 B-ALL samples. IGHV4-34, typically linked to autoreactive antibodies and underrepresented in germinal center and memory B-cells, was nonetheless found in 5 of 45 MM samples surveyed. Estimates of somatic hypermutation rates were calculated using the BCR pan-clonality assay. Most MM samples, as expected, contained some somatic hypermutation with 6 of 45 samples showing greater than 10% mutation rates. Automated lineage analysis, based on somatic hypermuation signatures within each sample, identified 8 of 45 MM samples which contained 5 or more clones in the primary clonal lineage, with one case containing a lineage with 23 clones. Two MM samples showed no somatic hypermutation as measured using the FR3 primers contained in the BCR pan-clonality assay. These samples were also evaluated using an FR1-J targeted NGS assay, which confirmed relatively low mutation rates for these MM samples at 0.44% and 1.3%, respectively. Conclusions These results demonstrate the utility of a novel assay for combined repertoire analysis of B cell receptor heavy and light chains in a single library preparation reaction. We expect this assay to simplify laboratory workflows and including analysis tools such as automated somatic hypermutation rate calculation and clonal lineage identification may open new paths for research in lymphoid cell disorders. For research use only. Disclosures Lowman: Thermo Fisher Scientific: Current Employment. Toro: Thermo Fisher Scientific: Current Employment. Pickle: Thermo Fisher Scientific: Current Employment. Ostresh: Thermo Fisher Scientific: Current Employment. Sarda: Thermo Fisher Scientific: Current Employment. Yang: Thermo Fisher Scientific: Current Employment.

scholarly journals Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

2017 ◽  
Author(s):  
Lovorka Stojic ◽  
Aaron Lun ◽  
Jasmin Mangei ◽  
Patrice Mascalchi ◽  
Valentina Quarantotti ◽  
...  
Keyword(s):  
Antisense Oligonucleotides ◽  
Noncoding Rna ◽  
Specific Activity ◽  
Transcriptional Analysis ◽  
Clonal Variation ◽  
Loss Of Function ◽  
Negative Controls ◽  
Whole Transcriptome ◽  
Target Effects

ABSTRACTLoss-of-function (LOF) methods, such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing, provide unparalleled power for studying the biological function of genes of interest. When coupled with transcriptomic analyses, LOF methods allow researchers to dissect networks of transcriptional regulation. However, a major concern is nonspecific targeting, which involves depletion of transcripts other than those intended. The off-target effects of each of these common LOF methods have yet to be compared at the whole-transcriptome level. Here, we systematically and experimentally compared non-specific activity of RNAi, antisense oligonucleotides and CRISPR interference (CRISPRi). All three methods yielded non-negligible offtarget effects in gene expression, with CRISPRi exhibiting clonal variation in the transcriptional profile. As an illustrative example, we evaluated the performance of each method for deciphering the role of a long noncoding RNA (lncRNA) with unknown function. Although all LOF methods reduced expression of the candidate lncRNA, each method yielded different sets of differentially expressed genes upon knockdown as well as a different cellular phenotype. Therefore, to definitively confirm the functional role of a transcriptional regulator, we recommend the simultaneous use of at least two different LOF methods and the inclusion of multiple, specifically designed negative controls.

scholarly journals Effect of Sodium Carboxymethylcellulose and Sorbitol on Anti-Peptic Ulcer Activity of Anredera cordifolia Leaves Extract

2019 ◽  
Vol 4 (1) ◽  
pp. 16
Author(s):  
Maria Ulfah ◽  
Revika Rachmaniar ◽  
Egi MR. Sudrajat ◽  
Rida W. Fadla ◽  
Hary S. Pinuji
Keyword(s):  
Body Weight ◽  
Peptic Ulcer ◽  
Normal Control ◽  
Wistar Rat ◽  
Positive Control ◽  
Negative Control ◽  
Sodium Carboxymethylcellulose ◽  
Freeze Dried ◽  
Male Wistar Rats ◽  
Negative Controls

Anredera cordifolia or binahong is one of the Indonesian medicinal plants that is used to treat peptic ulcer. The purpose of this study was to evaluate the effect of the addition of sodium carboxymethylcellulose (CMC) and sorbitol on anti-peptic ulcer activity of A. cordifolia leaves extracts in male Wistar rats. The plants were extracted using decoction method and freeze dried. Three liquid formulas were used i.e., i) a combination of sodium CMC and sorbitol; ii) only sorbitol; iii) extract only. The rats were divided into 6 groups, i.e., positive control (sucralfate 35 mg/kg body weight); negative control (80% ethanol); normal control; and 3 formulas. After the administration of the liquid formula, all groups, except normal control, were given 80% ethanol (l5 ml/kg body weight) to induce peptic ulcer. Antipeptic ulcer activity was evaluated using direct observation on rats gastric mucosa, and histopathology assessment. The result showed that the strongest anti-peptic ulcer  was shown by sorbitol only (96.95% inhibition),  followed by the combination of sodium CMC and sorbitol (92.68% inhibition). The formula which only contained extract showed only  31.70% inhibition.  Statistical analysis showed significant differences between formula 1 and 2 with negative controls. In conclusion, A. cordifolia leaves extract with the addition of sorbitol showed the strongest anti-peptic ulcer activity. Keyword: Anredera cordifolia, peptic ulcer, suspense, Wistar rat.

Abstract 2819: Cross-correlation Analysis of Myocardial Velocity is Superior to Conventional Time-to-Peak Parameters for Quantifying Left Ventricular Dyssynchrony

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Brandon K Fornwalt ◽  
Takeshi Arita ◽  
Mohit Bhasin ◽  
George Voulgaris ◽  
John D Merlino ◽  
...  
Keyword(s):  
Cross Correlation ◽  
Positive Control ◽  
Negative Control ◽  
Left Ventricular ◽  
Left Ventricular Dyssynchrony ◽  
Control Group ◽  
Time To Peak ◽  
Data Points ◽  
Negative Controls ◽  
Threshold Line

Background- A recent study showed that the most commonly used Tissue Doppler imaging (TDI) parameters to diagnose left ventricular dyssynchrony agree only 50% of the time. Most of these parameters require calculation of the ``time-to-peak” myocardial velocity. This ``time-to-peak” based analysis utilizes only one of >100 data points collected per heart cycle. Methods- We developed and tested a new dyssynchrony parameter, cross-correlation delay (XCD), that utilizes all velocity data points from 3 consecutive beats (~420 points). We hypothesized that XCD would be superior to existing methods at diagnosing dyssynchrony. We tested XCD on 11 members of a positive control group (echocardiographic responders to cardiac resynchronization therapy) and 12 members of a negative control group (normal echocardiogram and 12-lead ECG). We compared XCD to septal-to-lateral delay in time-to-peak (SLD), maximum difference in the basal 2- or 4-chamber times-to-peak (MaxDiff) and standard deviation of the 12 basal and mid-wall times-to-peak (Ts-SD). Results- An XCD threshold of 31ms discriminated between positive and negative controls with 100% sensitivity and specificity (Figure 1 ). SLD, MaxDiff and Ts-SD showed sensitivities of 36, 55 and 100% and specificities of 50, 42 and 50%, respectively. ROC analysis showed XCD and Ts-SD were superior to SLD and MaxDiff in discriminating between positive and negative controls (p<0.01). XCD was the only parameter which decreased after resynchronization in the positive controls (from 160±88ms to 69±61ms, p=0.003). Conclusion- XCD is superior to existing parameters at discriminating patients with LV dyssynchrony from those with normal function. Figure 1. XCD shows the greatest discrimination between positive and negative controls. Dyssynchrony values for each positive control are shown as x’s and values for each negative control are shown as circels. Different dyssynchrony parameters are shown in each subplot (A-D). Threshold values to diagnose dyssynchrony are plotted as horizontal lines in each figure. Note that x’s above the threshold line represent false positives while circles below the threshold line represent false negatives.

scholarly journals Essential oils as tick repellents on clothing

2019 ◽  
Vol 79 (2) ◽  
pp. 209-219 ◽  
Author(s):  
Oliver Soutar ◽  
Freya Cohen ◽  
Richard Wall
Keyword(s):  
Essential Oils ◽  
No Reduction ◽  
Positive Control ◽  
Negative Control ◽  
Tick Abundance ◽  
Spearmint Oil ◽  
Oregano Oil ◽  
Negative Controls ◽  
Tick Repellents

Abstract Essential oils show promise as natural alternatives to synthetic tick repellents, but few studies have investigated their repellent efficacy in vivo or under field conditions. Here, blanket-drags and standardised walks were employed to evaluate tick acquisition by 1 m2 cotton blankets or cotton trousers, respectively, in woodland edge habitats of known high tick abundance. Blankets and trousers had been treated with one of 5% oregano, rosemary, spearmint or thyme oils, 20% DEET (N,N-diethyl-3-methylbenzamide) (positive control) or ethanol excipient-only (negative control). The number of ticks present on the blankets or trousers differed significantly between treatments: spearmint oil treatments resulted in significantly fewer ticks than the negative controls for both blankets and trousers and significantly fewer ticks were present on the oregano oil treated blankets. For ticks that did attach to the trousers, the rate of drop off within 3 min was significantly higher for trousers treated with spearmint oil or thyme oil than ethanol, oregano oil and rosemary oil. No reduction in repellence was detected over a 24 h period between treatment and testing. The results suggest that 5% oregano and spearmint oils exhibit potential as natural clothing repellents, with an effective equivalence to 20% DEET.

Sign in / Sign up

Export Citation Format

Share Document