Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

How to avoid pitfalls in antibody use.

ABSTRACT: Antibody use is ubiquitous in the biomedical sciences. However, determining best research practices has not been trivial. Many commercially available antibodies and antibody-conjugates are poorly characterized and lack proper validation. Uncritical application of such useless tools has contributed to the reproducibility crisis in biomedical research. Despite early initiatives such as MIAPAR or PSI-PAR, a best practice guideline for antibody characterization is still not in prospect. Here, we analyze 24 antibody-related databases and compare their content with regard to validation aspects and coverage. We also provide a flowchart for end-users with all necessary steps to facilitate finding and choosing specific and sensitive antibodies for their experiments. Based on a growing demand for better and standardized validation procedures and characterization guidelines for antibody molecules we have summarized our findings in a five-point plan. We intend to keep the discussion alive and hope that properly used antibodies will remain as central to biomedicine as they are today.

SUBMITTER: Pauly D

PROVIDER: S-EPMC4722690 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

How to avoid pitfalls in antibody use.

Pauly Diana D Hanack Katja K

F1000Research 20150907

Antibody use is ubiquitous in the biomedical sciences. However, determining best research practices has not been trivial. Many commercially available antibodies and antibody-conjugates are poorly characterized and lack proper validation. Uncritical application of such useless tools has contributed to the reproducibility crisis in biomedical research. Despite early initiatives such as MIAPAR or PSI-PAR, a best practice guideline for antibody characterization is still not in prospect. Here, we ana ...[more]

PMID: 26834988

Similar Datasets

Quantification of Choriocapillaris with Phansalkar Local Thresholding: Pitfalls to Avoid.

Project description:PurposeTo demonstrate the proper use of the Phansalkar local thresholding method (Phansalkar method) in choriocapillaris (CC) quantification with optical coherence tomography angiography (OCTA).DesignRetrospective, observational case series.MethodsSwept source OCTA imaging was performed using 3×3 mm and 6×6 mm scanning patterns. The CC slab was extracted after semiautomatic segmentation of the retinal pigment epithelium/Bruch membrane complex. Retinal projection artifacts were removed before further analysis, and CC OCTA images from drusen eyes were compensated using a previously published strategy. CC flow deficits (FDs) were segmented with 2 previously published algorithms: the fuzzy C-means approach (FCM method) and the Phansalkar method. With the Phansalkar method, different parameters were tested and a local window radius of 1 to 15 pixels was used. FD density, mean FD size, and FD number were calculated for comparison.ResultsSix normal eyes from 6 subjects and 6 eyes with drusen secondary to age-related macular degeneration from 6 subjects were analyzed. With both 3×3 mm and 6×6 mm scans from all eyes, the FD metrics were highly dependent on the selection of the local window radius when using the Phansalkar method. Larger window radii resulted in higher FD density values. FD number increased with the increase in the window radius but then decreased, with an inflection point at about 1 to 2 intercapillary distances. Mean FD size decreased then increased with increasing window radii.ConclusionsMultiple parameters, especially the local window radius, should be optimized before using the Phansalkar method for the quantification of CC FDs with OCTA imaging. It is recommended that the proper use of the Phansalkar method should include the selection of the window radius that is related to the expected intercapillary distance in normal eyes.

| S-EPMC7214221 | biostudies-literature

Pitfalls in compressed sensing reconstruction and how to avoid them.

Project description:Multidimensional NMR can provide unmatched spectral resolution, which is crucial when dealing with samples of biological macromolecules. The resolution, however, comes at the high price of long experimental time. Non-uniform sampling (NUS) of the evolution time domain allows to suppress this limitation by sampling only a small fraction of the data, but requires sophisticated algorithms to reconstruct omitted data points. A significant group of such algorithms known as compressed sensing (CS) is based on the assumption of sparsity of a reconstructed spectrum. Several papers on the application of CS in multidimensional NMR have been published in the last years, and the developed methods have been implemented in most spectral processing software. However, the publications rarely show the cases when NUS reconstruction does not work perfectly or explain how to solve the problem. On the other hand, every-day users of NUS develop their rules-of-thumb, which help to set up the processing in an optimal way, but often without a deeper insight. In this paper, we discuss several sources of problems faced in CS reconstructions: low sampling level, missassumption of spectral sparsity, wrong stopping criterion and attempts to extrapolate the signal too much. As an appendix, we provide MATLAB codes of several CS algorithms used in NMR. We hope that this work will explain the mechanism of NUS reconstructions and help readers to set up acquisition and processing parameters. Also, we believe that it might be helpful for algorithm developers.

| S-EPMC5504175 | biostudies-literature

Potential Pitfalls in Wastewater Phosphorus Analysis and How to Avoid Them.

Project description:Due to the increasing adoption of nutrient discharge regulations, many research groups are stepping into new territory with phosphorus (P) measurements. Accurate reporting of P concentrations in effluent from novel wastewater treatment technologies is critical for protecting both environmental and human health. Analysis of P in wastewater is prone to pitfalls because of the (1) variety of chemical forms of P in wastewater (orthophosphate, condensed P, and organic P), (2) availability of different chemical assays for measuring different P forms, and (3) different conventions in the units for reporting P. Here, we present a case study highlighting how these pitfalls affect analysis and interpretation of P measurements. We show that, when used appropriately, commercially-available kits are indeed accurate tools for evaluating reactive P and total P concentrations. For both standard solutions and real wastewater, we systematically remove steps from the total P protocol to show how protocol deviations affect the results. While standard solutions are important for validating analytical methods, commercially-available wastewater standard solutions only contain P as orthophosphate (reactive P). We therefore demonstrate options for making a mixed-P standard solution containing acid-hydrolyzable and/or organic P compounds that can be used to validate both reactive P and total P assays.

| S-EPMC8168049 | biostudies-literature

Pitfalls in quantifying exploration in reward-based motor learning and how to avoid them.

Project description:When learning a movement based on binary success information, one is more variable following failure than following success. Theoretically, the additional variability post-failure might reflect exploration of possibilities to obtain success. When average behavior is changing (as in learning), variability can be estimated from differences between subsequent movements. Can one estimate exploration reliably from such trial-to-trial changes when studying reward-based motor learning? To answer this question, we tried to reconstruct the exploration underlying learning as described by four existing reward-based motor learning models. We simulated learning for various learner and task characteristics. If we simply determined the additional change post-failure, estimates of exploration were sensitive to learner and task characteristics. We identified two pitfalls in quantifying exploration based on trial-to-trial changes. Firstly, performance-dependent feedback can cause correlated samples of motor noise and exploration on successful trials, which biases exploration estimates. Secondly, the trial relative to which trial-to-trial change is calculated may also contain exploration, which causes underestimation. As a solution, we developed the additional trial-to-trial change (ATTC) method. By moving the reference trial one trial back and subtracting trial-to-trial changes following specific sequences of trial outcomes, exploration can be estimated reliably for the three models that explore based on the outcome of only the previous trial. Since ATTC estimates are based on a selection of trial sequences, this method requires many trials. In conclusion, if exploration is a binary function of previous trial outcome, the ATTC method allows for a model-free quantification of exploration.

| S-EPMC8382626 | biostudies-literature

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

Project description:The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.

| S-EPMC4080831 | biostudies-literature

Mandrills use olfaction to socially avoid parasitized conspecifics.

Project description:The evolutionary transition from a solitary to a social lifestyle entails an elevated parasite cost because the social proximity associated with group living favors parasite transmission. Despite this cost, sociality is widespread in a large range of taxonomic groups. In this context, hosts would be expected to have evolved behavioral mechanisms to reduce the risk of parasite infection. Few empirical studies have focused on the influence of pathogen-mediated selection on the evolution of antiparasitic behavior in wild vertebrates. We report an adaptive functional relationship between parasitism and social behavior in mandrills, associated with evidence that they are able to gauge parasite status of their group members. Using long-term observations, controlled experiments, and chemical analyses, we show that (i) wild mandrills avoid grooming conspecifics infected with orofecally transmitted parasites; (ii) mandrills receive significantly more grooming after treatment that targets these parasites; (iii) parasitism influences the host's fecal odors; and (iv) mandrills selectively avoid fecal material from parasitized conspecifics. These behavioral adaptations reveal that selecting safe social partners may help primates to cope with parasite-mediated costs of sociality and that "behavioral immunity" plays a crucial role in the coevolutionary dynamics between hosts and their parasites.

| S-EPMC5384805 | biostudies-literature

Vine tendrils use contact chemoreception to avoid conspecific leaves.

Project description:Movement and growth habit of climbing plants have attracted attention since the time of Charles Darwin; however, there are no reports on whether plants can choose suitable hosts or avoid unsuitable ones based on chemoreception. Here, I show that the tendrils of Cayratia japonica (Vitaceae) appear to avoid conspecific leaves using contact chemoreception for oxalates, which are highly concentrated in C. japonica leaves. The coiling experiments show that C. japonica has a flexible plastic response to avoid coiling around conspecific leaves. The coiling response is negatively correlated with the oxalate content in the contacted leaves. Experiments using laboratory chemicals indicate that the tendrils avoid oxalate-coated plastic sticks. These results indicate that the tendrils of C. japonica avoid coiling around a conspecific leaf based on contact chemoreception for oxalate compounds. The tendrils of climbing plants may function as a chemoreceptor system to detect the chemical cues of a contacted plant.

| S-EPMC5360923 | biostudies-literature

Intranasal Immunization of Mice to Avoid Interference of Maternal Antibody against H5N1 Infection.

Project description:Maternally-derived antibodies (MDAs) can protect offspring against influenza virus infection but may also inhibit active immune responses. To overcome MDA- mediated inhibition, active immunization of offspring with an inactivated H5N1 whole-virion vaccine under the influence of MDAs was explored in mice. Female mice were vaccinated twice via the intraperitoneal (IP) or intranasal (IN) route with the vaccine prior to mating. One week after birth, the offspring were immunized twice via the IP or IN route with the same vaccine and then challenged with a lethal dose of a highly homologous virus strain. The results showed that, no matter which immunization route (IP or IN) was used for mothers, the presence of MDAs severely interfered with the active immune response of the offspring when the offspring were immunized via the IP route. Only via the IN immunization route did the offspring overcome the MDA interference. These results suggest that intranasal immunization could be a suitable inoculation route for offspring to overcome MDA interference in the defense against highly pathogenic H5N1 virus infection. This study may provide references for human and animal vaccination to overcome MDA-induced inhibition.

| S-EPMC4900595 | biostudies-literature

Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

Project description:BackgroundCommunity assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates.AimsThis paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate.ResultsIt can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

| S-EPMC8763042 | biostudies-literature

Computational docking of antibody-antigen complexes, opportunities and pitfalls illustrated by influenza hemagglutinin.

Project description:Antibodies play an increasingly important role in both basic research and the pharmaceutical industry. Since their efficiency depends, in ultimate analysis, on their atomic interactions with an antigen, studying such interactions is important to understand how they function and, in the long run, to design new molecules with desired properties. Computational docking, the process of predicting the conformation of a complex from its separated components, is emerging as a fast and affordable technique for the structural characterization of antibody-antigen complexes. In this manuscript, we first describe the different computational strategies for the modeling of antibodies and docking of their complexes, and then predict the binding of two antibodies to the stalk region of influenza hemagglutinin, an important pharmaceutical target. The purpose is two-fold: on a general note, we want to illustrate the advantages and pitfalls of computational docking with a practical example, using different approaches and comparing the results to known experimental structures. On a more specific note, we want to assess if docking can be successful in characterizing the binding to the same influenza epitope of other antibodies with unknown structure, which has practical relevance for pharmaceutical and biological research. The paper clearly shows that some of the computational docking predictions can be very accurate, but the algorithm often fails to discriminate them from inaccurate solutions. It is of paramount importance, therefore, to use rapidly obtained experimental data to validate the computational results.

| S-EPMC3039950 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data