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A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated, quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist’s experiments, while more than half have even failed to reproduce their own experiments1. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique2,3. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g., DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE4), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common Standards and guidelines for quality assessment and reproducibility5.
In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models7,8, and tools9,10, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research.
This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of Stakeholders including, researchers, imaging scientists11, bioimage analysts, bioimage informatics developers, corporate partners, Funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREPLiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC.
To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
KEY COMPARISON
Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a key comparison, CCQM K55.c, was coordinated by the Bureau International des Poids et Mesures (BIPM) in 2012. Twenty National Measurement Institutes or Designated Institutes and the BIPM participated. Participants were required to assign the mass fraction of valine present as the main component in the comparison sample for CCQM-K55.c. The comparison samples were prepared from analytical grade L-valine purchased from a commercial supplier and used as provided without further treatment or purification.
Valine was selected to be representative of the performance of a laboratory's measurement capability for the purity assignment of organic compounds of low structural complexity [molecular weight range 100300] and high polarity (pKOW > –2).
The KCRV for the valine content of the material was 992.0 mg/g with a combined standard uncertainty of 0.3 mg/g. The key comparison reference value (KCRV) was assigned by combination of KCRVs assigned from participant results for each orthogonal impurity class. The relative expanded uncertainties reported by laboratories having results consistent with the KCRV ranged from 1 mg/g to 6 mg/g when using mass balance based approaches alone, 2 mg/g to 7 mg/g using quantitative 1H NMR (qNMR) based approaches and from 1 mg/g to 2.5 mg/g when a result obtained by a mass balance method was combined with a separate qNMR result.
The material provided several analytical challenges. In addition to the need to identify and quantify various related amino acid impurities including leucine, isoleucine, alanine and a-amino butyrate, care was required to select appropriate conditions for performing Karl Fischer titration assay for water content to avoid bias due to in situ formation of water by self-condensation under the assay conditions. It also proved to be a challenging compound for purity assignment by qNMR techniques.
There was overall excellent agreement between participants in the identification and the quantification of the total and individual related structure impurities, water content, residual solvent and total non-volatile content of the sample. Appropriate technical justifications were developed to rationalise observed discrepancies in the limited cases where methodology differences led to inconsistent results.
The comparison demonstrated that to perform a qNMR purity assignment the selection of appropriate parameters and an understanding of their potential influence on the assigned value is critical for reliable implementation of the method, particularly when one or more of the peaks to be quantified consist of complex multiplet signals.
The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to halophilic environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin and health care applications and is thus produced annually on a scale of tons in an industrial process using H. elongata as producer strain. This paper presents the complete genome sequence of H. elongata (4 061 296 bp) and includes experiments and analysis identifying and characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine degradation and its cyclic connection to ectoine synthesis. The degradation of ectoine (doe) proceeds via hydrolysis of ectoine (DoeA) to Nα-acetyl-L-2,4-diaminobutyric acid, followed by deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was derived that can be used to understand the way H. elongata survives under varying salt stresses and that provides a basis for a model-driven improvement of industrial ectoine production.
TEM Characterization of the Interface Quality of MOVPE Grown Strained InGaAs/GaAs Heterostructures
(1995)
DNA Microarrays, auch als DNA-Chips bekannt, werden verwendet,
um das Vorkommen von Genen bzw. Gentranskripten zu analysieren.
Sie finden breite Anwendung in der Diagnostik, der Genomanalyse
und bei der Erstellung von Genexpressionsprofilen. Vor der Analyse
muß auf Grund der oftmals geringen Menge an Probenmaterial eine
Vervielfältigung der Probe durchgeführt werden, die jedoch leicht zu
Fehlern führt. Im Rahmen dieses Projektes werden zwei experimentelle
Ansätze verfolgt, durch die ohne einen Verlust an Sensitivität
eine Vervielfältigung der Probe vermieden werden kann, 1) das Etablieren
eines RCA-basierten Microarray Assays und 2) die Optimierung
des Assays für die Detektion der Fluoreszenzsignale.
We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSB) and double-strand breaks (DSB), was determined by electrophoresis. The median lethal dose of D1/2 = 1.7 ± 0.3 Gy was found to be much smaller compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of DSB to SSB was found to be (1:12) as compared to 1:88) found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, cosolutes) for an electron energy range which is difficult to probe by standard methods.
In fields involving irradiated aqueous solutions, such as radiotherapy and nuclear waste remediation, it is often unclear whether the principal reactive species are OH° radicals or secondary (low-energy) electrons. This is mostly because both are rapidly attenuated in water. Presently a large part of the evidence for the involvement of low-energy electrons in biological radiation damage is based on 'dry' DNA samples. We demonstrate irradiation of DNA in solution by direct injection of electrons through a 40-nm thin SiO2 membrane, followed by in-situ detection of the DNA damage by a fluorescence-based method. Corresponding Monte Carlo simulations show that the spatial distribution of ionizing events in water with respect to the membrane is controlled by the electron impact energy. By immobilizing DNA to the solution side of the membrane, and because dynamics and reaction ranges of OH° radicals and low-energy electrons are dramatically different, it is possible to tune into the OH° radical or into the electron 'reaction modes' by simply changing the electron impact energy. Such experiments have the potential to provide important information on the radio-sensitivity at a level of a single biomolecule and to contribute to the development of new dosage concepts.
We report surface plasmon resonance (spr) and confocal fluorescence results concerning the interaction of a gene-5-protein (g5p) with single-stranded DNA oligonucleotides (dT25) tethered to a gold surface. The spr data show that a highly stable g5pssDNA complex is readily formed on a gold surface with koff = 1.7 × 10-3 s-1. The extent of the complexion indicated involvement of the cooperative proteinprotein interactions within the binding to DNA. In the experiments where dT25 coexist with g5p in the solution, the fluorescence data show that g5p also mediates the binding between the non-complementary oligonucleotides in the solution and those immobilised on the surface.
Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a key comparison, CCQM K55.b, was coordinated by the Bureau International des Poids et Mesures (BIPM) in 2010/2011. Nineteen national measurement institutes and the BIPM participated. Participants were required to assign the mass fraction of aldrin present as the main component in the comparison sample for CCQM-K55.b which consisted of technical grade aldrin obtained from the National Measurement Institute Australia that had been subject to serial recrystallization and drying prior to sub-division into the units supplied for the comparison.
Aldrin was selected to be representative of the performance of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molar mass range 300 Da to 500 Da] and low polarity (pKOW < -2) for which related structure impurities can be quantified by capillary gas phase chromatography (GC).
The key comparison reference value (KCRV) for the aldrin content of the material was 950.8 mg/g with a combined standard uncertainty of 0.85 mg/g. The KCRV was assigned by combination of KCRVs assigned by consensus from participant results for each orthogonal impurity class. The relative expanded uncertainties reported by laboratories having results consistent with the KCRV ranged from 0.3% to 0.6% using a mass balance approach and 0.5% to 1% using a qNMR method.
The major analytical challenge posed by the material proved to be the detection and quantification of a significant amount of oligomeric organic material within the sample and most participants relying on a mass balance approach displayed a positive bias relative to the KCRV (overestimation of aldrin content) in excess of 10 mg/g due to not having adequate procedures in place to detect and quantify the non-volatile content–specifically the non-volatile organics content–of the comparison sample.
There was in general excellent agreement between participants in the identification and the quantification of the total and individual related structure impurities, water content and the residual solvent content of the sample.
The comparison demonstrated the utility of 1H NMR as an independent method for quantitative analysis of high purity compounds. In discussion of the participant results it was noted that while several had access to qNMR estimates for the aldrin content that were inconsistent with their mass balance determination they decided to accept the mass balance result and assumed a hidden bias in their NMR data. By contrast, laboratories that placed greater confidence in their qNMR result were able to resolve the discrepancy through additional studies that provided evidence of the presence of non-volatile organic impurity at the requisite level to bring their mass balance and qNMR estimates into agreement.