Quality control for plant metabolomics: reporting MSI-compliant studies

The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study – the metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.     

Quantitative quality assurance in a community hospital pediatric intensive care unit.

Unbiased, objective evaluations of quality of care are preferred over subjective evaluations. We observed 681 admissions to a pediatric intensive care unit of a community hospital from 1989 through 1990 for outcomes and physiologic profiles of the patients on the admission day using the Pediatric Risk of Mortality score to assess severity of illness. Mortality adjusted for severity of illness was compared with that predicted from a pediatric intensive care unit of a tertiary medical center: 32.6 deaths were predicted based on the physiologic profiles, and 23 occurred. The number of outcomes and their distribution according to mortality risk indicated close agreement between observed and predicted results. Thus, a quality-assurance technique developed in tertiary care centers can be used to indicate a comparable level of care in a community hospital.     

Multiple category-lot quality assurance sampling: a new classification system with application to schistosomiasis control

Background

Originally a binary classifier, Lot Quality Assurance Sampling (LQAS) has proven to be a useful tool for classification of the prevalence of Schistosoma mansoni into multiple categories (≤10%, >10 and <50%, ≥50%), and semi-curtailed sampling has been shown to effectively reduce the number of observations needed to reach a decision. To date the statistical underpinnings for Multiple Category-LQAS (MC-LQAS) have not received full treatment. We explore the analytical properties of MC-LQAS, and validate its use for the classification of S. mansoni prevalence in multiple settings in East Africa.

Methodology

We outline MC-LQAS design principles and formulae for operating characteristic curves. In addition, we derive the average sample number for MC-LQAS when utilizing semi-curtailed sampling and introduce curtailed sampling in this setting. We also assess the performance of MC-LQAS designs with maximum sample sizes of n = 15 and n = 25 via a weighted kappa-statistic using S. mansoni data collected in 388 schools from four studies in East Africa.

Principle Findings

Overall performance of MC-LQAS classification was high (kappa-statistic of 0.87). In three of the studies, the kappa-statistic for a design with n = 15 was greater than 0.75. In the fourth study, where these designs performed poorly (kappa-statistic less than 0.50), the majority of observations fell in regions where potential error is known to be high. Employment of semi-curtailed and curtailed sampling further reduced the sample size by as many as 0.5 and 3.5 observations per school, respectively, without increasing classification error.

Conclusion/Significance

This work provides the needed analytics to understand the properties of MC-LQAS for assessing the prevalance of S. mansoni and shows that in most settings a sample size of 15 children provides a reliable classification of schools.     

Quality control: ER-associated degradation: Protein quality control and beyond

Even with the assistance of many cellular factors, a significant fraction of newly synthesized proteins ends up misfolded. Cells evolved protein quality control systems to ensure that these potentially toxic species are detected and eliminated. The best characterized of these pathways, the ER-associated protein degradation (ERAD), monitors the folding of membrane and secretory proteins whose biogenesis takes place in the endoplasmic reticulum (ER). There is also increasing evidence that ERAD controls other ER-related functions through regulated degradation of certain folded ER proteins, further highlighting the role of ERAD in cellular homeostasis.Newly synthesized membrane and secreted proteins enter the ER in an unfolded state through a protein-conducting channel named the translocon (Rapoport, 2007). In the ER, a myriad of chaperones and modifying enzymes assist their membrane integration and folding. In many cases folding involves post-translational modifications, such as glycosylation or disulfide bond formation (Braakman and Hebert, 2013). At this stage many proteins are also assembled into multisubunit complexes with defined stoichiometries. As newly synthesized proteins reach a native conformation, they leave the ER to perform their function elsewhere; either along the secretory pathway or outside of the cell.Despite all the resources dedicated to protein folding, a significant fraction of newly synthesized polypeptides entering the ER fails to acquire a native conformation (Hartl and Hayer-Hartl, 2009). The degree of misfolding of these proteins varies considerably and can have several causes such as mutations, substoichiometric amounts of a binding partner, or merely a shortage of chaperone availability. In most cases, the misfolded molecules are retained in the ER and eventually become substrates of the ER-associated protein degradation (ERAD), a collection of quality-control mechanisms that clears the ER from these potentially harmful species. Inactivation of ERAD results in the accumulation of misfolded proteins in the lumen and membrane of the ER, a condition known as ER stress that is common to several diseases (Walter and Ron, 2011). For this reason, ERAD plays a key role in ER homeostasis across eukaryotes. Genetic ablation of a number of ERAD components leads to embryonic lethality in mice, also highlighting the importance of this process in cellular and organismal homeostasis (Yagishita et al., 2005; Francisco et al., 2010; Eura et al., 2012). Whether this essential function of ERAD during mouse development is due to its role in the degradation of misfolded proteins remains to be determined.Certain folded, perfectly active proteins are also targeted by ERAD. However, their degradation is highly regulated and only occurs in the presence of a specific signal. The best-characterized regulated substrate is the 3-hydroxy-3-methylglutaryl acetyl-coenzyme-A reductase (HMGR), a key enzyme in sterol biosynthesis (Gil et al., 1985; Hampton et al., 1996; Bays et al., 2001a; Song et al., 2005). Both in yeast and in mammals, HMGR degradation by ERAD is part of a feedback inhibition system critical for sterol homeostasis. Interestingly, another enzyme of the sterol biosynthetic pathway, squalene monooxygenase (Erg1 in yeast and SQLE in mammals), was recently identified as a regulated ERAD substrate (Foresti et al., 2013). The degradation of Erg1/SQLE by ERAD is again part of a feedback inhibition system to prevent the accumulation of intermediate sterol metabolites, which are toxic for cells (Foresti et al., 2013). Recent evidence shows that regulation of the synthesis of sterols and other sterol-derived metabolites by ERAD is also present in plants (Doblas et al., 2013; Pollier et al., 2013). This evolutionarily conserved role of ERAD in sterol regulation might have been one of its primordial functions.The ERAD machinery is also exploited by certain viruses to degrade host proteins thereby escaping immune surveillance. Well characterized examples are the degradation of newly synthesized major histocompatibility complex class I (MHC I) heavy chain (Wiertz et al., 1996a) or CD4 molecules by the human cytomegalovirus or the immunodeficiency virus (HIV; Fujita et al., 1997; Schubert et al., 1998), respectively. Moreover, some bacterial toxins, such as cholera, and viruses, like simian virus 40 (SV40), travel to the ER retrogradely through the secretory pathway. At the ER these toxins and viruses exploit ERAD components to reach the cytosol, where ultimately they will act (Tsai et al., 2001; Schelhaas et al., 2007; Bernardi et al., 2008).Finally, ERAD components are also involved in the turnover of several soluble proteins in the cytoplasm and the nucleus of cells (Swanson et al., 2001; Ravid et al., 2006; Yamasaki et al., 2007). Most of these cases, however, involve only a subset of the ERAD steps and components. In sum, although a complete repertoire of substrates is not available, it is clear that misfolded proteins are not the exclusive clients of ERAD.

ERAD, linking ER quality control to cytoplasmic protein degradation

The earliest evidence for protein quality control at the ER came from observations that unassembled subunits of the T cell receptor were rapidly degraded in the cells (Lippincott-Schwartz et al., 1988). This degradation occurred independently of lysosomal proteases, leading to the proposal that the ER itself would house some uncharacterized proteolytic activity toward misfolded proteins. Then a landmark study in yeast showed that the degradation of a short-lived misfolded ER membrane protein was blocked in cells lacking Ubc6, a component of the ubiquitin conjugation machinery (Sommer and Jentsch, 1993). The ubiquitin system mediates the covalent attachment of ubiquitin, a small 76–amino acid protein, to target proteins in the cytoplasm by the sequential action of activating (E1), conjugating (E2), and ligase (E3) enzymes (Pickart, 2001). Ubiquitin-modified proteins are then recognized and degraded by the proteasome. The involvement of the ubiquitin–proteasome system in ER protein quality control was confirmed by studies on the degradation of mutant and wild-type cystic fibrosis transmembrane conductance regulator (CFTR), a large membrane protein with a complicated folding process (Jensen et al., 1995; Ward et al., 1995). Inhibition of proteasome function led to accumulation of CFTR molecules, and interestingly, a significant fraction of these was detected as ubiquitin conjugates (Jensen et al., 1995; Ward et al., 1995). Soon after, it became clear that a similar mechanism could also account for the degradation of luminal misfolded proteins such as CPY*, a mutant version of the yeast vacuolar carboxypeptidase Y and a prototype ERAD substrate (Hiller et al., 1996). Together, these papers demonstrated that aberrant proteins in the lumen and membrane of the ER are degraded in the cytoplasm where the components of the ubiquitin–proteasome system reside.

Ubiquitin ligase complexes: The hubs in ERAD

Subsequent genetic and biochemical studies, primarily in budding yeast but also in mammalian cells, identified many ERAD components and led to a general understanding of the organization of the pathway. An important realization was that the “one-size-fits-all” model does not apply to ERAD and that this pathway encompasses multiple branches with distinct specificity for different classes of misfolded proteins (Taxis et al., 2003; Vashist and Ng, 2004; Carvalho et al., 2006; Bernasconi et al., 2010; Christianson et al., 2012). However, irrespective of the branch, the same sequence of events leads to the degradation of all ERAD substrates (Fig. 1 A). The first step is the recognition of a substrate in the crowded ER environment. Then the substrate is transported across the ER lipid bilayer back into the cytoplasm, a step known as retrotranslocation. On the cytosolic side of the ER membrane, the substrate is ubiquitinated by a membrane-associated ubiquitin ligase (or E3 ligase). Subsequently, the ubiquitinated substrate is extracted from the membrane in an ATP-dependent manner and released in the cytoplasm for degradation by the proteasome. The execution of these steps is coordinated by a membrane-embedded protein complex named after the E3 ligase at its core. The canonical E3 ligases involved in ERAD are themselves multispanning membrane proteins, in which the RING (really interesting new gene) domain responsible for the ligase activity is in the cytoplasm. These E3 ligase complexes are best characterized in yeast (Fig. 1 B and Swanson et al., 2001) and Hrd1 (Bordallo et al., 1998; Bays et al., 2001a) assemble into the Doa10 and the Hrd1 complexes, respectively, each responsible for the degradation of a class of ERAD substrates (Carvalho et al., 2006).Open in a separate windowFigure 1.The different steps and branches in ERAD. (A) The events defining the ERAD of a generic luminal substrate with a misfolded domain (red star). Substrate recognition, retrotranslocation, and ubiquitination are coordinated by a membrane-embedded E3 ligase complex. Ubiquitin is depicted as small circles. (B) The E3 ligase complexes involved in ERAD in S. cerevisiae and their substrate specificities. ER proteins with a misfolded domain in the cytoplasm (ERAD-C substrates) are degraded via the Doa10 complex. Proteins with luminal (ERAD-L) or intramembrane (ERAD-M) misfolded domains are degraded via the Hrd1 complex. Misfolded domains on proteins are indicated by a red star. The Cdc48 cofactors Npl4 and Ufd1 are depicted as N and U, respectively.

Table 1.

Components of the yeast E3 ligase complexes and their mammalian counterparts

Protocols for the assurance of microarray data quality and process control

Microarrays represent a powerful technology that provides the ability to simultaneously measure the expression of thousands of genes. However, it is a multi-step process with numerous potential sources of variation that can compromise data analysis and interpretation if left uncontrolled, necessitating the development of quality control protocols to ensure assay consistency and high-quality data. In response to emerging standards, such as the minimum information about a microarray experiment standard, tools are required to ascertain the quality and reproducibility of results within and across studies. To this end, an intralaboratory quality control protocol for two color, spotted microarrays was developed using cDNA microarrays from in vivo and in vitro dose-response and time-course studies. The protocol combines: (i) diagnostic plots monitoring the degree of feature saturation, global feature and background intensities, and feature misalignments with (ii) plots monitoring the intensity distributions within arrays with (iii) a support vector machine (SVM) model. The protocol is applicable to any laboratory with sufficient datasets to establish historical high- and low-quality data.     

Quality leadership and quality control

Different quality control rules detect different analytical errors with varying levels of efficiency depending on the type of error present, its prevalence and the number of observations. The efficiency of a rule can be gauged by inspection of a power function graph. Control rules are only part of a process and not an end in itself; just as important are the trouble-shooting systems employed when a failure occurs. 'Average of patient normals' may develop as a usual adjunct to conventional quality control serum based programmes. Acceptable error can be based on various criteria; biological variation is probably the most sensible. Once determined, acceptable error can be used as limits in quality control rule systems.

A key aspect of an organisation is leadership, which links the various components of the quality system. Leadership is difficult to characterise but its key aspects include trust, setting an example, developing staff and critically setting the vision for the organisation. Organisations also have internal characteristics such as the degree of formalisation, centralisation, and complexity. Medical organisations can have internal tensions because of the dichotomy between the bureaucratic and the shadow medical structures.

     

Quality assurance in cytopathology. Recommendations and ongoing quality assurance activities of the American Society of Clinical Pathologists

The recommendations and activities of the American Society of Clinical Pathologists (ASCP) pertaining to quality assurance in cytopathology are reviewed. To assure the early detection of cervical cancer, the ASCP recommends that all women who are, or have been, sexually active should have an annual Papanicolaou smear examination, the reasons for which are discussed. To assure the optimal quality in the evaluation of these smears, the ASCP recommends that the screening should be performed (1) in an accredited laboratory by certified cytotechnologists, (2) for whom realistic workloads have been established, (3) under the supervision of a pathologist adequately trained in cytology, (4) who will maintain an ongoing quality assurance program. In addition, (5) Papanicolaou smear evaluations should be available to all patients at a reasonable cost and (6) the financial incentives for the performance of low-quality screening should be eliminated. The society's quality assurance activities discussed include the Check Sample program, self-assessment examinations, meetings and publications; planned additions to this arena include a challenge exam and proficiency survey mechanisms.     

100% rapid rescreening for quality assurance in a quality control program in a public health cytologic laboratory

OBJECTIVE: To verij5 the efficacy of the quality control (QC) program in a cytologic laboratwy with a rapid rescreening (RR) protocol. STUDY DESIGN: RR, according to the Turret RR method, of all samples initially screened as negative at the Laboratory of Cytology, Adolfo Lutz Institute, was performed. The slides were reviewed for 60 seconds. Suspect smears were fully checked by 2 reviewers to determine the final diagnoses. A total of 2954 sequential cytologic results were considered in this study. Of the 2954, 2568 (86.9%) were considered initially negative according to our internal QC, and these cases underwent RR. Also, 10% were randomly selected from these negative cases for full reviewing. The internal QC in our laboratory includes review of cases selected according to clinical and cytomorphologic criteria. RESULTS: Among the 2954 total cases, QC detected 386 (13%) atypias with final diagnoses reported according to The Bethesda System 2001 as follows: 82 (2.18%) low grade squamous intraepithelial lesions (LSILs), 35 (1.18%) high grade squamous intraepithelial lesions (HSILs), 2 (0.06%) squamous cell carcinomas, 105 (3.5%) atypical cells of undetermined significance (ASC-US), 4 (0.12%) atypical endocervical cells (AECs) and 158 (5.3%) unsatisfactory samples. RR of 2568 smears initially considered negative selected 194 (7.5%) slides. Of the 194, 146 (75.3%) were negative, 28 (14.4%) ASC-US, 5 (2.6%) AEC, 1 (0.5%) LSIL and 14 (7.2%) unsatisfactory. Full review of a 10% random fraction of the 2568 cases interpreted as negative did not detect lesions but did detect 5 (1.95%) unsatisfactory samples. CONCLUSION: Internal QC used in our laboratory based on clinical and cytomorphologic criteria to select cases for review proved to be an efficient method of detecting HSIL and cervical cancer. The consensus basis of this program strongly limits the false positive and false negative rates and also provides subjects with continuing education. One hundred percent RR is more efficient than 10% full reviewing in detecting cervical abnormalities.     

Overview of a quality assurance/quality control compliance program consistent with FDA regulations and policies for somatic cell and gene therapies: a four year experience

Somatic cell and gene therapy involve the application of biological technologies to an individual patient through the use of living cells which provide a therapeutic benefit (Aliski, 1991). Various forms of cellular and gene therapies are being developed and evaluated in an increasing number of clinical trials for congential and acquired disorders. The potential and progress of these therapeutic applications have resulted in an increasing effort by the Food and Drug Administration (FDA) to develop the regulatory framework under which these therapeutic approaches would insure safety and efficacy, the primary mandate of the FDA.Over five years ago Cellcor began to define the parameters, specifications, and conditions relevant to a Quality Assurance/Quality Control (QA/QC) program that has evolved to insure safety and maximize the efficacy of applications of the company'sex vivo technology, autolymphocyte therapy. Autolymphocyte therapy is an outpatient form of somatic cell immunotherapy based upon the infusion of T cells that have been activatedex vivo using a combination of previously generated autologous cytokines and an anti-CD3 monoclonal antibody.We have been able to demonstrate the feasibility for the safe, controlled, and consistent preparation and delivery of a cellular therapy by application of relevant GMP regulations. This presentation reviews aspects of this program and chronicles our experience which at present amounts to over 4400 infusions for over 700 patients. This program provides a high degree of assurance that a cellular therapy program can be carried out in a multisite mode involving hundreds of patients through the strict adherence to cGMP as set forth in existing regulations. It would be prudent that developers of cellular andex vivo gene therapies establish a similar cell processing and QA/QC infrastructure at an early developmental stage to optimize safety and reproducibility and facilitate regulatory review.     

Patterns of community structure in fishes: summary and overview

Synopsis This paper constitutes a review of topics and controversies that arose during and since the Cornell mini-symposium. A table of publications on fish community types not covered during the mini-symposium is presented, followed by discussions of three aspects of community structure in fishes. First, the general topic of temporal structure in fish communities is discussed, with emphasis on diel activity patterns, twilight changeover phenomena and the influence of predators on temporal behavior. This is followed by a section on the importance of ontogenetic changes in trophic, spatial and social activities of fish in a variety of communities. Finally, the topic of stochastic and deterministic processes in coral reef fish communities is reviewed, and methods of testing hypotheses and resolving differences of opinion are suggested. This section is concluded with a discussion of the possible influence of ecological interactions between larval fishes on reef fish community structure.This paper forms part of the proceedings of a mini-symposium convened at Cornell University, Ithaca, N.Y., 18–19 May 1976, entitled Patterns of Community Structure in Fishes (G. S. Helfman, ed.).     

Quality control and assurance from the development to the production of biopharmaceuticals.

Consumer and patient safety have become the prerequisites for (bio)pharmaceutical product development, production and marketing. The ability to provide an effective, pure, safe product is the primary factor determining the product's success. However, with an ever-increasing number of national and international regulations, 'quality assurance' has acquired a threatening ring for many project managers. Many think that ensuring and improving quality is expensive, but regulations aid public acceptance. Good manufacturing practice can be developed into a business asset and need not be seen as merely a regulatory hurdle.     

The use of latex beads in external quality assurance and internal quality control for routine semen analysis

The usefulness of latex beads of defined concentration was assessed as a substitute for sperm in the performance of External Quality Assurance (EQA) and Internal Quality Control (IQC) of semen analysis. Within the EQA programme, mean±SEM bias (%) was significantly reduced in 2007 compared to 2002 for both specialist (6.0%±5.4% vs. 55.0%±5.9%) and non-specialist (18.4%±5.9% vs. 90.9%±13.4%) laboratories (both p<0.0001), indicating improved accuracy over time. Within the IQC programme, the beads were used in the appraisal of two scientists, one experienced and one inexperienced, against a known standard. Beads were also used to calibrate eleven counting chambers, resulting in one old chamber being discarded due to its poor performance. The present study has shown that the use of a defined concentration of beads is an excellent adjunct to IQC and EQA programmes enabling the performance of both people and equipment to be assessed in an objective manner.     

Quality assurance issues and PACS

Quality assessment and assurance is a growing concern in all areas of health care. The concern is fueled by a body of evidence that indicates that quality of care is not optimal, and in many instances, is unacceptably low. Although different standards for quality have been proposed, health outcome is the ultimate standard, since improving health is the goal of the health care system. The effects of PACS on health outcome are not known. A PAC system has the potential to improve quality, especially if it makes the diagnostic process more efficient, but evidence that such improvement actually occurs is so far lacking.     

Data quality assurance and quality control measures in large multicenter stroke trials: the African-American Antiplatelet Stroke Prevention Study experience

Data quality assurance and quality control are critical to the effective conduct of a clinical trial. In the present commentary, we discuss our experience in a large, multicenter stroke trial. In addition to standard data quality control techniques, we have developed novel methods to enhance the entire process. Central to our methods is the use of clinical monitors who are trained in the techniques of data monitoring.     

Rapid pre-screening: a validated quality assurance measure in cervical cytology

We present the results of 3 years' experience of rapid pre-screening in cervical cytology. In our laboratory we rapidly pre-screen all smears. The performance of each primary screener can be assessed. In addition, the relative sensitivity and specificity of each rapid pre-screener can itself be continuously monitored using the final report as a yardstick. In our laboratory individual sensitivity of rapid pre-screening for the detection of high-grade abnormalities was in the range of 44-90% with an overall laboratory sensitivity of 69%. Specificity was in the range of 94-99% with an overall laboratory specificity of 98%. Rapid pre-screening allows checking of the checkers and pathologists and tends to promote uniformity in the assessment of smear adequacy. This form of continuous quality assurance is practical, convenient and acceptable to staff.     

Phytoplankton food quality control of planktonic food web processes

We developed a mechanistic model of nutrient, phytoplankton, zooplankton and fish interactions to test the effects of phytoplankton food quality for herbivorous zooplankton on planktonic food web processes. When phytoplankton food quality is high strong trophic cascades suppress phytoplankton biomass, the zooplankton can withstand intense zooplanktivory, and energy is efficiently transferred through the food web sustaining higher trophic level production. Low food quality results in trophic decoupling at the plant-animal interface, with phytoplankton biomass determined primarily by nutrient availability, zooplankton easily eliminated by fish predation, and poor energy transfer through the food web. At a given nutrient availability, food quality and zooplanktivory interact to determine zooplankton biomass which in turn determines algal biomass. High food quality resulted in intense zooplankton grazing which favored fast-growing phytoplankton taxa, whereas fish predation favored slow-growing phytoplankton. These results suggest algal food quality for herbivorous zooplankton can strongly influence the nature of aquatic food web dynamics, and can have profound effects on water quality and fisheries production. Handling editor: D. Hamilton