Standard operating procedures

Is biological research ready for the new wave of data-reporting standards currently under development?     

Effect of pre-analytical handling on haematological variables in minipigs

Pre-analytical handling may be an important determinant of haematological variables, if analysis is delayed. We investigated the effect of anticoagulants, i.e. tripotassium ethylenediamine-tetraacetic acid (EDTA) and citric acid, theophylline, adenosine, dipyridamole (CTAD), storage time (0.5, 1.5, 3.5, 5.5, 7.5, 25.5 and 27.5 h after blood sampling), and storage temperature (5 degrees C and 20 degrees C) on the variation in haemoglobin (HGB), red blood cell count (RBC), haematocrit (HCT), white blood cell count (WBC), and platelet count (PLT) in minipigs. Medians of HGB, RBC, HCT, WBC and PLT were significantly higher in EDTA tubes than in CTAD tubes due to the dilution effect of the anticoagulant. We found a minor significant increase in HCT after 25.5 h in blood stored at 20 degrees C, and at the same time a minor significant increase in WBC in EDTA tubes stored at 20 degrees C. We found a significant decrease in PLT in blood stored at 5 degrees C, especially in EDTA tubes. Minor variations were also observed in HGB and RBC. Our results indicate that PLT should only be measured in tubes placed at room temperature. If HCT or WBC analyses are to be performed on the day after blood sampling, the samples must be stored in a refrigerator until analysis. Our studies underline that time delay before analysis of haematological variables can cause increased variation, and should therefore be limited as far as possible in order to reduce the number of animals needed to make reliable conclusions.     

Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts

Metabolic profiling, metabolomic and metabonomic studies mainly involve the multicomponent analysis of biological fluids, tissue and cell extracts using NMR spectroscopy and/or mass spectrometry (MS). We summarize the main NMR spectroscopic applications in modern metabolic research, and provide detailed protocols for biofluid (urine, serum/plasma) and tissue sample collection and preparation, including the extraction of polar and lipophilic metabolites from tissues. 1H NMR spectroscopic techniques such as standard 1D spectroscopy, relaxation-edited, diffusion-edited and 2D J-resolved pulse sequences are widely used at the analysis stage to monitor different groups of metabolites and are described here. They are often followed by more detailed statistical analysis or additional 2D NMR analysis for biomarker discovery. The standard acquisition time per sample is 4-5 min for a simple 1D spectrum, and both preparation and analysis can be automated to allow application to high-throughput screening for clinical diagnostic and toxicological studies, as well as molecular phenotyping and functional genomics.     

Normalization techniques for PARAFAC modeling of urine metabolomic data

Introduction

One of the body fluids often used in metabolomics studies is urine. The concentrations of metabolites in urine are affected by hydration status of an individual, resulting in dilution differences. This requires therefore normalization of the data to correct for such differences. Two normalization techniques are commonly applied to urine samples prior to their further statistical analysis. First, AUC normalization aims to normalize a group of signals with peaks by standardizing the area under the curve (AUC) within a sample to the median, mean or any other proper representation of the amount of dilution. The second approach uses specific end-product metabolites such as creatinine and all intensities within a sample are expressed relative to the creatinine intensity.

Objectives

Another way of looking at urine metabolomics data is by realizing that the ratios between peak intensities are the information-carrying features. This opens up possibilities to use another class of data analysis techniques designed to deal with such ratios: compositional data analysis. The aim of this paper is to develop PARAFAC modeling of three-way urine metabolomics data in the context of compositional data analysis and compare this with standard normalization techniques.

Methods

In the compositional data analysis approach, special coordinate systems are defined to deal with the ratio problem. In essence, it comes down to using other distance measures than the Euclidian Distance that is used in the conventional analysis of metabolomic data.

Results

We illustrate using this type of approach in combination with three-way methods (i.e. PARAFAC) of a longitudinal urine metabolomics study and two simulations. In both cases, the advantage of the compositional approach is established in terms of improved interpretability of the scores and loadings of the PARAFAC model.

Conclusion

For urine metabolomics studies, we advocate the use of compositional data analysis approaches. They are easy to use, well established and proof to give reliable results.

     

Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders

Functional & Integrative Genomics - Metabolomics has become an important tool for clinical research, especially for analyzing inherited metabolic disorders (IMDs). The purpose of this study was...     

On the assessment of the stability of vitrified cryo-media by differential scanning calorimetry: A new tool for biobanks to derive standard operating procedures for storage,access and transport

When a vitrified sample is heated over the glass transition temperature it may start to devitrify endangering the sample. The ability to estimate the stability of the vitrified state can help in the development of new vitrification media as well as handling procedures. By employing differential scanning calorimetry, we can measure the ice crystallization rate in a vitrified sample and thus study the devitrification kinetics. Using this technique, we have studied samples comprised of PBS with cryoprotective additives (CPA) as dimethylsulfoxide (Me₂SO), ethylene glycol (EG) and mixtures thereof, regarding the dependence of the devitrification kinetics on the CPA concentration. We found that already small concentration changes lead to significant changes in the devitrification times. Changing the CPA concentration by 4 wt% changed the devitrification time with a factor of 342 and 271 for Me₂SO and EG, respectively. Concentration changes in EG/Me₂SO mixtures was found to have a smaller impact on the devitrification kinetics compared to the pure CPA samples. Our data suggest that these significant increases in the devitrification times are primarily due to a relation between nucleation rates and the CPA concentration. Finally, we investigated an established vitrification medium used to preserve human embryonic stem cells. This medium was found to have the poorest glass stability in this study and reflects the tradeoff between stability and biocompatibility. The present work finally provides a tool to evaluate handling and storage procedures when employing vitrification as a cryopreservation method and underlines the importance of these.     

Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data

We explore the utility of p-value weighting for enhancing the power to detect differential metabolites in a two-sample setting. Related gene expression information is used to assign an a priori importance level to each metabolite being tested. We map the gene expression to a metabolite through pathways and then gene expression information is summarized per-pathway using gene set enrichment tests. Through simulation we explore four styles of enrichment tests and four weight functions to convert the gene information into a meaningful p-value weight. We implement the p-value weighting on a prostate cancer metabolomic dataset. Gene expression on matched samples is used to construct the weights. Under certain regulatory conditions, the use of weighted p-values does not inflate the type I error above what we see for the un-weighted tests except in high correlation situations. The power to detect differential metabolites is notably increased in situations with disjoint pathways and shows moderate improvement, relative to the proportion of enriched pathways, when pathway membership overlaps.     

Adaptive strategies for post-renal handling of urine in birds

Birds are a diverse vertebrate class in terms of diet and habitat, but they share several common physiological features, including the use of uric acid as the major nitrogenous waste product and the lack of a urinary bladder. Instead, ureteral urine refluxes from the urodeum into the more proximal coprodeum and portions of the hindgut (colon or rectum and ceca). This presents a potential problem in that hyperosmotic ureteral urine in contact with the permeable epithelia of these tissues would counteract renal osmotic work. This review describes and provides examples of different strategies used by avian species to balance renal and post-renal changes in urine composition. The strategies described include: 1. a "reptilian" mode, with moderate renal concentrating ability, but high rates of post-renal salt and water resorption; 2. the "mammalian" strategy, in which the coprodeum effectively functions like a mammalian urinary bladder, preserving the osmotic concentrating work of the kidney; 3. an interaction strategy, in which post-renal transport processes are hormonally regulated in order to optimize renal function under varying conditions of salt or water stress; 4. the salt gland strategy seen in marine or estuarine birds with functional salt glands, in which post-renal transport mechanisms are used to conserve urinary water and to recycle excess NaCl to the nasal salt glands. Finally, we also describe some features of an as-yet unstudied group of birds, the birds of prey. At least some species in this group are relatively good renal concentrators, and would be predicted to have post-renal mechanisms to preserve this work. This new synthesis illustrates the marked diversity of adaptive mechanisms used by avian species to maintain osmotic homeostasis.     

The development of metabolomic sampling procedures for Pichia pastoris, and baseline metabolome data

Metabolic profiling is increasingly being used to investigate a diverse range of biological questions. Due to the rapid turnover of intracellular metabolites it is important to have reliable, reproducible techniques for sampling and sample treatment. Through the use of non-targeted analytical techniques such as NMR and GC-MS we have performed a comprehensive quantitative investigation of sampling techniques for Pichia pastoris. It was clear that quenching metabolism using solutions based on the standard cold methanol protocol caused some metabolite losses from P. pastoris cells. However, these were at a low level, with the NMR results indicating metabolite increases in the quenching solution below 5% of their intracellular level for 75% of metabolites identified; while the GC-MS results suggest a slightly higher level with increases below 15% of their intracellular values. There were subtle differences between the four quenching solutions investigated but broadly, they all gave similar results. Total culture extraction of cells + broth using high cell density cultures typical of P. pastoris fermentations, was an efficient sampling technique for NMR analysis and provided a gold standard of intracellular metabolite levels; however, salts in the media affected the GC-MS analysis. Furthermore, there was no benefit in including an additional washing step in the quenching process, as the results were essentially identical to those obtained just by a single centrifugation step. We have identified the major high-concentration metabolites found in both the extra- and intracellular locations of P. pastoris cultures by NMR spectroscopy and GC-MS. This has provided us with a baseline metabolome for P. pastoris for future studies. The P. pastoris metabolome is significantly different from that of Saccharomyces cerevisiae, with the most notable difference being the production of high concentrations of arabitol by P. pastoris.     

Standard operating procedure for computing pangenome trees

We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen with emphasis on groups of gene families conserved to various degrees inside the pan-genome. The software is available for free as an R-package.     

Urine stability for metabolomic studies: effects of preparation and storage

Metabolomic studies attempt to identify and profile unique metabolic differences among test populations, which may be correlated with a specific biological stress or pathophysiology. Due to the ease of collection and the metabolite-rich nature of urine, it is frequently used as a bio-fluid for human and animal metabolic studies. High-resolution ¹H-NMR is an analytical tool used to qualitatively and quantitatively identify metabolites in urine. Urine samples were collected from healthy male and female subjects and prepared: raw, following centrifugation, filtration, or the addition of the bacteriostatic preservative sodium azide and analyzed by NMR. In addition, these samples were stored at room temperature (22 °C), in a refrigerator (4 °C), or in a deep-freeze (−80 °C). Samples were analyzed by NMR every week for a month and changes in concentrations of 55 easily identifiable metabolites were followed. The degree of change in metabolite concentrations following storage over a 4-week period were influenced by the different methods of sample preparation and storage. Significant changes in urine metabolites are likely due to bacterial contamination of the urine. Our study demonstrates that bacterial contamination of urine in normal individuals significantly alters the metabolic profile of urine over time and proper preparation and storage procedures must be followed to reduce these changes. By identifying appropriate methods of urine preparation and storage investigators will preserve the fidelity of the urine samples in order to better reflect the original metabolic state.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

Sampling and handling procedures for the polarographic measurement of oxygen in hypolimnetic waters

SUMMARY. A new method for collecting and handling water samples prior to their polarographic measurement is described. Its usefulness has been demonstrated by testing its ability to exclude oxygen from anoxic hypolimnetic samples. The criterion of detection was 15 μg1⁻¹ of oxygen for the 95% confidence level. Different sampling and different handling procedures were compared, and only one overall method proved to introduce no significant contamination.     

Two statistical criteria to choose the method for dilution correction in metabolomic urine measurements

Introduction

Different normalization methods are available for urinary data. However, it is unclear which method performs best in minimizing error variance on a certain data-set as no generally applicable empirical criteria have been established so far.

Objectives

The main aim of this study was to develop an applicable and formally correct algorithm to decide on the normalization method without using phenotypic information.

Methods

We proved mathematically for two classical measurement error models that the optimal normalization method generates the highest correlation between the normalized urinary metabolite concentrations and its blood concentrations or, respectively, its raw urinary concentrations. We then applied the two criteria to the urinary ¹H-NMR measured metabolomic data from the Study of Health in Pomerania (SHIP-0; n?=?4068) under different normalization approaches and compared the results with in silico experiments to explore the effects of inflated error variance in the dilution estimation.

Results

In SHIP-0, we demonstrated consistently that probabilistic quotient normalization based on aligned spectra outperforms all other tested normalization methods. Creatinine normalization performed worst, while for unaligned data integral normalization seemed to most reasonable. The simulated and the actual data were in line with the theoretical modeling, underlining the general validity of the proposed criteria.

Conclusions

The problem of choosing the best normalization procedure for a certain data-set can be solved empirically. Thus, we recommend applying different normalization procedures to the data and comparing their performances via the statistical methodology explicated in this work. On the basis of classical measurement error models, the proposed algorithm will find the optimal normalization method.

     

Minimum reporting standards for plant biology context information in metabolomic studies

Plant metabolomics has matured over the past 8 years. Plant biologists routinely use comprehensive analyses of plant metabolites to discover new responses to genetic or environmental perturbation, or to validate initial hypotheses on the function and in vivo action of gene products. The wealth of scientific findings has increasingly provoked interest to share and review raw or processed data from plant metabolomics reports. We here suggest a minimum of parameters to be reported in order to define details of experimental study designs in plant metabolomics studies.