scholarly journals Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for “Precision Medicine and Pharmacometabolomics Task Group”—The Metabolomics Society Initiative)

2018 ◽  
Vol 64 (8) ◽  
pp. 1158-1182 ◽  
Author(s):  
Jennifer A Kirwan ◽  
Lorraine Brennan ◽  
David Broadhurst ◽  
Oliver Fiehn ◽  
Marta Cascante ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Storage Temperature ◽  
White Paper ◽  
Sample Volume ◽  
Time Of Day ◽  
Sample Collection ◽  
Diverse Range ◽  
Metabolomics Society ◽  
Biological Interpretation ◽  
Evidence Based Guidelines

Abstract BACKGROUND The metabolome of any given biological system contains a diverse range of low molecular weight molecules (metabolites), whose abundances can be affected by the timing and method of sample collection, storage, and handling. Thus, it is necessary to consider the requirements for preanalytical processes and biobanking in metabolomics research. Poor practice can create bias and have deleterious effects on the robustness and reproducibility of acquired data. CONTENT This review presents both current practice and latest evidence on preanalytical processes and biobanking of samples intended for metabolomics measurement of common biofluids and tissues. It highlights areas requiring more validation and research and provides some evidence-based guidelines on best practices. SUMMARY Although many researchers and biobanking personnel are familiar with the necessity of standardizing sample collection procedures at the axiomatic level (e.g., fasting status, time of day, “time to freezer,” sample volume), other less obvious factors can also negatively affect the validity of a study, such as vial size, material and batch, centrifuge speeds, storage temperature, time and conditions, and even environmental changes in the collection room. Any biobank or research study should establish and follow a well-defined and validated protocol for the collection of samples for metabolomics research. This protocol should be fully documented in any resulting study and should involve all stakeholders in its design. The use of samples that have been collected using standardized and validated protocols is a prerequisite to enable robust biological interpretation unhindered by unnecessary preanalytical factors that may complicate data analysis and interpretation.

scholarly journals Current Issues in Measurement and Reporting of Urinary Albumin Excretion

2009 ◽  
Vol 55 (1) ◽  
pp. 24-38 ◽  
Author(s):  
W Greg Miller ◽  
David E Bruns ◽  
Glen L Hortin ◽  
Sverre Sandberg ◽  
Kristin M Aakre ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Reference Intervals ◽  
Time Of Day ◽  
Urinary Albumin ◽  
Sample Collection ◽  
Continuous Increase ◽  
Albumin Excretion ◽  
Urine Albumin ◽  
Progression Of Kidney Disease ◽  
Patient Preparation

Abstract Background: Urinary excretion of albumin indicates kidney damage and is recognized as a risk factor for progression of kidney disease and cardiovascular disease. The role of urinary albumin measurements has focused attention on the clinical need for accurate and clearly reported results. The National Kidney Disease Education Program and the IFCC convened a conference to assess the current state of preanalytical, analytical, and postanalytical issues affecting urine albumin measurements and to identify areas needing improvement. Content: The chemistry of albumin in urine is incompletely understood. Current guidelines recommend the use of the albumin/creatinine ratio (ACR) as a surrogate for the error-prone collection of timed urine samples. Although ACR results are affected by patient preparation and time of day of sample collection, neither is standardized. Considerable intermethod differences have been reported for both albumin and creatinine measurement, but trueness is unknown because there are no reference measurement procedures for albumin and no reference materials for either analyte in urine. The recommended reference intervals for the ACR do not take into account the large intergroup differences in creatinine excretion (e.g., related to differences in age, sex, and ethnicity) nor the continuous increase in risk related to albumin excretion. Discussion: Clinical needs have been identified for standardization of (a) urine collection methods, (b) urine albumin and creatinine measurements based on a complete reference system, (c) reporting of test results, and (d) reference intervals for the ACR.

scholarly journals Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA

2018 ◽  
Vol 115 (30) ◽  
pp. E7174-E7183 ◽  
Author(s):  
David G. Welkie ◽  
Benjamin E. Rubin ◽  
Yong-Gang Chang ◽  
Spencer Diamond ◽  
Scott A. Rifkin ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Continuous Light ◽  
Axial Rotation ◽  
Time Of Day ◽  
Negative Regulator ◽  
Photosynthetic Organisms ◽  
Environmental Responsiveness ◽  
Environmental Responses ◽  
Clock Protein

The recurrent pattern of light and darkness generated by Earth’s axial rotation has profoundly influenced the evolution of organisms, selecting for both biological mechanisms that respond acutely to environmental changes and circadian clocks that program physiology in anticipation of daily variations. The necessity to integrate environmental responsiveness and circadian programming is exemplified in photosynthetic organisms such as cyanobacteria, which depend on light-driven photochemical processes. The cyanobacterium Synechococcus elongatus PCC 7942 is an excellent model system for dissecting these entwined mechanisms. Its core circadian oscillator, consisting of three proteins, KaiA, KaiB, and KaiC, transmits time-of-day signals to clock-output proteins, which reciprocally regulate global transcription. Research performed under constant light facilitates analysis of intrinsic cycles separately from direct environmental responses but does not provide insight into how these regulatory systems are integrated during light–dark cycles. Thus, we sought to identify genes that are specifically necessary in a day–night environment. We screened a dense bar-coded transposon library in both continuous light and daily cycling conditions and compared the fitness consequences of loss of each nonessential gene in the genome. Although the clock itself is not essential for viability in light–dark cycles, the most detrimental mutations revealed by the screen were those that disrupt KaiA. The screen broadened our understanding of light–dark survival in photosynthetic organisms, identified unforeseen clock–protein interaction dynamics, and reinforced the role of the clock as a negative regulator of a nighttime metabolic program that is essential for S. elongatus to survive in the dark.

scholarly journals Comparison of Dilution on Eastern Box Turtle (Terrapene carolina carolina) and Marine Toad (Rhinella marinus) Blood Parameters as Measured on a Portable Chemistry Analyzer

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
John A. Griffioen ◽  
Devorah M. Stowe ◽  
Macy Trosclair ◽  
Larry J. Minter ◽  
Chelsey Vanetten ◽  
...  
Keyword(s):  
Sample Volume ◽  
Total Carbon ◽  
Ionized Calcium ◽  
Dilution Ratio ◽  
Sample Collection ◽  
Clinical Tool ◽  
Terrapene Carolina ◽  
Two Samples ◽  
Terrapene Carolina Carolina ◽  
Sample Dilution

Biochemical testing is an important clinical tool in evaluating the physiology of reptiles and amphibians. Suitable point of care analyzers can allow for rapid delivery of results, but small patient size can inhibit sufficient sample collection. This study evaluated the utility of sample dilution with sterile distilled water as a means of biochemical evaluation when sample volume is limited. Blood was collected from 12 eastern box turtles (Terrapene carolina carolina) and 12 marine toads (Rhinella marinus) and analyzed via i-STAT CHEM8+ cartridges. Two undiluted samples and two samples diluted 1 : 1 with sterile water were evaluated immediately following collection for each animal in the study. Analytes reported in the diluted samples were limited to glucose, ionized calcium, and total carbon dioxide. The expected dilution ratio value of diluted to undiluted samples was 0.5, of which glucose in both turtles and toads was nearest. Dilution ratio values for ionized calcium, however, were higher than expected in both turtles and toads. Sample dilution is not recommended for most analytes included on the CHEM8+ cartridge due to values occurring outside the limits of detection for the analyzer. Glucose and ionized calcium values obtained on diluted samples should be interpreted with caution but may provide clinical utility in reptile and amphibian patients where sample volume is limited.

scholarly journals A new soil core sampler for determination bulk density in soil profile

2011 ◽  
Vol 50 (No. 6) ◽  
pp. 250-256 ◽  
Author(s):  
P. Prikner ◽  
F. Lachnit ◽  
F. Dvořák
Keyword(s):  
Bulk Density ◽  
Soil Sample ◽  
Soil Profile ◽  
Soil Compaction ◽  
Sampling Methods ◽  
Sample Volume ◽  
Soil Core ◽  
Sample Collection ◽  
Core Sampler ◽  
Inner Diameter

The portable soil core sampler was engineered for gradual sampling of soil profile in the depth up to 0.5 m, which ensures extraction of the whole sample volume of soil profile in determinable depth. The portable soil core sampler was compared with the professional soil probe Eijkelkamp P1.31 (Eijkelkamp Agrisearch Equipment, Netherlands) in field conditions. The portable sampler was compared with the physical soil sample rings in laboratory conditions to eliminate all of possible restrictive aspects affecting the procedure of measurement. The portable soil core sampler with inner diameter 71 mm, depth 120 mmenables gradually take samples of soil profile by step of 50 mmand is able to detect possible local extremes. On the other hand a soil probe is not able to reach desired accuracy in taking of a&nbsp;soil sample. Values measured from a soil probe approximately taken by step of 150 mmare inaccurate. The values of bulk density of both sampling methods were variable at significant interval from 40 into 80 kg/m<sup>3</sup>. Different values could be caused by soil profile condition and by the use of different sampling methods. The design of a portable soil sampler should be of assistance in fast and precise soil profiling sample collection, which is required to determine bulk density of the soil, its variance depending on moisture content in soil compaction determining criteria.

scholarly journals Choline in Whole Blood and Plasma: Sample Preparation and Stability

2008 ◽  
Vol 54 (3) ◽  
pp. 590-593 ◽  
Author(s):  
Bingfang Yue ◽  
Elizabeth Pattison ◽  
William L Roberts ◽  
Alan L Rockwood ◽  
Oliver Danne ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Whole Blood ◽  
Storage Time ◽  
Storage Temperature ◽  
Sample Collection ◽  
Coronary Syndrome ◽  
Thaw Cycle ◽  
Freeze Thaw Cycle ◽  
Heparin Plasma ◽  
Liquid Chromatography Tandem Mass

Abstract Background: Choline is critical for a variety of biological functions and has been investigated as a biomarker for various pathological conditions including acute coronary syndrome. Methods: A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was used to quantify choline in whole blood and plasma in freshly collected samples prepared with ultrafiltration or protein precipitation. We investigated the effects of preanalytical variables including types of anticoagulants and storage temperature and time. Results: We observed no significant differences in whole-blood choline concentration in EDTA-anticoagulated vs heparin-anticoagulated samples: mean (SD) difference 0.9% (3.2%), P = 0.80. For plasma, choline concentrations with heparin in 5 of 12 volunteers were &gt;10% higher than with EDTA, P = 0.01. One freeze-thaw cycle led to significant mean (SD) increases in choline concentrations in heparin whole blood, 19.3% (11.4%), P &lt;0.01, and the effect was not significant for other sample types studied (P &gt;0.33). For freshly collected samples stored at ambient temperature, choline concentrations in all types of samples increased with storage time. For EDTA whole blood, EDTA plasma, and heparin plasma, the choline concentration increased for the first 60 min and then stabilized. For heparin whole blood, the choline concentration continued to increase linearly with storage time for &gt;4 h, at which time the choline concentrations were increased by approximately 50%. Conclusions: Sample collection, storage, and sample preparation procedures are critical for clinical measurements of choline in whole blood and plasma.

Effect of sample storage temperature and buffer formulation on faecal immunochemical test haemoglobin measurements

2017 ◽  
Vol 24 (4) ◽  
pp. 176-181 ◽  
Author(s):  
Erin L Symonds ◽  
Stephen R Cole ◽  
Dawn Bastin ◽  
Robert JL Fraser ◽  
Graeme P Young
Keyword(s):  
Room Temperature ◽  
Storage Temperature ◽  
Test Accuracy ◽  
Sample Collection ◽  
Storage Duration ◽  
Initial Concentration ◽  
Faecal Immunochemical Test ◽  
Immunochemical Test ◽  
New Formulation ◽  
And Storage

Objectives Faecal immunochemical test accuracy may be adversely affected when samples are exposed to high temperatures. This study evaluated the effect of two sample collection buffer formulations (OC-Sensor, Eiken) and storage temperatures on faecal haemoglobin readings. Methods Faecal immunochemical test samples returned in a screening programme and with ≥10 µg Hb/g faeces in either the original or new formulation haemoglobin stabilizing buffer were stored in the freezer, refrigerator, or at room temperature (22℃–24℃), and reanalysed after 1–14 days. Samples in the new buffer were also reanalysed after storage at 35℃ and 50℃. Results were expressed as percentage of the initial concentration, and the number of days that levels were maintained to at least 80% was calculated. Results Haemoglobin concentrations were maintained above 80% of their initial concentration with both freezer and refrigerator storage, regardless of buffer formulation or storage duration. Stability at room temperature was significantly better in the new buffer, with haemoglobin remaining above 80% for 20 days compared with six days in the original buffer. Storage at 35℃ or 50℃ in the new buffer maintained haemoglobin above 80% for eight and two days, respectively. Conclusion The new formulation buffer has enhanced haemoglobin stabilizing properties when samples are exposed to temperatures greater than 22℃.

scholarly journals Fecal Sample Collection Methods and Time of Day Impact Microbiome Composition and Short Chain Fatty Acid Concentrations

2021 ◽  
Author(s):  
Jacquelyn Jones ◽  
Stacey Reinke ◽  
Alishum Ali ◽  
Debra Palmer ◽  
Claus T. Christophersen
Keyword(s):  
Fatty Acid ◽  
Fecal Sample ◽  
Short Chain Fatty Acid ◽  
Time Of Day ◽  
Chain Fatty Acid ◽  
Short Chain ◽  
Its2 Region ◽  
Rrna Gene ◽  
Sample Collection ◽  
Collection Methods

Abstract Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgeneGUT tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist microbiome investigators plan their fecal sample collection and storage procedures for multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.

scholarly journals Storage Procedures Affect pH, Electrical Conductivity, and Nutrient Concentrations of Pour-through Leachate from Pine Bark and Peat-based Substrates

HortScience ◽  
2020 ◽  
Vol 55 (10) ◽  
pp. 1597-1604
Author(s):  
Andrea C. Landaverde ◽  
Jacob H. Shreckhise ◽  
James E. Altland
Keyword(s):  
Electrical Conductivity ◽  
Storage Time ◽  
Storage Temperature ◽  
Chemical Properties ◽  
Pine Bark ◽  
Nutrient Concentrations ◽  
Sample Collection ◽  
Nutrient Analysis ◽  
Preservation Methods ◽  
Total Dissolved Nitrogen

The pour-through (PT) method is used in greenhouse and nursery production to monitor nutrient availability in soilless substrates. Efficacy of this method is based on the assumption that chemical properties of extracted solutions remain stable from the moment of collection until analysis. Extracted substrate solution can be analyzed directly in the greenhouse or sent to laboratories for complete nutritional analysis; thus, proper sample preservation methods (e.g., filtration and low temperatures) are critical for reducing sample contamination or degradation during storage. However, evidence of how these preservation methods affect chemical characteristics of PT samples is limited. The objective of this study was to evaluate the effect of storage time, storage temperature, and filtration of PT samples on pH, electrical conductivity (EC), and nutrient concentrations from pine bark– and peat-based substrates. PT extracts were obtained from liquid-fertilized fallow pots of either 100% milled pine bark (Expt. 1) or a 4 sphagnum peat: 1 perlite (by volume) substrate (Expt. 2). Aliquots of PT extract were either filtered or nonfiltered and then stored in plastic bottles at −22, 4, or 20 °C. EC, pH, and nutrient concentrations were analyzed at 0, 1, 7, and 30 days after PT sample collection. EC and pH in PT extracts of peat and pine bark, respectively, changed 1 day after collection. Storage time had the greatest effect on nutrient concentrations of samples stored at 20 °C. However, at day 30, nutrient concentrations had also changed in samples stored at 4 and −22 °C. Analytes that fluctuated most in both experiments and across all preservation treatments were dissolved organic carbon, total dissolved nitrogen, NO3−-N, and PO43−-P, whereas Ca2+, Mg2+, and SO42−-S were more stable in PT samples. This research suggests EC and pH should be analyzed immediately, whereas samples requiring nutrient analysis should be filtered immediately after collection, stored at 4 or −22 °C (preferably −22 °C), and analyzed within 7 days of collection.

Conservation Technology

2021 ◽  
Keyword(s):  
Environmental Changes ◽  
Large Data ◽  
Scientific Data ◽  
Camera Traps ◽  
Data Sets ◽  
Computer Algorithms ◽  
Diverse Range ◽  
Conservation Technology ◽  
Available Technology ◽  
International Experts

The global loss of biodiversity is occurring at an unprecedented pace. Despite the considerable effort devoted to conservation science and management, we still lack the basic data on the distribution and density of most animal and plant species, which in turn hampers our efforts to study changes over time. In addition, we often lack behavioural data from the very animals most influenced by environmental changes; this is largely due to the financial and logistical limitations associated with gathering scientific data on animals that are either widely distributed, cryptic, or negatively influenced by human presence. To overcome these limitations, conservationists are increasingly employing technology to facilitate such data collection. The use of camera traps, acoustic sensors, satellite data, drones, and sophisticated computer algorithms to analyse the large data sets collected are becoming increasingly common. Although there are several specialist books on some of these technologies, there is currently no overarching volume that describes the available technology for conservation and evaluates its varied applications. This edited volume will fill this void, bringing together a team of international experts using a diverse range of approaches.

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