scholarly journals Standard Sample Storage Conditions Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns

2021 ◽  
Author(s):  
Casper S. Poulsen ◽  
Rolf Sommer Kaas ◽  
Frank M. Aarestrup ◽  
Sünje Johanna Pamp
Keyword(s):  
Antimicrobial Resistance ◽  
Dna Sequencing ◽  
Storage Conditions ◽  
Systematic Effect ◽  
Sample Storage ◽  
Sequencing Data ◽  
Freezing And Thawing ◽  
Microbiome Composition ◽  
Freeze Thaw ◽  
Eukaryotic Microorganisms

Storage of biological specimens is crucial in the life and medical sciences. The storage conditions for samples can be different for a number of reasons, and it is unclear which effect this can have on the inferred microbiome composition in metagenomics analyses. Here, we assess the effect of common storage temperatures (deep freezer: -80°C, freezer: -20°C, fridge: 5°C, room temperature: 22°C) and storage times, (immediate sample processing: 0h, next day: 16h, over weekend: 64h, and longer term: 4, 8, 12 months), as well as repeated sample freezing and thawing (2-4 freeze-thaw cycles). We examine two different pig feces and sewage samples, unspiked and spiked with a mock community, and in triplicates, respectively, amounting to a total of 438 samples (777 Gbp; 5.1 billion reads). Storage conditions had a significant and systematic effect on the taxonomic and functional composition of microbiomes. Distinct microbial taxa and antimicrobial resistance classes were in some situations similarly effected across samples, while others were not, suggesting an impact of individual inherent sample characteristics. With an increasing number of freeze-thaw cycles, an increasing abundance of Firmicutes, Actinobacteria, and eukaryotic microorganisms was observed. We include recommendations for sample storage, and strongly suggest including more detailed information in the metadata together with the DNA sequencing data in public repositories to better facilitate meta-analyses and reproducibility of findings. IMPORTANCE: Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and find significant and, in part, systematic effects. Repeated freeze-thaw cycles could be used to improve the detection of microorganisms with more rigid cell walls, including parasites. We provide a dataset that could also be used for benchmarking algorithms to identify and correct for batch effects. Overall, the findings suggest that all samples of a microbiome study should be stored in the same way. Furthermore, there is a need to mandate more detailed information about sample storage and processing published together with the DNA sequencing data at INSDC (ENA/EBI, NCBI, DDBJ) or other repositories.

scholarly journals Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns

2021 ◽  
Author(s):  
Casper Sahl Poulsen ◽  
Rolf Sommer Kaas ◽  
Frank M. Aarestrup ◽  
Sünje Johanna Pamp
Keyword(s):  
Antimicrobial Resistance ◽  
Dna Isolation ◽  
Standard Sample ◽  
Storage Conditions ◽  
Library Preparation ◽  
Sample Storage ◽  
Sequencing Technology ◽  
Microbiome Composition ◽  
Resistance Patterns ◽  
Systematic Effects

Previous research has reported effects of DNA isolation, library preparation, and sequencing technology on metagenomics-based microbiome composition; however, the effect of biospecimen storage conditions has not been thoroughly assessed. We examined the effect of common sample storage conditions on metagenomics-based microbiome composition and found significant and, in part, systematic effects.

Effect of Sample Storage Conditions on Body Burden Analysis of Organic Contaminants in Unionid Mussels

1992 ◽  
Vol 27 (4) ◽  
pp. 833-844 ◽  
Author(s):  
Micheline Hanna
Keyword(s):  
Organic Contaminants ◽  
Body Burden ◽  
Storage Conditions ◽  
The Body ◽  
Sample Storage ◽  
Pcb Congeners ◽  
Unionid Mussels ◽  
Group A ◽  
The Difference ◽  
Group B

Abstract In order to quantitatively assess the effect of sample storage conditions on the body burden analysis of organic contaminants, a comparative analysis was carried out on the unionid mussel Elliptic complanata. The mussels were divided into two groups, each with distinct storage conditions, while Group A was kept in the freezer at −20°C, Group B was kept in the refrigerator for five days at 5°C. All the compounds present in the control were also present in Group B samples. Analysis of the organic contaminants in each of these two groups showed that for total PCB concentrations, the two treatments were not significantly different; however when compared individually 6 of the 13 PCB congeners showed significant differences. The observed differences were relatively small for individual PCB congeners (7.1 to 15.3%), higher for chlorobenzenes (10.5 to 36.4%), and yet higher for HCE (44.1%); the difference for HCE, although large is nevertheless not significant, even if only marginally so.

scholarly journals Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Leah L. Weber ◽  
Mohammed El-Kebir
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Evolutionary Process ◽  
Treatment Decision ◽  
Real Data ◽  
Current Data ◽  
Fast Method ◽  
Sequencing Data ◽  
Evolutionary Trajectory ◽  
Cancer Types

Abstract Background Cancer arises from an evolutionary process where somatic mutations give rise to clonal expansions. Reconstructing this evolutionary process is useful for treatment decision-making as well as understanding evolutionary patterns across patients and cancer types. In particular, classifying a tumor’s evolutionary process as either linear or branched and understanding what cancer types and which patients have each of these trajectories could provide useful insights for both clinicians and researchers. While comprehensive cancer phylogeny inference from single-cell DNA sequencing data is challenging due to limitations with current sequencing technology and the complexity of the resulting problem, current data might provide sufficient signal to accurately classify a tumor’s evolutionary history as either linear or branched. Results We introduce the Linear Perfect Phylogeny Flipping (LPPF) problem as a means of testing two alternative hypotheses for the pattern of evolution, which we prove to be NP-hard. We develop Phyolin, which uses constraint programming to solve the LPPF problem. Through both in silico experiments and real data application, we demonstrate the performance of our method, outperforming a competing machine learning approach. Conclusion Phyolin is an accurate, easy to use and fast method for classifying an evolutionary trajectory as linear or branched given a tumor’s single-cell DNA sequencing data.

scholarly journals Strength and Microscopic Damage Mechanism of Yellow Sandstone with Holes under Freezing and Thawing

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Huren Rong ◽  
Jingyu Gu ◽  
Miren Rong ◽  
Hong Liu ◽  
Jiayao Zhang ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Pore Size ◽  
Power Function ◽  
Damage Mechanism ◽  
Uniaxial Compression Test ◽  
Freezing And Thawing ◽  
Freeze Thaw ◽  
Thaw Cycle ◽  
Freeze Thaw Cycle ◽  
Microscopic Damage

In order to study the damage characteristics of the yellow sandstone containing pores under the freeze-thaw cycle, the uniaxial compression test of saturated water-stained yellow sandstones with different freeze-thaw cycles was carried out by rock servo press, the microstructure was qualitatively analyzed by Zeiss 508 stereo microscope, and the microdamage mechanism was quantitatively studied by using specific surface area and pore size analyzer. The mechanism of weakening mechanical properties of single-hole yellow sandstone was expounded from the perspective of microstructure. The results show the following. (1) The number of freeze-thaw cycles and single-pore diameter have significant effects on the strength and elastic modulus of the yellow sandstone; the more the freeze-thaw cycles and the larger the pore size, the lower the strength of the yellow sandstone. (2) The damage modes of the yellow sandstone containing pores under the freeze-thaw cycle are divided into five types, and the yellow sandstone with pores is divided into two areas: the periphery of the hole and the distance from the hole; as the number of freeze-thaw cycles increases, different regions show different microscopic damage patterns. (3) The damage degree of yellow sandstone is different with freeze-thaw cycle and pore size. Freeze-thaw not only affects the mechanical properties of yellow sandstone but also accelerates the damage process of pores. (4) The damage of the yellow sandstone by freeze-thaw is logarithmic function, and the damage of the yellow sandstone is a power function. The damage equation of the yellow sandstone with pores under the freezing and thawing is a log-power function nonlinear change law and presents a good correlation.

Review of Strength and Failure Criteria for Concrete After Freeze-Thaw Damage

2012 ◽  
Vol 253-255 ◽  
pp. 456-461
Author(s):  
Yan Fu Qin ◽  
Bin Tian ◽  
Gang Xu ◽  
Xiao Chun Lu
Keyword(s):  
Normal State ◽  
Concrete Strength ◽  
Failure Criteria ◽  
Concrete Durability ◽  
Freezing And Thawing ◽  
Normal Concrete ◽  
Strength Criteria ◽  
Freeze Thaw ◽  
Ordinary Concrete ◽  
Concrete Failure

Frost resistance research is one of the important subject of concrete durability, however strength criteria is an important part of the study of mechanical behavior of concrete. So far, about concrete failure criteria are almost for normal concrete, which the domestic and overseas scholars have comparative detailed research in every respect to it, and to freeze-thaw damage of concrete but few research. Based on the summary of the existing ordinary concrete strength and failure criteria in normal state and after freeze-thaw damage，this paper have a brief comment of failure criteria on concrete after freeze-thaw damage. For later research about concrete strength and failure criteria under freezing and thawing cycle provide the reference.

scholarly journals Supplementation of freezing and thawing media with brain-derived neurotrophic factor protects human sperm from freeze-thaw-induced damage

2016 ◽  
Vol 106 (7) ◽  
pp. 1658-1665.e4 ◽  
Author(s):  
Atefeh Najafi ◽  
Ebrahim Asadi ◽  
Adel R. Moawad ◽  
Saideh Mikaeili ◽  
Fardin Amidi ◽  
...  
Keyword(s):  
Neurotrophic Factor ◽  
Human Sperm ◽  
Brain Derived Neurotrophic Factor ◽  
Freezing And Thawing ◽  
Freeze Thaw

scholarly journals The effect of storage conditions on samples for the evaluation of copper status in blesbok (Damaliscus pygargus phillipsi)

2002 ◽  
Vol 73 (3) ◽  
Author(s):  
M. Quan ◽  
M.S. Mulders ◽  
D.G.A. Meltzer
Keyword(s):  
Superoxide Dismutase ◽  
Liquid Nitrogen ◽  
Liver Tissue ◽  
Room Temperature ◽  
Storage Conditions ◽  
Superoxide Dismutase Activity ◽  
Activity Levels ◽  
Sample Storage ◽  
Live Animal ◽  
Jersey Cows

Investigaltions to determine the effect of sample storage on the concentration of copper in liver tissue and on the activity of erythrocyte superoxide dismutase were undertaken in preparation for a study of blesbok (Damaliscus pygargus phillipsi) that were suspected to be suffering from copper deficiency. Two liver samples were collected from each of 20 culled blesbok in a manner that simulated the collection of biopsies from the live animal. These samples were stored either in 10 % formalin or frozen at -20 °C until analysed 4 1/2 months later. The effect of different methods of sample storage on superoxide dismutase activity was determined. Erythrocytes collected from 3 Jersey cows and 5 culled blesbok were washed and divided into 0.5m portions, stored at room temperature (~20 °C), in a refrigerator (4 °C), frozen at -20 °C in a freezer, and in liquid nitrogen (-200 °C). An analysis of superoxide dismutase activity was undertaken using a commercial assay kit at intervals of 2-4 days until the levels of activity had fallen significantly. The copper concentration in formalin-preserved liver samples was significantly lower than that measured in frozen liver tissue apparently as a result of leaching. The activity of superoxide dismutase in cattle blood was unchanged for 4 days at room temperature but fell appreciably after 2 days at 4 °C and -20 °C. Enzyme activity remained unchanged for 200 days in erythrocytes stored in liquid nitrogen. Superoxide dismutase activity levels in healthy blesbok were considerably lower than those measured in Jersey cows and remained unaffected for up to 6 days in samples stored at 4 °C and 20 °C. The level of activity fell significantly thereafter. Samples stored in liquid nitrogen were unchanged after 40 days.

scholarly journals USING SMOS PASSIVE MICROWAVE DATA TO DEVELOP SMAP FREEZE/THAW ALGORITHMS ADAPTED FOR THE CANADIAN SUBARCTIC

2015 ◽  
Vol XL-1-W5 ◽  
pp. 365-368 ◽  
Author(s):  
P. Kalantari ◽  
M. Bernier ◽  
K. C. McDonal ◽  
J. Poulin
Keyword(s):  
Land Cover ◽  
Time Series Data ◽  
Passive Microwave ◽  
Soil Freezing ◽  
Series Data ◽  
Freezing And Thawing ◽  
Freeze Thaw ◽  
Thaw Cycle ◽  
Freeze Thaw Cycle ◽  
The Impact

Seasonal terrestrial Freeze/Thaw cycle in Northern Quebec Tundra (Nunavik) was determined and evaluated with passive microwave observations. SMOS time series data were analyzed to examine seasonal variations of soil freezing, and to assess the impact of land cover on the Freeze/Thaw cycle. Furthermore, the soil freezing maps derived from SMOS observations were compared to field survey data in the region near Umiujaq. The objective is to develop algorithms to follow the seasonal cycle of freezing and thawing of the soil adapted to Canadian subarctic, a territory with a high complexity of land cover (vegetation, soil, and water bodies). Field data shows that soil freezing and thawing dates vary much spatially at the local scale in the Boreal Forest and the Tundra. The results showed a satisfactory pixel by pixel mapping for the daily soil state monitoring with a > 80% success rate with in situ data for the HH and VV polarizations, and for different land cover. The average accuracies are 80% and 84% for the soil freeze period, and soil thaw period respectively. The comparison is limited because of the small number of validation pixels.

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