Reproducibility of animal research in light of biological variation

Voelkl, Bernhard; Altman, Naomi; Forsman, Anders; Forstmeier, Wolfgang; Gurevitch, Jessica; Jarić, Ivana; Karp, Natasha A.; Kas, Martien; Schielzeth, Holger; Casteele, Tom Van de; Würbel, Hanno

doi:10.1038/s41583-020-0313-3

Cited by 256 publications

(284 citation statements)

References 124 publications

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“…Therefore, this model can also be used in laboratories that do not have an animal experimental unit. Due to a high biological variation, animal experimentation is influenced by both genotype and environmental conditions resulting in an impaired reproducibility 62 , 63 . Standardization of experimental setup may be one way to address this problem 64 , 65 .…”

Section: Discussionmentioning

confidence: 99%

Monitoring of tumor growth and vascularization with repetitive ultrasonography in the chicken chorioallantoic-membrane-assay

Eckrich

Kugler

Buhr

et al. 2020

Sci Rep

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The chorioallantoic-membrane (CAM)-assay is an established model for in vivo tumor research. Contrary to rodent-xenograft-models, the CAM-assay does not require breeding of immunodeficient strains due to native immunodeficiency. This allows xenografts to grow on the non-innervated CAM without pain or impairment for the embryo. Considering multidirectional tumor growth, limited monitoring capability of tumor size is the main methodological limitation of the CAM-assay for tumor research. Enclosure of the tumor by the radiopaque eggshell and the small structural size only allows monitoring from above and challenges established imaging techniques. We report the eligibility of ultrasonography for repetitive visualization of tumor growth and vascularization in the CAM-assay. After tumor ingrowth, ultrasonography was repetitively performed in ovo using a commercial ultrasonographic scanner. Finally, the tumor was excised and histologically analyzed. Tumor growth and angiogenesis were successfully monitored and findings in ultrasonographic imaging significantly correlated with results obtained in histological analysis. Ultrasonography is cost efficient and widely available. Tumor imaging in ovo enables the longitudinal monitoring of tumoral development, yet allowing high quantitative output due to the CAM-assays simple and cheap methodology. Thus, this methodological novelty improves reproducibility in the field of in vivo tumor experimentation emphasizing the CAM-assay as an alternative to rodent-xenograft-models.

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Section: Discussionmentioning

confidence: 99%

Monitoring of tumor growth and vascularization with repetitive ultrasonography in the chicken chorioallantoic-membrane-assay

Eckrich

Kugler

Buhr

et al. 2020

Sci Rep

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“…More recently, single cell transcriptional profiling of aging C57BL/6NJ mice has been reported for multiple tissues, including kidney [6]. When aging studies are carried out in single inbred strains, they may display specific and idiosyncratic patterns of aging and thus lack generalizability beyond the particular strain studied [7]. In order to capture the full range of pathologies associated with the aging kidney, a genetically diverse set of animals is required.…”

Section: Introductionmentioning

confidence: 99%

Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney

Takemon

Chick

Gyuricza

et al. 2020

Preprint

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The kidney is an excellent model for studying organ aging. Kidney function shows steady decline with age and is easy to assay using urine or blood samples. However, little is known about the molecular changes that take place in the kidney during the aging process. In order to better understand the molecular changes that occur with age, we measured mRNA and protein levels in 188 genetically diverse mice at ages 6, 12, and 18 months. We observed distinctive change in mRNA and protein levels as a function of age. Changes in both mRNA and protein are associated with increased immune infiltration and decreases in mitochondrial function. Proteins show a greater extent of change and reveal changes in a wide array of biological processes including unique, organ-specific features of aging in kidney. Most importantly, we observed functionally important age-related changes in protein that occur in the absence of corresponding changes in mRNA. Our findings suggest that mRNA profiling alone provides an incomplete picture of molecular aging in the kidney and that examination of changes in proteins is essential to understand aging processes that are not transcriptionally regulated.

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“…Changes in average relative abundances are just presented descriptively, changes over time and comparisons between groups should be interpreted with caution due to the small number of individuals in each group. We did not conduct statistical tests to assess changes in relative abundance due to the low statistical power, inter-individual variability, and large number of relevant comparisons [36]. The most abundant phyla in the oral and faecal microbiota of both cows and calves were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes; the changes in the relative abundance of these phyla between calving and four-weeks are displayed in Supplementary Figure 1.…”

Section: Resultsmentioning

confidence: 99%

Maternal influences on oral and faecal microbiota maturation in neonatal calves in beef and dairy production systems

Barden

Richards‐Rios

Ganda

et al. 2020

Preprint

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Abstract Background: The dam is considered an important source of microbes for the calf; consequently, the development of calf microbiota may vary with farming system due to differences between the contact the calf has with the dam. The objective of this study was to characterise the early changes in the composition of oral and faecal microbiota in beef and dairy calves (N = 10) using high-throughput sequencing of the 16S rRNA gene. The microbiota of calves was compared to selected anatomical niches on their dams which were likely to contribute to the vertical transfer of microbes. Results: A total of 14,125 amplicon sequence variants (ASVs) were identified and taxonomically assigned. The oral microbiota of calves and their dams were composed of more similar microbes after the first four weeks of life than immediately after calving. The faecal microbiota of four-week old calves was composed of microbes which were more similar to those found in the oral microbiota of calves and adult cows than the faecal microbiota of adult cows. Specific ASVs were identified in the oral microbiota of four-week old calves that were also present in cow niches at calving, whereas very few ASVs were present in the calf faecal microbiota at four-weeks of age were present in any adult cow niche at calving. These results were observed in both beef and dairy calves. Conclusions: We did not observe any marked differences in the maturation of the oral and faecal microbiota between beef or dairy calves, despite dairy calves having very limited contact with their dam. This suggests the development of gastrointestinal microbiota in calves may not be affected by continued vertical transmission of microbes from the dam. Although the calf faecal microbiota changed over the first four-weeks of life, it was composed of microbes which were phylogenetically closer to those in the oral microbiota of calves and adult cows than the faeces of adult cows. There was little evidence of persistent microbial seeding of the calf faeces from anatomical niches on the cow at calving in either beef or dairy animals.

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Reproducibility of animal research in light of biological variation

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Cited by 256 publications

References 124 publications

Monitoring of tumor growth and vascularization with repetitive ultrasonography in the chicken chorioallantoic-membrane-assay

Monitoring of tumor growth and vascularization with repetitive ultrasonography in the chicken chorioallantoic-membrane-assay

Proteomic and transcriptomic profiling reveal different aspects of aging in the kidney

Maternal influences on oral and faecal microbiota maturation in neonatal calves in beef and dairy production systems

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