Annotation depth confounds direct comparison of gene expression across species

BACKGROUND

Comparisons of the molecular framework among organisms can be done on both structural and functional levels. One of the most common top-down approaches for functional comparisons is RNA sequencing. This estimation of organismal transcriptional responses is of interest for understanding evolution of molecular activity, which is used for answering a diversity of questions ranging from basic biology to pre-clinical species selection and translation. However, direct comparison between species is often hindered by evolutionary divergence in structure of molecular framework, as well as large difference in the depth of our understanding of the genetic background between humans and other species. Here, we focus on the latter. We attempt to understand how differences in transcriptome annotation affect direct gene abundance comparisons between species.

RESULTS

We examine and suggest some straightforward approaches for direct comparison given the current available tools and using a sample dataset from human, cynomolgus monkey, dog, rat and mouse with a common quantitation and normalization approach. In addition, we examine how variation in genome annotation depth and quality across species may affect these direct comparisons.

CONCLUSIONS

Our findings suggest that further efforts for better genome annotation or computational normalization tools may be of strong interest.

In vivo models to evaluate ingestible devices: Present status and current trends

Evaluation of orally ingestible devices is critical to optimize their performance early in development. Using animals as a pre-clinical tool can provide useful information on functionality, yet it is important to recognize that animal gastrointestinal physiology, pathophysiology and anatomy can differ to that in humans and that the most suitable species needs to be selected to inform the evaluation. There has been a move towards in vitro and in silico models rather than animal models in line with the 3Rs (Replacement, Reduction and Refinement) as well as the better control and reproducibility associated with these systems. However, there are still instances where animal models provide the greatest understanding. This paper provides an overview of key aspects of human gastrointestinal anatomy and physiology and compares parameters to those reported in animal species. The value of each species can be determined based upon the parameter of interest from the ingested device when considering the use of pre-clinical animal testing.