Eichner, C. | bioRxiv Science

bioRxiv2020

Increased Sensitivity and Signal-to-Noise Ratio in Diffusion-Weighted MRI using Multi-Echo Acquisitions

Post-mortem diffusion MRI (dMRI) enables acquisitions of structural imaging data with otherwise unreachable resolutions - at the expense of longer scanning times. These data are typically acquired using highly segmented image acquisition strategies, thereby resulting in an incomplete signal decay before the MRI encoding continues. Especially in dMRI, with low signal intensities and lengthy contrast encoding, such temporal inefficiency translates into reduced image quality and longer scanning times. This study introduces Multi Echo (ME) acquisitions to dMRI on a human MRI system - a time-efficient approach, which increases SNR (Signal-to-Noise Ratio) and reduces noise bias for dMRI images. The benefit of the introduced ME dMRI method was validated using numerical Monte Carlo simulations and showcased on a post-mortem brain of a wild chimpanzee. The proposed Maximum Likelihood Estimation echo combination results in an optimal SNR without detectable signal bias. The combined strategy comes at a small price in scanning time (here 30% additional) and leads to a substantial SNR increase (here up to 1.9x which is equivalent to 3.6 averages) and a general reduction of the noise bias.

neuroscience↗

bioRxiv2019

Host gill attachment enables blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae, and alters parasite development and transcriptome

Blood-feeding is a common strategy among parasitizing arthropods, including the ectoparasitic salmon louse (Lepeophtheirus salmonis), feeding off its salmon hosts skin and blood. Blood is rich in nutrients, among these iron and heme. These are essential molecules for the louse, yet their oxidative properties render them toxic to cells if not handled properly. Blood-feeding might therefore alter parasite gene expression. We infected Atlantic salmon with salmon louse copepodids and sampled the lice in two different experiments at day 10 and 18 post infestation. Parasite development and presence of host blood in their intestines were determined. We find that lice start feeding on blood when becoming mobile preadults if sitting on the fish body, however they may initiate in blood-feeding at the chalimus I stage if attached to gills. Lice attached to gills develop at a slower rate. Lice of similar instar age from gills versus lice from skin epidermis were analyzed for gene expression by RNA-sequencing in samples taken at day 10 for both experiments and at day 18 for one of the experiments. By differential expression analysis, we found 355 transcripts elevated in lice sampled from gills and 202 transcripts elevated in lice sampled from skin consistent in all experiments. Genes annotated with "peptidase activity" are among the ones elevated in lice sampled from gills, while in the other group genes annotated with "phosphorylation" and "phosphatase" is pervasive. Transcripts elevated in lice sampled from gills are often genes relatively highly expressed in the louse intestine compared with other tissues, while this was not the case for transcripts found elevated in lice sampled from skin. In both groups, more than half the transcripts are from genes higher expressed after attachment. In conclusion, blood-feeding results in an alteration in gene expression, and a premature onset of blood-feeding likely causes the parasite to develop at a slower pace.

bioinformatics↗