Biology subjects

Hanson, J.

Publications and source records attributed to Hanson, J..

4 recordsLinked to original sources

bioRxiv2020

Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture and Dynamics

The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of GTP nucleotides. Among post-translational modifications initiated at the ER level, glycosylation is the most common reaction. However, our understanding of the impact of glycosylation on ER structure remains unclear. Here, we show that Exostosin-1 (EXT1) glycosyltransferase, an enzyme involved in N-glycosylation, is a key regulator of ER morphology and dynamics. We have integrated multi-omics data and super-resolution imaging to characterize the broad effect of EXT1 inactivation, including ER shape-dynamics-function relationships in mammalian cells. We have observed that, inactivating EXT1 induces cell enlargement and enhances metabolic switches such as protein secretion. In particular, suppressing EXT1 in mouse thymocytes causes developmental dysfunctions associated to ER network extension. Our findings suggest that EXT1 drives glycosylation reactions involving ER structural proteins and high-energy nucleotide sugars, which might also apply to other organelles.

cell biology↗

bioRxiv2020

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

genomics↗

bioRxiv2020

Quantifying Numerical and Spatial Reliability of Amygdala and Hippocampal Subdivisions in FreeSurfer

On-going, large-scale neuroimaging initiatives can aid in uncovering neurobiological causes and correlates of poor mental health, disease pathology, and many other important conditions. As projects grow in scale with hundreds, even thousands, of individual participants and scans collected, quantification of brain structures by automated algorithms is becoming the only truly tractable approach. Here, we assessed the spatial and numerical reliability for newly deployed automated segmentation of hippocampal subfields and amygdala nuclei in FreeSurfer 7. In a sample of participants with repeated structural imaging scans (N=923), we found numerical reliability (as assessed by intraclass correlations, ICCs) was reasonable: [~]95% of hippocampal subfields have "excellent" numerical reliability (ICCs[≥]0.90), however, only 67% of amygdala subnuclei met this same threshold. Spatial reliability was similarly reasonable, with 58% of hippocampal subfields and 44% of amygdala subnuclei having Dice coefficients[≥]0.70. Notably, multiple regions had poor numerical and/or spatial reliability. We also examined correlations between spatial reliability and person-level factors (e.g., participant age; T1 image quality). Both sex and image scan quality were related to variations in spatial reliability metrics. Examined collectively, our work suggests caution should be exercised for a few hippocampal subfields and amygdala nuclei with more variable reliability.

neuroscience↗

bioRxiv2019

Transcriptome and translatome profiling and translational network analysis during seed maturation reveals conserved transcriptional and distinct translational regulatory patterns

Seed maturation is an important plant developmental process that follows embryo development. It is associated with a series of physiological changes such as the establishment of desiccation tolerance, seed longevity and seed dormancy. However, the translational dynamics associated with seed maturation, especially its connection with seed germination remains largely elusive. Here transcriptome and translatome profiling were performed during seed maturation. During seed maturation we observed a gradual disappearance of polysomes and a relative increase of monosomes, indicating a gradual reduction of global translation. Comparing the levels of polysomal associated mRNAs with total mRNA levels showed that thousands of genes are translationally regulated at early sates of maturation, as judged by dramatic changes in polysomal occupancy. By including previous published data from germination and seedling establishment, a translational regulatory network: SeedTransNet was constructed. Network analysis identified hundreds of gene modules with distinct functions and transcript sequence features indicating the existence of separate translational regulatory circuits possibly acting through specific regulatory elements. The regulatory potential of one such element was confirmed in vivo. The network identified several seed maturation associated genes as central nodes, and we could confirm the importance of many of these hub genes with a maturation associated seed phenotype by mutant analysis. One of the identified regulators an AWPM19 family protein PM19-Like1 (PM19L1) was shown to regulate seed dormancy and longevity. This putative RBP also affects the transitional regulation of one its, by the SeedTransNet identified, target mRNAs. Our data shows the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

systems biology↗