Biology subjects

Norris, A.

Publications and source records attributed to Norris, A..

22 records · Page 2Linked to original sources

bioRxiv2019

Optimal Multichannel Artifact Prediction and Removal for Brain Machine Interfaces and Neural Prosthetics

Neural implants that electrically stimulate neural tissue such as deep brain stimulators, cochlear implants (CI), and vagal nerve stimulators are becoming the routine treatment options for various diseases. Optimizing electrical stimulation paradigms requires closed-loop stimulation using simultaneous recordings of evoked neural activity in real time. Stimulus-evoked artifacts at the recording site are generally orders of magnitude larger than the neural signals, which challenge the interpretation of evoked neural activity. We developed a generalized artifact removal algorithm that can be applied in a variety of neural recording modalities. The procedure leverages known electrical stimulation currents to derive optimal filters that are used to predict and remove artifacts. We validated the procedure using paired recordings and electrical stimulation from sciatic nerve axons, high-rate bilateral CI stimulation, and concurrent multichannel stimulation in auditory midbrain and recordings in auditory cortex. We demonstrate a vast enhancement in the quality of recording even for high-throughput multi-site stimulation with typical improvements in the signal-to-noise ratio between 20-40 dB. The algorithm is efficient, can be scaled to arbitrary number of sites, and is applicable in range of recording modalities. It has numerous benefits over existing approaches and thus should be valuable for emerging neural recording and stimulation technologies.

neuroscience↗

bioRxiv2019

Cellular contractility coordinates cytoskeletal dynamics and cell behaviour during Drosophila abdominal morphogenesis

During morphogenesis, cells undergo various behaviours, such as migration and constriction, which need to be coordinated. How this is achieved remains elusive. During morphogenesis of the Drosophila adult abdominal epidermis, larval epithelial cells (LECs) migrate directedly before constricting apically and undergoing apoptosis. Here, we study the mechanisms underlying the transition from migration to constriction. We show that LECs possess a pulsatile apical actomyosin network and that a change in network polarity underlies behavioural change. Exploring the properties of the contractile network, we find that the level of cell contractility impacts on the networks behaviour, as well as on overall cytoskeletal architecture and cell behaviour. We also find that pulsed contractions occur only in cells with intermediate levels of contractility. Furthermore, increasing levels of the small Rho GTPase Rho1 disrupts pulsed contractions, and instead leading to cells that cycle between two states, characterised by a junctional cortical and an apicomedial actin network. Our results highlight that behavioural change relies on tightly controlled cellular contractility. Moreover, we show that constriction can occur without pulsed contractions, raising questions about their contribution to constriction.

cell biology↗

bioRxiv2019

Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

1.Domestication of Atlantic salmon started approximately forty years ago, using both artificial and natural selection strategies. Such selection methods are likely to have imposed distinctive selection signatures on the salmon genome. Therefore, identifying differences in selection signatures may give insights into the mechanism of selection and candidate genes of biological and productive interest. Here, we used two complementary haplotype-based statistics, the within-population integrated Haplotype Score test (|iHS|) and the cross-population Extended Haplotype Homozygosity test (XP-EHH) to compare selection signatures in four populations of Atlantic salmon with a common genetic origin. Using |iHS| we found 24, 14, 16 and 26 genomic regions under selection in Pop-A, Pop-B, Pop-C, and Pop-D, respectively. While using the XP-EHH test we identified 27, 25 and 15 potential selection regions in Pop-A/Pop-B, Pop-A/Pop-C and Pop-A/Pop-D, respectively. These genomic regions harbor important genes such igf1r and sh3rf1 which have been associated with growth related traits in other species. Our results contribute to the detection of candidate genes of interest and help to understand the evolutionary and biological mechanisms for controlling complex traits under selection in Atlantic salmon.

genetics↗

bioRxiv2018

Reporter Ion Data Analysis Reduction (R.I.D.A.R) for isobaric proteomics quantification studies

Isobaric labeling-based relative quantification techniques such as iTRAQ and TMT were introduced 15 years ago and are now nearly ubiquitous in shotgun proteomics labs around the world. The methods for data processing in these experiments has changed little since inception, with peptide database searching of all MS/MS spectra occurring concurrent or asynchronous to the quantification of the reporter fragment regions. In this study we present an alternative method for data processing whereby the reporter ion region of all MS/MS spectra are first examined and spectra that are not quantitatively interesting to the end user are discarded. The remaining MS/MS spectra that are retained can then be more rapidly searched for computationally expensive database alterations such as post-translational modifications and single amino acid variations in more practical time. We have termed this method Reporter Ion Data Analysis Reduction (RIDAR). To demonstrate the application of RIDAR, we reprocess a recent CPTAC 2 study containing approximately 7.8 million MS/MS spectra. Post RIDAR processing we can search this public dataset versus a human canonical FASTA database and a compiled proteogenomic database of over 875,000 known cancer mutations in a single day on a standard desktop computer, a time reduction of 85% compared to the conventional workflow. With the rapidly increasing size and density of shotgun proteomics data files, RIDAR facilitates rapid analysis of large proteomics datasets for researchers without access to high performance computational resources.\n\nAbstract Graphic\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC=\"FIGDIR/small/437210_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (14K):\norg.highwire.dtl.DTLVardef@1bcf00eorg.highwire.dtl.DTLVardef@134510eorg.highwire.dtl.DTLVardef@1b594b4org.highwire.dtl.DTLVardef@35e268_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗