Biology subjects

Ellis, M.

Publications and source records attributed to Ellis, M..

22 records · Page 2Linked to original sources

bioRxiv2020

Disinhibition of the orbitofrontal cortex biases goal-directed behaviour in obesity

The lateral orbitofrontal cortex (lOFC) receives sensory information about food and integrates these signals with expected outcomes to guide future actions, and thus may play a key role in a distributed network of neural circuits that regulate feeding behaviour. Here, we reveal a novel role for the lOFC in the cognitive control of behaviour in obesity. Food-seeking behaviour is biased in obesity such that in male obese mice, behaviours are less flexible to changes in the perceived value of the outcome. Obesity is associated with reduced lOFC inhibitory drive, and chemogenetic reduction in GABAergic neurotransmission in the lOFC induces obesity-like impairments in goal-directed behaviour. Conversely, pharmacological or optogenetic restoration of inhibitory neurotransmission in the lOFC of obese mice reinstates flexible behaviour. Our results indicate that obesity-induced disinhibition of the lOFC leads to a failure to update changes in the value of food with satiety, which in turn may influence how individuals make decisions in an obesogenic environment.

neuroscience↗

bioRxiv2018

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

Recent advances in long-read sequencing enable the characterization of genome structure and its intra- and inter-species variation at a resolution that was previously impossible. Detecting overlaps between reads is integral to many long-read genomics pipelines, such as de novo genome assembly. While longer reads simplify genome assembly and improve the contiguity of the reconstruction, current long-read technologies come with high error rates. We present Berkeley Long-Read to Long-Read Aligner and Overlapper (BELLA), a novel algorithm for computing overlaps and alignments via sparse matrix-matrix multiplication that balances the goals of recall and precision, performing well on both. We present a probabilistic model that demonstrates the feasibility of using short k-mers for detecting candidate overlaps. We then introduce a notion of reliable k-mers based on our probabilistic model. Combining reliable k-mers with our binning mechanism eliminates both the k-mer set explosion that would otherwise occur with highly erroneous reads and the spurious overlaps from k-mers originating in repetitive regions. Finally, we present a new method based on Chernoff bounds for separating true overlaps from false positives using a combination of alignment techniques and probabilistic modeling. Our methodologies aim at maximizing the balance between precision and recall. On both real and synthetic data, BELLA performs amongst the best in terms of F1 score, showing performance stability which is often missing for competitor software. BELLAs F1 score is consistently within 1.7% of the top entry. Notably, we show improved de novo assembly results on synthetic data when coupling BELLA with the Miniasm assembler.

bioinformatics↗

bioRxiv2018

Guiding dose selection of monoclonal antibodies using a new parameter (AFTIR) for characterizing ligand binding systems

Guiding the dose selection for monoclonal antibody oncology drugs is often done using methods for predicting the receptor occupancy of the drug in the tumor. In this manuscript, previous work on characterizing target inhibition at steady state using the AFIR metric [1] is extended to include a \"target-tissue\" compartment and the shedding of membrane-bound targets. A new potency metric AFTIR (Averarge Free Tissue target to Initial target ratio at steady state) is derived, and it depends on only four key quantities: the equilibrium binding constant, the fold-change in target expression at steady state after binding to drug, the biodistribution of target from circulation to target tissue, and the average drug concentration in circulation. The AFTIR metric is useful for guiding dose selection, for efficiently performing sensitivity analyses, and for building intuition for more complex target mediated drug disposition models. In particular, reducing the complex, physiological model to four key parameters needed to predict target inhibition helps to highlight specific parameters that are the most important to estimate in future experiments to guide drug development.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC=\"FIGDIR/small/432500_fig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@6895d7org.highwire.dtl.DTLVardef@4566e0org.highwire.dtl.DTLVardef@6515e8org.highwire.dtl.DTLVardef@8168ea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1C_FLOATNO Graphical Abstract\n\nC_FIG

pharmacology and toxicology↗

bioRxiv2018

LRRK2 kinase inhibitors induce a reversible effect in the lungs of non-human primates with no measurable pulmonary deficits

Putative gain-of-function mutations in leucine-rich repeat kinase 2 (LRRK2), resulting in increased kinase activity and cellular toxicity, are a leading genetic cause of Parkinsons disease (PD). Hence, there is strong interest in developing LRRK2 kinase inhibitors as a disease-modifying therapy. Published reports that repeat dosing with two LRRK2 kinase inhibitors (GNE-7915 and GNE-0877) induce histopathological changes in the lung of non-human primates Fuji et al. 2015 (1) raised concerns about potential safety liability of LRRK2 kinase inhibitors. In the present study, we sought to determine whether previously observed effects in the lung: (a) represent on-target pharmacology, but with the potential for margin of safety, (b) are reversible upon drug withdrawal, and (c) are associated with pulmonary function deficits. To this end, we evaluated the histopathological effects, toxicokinetics and target inhibition of three structurally diverse LRRK2 kinase inhibitors, GNE-7915 (30 mg/kg, BID, as a positive control), MLi-2 (15 and 50 mg/kg, QD) and PFE-360 (3 and 6 mg/kg, QD) following 2 weeks of dosing in non-human primates. Subsets of animals dosed with GNE-7915 or MLi-2 were evaluated after 2-week dose-free periods. All three LRRK2 kinase inhibitors induced mild cytoplasmic vacuolation of type II pneumocytes, as reported previously, confirming an on-target effect of these compounds. Interestingly, despite lower doses of both PFE-360 and MLi-2 producing nearly complete inhibition of LRRK2 kinase activity in the brain as assessed by levels of pS935-LRRK2, histopathological changes in lung were absent in animals treated with low-dose PFE-360 and observed only sporadically in the low-dose MLi-2 group. The lung effect was fully reversible at 2 weeks post-dosing of GNE-7915. In a second study of identical dosing with MLi-2 and GNE-7915, no deficits were observed in a battery of translational pulmonary functional tests. In aggregate, these results do not preclude the development of LRRK2 kinase inhibitors for clinical investigation in Parkinsons disease.

pharmacology and toxicology↗