Biology subjects

Jensen, P.

Publications and source records attributed to Jensen, P..

30 records · Page 2Linked to original sources

bioRxiv2022

Improving an rRNA depletion protocol with statistical design of experiments

rRNA depletion is the most expensive step in prokaryotic RNA-seq library preparation. rRNA is so abundant that small increases in depletion efficiency lead to large changes in mRNA sequencing coverage. A variety of commercial and home-made methods exist to lower the cost or increase the efficiency of rRNA removal. Many of these techniques are suboptimal when applied to new species of bacteria or when the protocol or reagents need to be changed. Re-optimizing a protocol by trial-and-error is an expensive and laborious process. Systematic frameworks like the statistical design of experiments (DOE) can improve processes by exploring the quantitative relationship between multiple factors. DOE allows experimenters to find factor interactions that may not be apparent when factors are studied in isolation. We used DOE to optimize an rRNA depletion protocol by updating reagents and identifying factors that maximize rRNA removal and minimize cost. The optimized protocol more efficiently removes rRNA, uses fewer reagents, and is less expensive than the original protocol. Our optimization required only 17 experiments and identified two significant interactions among three factors. Overall, our approach demonstrates the utility of a rational, DOE framework for improving complex protocols.

systems biology↗

bioRxiv2021

Chemogenetic activation of Locus Coeruleus Noradrenergic Neurons Modulates the Default Mode Network

The default mode network (DMN) of the brain is involved in cognition, emotion regulation, impulsivity, and balancing between internally and externally focused states. DMN dysregulation has been implicated in several neurological and neuropsychiatric disorders. In this study, we used functional magnetic resonance imaging (fMRI), positron emission tomography (PET), and spectral fiber-photometry to investigate the selective neuromodulatory effect of norepinephrine (NE)-releasing noradrenergic neurons in the locus coeruleus (LC) on the DMN in mice. Chemogenetic-induced tonic LC-NE activity decreased cerebral blood volume (CBV) and glucose uptake, and increased synchronous low frequency fMRI activity within the frontal cortices of the DMN. Fiber-photometry results corroborated these findings, showing that LC-NE activation induced NE release, enhanced calcium-weighted neuronal spiking, and reduced CBV in the anterior cingulate cortex. These data suggest that LC-NE alters conventional stimulus-evoked coupling between neuronal activity and CBV in the frontal DMN. We also demonstrated that chemogenetic activation of LC-NE neurons strengthened functional connectivity within the frontal DMN, and this effect was causally mediated by reduced modulatory inputs from retrosplenial and hippocampal regions to the association cortices of the DMN.

neuroscience↗

bioRxiv2021

A novel post-translational proteomics platform identifies neurite outgrowth impairments in Parkinson's disease GBA-N370S dopamine neurons

The causes of Parkinsons disease (PD) likely involve complex interactions between environmental factors and susceptibility genes with variants at the GBA locus encoding the glucocerebrosidase (GCase) enzyme being the strongest common genetic risk factor for PD. To understand GBA-related disease mechanisms, we used a novel multipart-enrichment proteomics and post-translational modification workflow to simultaneously identify peptides with phosphorylation, reversible cysteine-modifications or sialylated N-linked glycosylation, alongside unmodified proteins. We identified large numbers of dysregulated proteins and post-translational modifications (PTMs) in heterozygous GBA-N370S PD patient induced pluripotent stem cells (iPSC)-derived dopamine neurons. Alterations in glycosylation status of lysosomal proteins identified disturbances in the autophagy-lysosomal pathway, concurrent with upstream perturbations in mTOR phosphorylation and activity in GBA-N370S iPSC-dopamine neurons. In addition, the strategy revealed several native and modified proteins encoded by PD-associated genes to be dysregulated in GBA-N370S neurons, enhancing our understanding of the wider role of GBA mutations on the neuronal proteome. Integrated pathway analysis of all datasets revealed impaired neuritogenesis in GBA-N370S PD iPSC-dopamine neurons and identified tau (MAPT) as a key mediator of this process. Using a functional assay, we confirmed neurite outgrowth deficits in GBA-N370S PD neurons and a central role for tau in this process. Furthermore, pharmacological restoration of GCase activity in GBA-N370S PD patient neurons rescued the neurite outgrowth deficit. Overall, this study demonstrates the potential of PTMomics to elucidate novel neurodegeneration-associated pathways and identify phenotypes and potential drug targets in complex disease models.

neuroscience↗

bioRxiv2020

Mutations on a novel brain-specific isoform of PGC1α leads to extensive upregulation of neurotransmitter-related genes and sexually dimorphic motor deficits in mice

The peroxisome proliferator-activated receptor gamma co-activator 1 alpha (PGC1) is known as a transcriptional co-activator in peripheral tissues but its function in the brain remains poorly understood. Various brain-specific Pgc1 isoforms have been reported in mice and humans, including transcripts derived from a novel promoter about [~]580 Kb upstream from the reference gene. These isoforms incorporate repetitive sequences from the simple sequence repeat (SSR) and short interspersed nuclear element (SINE) classes and are predicted to give rise to proteins with distinct amino-termini. In this study, we show that a SINE-containing isoform is the predominant form of Pgc1 expressed in neurons. We then generated a mouse carrying a mutation within the SINE to study its functional role in the brain. By combining genomics, biochemical and behavioural approaches, we show that this mutation leads to impaired motor coordination in females, but not male mice, associated with the upregulation of hundreds of cerebellar genes. Moreover, our analysis suggests that known nuclear receptors interact with this isoform of PGC1 in the brain to carry out the female transcriptional program. These data expand our knowledge on the role of Pgc1 in the brain and help explain its conflicting roles in neurological disease and behavioural outcomes.

neuroscience↗

bioRxiv2020

Synaptic transmission induces site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals

Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show a novel potential modulator of synaptic transmission, sialylation of N-linked glycosylation. The negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after five seconds depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.

neuroscience↗

bioRxiv2019

A role for the locus coeruleus in the modulation of feeding

Recent data suggest that LC-NE neurons play a role in fear-induced suppression of feeding, but their endogenous activity in naturally behaving animals has not been explored. We found that endogenous activity of LC-NE neurons was enhanced during food approach and suppressed during food consumption, and that these food-evoked LC-NE responses were attenuated in sated mice. Interestingly, visual-evoked LC-NE activity was also attenuated in sated mice, demonstrating that internal satiety state modulates LC-NE encoding of multiple behavioral states. We also found that food intake could be attenuated by brief or longer durations of LC-NE activation. Lastly, we demonstrated that activation of LC neurons suppresses feeding and enhances avoidance and anxiety-like responding through a projection to the lateral hypothalamus. Collectively, our data suggest that LC-NE neurons modulate feeding by integrating both external cues (e.g., anxiogenic environmental cues) and internal drives (e.g., nutritional state).

neuroscience↗

bioRxiv2019

Elimination of galanin synthesis in noradrenergic neurons reduces galanin in select brain areas and promotes active coping behaviors

Accumulating evidence indicates that disruption of galanin signaling is associated with neuropsychiatric disease, but the precise functions of this neuropeptide remain largely unresolved due to lack of tools for experimentally disrupting its transmission in a cell type-specific manner. To examine the function of galanin in the noradrenergic system, we generated and crossed two novel knock-in mouse lines to create animals lacking galanin specifically in noradrenergic neurons (GalcKO-Dbh). We observed reduced levels of galanin peptide in pons, hippocampus, and prefrontal cortex of GalcKO-Dbh mice, indicating that noradrenergic neurons are a significant source of galanin to those brain regions, while midbrain and hypothalamic galanin levels were comparable to littermate controls. In these same brain regions, we observed no change in levels of norepinephrine or its major metabolite at baseline or after an acute stressor, suggesting that loss of galanin does not affect noradrenergic synthesis or turnover. GalcKO-Dbh mice had normal performance in tests of depression, learning, and motor-related behavior, but had an altered response in some anxiety-related tasks. Specifically, GalcKO-Dbh mice showed increased marble and shock probe burying and had a reduced latency to eat in a novel environment, indicative of a more proactive coping strategy. Together, these findings indicate that noradrenergic neurons provide a significant source of galanin to discrete brain areas, and noradrenergic-specific galanin opposes adaptive coping responses.

neuroscience↗

bioRxiv2019

Phosphoproteomic identification of Xin as a novel requirement for skeletal muscle disuse atrophy

BackgroundImmobilization of skeletal muscle in a stretched position is associated with marked protection against disuse atrophy. Some intramyocellular changes in known proteins and post-translational modifications were previously linked to this phenomenon but there are likely many presently unknown proteins and post-translational modifications that contribute to this beneficial effect.\n\nMethodsTo identify novel proteins and phosphorylation events involved in stretch-induced reduction of disuse atrophy, we conducted a global unbiased screen of the changes occurring in skeletal muscle in control vs. 1 day and 1 week stretched cast-immobilized mouse tibialis anterior muscle, using quantitative tandem mass spectrometry on HILIC-fractionated muscle peptides with follow-up studies in transgenic mice and humans.\n\nResultsOur mass spectrometry analyses detected 11714 phosphopeptides and 2081 proteins, of which 53 phosphopeptides and 5 proteins, 125 phosphopeptides and 43 proteins were deregulated after 1D and 7D of stretched immobilization, respectively. The sarcomere and muscle tendinous junction-associated putative multi-adaptor protein Xin was among the most highly upregulated proteins both in terms of phosphorylation and protein expression and was confirmed to increase with stretch but not disuse atrophy in mice and to increase and decrease with exercise and cast immobilization, respectively, in humans. Xin-/- mice were partially protected against disuse but not denervation atrophy in both stretched and flexed immobilized muscles compared to WT.\n\nConclusionThis study identified Xin as a novel protein involved in disuse atrophy and also provides a resource to guide future hypothesis-driven investigations into uncovering critical factors in the protection against disuse atrophy.

physiology↗

bioRxiv2018

droplet-Tn-Seq combines microfluidics with Tn-Seq identifying complex single-cell phenotypes

While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. droplet-Tn-seq solves that problem by microfluidics facilitated encapsulation of individual transposon mutants into liquid-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Importantly, all advantages of Tn-Seq are conserved, while reducing costs and greatly extending its applicability.

microbiology↗

bioRxiv2018

CREBBP and WDR 24 Affects Quantitative Variation in Red Colouration in the Chicken

Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signaling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilizing a domestic x wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red colouration in chickens. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.

genetics↗

bioRxiv2017

CA2 Neuronal Activity Controls Hippocampal Oscillations and Social Behavior

Hippocampal oscillations arise from coordinated activity among distinct populations of neurons and are associated with cognitive functions and behaviors. Although much progress has been made toward identifying the relative contribution of specific neuronal populations in hippocampal oscillations, far less is known about the role of hippocampal area CA2, which is thought to support social aspects of episodic memory. Furthermore, the little existing evidence on the role of CA2 in oscillations has led to conflicting conclusions. Therefore, we sought to identify the specific contribution of CA2 pyramidal neurons to brain oscillations using a controlled experimental system. We used excitatory and inhibitory DREADDs in transgenic mice to acutely and reversibly manipulate CA2 pyramidal cell activity. Here, we report on the role of CA2 in hippocampal-prefrontal cortical network oscillations and social behavior. We found that excitation or inhibition of CA2 pyramidal cells bidirectionally regulated hippocampal and prefrontal cortical low gamma oscillations and inversely modulated hippocampal ripple oscillations. Further, CA2 inhibition impaired social approach behavior. These findings support a role for CA2 in low gamma generation and ripple modulation within the hippocampus and underscore the importance of CA2 neuronal activity in extrahippocampal oscillations and social behavior.

neuroscience↗

bioRxiv2017

Genetics and genomics of social behaviour in a chicken model

The identification of genes affecting behaviour can be problematic, yet their identification allows a raft of possibilities. Sociality and social behaviour can have multiple definitions, though at its core it is the desire to seek contact with con- or hetero-specifics. The identification of genes affecting sociality can therefore give insights into the maintenance and establishment of sociality. In this study we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement (SR) behaviour. A total of 24 SR QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamus tissue. Correlations between overlapping QTL and eQTL indicated 5 strong candidate genes, with the gene TTRAP being strongly significantly correlated with multiple aspects of SR behaviour, as well as possessing a highly significant eQTL. The distribution of eQTL can also indicate the genetic mechanisms underlying domestication itself. Multiple eQTL were found to in discrete clusters, however tests for pleiotropy show that these blocks were primarily linked in origin. This suggests that clustered genetic modules, rather than pure pleiotropy (as hypothesised by the neural crest theory) appears to be driving domestication in the chicken.

genetics↗