Biology subjects

Rees, A.

Publications and source records attributed to Rees, A..

5 recordsLinked to original sources

bioRxiv2024

Exploiting facial side similarities to improve AI-driven sea turtle photo-identification systems

AO_SCPLOWBSTRACTC_SCPLOWAnimal Photo-identification (photo-ID) denotes the process of identifying individual animals based on their unique and stable morphological characteristics. It has been proven to be a particularly useful tool for a variety of studies on sea turtles increasing the knowledge of their ecology and informing conservation efforts. The photo-ID process in sea turtles is predominantly based on the geometric patterns of the scales of their two head sides which are unique to every individual, and also different from side to side. As such, both manual and automated photo-ID techniques are performed under a side-specific image retrieval setting. There, a query image showing a single profile of an unknown individual, either left or right, is only compared to images of previously identified individuals showing the same side. Here, by employing the recently introduced state-of-the-art deep feature extractor MegaDescriptor, we show for the first time an inherit deep visual similarity between left and right facial profiles of the same individuals in three sea turtle species. We show that the similarity between the left and right profiles of the same individual with respect to geometry, coloration and pigmentation, is on average higher than the similarity between profiles of different individuals. The similarity is detectable even when images are taken years apart and under diverse settings and conditions. We perform several image retrieval experiments under scenarios which mimic realistic sea turtle photo-ID matching processes, where we also allow comparisons of opposite sides in the matching process which have no spatial overlap. We show that the detection and exploitation of this similarity is translated to improved accuracies when compared to the traditional side-specific image retrieval setting. Notably this similarity cannot be detected and thus neither explored by the so-far state-of-the-art sea turtle photo-ID automated methods such as those based on SIFT. Our work leads to a change of paradigm for the sea turtle photo-ID workflows which will be further facilitated by the constant improvement of deep feature-based re-identification methods and paves the path for adopting similar workflows in other animal species as well.

ecology↗

bioRxiv2023

Motor, somatosensory, and executive cortical areas directly modulate firing activity in the auditory midbrain

We have recently reported that the central nucleus of the inferior colliculus (the auditory midbrain) is innervated by glutamatergic pyramidal cells originating not only in auditory cortex (AC) but also in multiple non-auditory regions of the cerebral cortex. Using optogenetics and electrical stimulation, we investigated the functional properties of these descending connections in vivo in anaesthetised rats. A retrograde virus encoding green fluorescent protein (GFP) and channelrhodopsin (ChR2) injected into the central nucleus of the inferior colliculus (ICC), labelled discrete groups of cells in multiple areas of the cerebral cortex. Light stimulation of AC and M1 caused local activation of cortical neurones and increased the firing rate of neurones in ICc indicating a direct excitatory input from AC and M1 to ICC. Electrical stimulation of M1, secondary motor, somatosensory and prefrontal cortical regions evoked short, fixed latency firing events in ICC as well as longer latency, longer duration increases in firing activity. The short latency events were singular spikes of consistent shape and size likely resulting from monosynaptic excitation of individual ICC units. The longer latency responses comprised multiple units and spikes occurred with significant temporal jitter suggesting polysynaptic activation of local circuits within the ICC. The probability of the monosynaptic event, the magnitude of the polysynaptic response, and the area of ICC affected were dependent on the stimulus current. Our data are consistent with cortical regions exerting an important excitatory direct and indirect regulation of ICc neurones. Significance statementWe have recently described inputs from motor, somatosensory, and executive cortices to the inferior colliculus (IC, auditory midbrain). Here we provide functional evidence for such connections. Optogenetics, using a retrograde virus encoding channelrhodopsin injected into IC revealed a direct excitatory influence of neurones in auditory and motor cortices on firing in IC. Electrical stimulation of discrete cortical regions revealed that multiple non-auditory cortical regions have a direct monosynaptic excitatory influence on neurones in the IC which, in turn, activates local circuits increasing the firing probability of multiple neurones in the IC. This is the first evidence for circuitry by which auditory processing can be influenced at an early stage by activity in the sensory, motor and executive domains.

neuroscience↗

bioRxiv2021

Nitric oxide signalling underlies salicylate-induced increases in neuronal firing in the inferior colliculus: a central mechanism of tinnitus?

The tinnitus-inducing agent salicylate reduces cochlear output but causes hyperactivity in higher auditory centres, including the inferior colliculus (the auditory midbrain). Using multi-electrode recording in anaesthetised guinea pigs (Cavia porcellus), we addressed the hypothesis that salicylate-induced hyperactivity in the inferior colliculus involves nitric oxide signalling secondary to increased ascending excitatory input. In the inferior colliculus, systemic salicylate (200 mg/kg i.p., 0 h) markedly increased spontaneous and sound-driven neuronal firing (3-6 h post drug) with both onset and sustained responses to pure tones being massively increased. Reverse microdialysis of increasing concentrations of salicylate directly into the inferior colliculus (100 {micro}M-10 mM, from 0 h) failed to mimic systemic salicylate. In contrast, it caused a small, transient, increase in sound-driven firing (1 h), followed by a larger sustained decrease in both spontaneous and sound-driven firing (2-5 h). When salicylate was given systemically, reverse microdialysis of the neuronal nitric oxide synthase inhibitor L-methyl arginine into the inferior colliculus (500 mM, 2-6 h) completely blocked the salicylate-induced increase in spontaneous and sound-driven neuronal firing. Our data indicate that systemic salicylate induces neuronal hyperactivity in the auditory midbrain via a mechanism outside the inferior colliculus, presumably upstream in the auditory pathway; and that the mechanism is ultimately dependent on nitric oxide signalling within the inferior colliculus. Given that nitric oxide is known to mediate NMDA receptor signalling in the inferior colliculus, we propose that salicylate activates an ascending glutamatergic input to the inferior colliculus and that this is an important mechanism underlying salicylate-induced tinnitus. Graphical abstractTinnitus is associated with increased activity in the central auditory pathway, an effect replicated by high dose sodium salicylate. Here we show that salicylate-induced increases in neuronal activity in the auditory midbrain are mediated by nitric oxide signalling within this region. Nitric oxide is a key mediator of neuronal responses to NMDA receptor stimulation in this region. Our data support the hypothesis that tinnitus is mediated by increased ascending glutamatergic input to the auditory midbrain. O_FIG O_LINKSMALLFIG WIDTH=160 HEIGHT=200 SRC="FIGDIR/small/444151v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1d732dcorg.highwire.dtl.DTLVardef@14c2314org.highwire.dtl.DTLVardef@1930a33org.highwire.dtl.DTLVardef@82d799_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

A novel Ca2+ signalling pathway co-ordinates environmental phosphorus sensing and nitrogen metabolism in marine diatoms

Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients including phosphorus and nitrogen. Although it is well established that diatoms are common first-responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here we show that diatoms use a novel and highly-sensitive Ca2+-dependent signalling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient phosphorus. We demonstrate that phosphorus-Ca2+ signalling is essential for regulating diatom recovery from phosphorus limitation, by controlling rapid and substantial increases in nitrogen assimilation. Phosphorus-Ca2+ signalling thus mediates fundamental cross-talk between the vital nutrients P and N to maximise resource competition, and likely governs the success of diatoms as major bloom formers in regions of pulsed nutrient supply. Importantly, our study demonstrates that distinct mechanisms for nutrient sensing have evolved in photosynthetic eukaryotes.

microbiology↗

bioRxiv2019

Multiple non-auditory cortical regions innervate the auditory midbrain

Our perceptual experience of sound depends on the integration of multiple sensory and cognitive domains, but the networks sub-serving this integration are unclear. There are connections linking different cortical domains, however we do not know if there are also connections between multiple cortical domains and subcortical structures. Retrograde tracing in rats revealed that the inferior colliculus - the auditory midbrain - receives dense descending projections from not only the auditory cortex, but also the visual, somatosensory, motor, and prefrontal cortices. While all these descending connections are bilateral, those from sensory areas show a more pronounced ipsilateral dominance than those from motor and prefrontal cortices. Anterograde tracing from cortical areas identified by retrograde tracing, showed cortical fibres terminating in all three subdivisions of the inferior colliculus, targeting both inhibitory and excitatory neurons. These findings demonstrate that auditory perception is served by a network that includes extensive descending connections from sensory, behavioural, and executive cortices.

neuroscience↗