Biology subjects

Perry, R.

Publications and source records attributed to Perry, R..

9 recordsLinked to original sources

bioRxiv2023

Exploring the embodied mind: functional connectome fingerprinting of meditation expertise

BACKGROUNDShort mindfulness-based interventions have gained traction in research due to their positive impact on well-being, cognition, and clinical symptoms across various settings. However, these short-term trainings are viewed as preliminary steps within a more extensive transformative path, presumably leading to long-lasting trait changes. Despite this, little is still known about the brain correlates of these meditation traits. METHODTo address this gap, we investigated the neural correlates of meditation expertise in long-term Buddhist practitioners, comparing the large-scale brain functional connectivity of 28 expert meditators with 47 matched novices. Our hypothesis posited that meditation expertise would be associated with specific and enduring patterns of functional connectivity present during both meditative (open monitoring/open presence and loving-kindness compassion meditations) and non-meditative resting states, as measured by connectivity gradients. RESULTSApplying a support vector classifier to states not included in training, we successfully decoded expertise as a trait, demonstrating its non-state-dependent nature. The signature of expertise was further characterized by an increased integration of large-scale brain networks, including the dorsal and ventral attention, limbic, frontoparietal and somatomotor networks. The latter correlated with a higher ability to create psychological distance from thoughts and emotions. CONCLUSIONSuch heightened integration of bodily maps with affective and attentional networks in meditation experts could point toward a signature of the embodied cognition cultivated in these contemplative practices.

neuroscience↗

bioRxiv2023

The first proof of concept demonstration of nanowarming in coral tissue

Climate change is causing ocean acidification and warming, resulting in mass bleaching and death of corals globally. Cryopreservation and biobanking to secure the genetics of threatened populations is currently limited to coral sperm and larvae, which are only available during brief annual spawning events and are impacted by ocean warming, so there is an urgent need for methods to enable biobanking activities year-round. Here, we used vitrification and nanowarming to successfully recover adult coral tissues in a novel sample type, the single-polyp microfragment (SPMF). Fluorescence and confocal microscopy showed clearly defined tissues and green fluorescent protein fluorescence around the polyp mouth post-warming in 43.3% of SPMFs at 24 hours post-warming, and 30.0% at one month. These advances provide a basis for continued research and development of a field-ready protocol for cryopreservation of adult coral tissues, to permit biobanking of threatened coral species throughout the year and support reef restoration efforts.

ecology↗

bioRxiv2023

Cryopreservation and revival of Hawaiian stony corals via isochoric vitrification

Corals are under siege by both local and global threats, creating a wordwide reef crisis. Cryopreservation is an important intervention measure and a vital component of the modern coral conservation toolkit, but preservation techniques are currently limited to sensitive reproductive materials that can only be obtained a few nights per year during spawning. Here, we report the first successful cryopreservation and revival of cm-scale coral fragments via mL-scale isochoric vitrification. We demonstrate coral viability at 24h post-thaw using a calibrated oxygen-uptake respirometry technique, and further show that the method can be applied in a passive, electronics-free configuration. Finally, we detail a complete prototype coral cryopreservation pipeline, which provides a platform for essential next steps in modulating postthaw stress and initiating long-term growth. These findings pave the way towards an approach that can be rapidly deployed around the world to secure the biological genetic diversity of our vanishing coral reefs.

biophysics↗

bioRxiv2023

Metrics of Coral Microfragment Viability

Coral reefs are being degraded at unprecedented rates and decisive intervention actions are urgently needed to help them. One such intervention in aid of reefs is coral cryopreservation. Although the cryopreservation of coral sperm and larvae has been achieved, preservation of coral fragments including both its tissue and skeleton, has not. The goal of this paper was to understand and assess the physiological stressors that might underlie coral fragment cryopreservation and the long-term consequences of these physiological exposures to continued growth. Therefore, we assessed small fragments ([~]0.5 x0.5 mm2) from the Hawaiian coral, Porites compressa, examining: 1) the sensitivity of the fragments and their algal symbionts to chilling temperatures; 2) the sensitivity of the coral to complex cryoprotectants; 3) methods to safely remove the algal symbionts from the coral fragment for cryopreservation, given the two symbiotic partners may require different cryopreservation protocols; 4) continued growth over time of coral fragments once returned to running seawater after treatment exposures; and, 5) assessment of health and viability of microfragments after treatments examining the distribution of green fluorescent protein and fluorescent symbionts. Technological advances in cryo-technology promise to support successful coral fragment cryopreservation soon, and its success could help secure much of the genetic and biodiversity of reefs in the next decade.

cell biology↗

bioRxiv2022

Tank Fouling Community Enhances Coral Microfragment Growth

Anthropogenic stressors threaten reefs worldwide and natural in situ coral reproduction may be inadequate to meet this challenge. Land-based culture can provide increased coral growth, especially with microfragments. We tested whether culture methods using different algal fouling communities could improve the growth and health metrics of microfragments of the Hawaiian coral, Porites compressa. Culture method fouling communities were: 1) similar to a reef environment (Mini Reef); 2) clean tanks managed to promote crustose coralline algae (Clean Start); and, 3) tanks curated beforehand with poorly-competing algae (Green Film) assessed in winter and summer months. The Green Film method during the winter produced the fastest microfragment mean growth at 28 days until the first row of new polyps developed and the highest tank metric scores. Time efficient, standardized methods for land-based culture designed to maximize growth and production of coral fragments will contribute considerably to the success of large scale restoration efforts.

zoology↗

bioRxiv2022

Securing algal endosymbiont communities for reef-building corals

Photosynthetic dinoflagellates that live in symbiosis with corals (family Symbiodiniaceae) are fundamental for the survival of coral reef ecosystems. During coral bleaching events, it is assumed that these symbionts remain available in the water column, in sediments, or are seeded from unbleached coral colonies. Yet, this hypothesis has not been verified and it remains unclear whether some diversity of Symbiodiniaceae may be lost in the process. Culture methods have been developed for some Symbiodiniaceae, but for the vast majority of these photosynthetic symbionts, known culture methods are not successful at maintaining them for extensive periods. For these unculturable symbionts, cryopreservation, which places cells and tissues in suspended animation for days to decades, offers the best hope for saving the biodiversity of these crucial coral partners. Some cryopreservation processes use slow freezing, but if the cells are sensitive to low temperatures, as is the case for Symbiodiniaceae, then rapid freezing, called vitrification, is needed. We here, tested two published vitrification protocols that had been designed for algal symbionts extracted from Hawaiian corals, but we were unable to recover living symbionts after vitrification and warming. Therefore, we report a successful optimisation of the former vitrification protocols, which we tested on algal symbionts freshly extracted from three Hawaiian coral species, the development of ultra-rapid laser-warming cryopreservation techniques for symbionts, and banking procedures for algal symbionts. We also present some successful uptake of cryopreserved algal symbionts by coral larvae, although at a low rate. It is unclear why the former vitrification protocols failed but we propose that it may have been related to thermal stress and bleaching events that occurred on several occasions throughout the Hawaiian Islands. Maintenance of biodiversity is essential for sustaining functional, productive ecosystems with the adaptability to effectively recover from disturbances. By successfully cryopreserving and banking coral symbionts, we provide a critically needed component for securing Symbiodiniaceae biodiversity into the future.

zoology↗

bioRxiv2022

Evidence of hatch-time based growth compensation in the early life history of two salmonid fishes

Initial body size can indicate quality within-species, with large size increasing the likelihood of survival. However, some populations or individuals may have body size disadvantages due to spatial/temporal differences in temperature, photoperiod, or food availability. Across-populations animals often have locally adapted physiology to compensate for poor environmental influences on development and growth, while within-populations behavioural adjustments that increase food intake after periods of deprivation provide opportunities to catch up (growth compensation). We posit a theoretical extension of growth compensation to include within-population differences related to short growing seasons due to delayed hatch time. We tested the hypothesis that individual fish that hatch later grow faster than those that hatch earlier. The relative magnitude of such a response was compared to growth variation among populations and between related species. We sampled young of the year Arctic charr and brook trout from five rivers in northern Labrador. Daily increments from otoliths were used to back-calculate size to a common age and calculate growth rates. Supporting the hypothesis, older fish were not larger at capture than younger fish, because animals that hatched later grew faster which may indicate age-based growth compensation.

ecology↗

bioRxiv2020

Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut.

Zinc is an essential cofactor for bacterial metabolism, and many Enterobacteriaceae express the zinc transporters ZnuABC and ZupT to acquire this metal in the host. Unexpectedly, the probiotic bacterium Escherichia coli Nissle 1917 exhibited appreciable growth in zinc-limited media even when these transporters were deleted. By utilizing in vitro and in vivo studies, as well as native spray metal infusion mass spectrometry and ion identity molecular networking, we discovered that Nissle utilizes yersiniabactin as a zincophore. Indeed, yersiniabactin enables Nissle to scavenge zinc in zinc-limited media, to resist calprotectin-mediated zinc sequestration, and to thrive in the inflamed gut. Moreover, we discovered that yersiniabactins affinity for iron or zinc changes in a pH-dependent manner, with higher affinity for zinc as the pH increased. Altogether, we demonstrate that siderophore metal affinity can be influenced by the local environment and reveal a mechanism of zinc acquisition available to many commensal and pathogenic Enterobacteriaceae.

microbiology↗

bioRxiv2018

Extensive Secondary Contact Among Three Glacial Lineages of Arctic Char (Salvelinus alpinus) in Newfoundland and Labrador

We sequenced a portion of the D-loop region in over 1000 Arctic char (Salvelinus alpinus) samples from 67 locations across Newfoundland and Labrador to assess the extent of secondary contact among the Arctic, Atlantic, and Acadian glacial lineages in Newfoundland and Labrador. Within Labrador, the Arctic and Atlantic lineages were widespread. Two locations (one landlocked and one with access to the sea) also contained individuals of the Acadian lineage, constituting the first record of this lineage in Labrador. Atlantic and Acadian lineage individuals were found in both eastern and western Newfoundland. Multiple sampling locations in Newfoundland and Labrador contained fish of two or more different glacial lineages, implying their introgression. Glacial lineage did not appear to dictate contemporary genetic divergence between the pale and dark morph of char present in Gander Lake, Newfoundland. Both were predominately of the Atlantic lineage, suggesting the potential for their divergence in sympatry. This study reveals Newfoundland and Labrador to be a unique junction of three glacial lineages which have likely hybridized extensively in this region.

evolutionary biology↗