Biology subjects

Bell, T.

Publications and source records attributed to Bell, T..

31 records · Page 2Linked to original sources

bioRxiv2020

Uneven protection of persistent giant kelp forest in the Northeast Pacific Ocean

In most regions, the distribution of marine forests and the efficacy of their protection is unknown. We mapped the persistence of giant kelp forests across ten degrees of latitude in the Northeast Pacific Ocean and found that 7.7% of giant kelp is fully protected, with decreasing percentages from north to south. Sustainability goals should prioritize kelp mapping and monitoring, while protection and climate adaption targets should account for habitat dynamics.

ecology↗

bioRxiv2020

Systematic variation in the temperature dependence of bacterial carbon use efficiency

Understanding the temperature dependence of carbon use efficiency (CUE) is critical for understanding microbial physiology, population dynamics, and community-level responses to changing environmental temperatures 1,2. Currently, microbial CUE is widely assumed to decrease with temperature 3,4. However, this assumption is based largely on community-level data, which are influenced by many confounding factors 5, with little empirical evidence at the level of individual strains. Here, we experimentally characterise the CUE thermal response for a diverse set of environmental bacterial isolates. We find that contrary to current thinking, bacterial CUE typically responds either positively to temperature, or has no discernible temperature response, within biologically meaningful temperature ranges. Using a global data-synthesis, we show that our empirical results are generalisable across a much wider diversity of bacteria than have previously been tested. This systematic variation in the thermal responses of bacterial CUE stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide fundamental new insights into microbial physiology, and a basis for more accurately modelling the effects of shorter-term thermal fluctuations as well as longer-term climatic warming on microbial communities.

microbiology↗

bioRxiv2020

Ultra-Low Colcemid Doses Induce Microtubule Dysfunction as Revealed by Super-Resolution Microscopy

Microtubule-interacting drugs, sometimes referred to as antimitotics, are used in cancer therapy to target and disrupt micro-tubules. However, their side effects require the development of safer drug regimens that still retain clinical efficacy. Currently, many questions remain regarding microtubule-interacting drugs at clinically relevant and ultra-low doses. Here, we use super-resolution microscopies (single molecule localization and optical fluctuation based) to reveal the initial microtubule dysfunctions caused by nanomolar concentrations of colcemid. Short exposure to 30 - 80 nM colcemid results in aberrant microtubule curvature while microtubule fragmentation is detected upon treatment with [≥]100 nM colcemid. Remarkably, even ultra-low doses (5 hours at <20 nM) led to subtle but significant microtubule architecture remodeling and suppression of microtubule dynamics. These challenges to microtubule function represent less severe precursor perturbations compared to the established antimitotic effects of microtubule-interacting drugs, and therefore offer potential for improved understanding and design of anti-cancer agents.

cell biology↗

bioRxiv2020

Intolerance of uncertainty is associated with heightened responding in the prefrontal cortex during instructed threat of shock

Heightened responding to uncertain threat is considered a hallmark of anxiety disorder pathology. Here, we sought to determine if individual differences in self-reported intolerance of uncertainty (IU), a key transdiagnostic dimension in anxiety-related pathology, underlies differential recruitment of neural circuitry during instructed outcome uncertainty of threat (n = 42). In an instructed threat of shock task, cues signalled uncertain threat of shock (50%) or certain safety from shock outcomes. Ratings of arousal and valence, skin conductance response (SCR) and functional magnetic resonance imaging were acquired. Overall, participants displayed greater ratings of arousal and negative valence, SCR, and amygdala activation to uncertain threat vs. safe cues. IU was not associated with greater arousal ratings, SCR or amygdala activation to uncertain threat vs. safe cues. However, we found that high IU was associated with greater ratings of negative valence and greater activity in the medial prefrontal cortex and dorsomedial rostral prefrontal cortex to uncertain threat vs safe cues. These findings suggest that during instructed outcome uncertainty of threat, individuals high in IU rate uncertain threat as aversive and engage prefrontal cortical regions known to be involved in safety-signalling and conscious threat appraisal. Taken together, these findings highlight the potential of IU in modulating safety-signalling and conscious appraisal mechanisms in situations with instructed outcome uncertainty of threat, which may be relevant to models of anxiety-related pathology.

neuroscience↗

bioRxiv2019

Productive bacterial communities exclude invaders

Experiments with artificial communities have suggested that invasion resistance in microbial communities is often a side-effect of community members contribution towards overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, few experiments have investigated this in natural microbial communities. We conducted experimental invasions of two bacterial species (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally-occurring microbial communities collected in the field. Using 16S amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.

ecology↗

bioRxiv2019

Microbial metabolically cohesive consortia and ecosystem functioning

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities, many excreted by-products of metabolism may also be resources. Microbial communities therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organisation between the species and the community level may be pervasive, where tightly-knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community-, and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.

microbiology↗

bioRxiv2019

Effects of Transcranial Direct Current Stimulation on GABA and Glutamate in Children: A Pilot Study

Transcranial direct current stimulation (tDCS) is a form of non-invasive brain stimulation that safely modulates brain excitability and has therapeutic potential for many conditions. Several studies have shown that anodal tDCS of the primary motor cortex (M1) facilitates motor learning and plasticity, but there is little information about the underlying mechanisms. Using magnetic resonance spectroscopy (MRS) it has been shown that tDCS can affect local levels of {gamma}-aminobutyric acid (GABA) and Glx (a measure of glutamate and glutamine combined) in adults, both of which are known to be associated with skill acquisition and plasticity; however this has yet to be studied in children and adolescents. This study examined GABA and Glx in response to conventional anodal tDCS (a-tDCS) and high definition tDCS (HD-tDCS) targeting the M1 in a pediatric population. Twenty-four typically developing, right handed children ages 12-18 years participated in five consecutive days of tDCS intervention (sham, a-tDCS or HD-tDCS) targeting the right M1 while training in a fine motor task (Purdue Pegboard Task) with their left hand. Glutamate and GABA were measured before and after the protocol (at day 5 and 6 weeks) using conventional MRS and GABA-edited MRS in the sensorimotor cortices. Glutamate measured in the left sensorimotor cortex was higher in the HD-tDCS group compared to a-tDCS and sham at 6 weeks (p = 0.001). No changes in GABA were observed in either sensorimotor cortex at any time. These results suggest that neither a-tDCS or HD-tDCS locally affect GABA and glutamate in the developing brain and therefore it may demonstrate different responses in adults.

neuroscience↗

bioRxiv2019

functionInk: An efficient method to detect functional groups in multidimensional networks reveals the hidden structure of ecological communities

O_LIComplex networks have been useful to link experimental data with mechanistic models, and have become widely used across many scientific disciplines. Recently, the increasing amount and complexity of data, particularly in biology, has prompted the development of multidimensional networks, where dimensions reflect the multiple qualitative properties of nodes, links, or both. As a consequence, traditional quantities computed in single dimensional networks should be adapted to incorporate this new information. A particularly important problem is the detection of communities, namely sets of nodes sharing certain properties, which reduces the complexity of the networks, hence facilitating its interpretation. C_LIO_LIIn this work, we propose an operative definition of "function" for the nodes in multidimensional networks, and we exploit this definition to show that it is possible to detect two types of communities: i) modules, which are communities more densely connected within their members than with nodes belonging to other communities, and ii) guilds, which are sets of nodes connected with the same neighbours, even if they are not connected themselves. We provide two quantities to optimally detect both types of communities, whose relative values reflect their importance in the network. C_LIO_LIThe flexibility of the method allowed us to analyze different ecological examples encompassing mutualistic, trophic and microbial networks. We showed that by considering both metrics we were able to obtain deeper ecological insights about how these different ecological communities were structured. The method mapped pools of species with properties that were known in advance, such as plants and pollinators. Other types of communities found, when contrasted with external data, turned out to be ecologically meaningful, allowing us to identify species with important functional roles or the influence of environmental variables. Furthermore, we found the method was sensitive to community-level topological properties like the nestedness. C_LIO_LIIn ecology there is often a need to identify groupings including trophic levels, guilds, functional groups, or ecotypes.The method is therefore important in providing an objective means of distinguishing modules and guilds. The method we developed, functionInk (functional linkage), is computationally efficient at handling large multidimensional networks since it does not require optimization procedures or tests of robustness. The method is available at: HTTPS://GITHUB.COM/APASCUALGARCIA/FUNCTIONINK. C_LI

bioinformatics↗

bioRxiv2019

Community-level signatures of ecological succession in natural bacterial communities

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We present an integrative top-down analysis of over 700 bacterial communities sampled from water-filled beech tree-holes in the United Kingdom at distances between <5m to >100km, combining an analyses of community composition (16S rRNA sequencing) with assays of community functional capacity (exo-enzymatic activities, ATP production, CO2 dissipation and yield). The communities were grown in laboratory conditions in a complex growth medium, what allowed us to investigate the relationship between composition and function, excluding confounding environmental factors. We found a distance-decay trend in the similarity of the communities, and simulated data allowed us to reject the hypothesis that stochastic processes dominated the assembly of the communities, suggesting that niche effects prevailed. Consistent with this idea, clustering of communities lead us to identify six distinct community classes encompassing samples collected at often distant locations. Using structural equation modelling, we explored how functions were interrelated, demonstrating that a representative functional signature can be associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions with PiCRUST. Notably, this approach allowed us to show that these classes contain distinct genetic repertoires reflecting community-level ecological strategies. We finally formulated an over-arching ecological hypothesis about how local conditions drive succession in these habitats. The ecological strategies resemble the classical distinction between r- and K-strategists and could be extrapolated to other systems, suggesting that a coarse grained picture of microbial ecological succession may be explained by relatively simple ecological mechanisms.

microbiology↗

bioRxiv2019

Metabolic rates of prokaryotic microbes may inevitably rise with global warming

Understanding how the metabolic rates of prokaryotes respond to temperature is fun-damental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima [lsim] 45{degrees}C), but not thermophiles ({gtrsim} 45{degrees}C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Given that climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, carbon efflux, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.

ecology↗

bioRxiv2018

Regional Striatal Cholinergic Involvement in Human Behavioural Flexibility

Animal studies have shown that the striatal cholinergic system plays a role in behavioural flexibility but, until recently, this system could not be studied in humans due to a lack of appropriate non-invasive techniques. Using proton magnetic resonance spectroscopy (1H-MRS) we recently showed that the concentration of dorsal striatal choline (an acetylcholine precursor) changes during reversal learning (a measure of behavioural flexibility) in humans. The aim of the present study was to examine whether regional average striatal choline was associated with reversal learning. We measured choline at rest in both the dorsal and ventral striatum using 1H-MRS and examined its relationship with performance on a probabilistic learning task with a reversal component. Task performance was described using a simple reinforcement learning model that dissociates the contributions of positive and negative prediction errors to learning. Average levels of choline in the dorsal striatum were associated with performance during reversal, but not during initial learning. Specifically, lower levels of choline in the dorsal striatum were associated with a lower number of perseverative trials. Moreover, choline levels explained inter-individual variance in perseveration over and above that explained by learning from negative prediction errors. These findings suggest that the dorsal striatal cholinergic system plays an important role in behavioural flexibility, in line with evidence from the animal literature and our previous work in humans. Additionally, this work provides further support for the idea of measuring choline with 1H-MRS as a non-invasive way of studying human cholinergic neurochemistry.\n\nSIGNIFICANCE STATEMENTBehavioural flexibility is a crucial component of adaptation and survival, as well as everyday living. Evidence from the animal literature shows the striatal cholinergic system is fundamental to reversal learning, a key paradigm for studying behavioural flexibility. However, this system remains understudied in humans, largely due to a lack of non-invasive techniques. Using proton magnetic resonance spectroscopy (1H-MRS), we showed that choline levels at rest in the dorsal striatum are associated with individual differences in performance specifically during reversal learning. These novel findings help to bridge the gap between animal studies of the striatal cholinergic system and human studies of basal ganglia function, by demonstrating the importance of cholinergic function in the dorsal striatum in human behavioural flexibility. Importantly, the methods described here can not only be applied to furthering our understanding of healthy human neurochemistry, but can also be applied to extending our understanding of cholinergic disorders.

neuroscience↗

bioRxiv2018

Thalamostriatal Interactions in Human Reversal Learning

Cognitive flexibility is crucial for adaptation and is disrupted in neuropsychiatric disorders and psychopathology. Human studies of flexibility using reversal learning tasks typically contrast error trials before and after reversal, which provides little information about the mechanisms that support learning and expressing a new response. However, animal studies suggest a specific role in this latter process for the connections between the dorsal striatum and the centromedian parafascicular (CM-Pf) thalamus, a system which may recruit the striatal cholinergic interneurons, but which is not well understood in humans. This study investigated the role of this system in human probabilistic reversal learning, specifically with respect to learning a new response strategy, contrasting its function to that of the better understood orbitoftontal-striatal systems. Using psychophysiological interaction (PPI) analysis of functional magnetic resonance imaging (fMRI) data we show that connectivity between the striatum and both the lateral orbitofrontal cortex (lOFC) and CM-Pf pathways increased during reversal, but not initial learning. However, while the strength of lOFC-striatal connectivity was associated with the speed of the reversal, the strength of CM-Pf-striatal connectivity was associated specifically with the quality of the reversal (reduced regressive errors). These findings expand our understanding of flexibility mechanisms in the human brain, bridging the gap with animal studies of this system.

neuroscience↗

bioRxiv2017

Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available on https://citrusgreening.org/.

genomics↗