Biology subjects

Brown, J.

Publications and source records attributed to Brown, J..

13 recordsLinked to original sources

bioRxiv2018

Elimination of peripheral auditory pathway activation does not affect motor responses from ultrasound neuromodulation

Recent studies in a variety of animal models including rodents, monkeys, and humans suggest that transcranial focused ultrasound (tFUS) has considerable promise for non-invasively modulating neural activity with the ability to target deep brain structures. However, concerns have been raised that motor responses evoked by tFUS may be due to indirect activation of the auditory pathway rather than direct activation of motor circuits. In this study, tFUS-induced electromyography (EMG) signals were recorded and analyzed in wild-type (WT) normal hearing mice and two strains of genetically deaf mice to examine the involvement of the peripheral auditory system in tFUS-stimulated motor responses. In addition, auditory brainstem responses (ABRs) were measured to elucidate the effect of the tFUS stimulus envelope on auditory and motor responses. We also varied the tFUS stimulation duration to measure its effect on motor response duration. We show, first, that the sharp edges in a tFUS rectangular envelope stimulus activate the peripheral afferent auditory pathway and, second, that smoothing these edges eliminates the auditory responses without affecting the motor responses in normal hearing WT mice. We further show that by eliminating peripheral auditory activity using two different strains of deaf knockout mice, motor responses are the same as in normal hearing WT mice. Finally, we demonstrate a high correlation between tFUS pulse duration and EMG response duration. These results support the concept that tFUS-evoked motor responses are not a result of stimulation of the peripheral auditory system.

neuroscience↗

bioRxiv2018

Nested phylogenetic conflicts and deep phylogenomics in plants

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a dataset in order to resolve recalcitrant relationships and, importantly, identify what the dataset is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant dataset. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific dataset to address deep phylogenetic relationships while also identifying the inferential boundaries of the dataset.

evolutionary biology↗

bioRxiv2018

Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88

A novel concept has emerged whereby the higher-order self-assembly of proteins provides a simple and robust mechanism for signal amplification. This appears to be a universal signalling mechanism within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns need to trigger a strong, binary response within cells. Previously, multiple structural studies have been limited to single domains, expressed and assembled at high protein concentrations. We therefore set out to develop new in vitro strategies to characterise the behaviour of full-length proteins at physiological levels. In this study we focus on the adaptor protein MyD88, which contains two domains with different self-assembly properties: a TIR domain that can polymerise similarly to the TIR domain of Mal, and a Death Domain that has been shown to oligomerise with helical symmetry in the Myddosome complex. To visualize the behaviour of full-length MyD88 without purification steps, we use single-molecule fluorescence coupled to eukaryotic cell-free protein expression. These experiments demonstrate that at low protein concentration, only full-length MyD88 forms prion-like polymers. We also demonstrate that the metastability of MyD88 polymerisation creates the perfect binary response required in innate signalling: the system is silenced at normal concentrations but upstream signalling creates a \"seed\" that triggers polymerisation and amplification of the response. These findings pushed us to re-interpret the role of polymerisation in MyD88-related diseases and we studied the impact of disease-associated point mutations L93P, R196C and L252P/L265P at the molecular level. We discovered that all mutations completely block the ability of MyD88 to polymerise. We also confirm that L252P, a gain-of-function mutation, allows the MyD88 mutant to form extremely stable oligomers, even when expressed at low nanomolar concentrations. Thus, our results are consistent with and greatly add to the findings on the Myddosomes digital all-or-none responses and the behaviour of the oncogenic mutation of MyD88.

molecular biology↗

bioRxiv2018

The immune checkpoint kick start: Optimization of neoadjuvant combination therapy using game theory

An upcoming clinical trial at the Moffitt Cancer Center for women with stage 2/3 ER+breast cancer combines an aromatase inhibitor and a PD-L1 checkpoint inhibitor, and aims to lower a preoperative endocrine prognostic index (PEPI) that correlates with relapse-free survival. PEPI is fundamentally a static index, measured at the end of neoadjuvant therapy before surgery. We develop a mathematical model of the essential components of the PEPI score in order to identify successful combination therapy regimens that minimize both tumor burden and metastatic potential, based on time-dependent trade-offs in the system. We consider two molecular traits, CCR7 and PD-L1 which correlate with treatment response and increased metastatic risk. We use a matrix game model with the four phenotypic strategies to examine the frequency-dependent interactions of cancer cells. This game was embedded into an ecological model of tumor population growth dynamics. The resulting model predicts both evolutionary and ecological dynamics that track with changes in the PEPI score. We consider various treatment regimens based on combinations of the two therapies with drug holidays. By considering the trade off between tumor burden and metastatic potential, the optimal therapy plan was found to be a 1 month kick start of the immune checkpoint inhibitor followed by five months of continuous combination therapy. Relative to a protocol with both therapeutics given together from the start, this delayed regimen results in transient sub-optimal tumor regression while maintaining a phenotypic constitution that is more amenable to fast tumor regression for the final five months of therapy. The mathematical model provides a useful abstraction of clinical intuition, enabling hypothesis generation and testing of clinical assumptions.

cancer biology↗

bioRxiv2018

The dynamic tumor ecosystem: how cell turnover and trade-offs affect cancer evolution

AO_SCPCAPBSTRACTC_SCPCAPTumors are not static masses of cells but rather dynamic ecosystems where cancer cells experience constant turnover and evolve fitness-enhancing phenotypes. Selection for different phenotypes may vary with 1) the tumor niche (edge or core), 2) cell turnover rates, 3) the nature of the tradeoff between traits (proliferation vs migration), and 4) whether deaths occur in response to demographic or environmental stochasticity. In an agent based, spatially-explicit model, we observe how two traits (proliferation rate and migration speed) evolve under different trade-off conditions with different turnover rates. Migration rate is favored over proliferation at the tumors edge and vice-versa for the interior. Increasing cell turnover rates only slightly slows the growth of the tumor, but accelerates the rate of evolution for both proliferation and migration. The absence of a tradeoff favors ever higher values for proliferation and migration. A convex tradeoff tends to favor proliferation over migration while often promoting the coexistence of a generalist and specialist phenotype. A concave tradeoff slows the rate of evolution, and favors migration at low death rates and proliferation at higher death rates. Mortality via demographic stochasticity favors proliferation at the expense of migration; and vice-versa for environmental stochasticity. All of these factors and their interactions contribute to the ecology of the tumor, tumor heterogeneity, trait evolution, and phenotypic variation. While diverse, these effects may be predictable and empirically accessible.

ecology↗

bioRxiv2018

Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

BackgroundPlants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The scale of the contribution of alternative splicing (AS) to stress responses has been underestimated due to limitations in RNA-seq analysis programs and poor representation of AS transcripts in plant databases. Significantly, the dynamics of the AS response have not been investigated but this is now possible with accurate transcript quantification programs and AtRTD2, a new, comprehensive transcriptome for Arabidopsis.\n\nResultsUsing ultra-deep RNA-sequencing of a time-course of Arabidopsis thaliana plants exposed to cold treatment, we identified 8,949 genes with altered expression of which 2,442 showed significant differential alternative splicing (DAS) and 1,647 genes were regulated only at the level of AS (DAS-only). The high temporal resolution demonstrated the rapid induction of both transcription and AS resulting in coincident waves of differential expression (transcription) and differential alternative splicing in the first 6-9 hours of cold. The differentially expressed and DAS gene sets were largely non-overlapping, each comprising thousands of genes. The dynamic analysis of AS identified genes with rapid and sensitive AS within 3 h of transfer to the cold (early AS genes), which were enriched for splicing and transcription factors. A detailed investigation of the novel cold-response DAS-only gene, U2B\"-LIKE, suggested that it regulates AS and is required for tolerance to freezing.\n\nConclusionsOur data indicate that transcription and AS are the major regulators of transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.

genomics↗

bioRxiv2017

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the novel products of phylogenomic inference - such as newly supported clade concepts - have not kept pace. However, the ability to verbalize both node concept congruence and conflict across multiple, (in effect) simultaneously endorsed phylogenomic hypotheses, is a critical prerequisite for building synthetic data environments for biological systematics, thereby also benefitting other domains impacted by these (conflicting) inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC-5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC-5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recently published phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the \"neoavian explosion\" region. According to our representations, this conflict is constituted by 26 instances of input \"whole concept\" overlap. These instances are further resolvable in the output labeling schemes and visualizations as \"split concepts\", thereby providing the provenance services needed to build truly synthetic phylogenomic data environments. Because the RCC-5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers - even and especially when we are not in agreement with each other.

evolutionary biology↗

bioRxiv2017

The Population Dynamics of Obligately Cooperative Species Are Inherently Unstable

Cooperation significantly impacts a species population dynamics as individuals choose others to associate with based upon fitness opportunities. Models of these dynamics typically assume that individuals can freely move between groups. Such an assumption works well for facultative co-operators (e.g. flocking birds, schooling fish, and swarming locusts) but less so for obligate co-operators (e.g. canids, cetaceans, and primates). With obligate co-operators, the fitness consequences from associations are stronger compared to facultative co-operators. Consequently, individuals within a group should be more discerning and selective over their associations, rejecting new members and even removing current members. Incorporating such aspects into population models may better reflect obligately cooperative species. In this paper, we create and analyze a model of the population dynamics of obligate co-operators. In our model, a behavioral game determines within-group population dynamics that then spill over into between-group dynamics. Our analysis shows that group number increases when population dynamics are stable, but additional groups lead to unstable population dynamics and an eventual collapse of group numbers. Using a more general analysis, we identify a fundamental mismatch between the stability of the behavioral dynamics and the stability of the population dynamics. When one is stable, the other is not. Our results suggest that group turnover may be inherent to the population dynamics of obligate co-operators. The instability arises from a non-chaotic deterministic process, and such dynamics should be predictable and testable.

ecology↗

bioRxiv2017

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the \"Candidate phylum SPAM\" represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66%-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual SPAM cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior metagenomic studies. Based on these observations, we propose renaming SPAM to \"Candidate phylum Solagigasbacteria\". Current evidence suggests that Solagigasbacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers and the deep subsurface, with no reports from marine environments to date.

microbiology↗

bioRxiv2017

A pesticide paradox: Fungicides indirectly increase fungal infections

There are many examples where the use of chemicals have had profound unintended consequences, such as fertilizers reducing crop yields (paradox of enrichment) and insecticides increasing insect pests (by reducing natural biocontrol). Recently, the application of agrochemicals, such as agricultural disinfectants and fungicides, has been explored as an approach to curb the pathogenic fungus, Batrachochytrium dendrobatidis (Bd), which is associated with worldwide amphibian declines. However, the long-term, net effects of early-life exposure to these chemicals on amphibian disease risk have not been thoroughly investigated. Using a combination of laboratory experiments and analysis of data from the literature, we explored the effects of fungicide exposure on Bd infections in two frog species. Extremely low concentrations of the fungicides azoxystrobin, chlorothalonil, and mancozeb were directly toxic to Bd in culture. However, estimated environmental concentrations of the fungicides did not reduce Bd on Cuban tree frog (Osteopilus septentrionalis) tadpoles exposed simultaneously to any of these fungicides and Bd, and fungicide exposure actually increased Bd-induced mortality. Additionally, exposure to any of these fungicides as tadpoles resulted in higher Bd abundance and greater Bd-induced mortality when challenged with Bd post-metamorphosis, an average of 71 days after their last fungicide exposure. Analysis of data from the literature revealed that previous exposure to the fungicide itraconazole, which is commonly used to clear Bd infections, made the critically endangered booroolong frog (Litoria booroolongensis) more susceptible to Bd. Finally, a field survey revealed that Bd prevalence was positively associated with concentrations of fungicides in ponds. Although fungicides show promise for controlling Bd, these results suggest that, if fungicides do not completely eliminate Bd or if Bd re-colonizes, exposure to fungicides has the potential to do more harm than good. To ensure that fungicide applications have the intended consequence of curbing amphibian declines, researchers must identify which fungicides do not compromise the pathogen resistance mechanisms of amphibians.

ecology↗

bioRxiv2017

BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal

All current nanopore basecalling applications begin with the segmentation of raw signal into discrete events, which are ultimately processed into called bases. We propose the basecRAWller algorithm, a pair of unidirectional recurrent neural networks that enables the calling of DNA bases in real time directly from the rawest form of nanopore output. This shift in nanopore basecalling provides a number of advantages over current processing pipelines including: 1) streaming basecalling, 2) tunable ratio of insertions to deletions, and 3) potential for streaming detection of modified bases. Key to the streaming basecalling capability is sequence prediction at a delay of less than 1/100th of a second, allowing future signal to continuously modulate sequence prediction. BasecRAWller is computationally efficient enabling basecalling at speeds faster than current nanopore instrument measurement speeds on a single core. Further, basecalling can be paused and resumed without any change in the resulting predicted sequence, transforming the potential applications for dynamic read rejection capabilities. The basecRAWller algorithm provides an alternative approach to nanopore basecalling at comparable accuracy and provides the community with the capacity to train their own basecRAWller neural networks with minimal effort.

bioinformatics↗

bioRxiv2017

The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies

Recent developments in phylogenetic methods and data acquisition have allowed for the construction of large and comprehensive phylogenetic relationships. Published phylogenies represent an enormous resource that not only facilitate the resolution of questions related to comparative biology, but also provide a resource on which to gauge the development of consensus across the tree of life. From the Open Tree of Life, we gathered 290 avian phylogenies representing all major groups that have been published over the last few decades and analyzed how concordance and conflict develop among these trees through time. Nine large scale backbone trees (including a new synthetic tree from this study) were used for the consensus assessment. We found that conflicts were over-represented both along the backbone (higher-level neoavian relationships) and within the oscine Passeriformes. Importantly, although we have made major strides in our knowledge of major clades, recent published comprehensive trees, as well as trees of individual clades, continue to contribute significantly to the resolution of clades in the avian phylogeny. These findings are somewhat unexpected, given that birds constitute a relatively well-studied and small clade of the tree of life (i.e., Aves). Therefore, our analysis highlights that much work is still needed before we can confidently resolve the less well studied areas of the tree of life.

evolutionary biology↗

bioRxiv2016

Behavioral evidence for feedback gain control by the inhibitory microcircuit of the substantia nigra

We recently demonstrated that the collaterals of substantia nigra (SN) projection neurons can implement divisive feedback inhibition, or gain control (Brown et al., 2014). While in vivo recordings were consistent with divisive feedback inhibition, a causal test was lacking. A gain control model of the nigral microcircuit implies behavioral effects of disrupting intranigral inhibition that are distinct from previous functional models. To test the model predictions experimentally, we develop a chemogenetic approach that can selectively suppress synaptic release within the substantial nigra without affecting the propagation of activity to extranigral targets. We observe behavioral consequences of suppressing intranigral inhibition that are uniquely consistent with a gain control model. Our data further suggest that if endogenous metabotropic signaling can modulate intranigral synapses, this would provide a circuit mechanism for an exploitation/exploration trade-off in which the timing and variability of goal-directed movements are controlled independently of changes in action.

neuroscience↗