Biology subjects

Hawes, I.

Publications and source records attributed to Hawes, I..

5 recordsLinked to original sources

bioRxiv2021

Analogue representation of a spatial memory by ramp-like neural activity in retrohippocampal cortex

Neurons in the retrohippocampal cortices play crucial roles in spatial memory. Many retrohippocampal neurons have firing fields that are selectively active at specific locations, with memory for rewarded locations associated with reorganisation of these firing fields. Whether this is the sole strategy for representing spatial memories is unclear. Here, we demonstrate that during a spatial memory task retrohippocampal neurons encode location through ramping activity that extends within segments of a linear track approaching and following a reward, with the rewarded location represented by offsets or switches in the slope of the ramping activity. These ramping representations could be maintained independently of trial outcome and cues that mark the reward location, indicating that they result from recall of the track structure. During recordings in an open arena, neurons that generated ramping activity during the spatial memory task were more numerous than grid or border cells, with a majority showing spatial firing that did not meet criteria for classification as grid or border representations. Encoding of rewarded locations through offsets and switches in the slope of ramping activity also emerged in recurrent neural networks trained to solve a similar location memory task. Impaired performance of these networks following disruption of outputs from ramping neurons is consistent with this coding strategy supporting navigation to recalled locations of behavioural significance. We hypothesise that retrohippocampal ramping activity mediates readout of learned models for goal-directed navigation.

neuroscience↗

bioRxiv2020

Environmental controls and habitat connectivity of phototrophic microbial mats and bacterioplankton communities in an Antarctic freshwater system

Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA sequencing, we evaluated the structure of microbial mat and planktonic communities within a connected watershed in the McMurdo Wright Valley, Antarctica to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined benthic and planktonic samples from glacial Lake Brownworth, the perennially ice-covered Lake Vanda, and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar between them. Despite the higher connectivity between bacterial communities in the shallow parts of the system, environmental filtering dominated over dispersal in driving bacterial community structure. Functional metagenomics predictions identified genes related to degradation of halogenated aromatic compounds in surface microbial mats exposed to changes in water regimes, which progressively disappeared with increasing depth. Shifting environmental conditions due to increasing connectivity, rather than dispersal, may become the dominant drivers of bacterial diversity and functioning in Antarctic freshwater ecosystems.

ecology↗

bioRxiv2019

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica

Ecological communities are commonly thought to be controlled by the dynamics of energy flow through environments. Two of the most important energetic constraints on all communities are photosynthetically active radiation (PAR) and oxygen concentration ([O2]). Microbial mats growing on the bottom of Lake Fryxell, Antarctica, span environmental gradients in PAR and [O2], which we used to test the extent to which each controls community structure. Metagenomic analyses showed variation in the diversity and relative abundances of Archaea, Bacteria, and Eukaryotes across three [O2] and PAR conditions. Where [O2] saturated the mats or was absent from the overlying water, PAR structured the community. Where [O2] varied within mats, microbial communities changed across covarying PAR and [O2] gradients. Diversity negatively correlated with [O2] and PAR through mat layers in each habitat suggesting that, on the millimeter-scale, communities are structured by the optimization of energy use. In contrast, [O2] positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. The benthic microbial communities in Lake Fryxell are thus structured by energy flow in a scale-dependent manner.

microbiology↗

bioRxiv2019

Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis

BackgroundSince 2014, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM). Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF) and only inconsistently identified from the respiratory tract, serum, or stool.\n\nMethodsWe interrogated CSF from children with AFM (n=42) and pediatric controls with other neurologic diseases (OND) (n=58). Samples were incubated with T7 bacteriophage expressing 481,966 sixty-two amino acid peptides with a fourteen amino acid overlap tiled across all known vertebrate virus and arbovirus genomes, an adaption of the VirScan method. Antibody-bound phage were deep sequenced to quantify enriched peptides with normalized counts expressed as reads per hundred thousand (rpK). EV antibody findings were confirmed with ELISA using whole viral protein 1 (VP1) from contemporary enterovirus (EV) A71 and D68 strains. Separately, metagenomic next-generation sequencing (mNGS) of CSF RNA, both unbiased and with targeted enrichment for EVs, was performed.\n\nResultsThe most significantly enriched viral family by VirScan of CSF in AFM versus OND controls was Picornaviridae (mean rpK 11,266 versus mean rpK 950, p-adjusted < 0.001, Wilcoxon signed-rank test with Bonferroni adjustment). Enriched Picornaviridae peptides belonged almost entirely to the genus Enterovirus. The mean EV VP1 ELISA signal in AFM (mean OD 0.51) was significantly higher than OND controls (mean OD 0.08, p-value < 0.001, Mann-Whitney test). mNGS did not detect additional enterovirus RNA in CSF.\n\nConclusionDespite the rare detection of EV RNA in the CNS of patients with AFM, a pan-viral serologic assay identified high levels of CSF EV antibodies in AFM CSF compared to CSF from OND controls. These results provide further evidence for a causal role of non-polio enteroviruses in AFM.

microbiology↗

bioRxiv2018

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium

Atmospheric oxygen level rose dramatically around 2.4 billion years ago due to oxygenic photosynthesis by the Cyanobacteria. The oxidation of surface environments permanently changed the future of life on Earth, yet the evolutionary processes leading to oxygen production are poorly constrained. Partial records of these evolutionary steps are preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Melainabacteria, crown-group Cyanobacteria, and Gloeobacter, representing the earliest-branching Cyanobacteria capable of oxygenic photosynthesis. Here, we describe nearly complete, metagenome assembled genomes of an uncultured organism phylogenetically placed between the Melainabacteria and crown-group Cyanobacteria, for which we propose the name Candidatus Aurora vandensis {au.rora Latin noun dawn and vand.ensis, originating from Vanda}.\n\nThe metagenome assembled genome of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many extrinsic proteins associated with the photosystems in other species are, however, missing or poorly conserved. The assembled genome also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Based on the content of the genome, we propose an evolutionary model for increasing efficiency of oxygenic photosynthesis through the evolution of extrinsic proteins to stabilize photosystem II and I reaction centers and improve photon capture. This model suggests that the evolution of oxygenic photosynthesis may have significantly preceded oxidation of Earths atmosphere due to low net oxygen production by early Cyanobacteria.

microbiology↗