Biology subjects

Palmer, S.

Publications and source records attributed to Palmer, S..

24 records · Page 2Linked to original sources

bioRxiv2021

In-depth characterization of HIV-1 reservoirs reveals links to viral rebound during treatment interruption

The HIV-1 reservoir is composed of cells harboring latent proviruses that are capable of contributing to viremia upon antiretroviral treatment (ART) interruption. Although this reservoir is known to be maintained by clonal expansion, the contribution of large, infected cell clones to residual viremia and viral rebound remains underexplored. Here, we conducted an extensive analysis on four ART-treated individuals who underwent an analytical treatment interruption (ATI). We performed subgenomic (V1-V3 env), near full-length proviral and integration site sequencing, and used multiple displacement amplification to sequence both the integration site and provirus from single HIV-infected cells. We found eight proviruses that could phylogenetically be linked to plasma virus obtained before or during the ATI. This study highlights a role for HIV-infected cell clones in the maintenance of the replication-competent reservoir and suggests that infected cell clones can directly contribute to rebound viremia upon ATI.

microbiology↗

bioRxiv2020

The Atlas of the In Vivo HIV CD4 T Cell Reservoir

ABSTRACTThe latent reservoir is a main barrier for curing HIV. But because latently-infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently-infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. Most importantly, by selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells, thereby validating the PP-SLIDE approach for reservoir characterization. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies of HIV persistence.Competing Interest StatementThe authors have declared no competing interest.View Full Text

immunology↗

bioRxiv2020

Spatially displaced excitation contributes to the encoding of interrupted motion by the retinal direction-selective circuit

Spatially distributed excitation and inhibition collectively shape a visual neurons receptive field (RF) properties. In the direction-selective circuit of the mammalian retina, the role of strong null-direction inhibition of On-Off direction-selective ganglion cells (ON-OFF DSGCs) on their direction selectivity is well-studied. However, how excitatory inputs influence the On-Off DSGCs visual response is underexplored. Here, we report that On-Off DSGCs have a spatially displaced glutamatergic receptive field along their preferred-null motion axis. This displaced receptive field contributes to DSGC null-direction spiking during interrupted motion trajectories. Theoretical analyses indicate that population responses during interrupted motion may help populations of On-Off DSGCs signal the spatial location of moving objects in complex, naturalistic visual environments. Our study highlights that the direction-selective circuit exploits separate sets of mechanisms under different stimulus conditions, and these mechanisms may help encode multiple visual features.

neuroscience↗

bioRxiv2020

sangeranalyseR: simple and interactive analysis of Sanger sequencing data in R

SummarysangeranalyseR is an interactive R/Bioconductor package and two associated Shiny applications designed for analysing Sanger sequencing from data from the ABIF file format in R. It allows users to go from loading reads to saving aligned contigs in a few lines of R code. sangeranalyseR provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, viewing chromatograms, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. sangeranalyseR comes with extensive online documentation, and outputs detailed interactive HTML reports. Availability and implementationsangeranalyseR is implemented in R and released under an MIT license. It is available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR) and on Github (https://github.com/roblanf/sangeranalyseR). Contactkuanhao.chao@gmail.com Supplementary informationDocumentation at https://sangeranalyser.readthedocs.io/.

bioinformatics↗

bioRxiv2019

Axonal gap junctions in the fly visual system enable fast prediction for evasive flight maneuvers

The visual system must make predictions to compensate for inherent delays in its processing. Yet little is known, mechanistically, about how prediction aids natural behaviors. Here, we show that despite a 20-30ms intrinsic processing delay, the vertical motion sensitive (VS) network of the blowfly achieves maximally efficient prediction. This prediction enables the fly to fine-tune its complex, yet brief, evasive flight maneuvers according to its initial ego-rotation at the time of detection of the visual threat. Combining a rich database of behavioral recordings with detailed compartmental modeling of the VS network, we further show that the VS network has axonal gap junctions that are critical for optimal prediction. During evasive maneuvers, a VS subpopulation that directly innervates the neck motor center can convey predictive information about the flys future ego-rotation, potentially crucial for ongoing flight control. These results suggest a novel sensory-motor pathway that links sensory prediction to behavior. Author summarySurvival-critical behaviors shape neural circuits to translate sensory information into strikingly fast predictions, e.g. in escaping from a predator faster than the systems processing delay. We show that the fly visual system implements fast and accurate prediction of its visual experience. This provides crucial information for directing fast evasive maneuvers that unfold over just 40ms. Our work shows how this fast prediction is implemented, mechanistically, and suggests the existence of a novel sensory-motor pathway from the fly visual system to a wing steering motor neuron. Echoing and amplifying previous work in the retina, our work hypothesizes that the efficient encoding of predictive information is a universal design principle supporting fast, natural behaviors.

neuroscience↗

bioRxiv2018

Mangrove vegetation inspire a new approach to protect shorelines

I. AbstractMangroves are found worldwide across the rivers and coastlines in tropical regions. They are robust against storm surges and tsunamic for a long time. The roots have the most contributions for their resiliency and therefore can be inspired for future manmade structures. The motion of water in riverine mangrove forest is expected to be impacted by mangrove roots, which in turn disturb the transport of nutrients, contaminants, and residues in these systems. In this paper, a facile method for protecting shoreline is described and review and the significant impact of this method were reviewed. Bioinspired simplified models as and obstruction to water currents in shorelines, and coastal areas are presented. It was found that Mangrove roots produce complex flow structure interactions with their environment, which affect the nutrient, habitat and aquatic animals. Analysis of the flow structure behind the roots extend to a broad range of mangrove-inspired applications and provide understandings into flows that are more complex and more indicative of the flows encountered in the unidirectional riverine flow.

biophysics↗