Biology subjects

Wilson, M. A.

Publications and source records attributed to Wilson, M. A..

60 records · Page 4Linked to original sources

bioRxiv2019

An easy-to-assemble, robust, and lightweight drive implant for chronic tetrode recordings in freely moving animals

Tetrode arrays are the gold-standard method for neuronal recordings in many studies with behaving animals, especially for deep structures and chronic recordings. Here we outline an improved drive design for use in freely behaving animals. Our design makes use of recently developed technologies to reduce the complexity and build time of the drive while maintaining a low weight. The design also presents an improvement over many existing designs in terms of robustness and ease of use. We describe two variants: a 16 tetrode implant weighing [~]2 g for mice, bats, tree shrews and similar animals, and a 64 tetrode implant weighing [~]16 g for rats, and similar animals.These designs were co-developed and optimized alongside a new class of drive-mounted feature-rich amplifier boards with ultra-thin RF tethers, as described in an upcoming paper (Newman, Zhang et al., in prep). This design significantly improves the data yield of chronic electrophysiology experiments.

neuroscience↗

bioRxiv2019

Hippocampal Remapping as Hidden State Inference

Cells in the hippocampus tuned to spatial location (place cells) typically change their tuning when an animal changes context, a phenomenon known as remapping. A fundamental challenge to understanding remapping is the fact that what counts as a \"context change\" has never been precisely defined. Furthermore, different remapping phenomena have been classified on the basis of how much the tuning changes after different types and degrees of context change, but the relationship between these variables is not clear. We address these ambiguities by formalizing remapping in terms of hidden state inference. According to this view, remapping does not directly reflect objective, observable properties of the environment, but rather subjective beliefs about the hidden state of the environment. We show how the hidden state framework can resolve a number of puzzles about the nature of remapping.

neuroscience↗

bioRxiv2019

Twister3: a simple and fast microwire twister

We present Twister3, a microwire twisting machine. This device greatly increases the speed and repeatability of constructing twisted microwire neural probes (e.g. stereotrodes and tetrodes) compared to existing options. It is cheap, well documented, and all associated designs and source code are open-source. Twister3 is of interest to any lab performing twisted microwire neural recordings, for example, using tetrode drives.

neuroscience↗

bioRxiv2019

Aligning RNA-Seq reads to a sex chromosome complement informed reference genome increases ability to detect sex differences in gene expression

BackgroundHuman X and Y chromosomes share an evolutionary origin and, as a consequence, sequence similarity. We investigated whether sequence homology between the X and Y chromosomes affects alignment of RNA-Seq reads and estimates of differential expression. We tested the effects of using reference genomes and reference transcriptomes informed by the sex chromosome complement of the samples genome on measurements of RNA-Seq abundance and sex differences in expression. ResultsThe default genome includes the entire human reference genome (GRCh38), including the entire sequence of the X and Y chromosomes. We created two sex chromosome complement informed reference genomes. One sex chromosome complement informed reference genome was used for samples that lacked a Y chromosome; for this reference genome version, we hard-masked the entire Y chromosome. For the other sex chromosome complement informed reference genome, to be used for samples with a Y chromosome, we hard-masked only the pseudoautosomal regions of the Y chromosome, because these regions are duplicated identically in the reference genome on the X chromosome. We analyzed transcript abundance in the whole blood, brain cortex, breast, liver, and thyroid tissues from 20 genetic female (46, XX) and 20 genetic male (46, XY) samples. Each sample was aligned twice; once to the default reference genome and then independently aligned to a reference genome informed by the sex chromosome complement of the sample, repeated using two different read aligners, HISAT and STAR. We then quantified sex differences in gene expression using featureCounts to get the raw count estimates followed by Limma/Voom for normalization and differential expression. We additionally created sex chromosome complement informed transcriptome references for use in pseudo-alignment using Salmon. Transcript abundance was quantified twice for each sample; once to the default target transcripts and then independently to target transcripts informed by the sex chromosome complement of the sample. ConclusionsWe show that regardless of the choice of read aligner, using an alignment protocol informed by the sex chromosome complement of the sample results in higher expression estimates on the pseudoautosomal regions of the X chromosome in both genetic male and genetic female samples, as well as an increased number of unique genes being called as differentially expressed between the sexes. We additionally show that using a pseudo-alignment approach informed on the sex chromosome complement of the sample eliminates Y-linked expression in female XX samples. Author summaryThe human X and Y chromosomes share an evolutionary origin and sequence homology, including regions of 100% identity; this sequence homology can result in reads misaligning between the sex chromosomes, X and Y. We hypothesized that misalignment of reads on the sex chromosomes would confound estimates of transcript abundance if the sex chromosome complement of the sample is not accounted for during the alignment step. For example, because of shared sequence similarity, X-linked reads could misalign to the Y chromosome. This is expected to result in reduced expression for regions between X and Y that share high levels of homology. For this reason, we tested the effect of using a default reference genome versus a reference genome informed by the sex chromosome complement of the sample on estimates of transcript abundance in human RNA-Seq samples from whole blood, brain cortex, breast, liver, and thyroid tissues of 20 genetic female (46, XX) and 20 genetic male (46, XY) samples. We found that using a reference genome with the sex chromosome complement of the sample resulted in higher measurements of X-linked gene transcription for both male and female samples and more differentially expressed genes on the X and Y chromosomes. We additionally investigated the use of a sex chromosome complement informed transcriptome reference index for alignment free quantification protocols. We observed no Y-linked expression in female XX samples only when the transcript quantification was performed using a transcriptome reference index informed on the sex chromosome complement of the sample. We recommend that future studies requiring aligning RNA-Seq reads to a reference genome or pseudo-alignment with a transcriptome reference should consider the sex chromosome complement of their samples prior to running default pipelines.

evolutionary biology↗

bioRxiv2019

mPFC Spindle Cycles Organize Sparse Thalamic Activation and Recently Active CA1 cells During non-REM Sleep

Sleep oscillations in neocortex and hippocampus are critical for the integration of new episodic memories into stable generalized representations in neocortex. However, the role of the thalamus in this process is poorly understood. To determine the thalamic contribution to non-REM oscillations (sharp-wave ripples, SWRs; slow/delta; spindles), we recorded units and local field potentials (LFPs) simultaneously in the limbic thalamus, mPFC, and CA1 in rats. We report that the cycles of neocortical spindles provide a key temporal window that coordinates CA1 SWRs with sparse but consistent activation of thalamic units. Thalamic units were phase-locked to delta and spindles in mPFC, and fired at consistent lags with other thalamic units within spindles, while CA1 units that were active during spatial exploration were engaged in SWR-coupled spindles after behavior. The sparse thalamic firing could promote an incremental integration of recently acquired memory traces into neocortical schemas through the interleaved activation of thalamocortical cells.

neuroscience↗

bioRxiv2019

Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis

Summary ParagraphProtein dynamics play an important role in enzyme catalysis1-4. Many enzymes form covalent catalytic intermediates that can alter enzyme structure and conformational dynamics5,6. How these changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question in structural enzymology. Here, we use Mix-and-Inject Serial Femtosecond X-ray Crystallography (MISC) at an X-ray Free Electron Laser (XFEL)7-10, ambient temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in isocyanide hydratase (ICH) alters the enzymes conformational ensemble throughout the catalytic cycle. With MISC, we directly observe formation of a thioimidate covalent intermediate during ICH catalysis. The intermediate exhibits changes in the active site electrostatic environment, disrupting a hydrogen bond and triggering a cascade of conformational changes in ICH. X-ray-induced formation of a cysteine-sulfenic acid at the catalytic nucleophile (Cys101-SOH) with conventional crystallography at ambient temperature induces similar conformational shifts, demonstrating that these enzyme motions result from cysteine modification. Computer simulations show how cysteine modification-gated structural changes allosterically propagate through the ICH dimer. Mutations at Gly150 that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. Taken together, our results demonstrate the potential of mix-and-inject XFEL crystallography to capture otherwise elusive mechanistic details of enzyme catalysis and dynamics from microcrystalline samples7,11. This approach can connect conformational dynamics to function for the large class of systems that rely on covalently modified cysteine residues for catalysis or regulation, resolving long-standing questions about enzyme mechanism and functionally relevant non-equilibrium enzyme motions.

biochemistry↗