Biology subjects

Murray, K. D.

Publications and source records attributed to Murray, K. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations

Extensive laboratory experimentation has revealed conserved molecular pathways controlling growth and stress responses in plants, yet how these programs operate in natural settings remains poorly understood. We investigated transcriptome organization in wild populations of Arabidopsis thaliana by sampling plants from 60 natural sites in Europe and North America across two seasons. Transcriptomes varied extensively among individuals and showed largely continuous rather than discrete structure across geography and season. Although disease and microbial colonization were common in the wild, wild transcriptomes did not simply recapitulate canonical laboratory stress signatures. Measured microbial infection, environmental, and phenotypic variables explained only a modest fraction of total expression variation, but infection-associated signals accounted for the largest share of the explainable component. Consistent with this, biotic-response networks defined in controlled laboratory experiments were well conserved in wild transcriptomes, whereas control and abiotic-response networks were substantially reorganized. Together, these results suggest that while core transcriptional modules remain recognizable across environments, regulatory relationships among modules differ markedly between laboratory and natural contexts. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/711176v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1c89152org.highwire.dtl.DTLVardef@bcd1acorg.highwire.dtl.DTLVardef@6975a2org.highwire.dtl.DTLVardef@1a9e2fe_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Complex Genomic Structural Variation Underlies Climate Adaptation among Eucalyptus species

Climate change threatens global natural forest ecosystems, however, our limited understanding of adaptive genomic variation in wild forest trees restricts our ability to address this threat. Eucalyptus species likely harbour many climate adaptive alleles considering their long-standing evolutionary success across the Australian continent, yet their complex genomic variation and adaptive implications remain undercharacterised. Here, we present a comprehensive pangenome analysis of Eucalyptus viminalis using haplotype-resolved genomes and population-level long-read sequencing spanning the species natural distribution. We discovered complex and simple structural variants (SVs) that doubled the haploid genome length (530 Mbp haploid to 1.1 Gbp pan-genome). Landscape genomic analyses with SVs identified CHILL1, a 400-kb cold-adaptation locus underlined by complex structural variation. Validation across 434 accessions from three Eucalyptus species confirmed the large-effects of CHILL1, which outperforms species classification at predicting cold adaptation. These findings demonstrate that wild tree populations harbour critical adaptive alleles that can expedite climate-informed restoration.

genomics↗

bioRxiv2025

Kv2/Kv6.4 heteromeric potassium channels are expressed in spinal motor neurons and localized at C-bouton synapses

Voltage-gated K+ channels of the Kv2 family co-assemble with electrically silent KvS subunits in specific subpopulations of brain neurons, forming heteromeric Kv2/KvS channels with distinct functional properties. Little is known about the composition and function of Kv2 channels in spinal cord neurons, however. Here, we show that while Kv2.1 is broadly expressed in multiple classes of spinal cord neurons, the Kv6.4 "electrically-silent" subunit is specifically expressed in motor neurons. In motor neurons, we find that Kv6.4 protein is co-clustered with Kv2.1 and Kv2.2 subunits at endoplasmic reticulum-plasma membrane (ER-PM) junctions beneath C-bouton synapses. In Kv2.1 S590A mutant mice, in which Kv2.1 is unable to bind ER VAP proteins, Kv2.1 and Kv6.4 clustering at ER-PM junctions is severely reduced suggesting Kv2 channels are localized at ER-PM junctions by the same molecular mechanism in motor neurons and brain neurons. Moreover, clustering of Kv6.4, as well as the AMIGO-1 auxiliary subunit, are severely reduced in Kv2.1 knockout mice and moderately reduced in Kv2.2 knockout mice. Thus, expression and localization of Kv6.4 subunits is dependent on Kv2 subunits, likely through their co-assembly into heteromeric channels. Finally, we find that presynaptic C-boutons and postsynaptic clusters of the ER-resident sigma1-receptor are preserved in motor neurons of Kv2 knockout mice. Together, these findings identify a specific Kv2/KvS channel subtype expressed in motor neurons that localizes to C-bouton junctions where it could regulate neuronal excitability and signaling at ER-PM junctions.

neuroscience↗

bioRxiv2024

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

bioRxiv2024

Pangenomic context reveals the extent of intraspecific plant NLR evolution

Nucleotide-binding leucine-rich repeat (NLR) proteins are a major component of the plant immune system, which directly or indirectly detect molecular signals of pathogen invasion. Despite their critical role, the processes by which NLR genes diversify remain poorly characterised due to the extraordinary sequence, structural, and regulatory variability of NLRs, even among closely related individuals. To understand the evolution of NLR diversity in Arabidopsis thaliana, we leverage graph-based methods to define pangenomic NLR neighbourhoods in 17 genetically diverse genomes. We integrate full-length transcript and transposable element information to exhaustively annotate all intact and degraded NLRs, enabling exploration of the processes that underpin the birth, death and maintenance of NLR diversity within a species. Our main finding is that many uncorrelated mutational processes create NLR diversity, and that there is no single metric that captures on its own the true extent of NLR structural and sequence variation. This immense diversity in plant immune system diversification allows populations to survive the constant onslaught of pathogens, not unlike vertebrate adaptive immunity, where variation is also generated by a variety of complementary mechanisms, albeit at the level of individuals.

plant biology↗

bioRxiv2024

Neurosphere culture derived from aged hippocampal dentate gyrus

The neurosphere assay is the gold standard for determining proliferative and differentiation potential of neural progenitor cells (NPCs) in neurogenesis studies1-3. While several in vitro assays have been developed to model the process of neurogenesis, they have predominantly used embryonic and early postnatal NPCs derived from the dentate gyrus (DG). A limitation of these approaches is that they do not provide insight into adult-born NPCs, which are modeled to affect hippocampal function and diseases later in life. Here, we show a novel free-floating neurosphere culture system using NPCs isolated from the DG of mature adult and aged mice. The protocol outlines detailed steps on the isolation, propagation, and maintenance of neurospheres from adult and aged (>12 months old) mouse brain and how to differentiate cultured neurospheres into neurons and astrocytes. Culturing adult and aged NPCs provides an important in vitro model to (1) investigate cellular and molecular properties of this unique cell population and (2) expand the understanding of plasticity in the adult and aging brain. This protocol requires [~]2 hours to complete dissection, dissociation and culture plating, while differentiation to neuronal and astrocytic lineages takes 9 days. By focusing on neurospheres obtained from animals at later ages this model facilitates investigation of important biological questions related to development and differentiation of hippocampal neurons generated throughout adult life.

neuroscience↗

bioRxiv2024

Electrically silent KvS subunits associate with native Kv2 channels in brain and impact diverse properties of channel function

Voltage-gated K+ channels of the Kv2 family are highly expressed in brain and play dual roles in regulating neuronal excitability and in organizing endoplasmic reticulum - plasma membrane (ER- PM) junctions. Studies in heterologous cells suggest that the two pore-forming alpha subunits Kv2.1 and Kv2.2 assemble with "electrically silent" KvS subunits to form heterotetrameric channels with distinct biophysical properties. Here, using mass spectrometry-based proteomics, we identified five KvS subunits as components of native Kv2.1 channels immunopurified from mouse brain, the most abundant being Kv5.1. We found that Kv5.1 co-immunoprecipitates with Kv2.1 and to a lesser extent with Kv2.2 from brain lysates, and that Kv5.1 protein levels are decreased by 70% in Kv2.1 knockout mice and 95% in Kv2.1/2.2 double knockout mice. Multiplex immunofluorescent labelling of rodent brain sections revealed that in neocortex Kv5.1 immunolabeling is apparent in a large percentage of Kv2.1 and Kv2.2-positive layer 2/3 neurons, and in a smaller percentage of layer 5 and 6 neurons. At the subcellular level, Kv5.1 is co-clustered with Kv2.1 and Kv2.2 at ER-PM junctions in cortical neurons, although clustering of Kv5.1-containing channels is reduced relative to homomeric Kv2 channels. We also found that in heterologous cells coexpression with Kv5.1 reduces the clustering and alters the pharmacological properties of Kv2.1 channels. Together, these findings demonstrate that the Kv5.1 electrically silent subunit is a component of a substantial fraction of native brain Kv2 channels, and that its incorporation into heteromeric channels can impact diverse aspects of Kv2 channel function.

neuroscience↗

bioRxiv2023

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence.

Structural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of E. melliodora and E. sideroxylon, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, in E. melliodora and E. sideroxylon respectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.

genomics↗

bioRxiv2023

NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.

neuroscience↗

bioRxiv2023

Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Antibody-based imaging techniques rely on reagents whose performance may be application-specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique. Significance StatementArray tomography (AT) is a powerful volume microscopy technique for high-dimensional analysis of complex protein populations in cells and organelles, including synapses. AT involves the use of ultrathin serial sections embedded in resin and subjected to multiple rounds of immunofluorescence antibody (Ab) labeling and imaging. AT relies on antibody-based detection of proteins but because commercial antibodies are typically validated for other applications they often fail for AT. To identify antibodies with high probability of success in AT we developed a novel screening strategy and used this to create a comprehensive database of AT-validated antibodies for neuroscience.

neuroscience↗

bioRxiv2022

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

It has recently been proposed that the uneven distribution of epigenomic features might facilitate reduced mutation rate in constrained regions of the Arabidopsis thaliana genome, even though previous work had shown that it would be difficult for reduced mutation rates to evolve on a gene-by-gene basis. A solution to Lynchs equations for the barrier imposed by genetic drift on the evolution of targeted hypomutation can, however, come from epigenomic features that are enriched in certain portions of the genome, for example, coding regions of essential genes, and which simultaneously affect mutation rate. Such theoretical considerations draw on what is known about DNA repair guided by epigenomic features. A recent publication challenged these conclusions, because several mutation data sets that support a lower mutation rate in constrained regions suffered from variant calling errors. Here we show that neither homopolymer errors nor elevated mutation rates at transposable elements are likely to entirely explain reported mutation rate biases. Observed mutation biases are also supported by a meta-analysis of several independent germline mutation data sets, with complementary experimental data providing a mechanistic basis for reduced mutation rate in genes and specifically in essential genes. Finally, models derived from the drift-barrier hypothesis demonstrate that mechanisms linking DNA repair to chromatin marks and other epigenomic features can evolve in response to second-order selection on emergent mutation biases.

evolutionary biology↗

bioRxiv2021

Brain Iron Imaging Markers in the Presence of White Matter Hyperintensities

PurposeTo investigate the relationship between pathological brain iron deposition and white matter hyperintensities (WMHs) in cerebral small vessel disease (CSVD), via Monte Carlo simulations of magnetic susceptibility imaging and a novel imaging marker called the Expected Iron Coefficient (EIC). MethodsA synthetic pathological model of a different number of impenetrable spheres at random locations was employed to represent pathological iron deposition. The diffusion process was simulated with a Monte Carlo method with adjustable parameters to manipulate sphere size, distribution, and extracellular properties. Quantitative susceptibility mapping (QSM) was performed in a clinical dataset to study CSVD to derive and evaluate QSM, R2*, the iron microenvironment coefficient (IMC), and EIC in the presence of WMHs. ResultsThe simulations show that QSM signals increase in the presence of increased tissue iron, confirming that the EIC increases with pathology. Clinical results demonstrate that while QSM, R2*, and the IMC do not show differences in brain iron, the EIC does in the context of CSVD. ConclusionThe EIC is more sensitive to subtle changes in brain iron deposition caused by pathology, even when QSM, R2*, and the IMC do not.

pathology↗

bioRxiv2021

Increased Risk for Cerebral Small Vessel Disease is Associated with Quantitative Susceptibility Mapping in HIV Infected and Uninfected Individuals

The aim of this study was to assess in the context of cerebral small vessel disease (CSVD), cardiovascular risk factors and white matter hyperintensities (WMHs) were associated with brain tissue susceptibility as measured by quantitative susceptibility mapping (QSM). Given that CSVD is diagnosed by the presence of lacunar strokes, periventricular and deep WMHs, increased perivascular spaces, and microbleeds, we expected that QSM could capture changes in brain tissue due to underlying CSVD pathology. We compared a cohort of 101 HIV-infected individuals (mean age (SD) = 53.2 (10.9) years) with mild to moderate cardiovascular risk scores, as measured by the Reynolds risk score, to 102 age-matched controls (mean age (SD) = 50.3 (15.7) years) with similar Reynold scores. We performed brain MRI to assess CSVD burden by acquiring 3D T1-MPRAGE, 3D FLAIR, 2D T2-TSE, and mGRE for QSM. We found that signs of CSVD are significantly higher in individuals with HIV-infection compared to controls and that WMH volumes are significantly correlated with age and cardiovascular risk scores. Regional QSM was associated with cardiovascular risk factors, age, sex, and WMH volumes but not HIV status. These results suggest that QSM may be an early imaging marker reflective of alterations in brain microcirculation.

pathology↗

bioRxiv2020

Surface-Based Connectivity Integration

There has been increasing interest in jointly studying structural connectivity (SC) and functional connectivity (FC) derived from diffusion and functional MRI. However, several fundamental problems are still not well considered when conducting such connectome integration analyses, e.g., "Which structure (e.g., gray matter, white matter, white surface or pial surface) should be used for defining SC and FC and exploring their relationships", "Which brain parcellation should be used", and "How do the SC and FC correlate with each other and how do such correlations vary in different locations of the brain?". In this work, we develop a new framework called surface-based connectivity integration (SBCI) to facilitate the integrative analysis of SC and FC with a re-thinking of these problems. We propose to use the white surface (the interface of white matter and gray matter) to build both SC and FC since diffusion signals are in the white matter while functional signals are more present in the gray matter. SBCI also represents both SC and FC in a continuous manner at very high spatial resolution on the white surface, avoiding the need of pre-specified atlases which may bias the comparison of SC and FC. Using data from the Human Connectome Project, we show that SBCI can create reproducible, high quality SC and FC, in addition to three novel imaging biomarkers reflective of the similarity between SC and FC throughout the brain, called global, local, and discrete SC-FC coupling. Further, we demonstrate the usefulness of these biomarkers in finding group effects due to biological sex throughout the brain.

neuroscience↗

bioRxiv2019

A toolbox of nanobodies developed and validated for diverse neuroscience research applications

Nanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.

neuroscience↗

bioRxiv2019

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (LHeritier 1789; the \"eucalypts\") are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity ({pi} {approx} 0.05) and low genome-wide, inter-specific differentiation (FST = 0.15). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalised dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e., IBE). Eucalyptus sideroxylon showed much stronger IBD, and moderate IBE. These results highlight the vast adaptive potential of these species, and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.

evolutionary biology↗

bioRxiv2018

A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

Generating recombinant monoclonal antibodies (R-mAbs) from mAb-producing hybridomas offers numerous advantages that increase the effectiveness, reproducibility, and transparent reporting of research. We report here the generation of a novel resource in the form of a library of recombinant R-mAbs validated for neuroscience research. We cloned immunoglobulin G (IgG) variable domains from cryopreserved hybridoma cells and input them into an integrated pipeline for expression and validation of functional R-mAbs. To improve efficiency over standard protocols, we eliminated aberrant Sp2/0-Ag14 hybridoma-derived variable light transcripts using restriction enzyme treaent. Further, we engineered a plasmid backbone that allows for switching of the IgG subclasses without altering target binding specificity to generate R-mAbs useful in simultaneous multiplex labeling experiments not previously possible. The method was also employed to rescue IgG variable sequences and generate functional R-mAbs from a non-viable cryopreserved hybridoma. All R-mAb sequences and plasmids will be archived and disseminated from open source suppliers.

neuroscience↗

bioRxiv2018

Population structure of the Brachypodium species complex and genome wide association of agronomic traits in response to climate.

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of the Brachypodium species complex and allow powerful complex trait dissection within this new grass model species.

plant biology↗