A5078210447- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Prosthetics and Rehabilitation Robotics
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Muscle activation and electromyography studies
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Diabetic Foot Ulcer Assessment and Management
- Genetic and phenotypic traits in livestock
- Genetics and Plant Breeding
- Algorithms and Data Compression
- Photosynthetic Processes and Mechanisms
- Molecular Biology Techniques and Applications
- Mollusks and Parasites Studies
- Invertebrate Taxonomy and Ecology
- Species Distribution and Climate Change
- Wheat and Barley Genetics and Pathology
- Plant Pathogens and Fungal Diseases
- Stroke Rehabilitation and Recovery
- Forest Insect Ecology and Management
- Catalysis and Oxidation Reactions
- DNA Repair Mechanisms
- Spinal Cord Injury Research
- Spectroscopy and Laser Applications
Australian National University
2015-2024
University College Cork
2024
Max Planck Institute for Biology
2022-2024
Max Planck Institute for Developmental Biology
2022
Australian Research Council
2014-2018
ARC Centre of Excellence in Plant Energy Biology
2015-2018
University of Strathclyde
2013-2018
<ns3:p>The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. provides implementations of probabilistic k-mer counting data structure, compressible De Bruijn graph representation, partitioning, and digital normalization. implemented in C++ Python, under the BSD license at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri"...
Stress recovery may prove to be a promising approach increase plant performance and, theoretically, mRNA instability facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) methylome profiling during repeated excess-light stress was performed at intervals as short 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid For instance, HSP101 abundance declined 2-fold every 5.1 term this phenomenon gene downregulation (RRGD), whereby...
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression reproduction. Despite the need to conserve genome architecture, high level structural variation has been observed species. As species separate diverge, also diverges, becoming increasingly poorly conserved as divergence time increases. However, plant genomes, processes are not...
Closely related species often use the same genes to adapt similar environments. However, we know little about why such possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation climate presents a natural laboratory test these ideas, as even distantly must contend with stresses. Here, re-analyse genomic data from thousands of individuals 25 plant diverged lodgepole pine Arabidopsis (~300 Myr). We for genetic repeatability based on...
Abstract Summary We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in read, even presence of sequencing errors. The is able to handle combinatorial indexing, indices differing length and several mismatches per sequence. Availability implementation implemented C, used as command-line program on Unix-like systems. available online at https://github.com/kdmurray91/axe, Debian/Ubuntu distributions GNU/Linux package...
Coevolution between interacting species is thought to increase biodiversity, but evidence linking microevolutionary processes macroevolutionary patterns scarce. We leveraged two decades of behavioral research coupled with historical DNA analysis reveal that coevolution hosts underpins speciation in brood-parasitic bronze-cuckoos. At a scale, we show highly virulent taxa have higher rates and are more likely speciate sympatry than less-virulent nonparasitic relatives. the process underlying...
In this study, we investigated and compared the dynamic interface pressure distribution of hands-off hands-on transtibial prosthetic systems by means mapping. Of 48 established unilateral amputees recruited, half (n = 24) had been wearing pressure-cast prostheses (IceCast Compact) other hand-cast sockets patellar tendon bearing design. We measured profile more than 90% area within each socket four Tekscan F-Scan transducer arrays. between concepts. found that at limb-socket was similar for...
Thigmomorphogenesis is viewed as being a response process of acclimation to short repetitive bursts mechanical stimulation or touch. The underlying molecular mechanisms that coordinate changes in how touch signals lead long-term morphological are enigmatic. Touch responsive gene expression rapid and transient, no transcription factor DNA regulatory motif has been reported could confer genome wide stimulus. We report here on chromatin modifying enzyme, SDG8/ASHH2, which can regulate the many...
Abstract Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal selection. Eucalyptus (L'Héritier 1789; the “eucalypts”) foundation tree that provide essential habitat modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation two woodland eucalypt species, using whole‐genome sequencing 388 individuals albens sideroxylon . We found exceptionally...
Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation directly from sequencing data has the potential overcome reference genome bias, and verify that belong correct lineage before conclusions are drawn using mislabelled, or misidentified samples. We present k-mer Weighted Inner...
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods assessment. Here, we identify set orthologous single-copy genes transcriptome for the land snails slugs (Eupulmonata) using thorough approach determination involving manual alignment curation, gene tree...
Abstract Genotype‐environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype‐by‐sequencing data provide robust inferences for environmental adaptation. In many cases, default filtering thresholds minor allele frequency and missing are applied regardless sample size, having unknown impacts on results, negatively affecting management strategies. Here, investigate effects GEA results potential...
Amputee satisfaction with cosmesis and the importance they place on design have not been published in literature.To investigate current levels of amputees United Kingdom their placed attributes to inform future redesign.Cross-sectional questionnaire study.Questionnaires were administered lower limb Kingdom. Satisfaction scores overall ranking features calculated. Statistically significant relationships between two demographic, or variables tested using Fisher's exact tests (one-tailed) at a...
Abstract Synteny, the ordering of sequences within homologous chromosomes, must be maintained genomes sexually reproducing species for sharing alleles and production viable, offspring. However, when closely related are compared, a loss synteny is often observed. Unequal recombination primary mechanism behind loss, occurring more in transposon rich regions, resulting formation chromosomal rearrangements. To examine patterns among three related, interbreeding, wild Eucalyptus species, we...
Abstract Structural variations (SVs) play a significant role in speciation and adaptation many species, yet few studies have explored the prevalence impact of different categories SVs. We conducted comparative analysis long-read assembled reference genomes closely related Eucalyptus species to identify candidate SVs potentially influencing adaptation. Interspecies can be either fixed differences or polymorphic one both species. To describe SV patterns, we employed short-read whole-genome...
In plants, the molecular function(s) of nucleus-localized 5′-3′ EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis RNA ends, we documented dramatic increase in uncapped substrates XRNs both sal1 xrn2xrn3 mutants. We found that major consequence reducing SAL1 or XRN was Polymerase II 3′ read-through. This occurred at 72% expressed genes, demonstrating...
Nucleotide-binding leucine-rich repeat (NLR) proteins are a major component of the plant immune system, which directly or indirectly detect molecular signals pathogen invasion. Despite their critical role, processes by NLR genes diversify remain poorly characterised due to extraordinary sequence, structural, and regulatory variability NLRs, even among closely related individuals. To understand evolution diversity in Arabidopsis thaliana, we leverage graph-based methods define pangenomic...
Abstract The development of model systems requires a detailed assessment standing genetic variation across natural populations. Brachypodium species complex has been promoted as plant for grass genomics with translation to small grain and biomass crops. To capture the diversity within this complex, thousands accessions from around globe were collected genotyped by sequencing. Overall, 1897 samples classified into two diploid or allopolyploid species, then further grouped distinct inbred...
This study compared the general activity during 1 week and detailed a 24-hr period of 48 established unilateral transtibial prostheses users. Activity was measured by instrumenting their prescribed prosthesis, which they have been using for minimum 6 months, with ActivPAL™ monitor. Half (n = 24) were fitted prosthesis total surface bearing (TSB) pressure-cast sockets ("hands-off" group), other half had wearing hand-cast patellar tendon-bearing (PTB) ("hands-on" group). As prerequisite,...
Abstract Here we implement a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in read, even presence of sequencing errors. The is able to handle combinatorial indexing, indices differing length, and several mismatches per sequence.
Acanthophis is a comprehensive pipeline for the joint analysis of both host genetic variation and in composition abundance host-associated microbiomes (together, "hologenome").Implemented Snakemake (Köster & Rahmann, 2012), handles data from raw FASTQ read files through quality control, alignment reads to plant reference, variant calling, taxonomic classification quantification microbes, metagenome analysis.The workflow contains numerous practical optimisations, reduce disk space usage...
Reduced function and health in individuals with lower limb amputation is well documented. Step count measurement could facilitate rehabilitation help monitor functional outcomes.To determine whether mean daily step changed between in-patient consecutive leave periods.Observational study.Nine bilateral traumatic amputations attending at the Defence Medical Rehabilitation Centre during a 4-month period were invited to participate study (two transfemoral, two transfemoral/knee disarticulation,...
Abstract Genomes have a highly organised architecture (non-random organisation of functional and non-functional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression reproduction. Despite the need to conserve genome architecture, surprisingly high level structural variation has been observed species. As species separate diverge, also diverges, becoming increasingly poorly conserved as divergence time increases. However, plant...