Matthew Durrant

Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured… Show more

Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design. Show less

My Role: First Author

Abstract

Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold… Show more

My Role: First Author

Abstract

Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40–75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks. Show less

My Role: Middle Author
Performed allele-specific expression analysis and helped with data quality control.

Abstract

Acute physical activity leads to several changes in metabolic, cardiovascular, and immune pathways. Although studies have examined selected changes in these pathways, the system-wide molecular response to an acute bout of exercise has not been fully characterized. We performed longitudinal multi-omic profiling of plasma and peripheral blood mononuclear cells… Show more

My Role: Middle Author
Performed allele-specific expression analysis and helped with data quality control.

Abstract

Acute physical activity leads to several changes in metabolic, cardiovascular, and immune pathways. Although studies have examined selected changes in these pathways, the system-wide molecular response to an acute bout of exercise has not been fully characterized. We performed longitudinal multi-omic profiling of plasma and peripheral blood mononuclear cells including metabolome, lipidome, immunome, proteome, and transcriptome from 36 well-characterized volunteers, before and after a controlled bout of symptomlimited exercise. Time-series analysis revealed thousands of molecular changes and an orchestrated choreography of biological processes involving energy metabolism, oxidative stress, inflammation, tissue repair, and growth factor response, as well as regulatory pathways. Most of these processes were dampened and some were reversed in insulin-resistant participants. Finally, we discovered biological pathways involved in cardiopulmonary exercise response and developed prediction models revealing potential resting blood based biomarkers of peak oxygen consumption. Show less

My Role: First Author

Abstract

Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased detection of MGEs remains challenging. Here, we describe MGEfinder , a bioinformatic toolbox that identifies integrative MGEs and their insertion sites using short-read sequencing data. MGEfinder identifies the DNA- sequence site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374… Show more

My Role: First Author

Abstract

Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased detection of MGEs remains challenging. Here, we describe MGEfinder , a bioinformatic toolbox that identifies integrative MGEs and their insertion sites using short-read sequencing data. MGEfinder identifies the DNA- sequence site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of nine prevalent bacterial pathogens, and we identify thousands of known and novel MGEs, including many candidate insertion sequences, conjugative transposons, and prophage elements. We find that the MGE repertoire and insertion rates vary considerably across species, and that integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. We also find that MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Finally, we identify a set of thousands of DNA mobility genes, many of unknown function. Show less

My Role: Second Author
Analyzed RNA sequencing data to identify changes in allele-specific expression during a 10-year period of aging.

Background
Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older… Show more

My Role: Second Author
Analyzed RNA sequencing data to identify changes in allele-specific expression during a 10-year period of aging.

Background
Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age.

Results
We perform RNA sequencing in whole blood from the same individuals at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging at a population and individual level. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age. We identify 1291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories. Further, we observe a strong correlation of genetic effects on expression and splicing between the two ages, with a small subset of tested genes showing a reduction in genetic associations with expression and splicing in older age.

Conclusions
These findings demonstrate that, although the transcriptome and its genetic regulation is mostly stable late in life, a small subset of genes is dynamic and is characterized by a reduction in genetic regulation, most likely due to increasing environmental variance with age. Show less

A commentary on the interesting findings of a paper published by Zeevi et al. titled "Structural variation in the gut microbiome associates with host health".

My Role: First Author

Summary

- Herbivory‐induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores’ oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses.
- We analyzed herbivory‐induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a… Show more

My Role: First Author

Summary

- Herbivory‐induced defenses are specific and activated in plants when elicitors, frequently found in the herbivores’ oral secretions, are introduced into wounds during attack. While complex signaling cascades are known to be involved, it remains largely unclear how natural selection has shaped the evolution of these induced defenses.
- We analyzed herbivory‐induced transcriptomic responses in wild tobacco, Nicotiana attenuata, using a phylotranscriptomic approach that measures the origin and sequence divergence of herbivory‐induced genes.
- Highly conserved and evolutionarily ancient genes of primary metabolism were activated at intermediate time points (2–6 h) after elicitation, while less constrained and young genes associated with defense signaling and biosynthesis of specialized metabolites were activated at early (before 2 h) and late (after 6 h) stages of the induced response, respectively – a pattern resembling the evolutionary hourglass pattern observed during embryogenesis in animals and the developmental process in plants and fungi.
- The hourglass patterns found in herbivory‐induced defense responses and developmental process are both likely to be a result of signaling modularization and differential evolutionary constraints on the modules involved in the signaling cascade. Show less

My Role: First Author

Background
The S31N amantadine-resistance mutation in the influenza A M2 sequence currently occurs more frequently in nature than the S31 wild type. Overcoming the resistance of the S31N mutation is the primary focus of M2 researchers who aim to develop novel antiviral therapies. Recent studies have noted a possible rise in frequency of the V27A/S31N double amantadine-resistance mutation in recent years. The purpose of this study is to investigate this recent… Show more

My Role: First Author

Background
The S31N amantadine-resistance mutation in the influenza A M2 sequence currently occurs more frequently in nature than the S31 wild type. Overcoming the resistance of the S31N mutation is the primary focus of M2 researchers who aim to develop novel antiviral therapies. Recent studies have noted a possible rise in frequency of the V27A/S31N double amantadine-resistance mutation in recent years. The purpose of this study is to investigate this recent rise in frequency of the double mutation and any possible bias of the other mutations toward co-occurrence with S31N or S31 strains.

Results
The primary dataset used for this study was comprised of 24,152 influenza A M2 channel sequences which were downloaded from UniProt. There is an increased frequency for the S31N/V27A dual AR mutation in recent years, especially in swine. A test for difference in two proportions indicates that the V27A mutation is co-occurring with S31N more often than expected (p-value < 0.001) when considering individual amino acid frequencies. At the same time, the different propensities for the V27A as compared to the V27T dual mutant may reflect differences in viral fitness or protein energetics, and this information could be exploited to focus drug development so as to reduce further drug insensitivity.

Conclusions
The development of the S31N/V27A variant in the Midwestern US swine may be a harbinger of novel human strain development. V27A/S31N is a possible path forward for the evolution of M2 which may convey a new level of drug resistance and should receive attention in drug design. Show less