Biology subjects

Shaw, J.

Publications and source records attributed to Shaw, J..

31 records · Page 2Linked to original sources

bioRxiv2022

Seed-chain-extend alignment is accurate and runs in close to O(m log n) time for similar sequences: a rigorous average-case analysis

Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence alignment employed by modern sequence aligners. While effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist for seed-chain-extend. In this work, we give the first rigorous bounds for the efficacy of seed-chain-extend with k-mers in expectation. Assume we are given a random nucleotide sequence of length ~ n that is indexed (or seeded) and a mutated substring of length ~ m [≤] n with mutation rate{theta} < 0.206. We prove that we can find a k ={Theta} (log n) for the k-mer size such that the expected runtime of seed-chain-extend under optimal linear gap cost chaining and quadratic time gap extension is O(mnf({theta}) log n) where f({theta}) < 2.43 {middle dot}{theta} holds as a loose bound. The alignment also turns out to be good; we prove that more than [Formula] fraction of the homologous bases are recoverable under an optimal chain. We also show that our bounds work when k-mers are sketched, i.e. only a subset of all k-mers is selected, and that sketching reduces chaining time without increasing alignment time or decreasing accuracy too much, justifying the effectiveness of sketching as a practical speedup in sequence alignment. We verify our results in simulation and on real noisy long-read data and show that our theoretical runtimes can predict real runtimes accurately. We conjecture that our bounds can be improved further, and in particular, f({theta}) can be further reduced.

bioinformatics↗

bioRxiv2022

How to optimally sample a sequence for rapid analysis

We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimizers, syncmers, and minimally-overlapping words, were developed by heuristic intuition, and are not optimal. We present a sequence-sampling approach that provably optimizes sensitivity for a whole class of sequence comparison methods, for randomly-evolving sequences. It it likely near-optimal for a wide range of alignmentbased and alignment-free analyses. For real biological DNA, it increases specificity by avoiding simple repeats. Our approach generalizes universal hitting sets (which guarantee to sample a sequence at least once), and polar sets (which guarantee to sample a sequence at most once). This helps us understand how to do rapid sequence analysis as accurately as possible.

bioinformatics↗

bioRxiv2022

A comparison between Mini-loop mediated isothermal amplification and polymerase spiral reaction for selective amplification of short template DNA

Isothermal amplification of circulating tumour-derived DNA (ctDNA) in the blood plasma could provide a rapid and cost effective alternative to PCR and NGS approaches for real-time cancer monitoring. Several variations of isothermal technologies exist, typically designed over unconstrained template length. Here, we compared the amplification efficiency of a compact loop mediated isothermal amplification reaction (termed AS-Mini-LAMP) with polymerase spiral reaction (PSR) suitable for analysis of ctDNA. Utilising 4-primers and targeting a 155 bp template encompassing the estrogen receptor (ESR1) c.1138G>C (p.E380Q) missense mutation. Using synthetic E380Q template DNA and Bst2.0 polymerase, results demonstrate that AS-Mini-LAMP was capable of selective mutant allele DNA amplification to a limit of 1,000 mutant copies, whereas no specific amplification was observed by PSR. The alternative use of Bst3.0 polymerase for either AS-Mini-LAMP or PSR revealed non-canonical events that underpin potentially misleading results when employing isothermal chemistries. In conclusion, AS-Mini-LAMP is more suited to mutation detection than PSR.

molecular biology↗

bioRxiv2021

Theory of local k-mer selection with applications to long-read alignment

MotivationSelecting a subset of k-mers in a string in a local manner is a common task in bioinformatics tools for speeding up computation. Arguably the most well-known and common method is the minimizer technique, which selects the lowest-ordered k-mer in a sliding window. Recently, it has been shown that minimizers are a sub-optimal method for selecting subsets of k-mers when mutations are present. There is however a lack of understanding behind the theory of why certain methods perform well. ResultsWe first theoretically investigate the conservation metric for k-mer selection methods. We derive an exact expression for calculating the conservation of a k-mer selection method. This turns out to be tractable enough for us to prove closed-form expressions for a variety of methods, including (open and closed) syncmers, (, b, n)-words, and an upper bound for minimizers. As a demonstration of our results, we modified the minimap2 read aligner to use a more optimal k-mer selection method and demonstrate that there is up to an 8.2% relative increase in number of mapped reads. Availability and supplementary informationSimulations and supplementary methods available at https://github.com/bluenote-1577/local-kmer-selection-results. os-minimap2 is a modified version of minimap2 and available at https://github.com/bluenote-1577/os-minimap2. Contactjshaw@math.toronto.edu

bioinformatics↗

bioRxiv2021

The responsiveness of gait and balance outcomes to disease progression in Friedreich ataxia

ObjectiveTo identify gait and balance measures that are responsive to change during the timeline of a clinical trial in Friedreich ataxia (FRDA) we administered a battery of potential measures three times over a 12-month period. MethodsSixty-one ambulant individuals with FRDA underwent assessment of gait and balance at baseline, six months and 12 months. Outcomes included: GAITRite(R) spatiotemporal gait parameters; Biodex Balance System Postural Stability Test (PST) and Limits of Stability; Berg Balance Scale (BBS); Timed 25 Foot Walk Test; Dynamic Gait Index (DGI); SenseWear MF Armband step and energy activity; and the Friedreich Ataxia Rating Scale Upright Stability Subscale (FARS USS). The standardised response mean (SRM) or correlation coefficients were reported as effect size indices for comparison of internal responsiveness. Internal responsiveness was also analysed in subgroups. ResultsSenseWear Armband daily step count had the largest effect size of all the variables over six months (SRM=-0.615), while the PST medial-lateral index had the largest effect size (SRM=0.829) over 12 months. The FARS USS (SRM=0.824) and BBS (SRM=-0.720) were the only outcomes able to detect change over 12 months in all subgroups. The DGI was the most responsive outcome in children, detecting a mean change of -2.59 (95% CI -3.52 to -1.66, p<0.001, SRM=-1.429). ConclusionsThe FARS USS and BBS are highly responsive and can detect change in a wide range of ambulant individuals with FRDA. However, therapeutic effects in children may be best measured by the DGI.

neuroscience↗

bioRxiv2021

Using image-based haplotype alignments to map global adaptation of SARS-CoV-2

Quantifying evolutionary change among viral genomes is an important clinical device to track critical adaptations geographically and temporally. We built image-based haplotype-guided evolutionary inference (ImHapE) to quantify adaptations in expanding populations of non-recombining SARS-CoV-2 genomes. By combining classic population genetic summaries with image-based deep learning methods, we show that different rates of positive selection are driving evolutionary fitness and dispersal of SARS-CoV-2 globally. A 1.35-fold increase in evolutionary fitness is observed within the UK, associated with expansion of both the B.1.177 and B.1.1.7 SARS-CoV-2 lineages.

evolutionary biology↗

bioRxiv2020

Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing

Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem. We introduce two new mathematical formulations of polyploid haplotype phasing: (1) the min-sum max tree partition (MSMTP) problem, which is a more flexible graphical metric compared to the standard minimum error correction (MEC) model in the polyploid setting, and (2) the uniform probabilistic error minimization (UPEM) model, which is a probabilistic analogue of the MEC model. We incorporate both formulations into a long-read based polyploid haplotype phasing method called flopp. We show that flopp compares favorably to state-of-the-art algorithms--up to 30 times faster with 2 times fewer switch errors on 6x ploidy simulated data.

bioinformatics↗

bioRxiv2019

Impacts of intraspecific variability and local adaptation on the ecophysiology of mosses: an example with Sphagnum magellanicum

BackgroundBryophytes are a diverse plant group and are functionally different from vascular plants. Yet, plant ecology theories and hypotheses are often presented in an inclusive term. The trait-based approach to ecology is no exception; largely focusing on vascular plant traits and almost exclusively on interspecific traits. Currently, we lack information about the magnitude and the importance of intraspecific variability to the ecophysiology of bryophytes and how these might translate to local adaptation--a prerequisite for adaptive evolution. MethodWe used transplant and factorial experiments involving moisture and light to ask whether variability in traits between morphologically distinct individuals of Sphagnum magellanicum from habitat extremes was due to phenotypic plasticity or local adaptation and the implications for the ecophysiology of the species. Key ResultsWe found that the factors that discriminated between the plant origins in the field did not translate to their ecophysiological functioning and the pattern of variability changed with the treatments, which suggests that the trait responses were due largely to phenotypic plasticity. The trait responses suggest that the need for mosses to grow in clumps where they maintain a uniform growth rate may have an overriding effect on responses to environmental heterogeneity, and therefore a constraint for local adaptation. ConclusionThe circumstances under which local adaptation would be beneficial in this plant group is not clear. We conclude that extending the trait-based framework to mosses or making comparisons between mosses and vascular plants under any theoretical framework would only be meaningful to the extent that growth form and dispersal strategies are considered.

ecology↗

bioRxiv2019

The tunable intrahexamer heteroassembly mechanism of pseudoenzyme/enzyme pair, PDX1.2/PDX1.3, with its molecular impact on vitamin B6 regulation

Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically non-active. Yet many factors defining why one protein is active while its homolog is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme PDX1.2 positively regulates vitamin B6 production by association with its active catalytic homologs such as PDX1.3 through an unknown mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in hetero-complexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the hetero-complexes and identified symmetry- imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.

molecular biology↗

bioRxiv2018

Physiological regulation of bud burst in grapevine

The physiological constraints on bud burst in woody perennials, including the prerequisite for vascular development remain unresolved. Both light and tissue oxygen status have emerged as important cues for vascular development in other systems, however, light requirement appears to be facultative in grapevine, and the information related to the spatial variability of oxygen in buds is unclear. Here, we analysed apoplastic development at early stages of grapevine bud burst and combined molecular modelling with histochemical techniques to determine the pore size of cell walls in grapevine buds. The data demonstrate that quiescent grapevine buds were impermeable to apoplastic dyes (acid fuchsin and eosin Y) until after bud burst was established. The molecular exclusion size was calculated to be 2.1 nm, which would exclude most macromolecules except simple sugars and phytohormones. In vivo experiments show that grapevine buds were able to resume growth even following excision from the cane, and that the outer scales of grapevine buds may participate in the biochemical repression of bud burst. Furthermore, we demonstrate that the tissue oxygen partial pressure data correlated well with structural heterogeneity within the bud and differences in tissue density. These data consolidate evidence that the meristematic core becomes rapidly oxygenated during bud burst. Taken together, and when put in the context of earlier studies, these data provide solid evidence that the physiological and biochemical events that initiate bud burst reside within the bud, and question the role of long distance signalling in this developmental transition.\n\nHighlightsO_LIThe apoplastic pore size between the grapevine bud and the mother vine is dynamically regulated in the transition to bud burst.\nC_LIO_LIThe molecular exclusion size of the apoplastic connection between the bud and cane is calculated 2.1 nm prior to the initiation of bud burst.\nC_LIO_LIThe structural heterogeneity of the bud explains the spatial variance in tissue oxygen status, and the meristematic core is oxygenated during the initiation of bud burst.\nC_LIO_LILong distance maternal signals are not a requirement for bud burst.\nC_LI

plant biology↗

bioRxiv2018

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing. The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9x long read coverage, thus enabling high quality assembly of lowly abundant species (<1%). Furthermore, OPERA-MSs fine-grained clustering is able to deconvolute and assemble multiple genomes of the same species in a single sample, allowing us to study the complex dynamics of the human microbiome at the sub-species level. Applying nanopore sequencing to gut metagenomes of patients undergoing antibiotic treatment, we show that long reads can be obtained from stool samples in clinical studies to produce more meaningful metagenomic assemblies (up to 200x improvement over short-read assemblies), including the closed assembly of >80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences.

bioinformatics↗

bioRxiv2018

Chelation therapy using static magnetic field

Static magnetic field (SMF) is reported to mimic chelation agents. In thalassemia blood, SMF minimizes iron overloading effect. In such cells ROS level is reduced, in presence of moderate strength (70mT). Pilot study on transfusion dependent thalassemia, thalassemia carriers and normal red blood clearly indicate the differential effects of SMF on thalassemia, thalassemia carrier and normal cells. SMF also reduces ROS induced DNA damage in lymphocytes. A comparative study on the iron chelating drug deferasirox and SMF treated lymphocytes further confirm our main thesis. This non-invasive therapeutic regime for hemochromatosis may serve the dual purpose of treating, iron overloading and minimizing, cellular damage by lowering the ROS level.

epidemiology↗

bioRxiv2018

Targeting hepatitis C virus p7 channel activity reveals prospect for bimodal antiviral prophylaxis

Since the 1960s, a single class of agent has been licensed targeting virus-encoded ion channels, or \"viroporins\", contrasting the success of channel blocking drugs in other areas of medicine. Although resistance arose to these prototypic adamantane inhibitors of the influenza A virus (IAV) M2 proton channel, a growing number of clinically and economically important viruses are now recognised to encode essential viroporins providing potential targets for modern drug discovery.\n\nWe describe the first rationally designed viroporin inhibitor with a comprehensive structure-activity relationship (SAR). This step-change in understanding not only revealed a second biological function for the p7 viroporin from hepatitis C virus (HCV) during virus entry, but also enabled the synthesis of a labelled tool compound that retained biological activity. Hence, p7 inhibitors (p7i) represent a unique class of HCV antiviral targeting both the spread and establishment of infection, as well as a precedent for future viroporin-targeted drug discovery.

microbiology↗