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Evans, S.

Publications and source records attributed to Evans, S..

At least 19 recordsLinked to original sources

A Novel Computational Framework to Investigate the Biomechanics of Burrowing

Head-first burrowing likely imposes strong mechanical demands on the skull of fossorial vertebrates, but how cranial tissues respond to these loads remains obscure. Here, we developed a computational framework integrating the discrete element method (DEM) with finite element analysis (FEA) to investigate cranial biomechanics during burrowing. We used Blanus cinereus, a round-headed amphisbaenian, as a model to establish DEM predictions that were validated and calibrated against in vitro experiments across three substrates and compared with in vivo push forces. DEM-calibrated particle contact forces were then transferred to an anatomically detailed finite element model to quantify cranial loading. The analyses suggested that soft tissues accommodated substantial deformation, while the skull transmitted burrowing loads from the premaxilla towards the occipital region. Cranial sutures further redistributed stresses and strains within the skull. This validated DEM-FEA framework links particle-scale substrate interactions with internal cranial biomechanics and provides a quantitative approach for investigating the mechanics of head-first burrowing across fossorial vertebrates.

bioengineering↗

Engineering the NAT-ULT module increases seed number per pod in soybean

Seed number per pod is a major soybean yield-component trait, yet experimentally validated causal modules remain poorly defined. Here, we identify and functionally validate a soybean NAT-ULT regulatory module controlling ovule and seed number per pod. Through a visual screen of a fast-neutron-irradiated Glycine max cv. Williams 82 population, we isolated MO27, which increased four-seeded pod frequency from approximately 2-4% in wild type to 27-30%, without major changes in plant architecture, total pod number, or seed morphology. Comparative genome hybridization mapped the phenotype to a 46.7-kb chromosome 2 deletion containing GmNAT1 and chromosome 6 deletions encompassing GmULT-B1 and GmULT-B3. Ovule-clearing analysis showed that increased seed number originated before fertilization through elevated formation of four-ovule ovaries. CRISPR/Cas9-mediated mutagenesis of GmNAT1, GmULT-B1, and GmULT-B3 increased four-seeded pod frequency without detectable penalties in 100-seed weight, total pod number, or plant height. Tomato SlULT triple mutants also increased floral organ and locule number, supporting conserved ULT-like function in reproductive organ patterning. RNA-seq interaction analysis revealed a chromosome 6-dominant transcriptional state, accompanied by selective non-additive reprogramming of hormone/ovule-number and cell-wall-remodeling modules. Integrated genetic and transcriptomic analyses support a hierarchical model in which NAT-ULT perturbation may enhance meristematic competence and remodel reproductive developmental programs, while additional fast-neutron-background-associated transcriptional changes may further modulate the phenotype. These findings define NAT-ULT as a molecular target for engineering soybean seed number per pod.

plant biology↗

Reading ability in both deaf and hearing adults is linked to neural representations of abstract phonology derived from visual speech

Reading is central to academic and vocational success. Some deaf children face reading challenges due to limited access to spoken or signed language. Robust phonological representations are key to reading development in hearing children. Spoken language phonology may be one of many contributors to reading development in deaf children. Indeed, speechreading ability correlates with reading skill in both deaf and hearing individuals, suggesting it is linked to reading development regardless of hearing status. Further support for this hypothesis would be provided by evidence that similar neural representations of speech phonology are evoked by visual speech and other language forms (auditory speech and text), and that these neural representations are related to reading proficiency. We used fMRI and Representational Similarity Analysis (RSA) to identify shared neural representations of spoken language phonological structure. A group of deaf adult participants (N=22), with a mixture of sign language and spoken language backgrounds and reading abilities, were presented with single lexical items as visual speech and dynamic text (cursive text, revealed letter-by-letter to promote a phonological reading strategy). Adult hearing participants (N=25) were presented with the same words, but as visual speech and auditory speech. Shared neural representations of phonological structure of English words were found in each group in the superior and middle temporal cortex (STC/MTC) and these abstract representations were more similar across different language forms in better readers. Our data provide neurobiological evidence of the contribution of visual speech to abstract phonological representations of spoken language, that relate to reading proficiency, in both deaf and hearing adults. Significance StatementReading is an essential skill, yet some deaf children face reading challenges due to reduced access to signed or spoken language. In hearing children, successful reading depends on abstract phonological representations, but whether spoken language phonology relates to reading in deaf individuals remains unclear. Using fMRI and RSA, we show that deaf and hearing adults recruit neural representations of phonology that are shared by visual speech and other language forms (visual/auditory speech in hearing; visual speech/dynamic text in deaf) in the superior and middle temporal cortex. Critically, greater cross-modal alignment of neural representations of phonological structure was associated with better reading in both groups. These findings provide neurobiological evidence that visual speech contributes to phonological representations that relate to reading, regardless of hearing status.

neuroscience↗

Community Challenge towards Consensus on Characterization of Biological Tissue: C4Bios First Findings

This study investigates methodological variability across various expert laboratories worldwide, with regards to characterizing the mechanical properties of biological tissues. Two testing rounds were conducted on the specific use case of uniaxial tensile testing of porcine aorta. In the first round, 24 labs were invited to apply their established methods to assess inter-laboratory variability. This revealed significant methodological diversity and associated variability in the stress-stretch results, underscoring the necessity for a standardized approach. In the second round, a consensus protocol was collaboratively developed and adopted by 19 labs in an attempt to minimize variability. This involved standardized sample preparation and uniformity in testing protocol, including the use of a common cutting and thickness measurement tool. Despite protocol harmonization, significant variability persisted across labs, which could not be solely attributed to inherent biological differences in tissue samples. These results illustrate the challenges in unifying testing methods across different research settings, underlining the necessity for further refinement of testing practices. Enhancing consistency in biomechanical experiments is pivotal when comparing results across studies, as well as when using the resulting material properties for in silico simulations in medical research.

bioengineering↗

Cyanamide-inducible expression of homing nuclease I-SceI for iterative genome engineering and parallel promoter characterisation in Saccharomyces cerevisiae

In synthetic biology, microbial chasses including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale. Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements, such as the galactose-inducible (GAL) promoter in S. cerevisiae. Here, we prototyped the cyanamide-induced I-SceI-mediated double-strand DNA breaks (DSBs) for selectable marker recycling in yeast metabolic engineering. We further combined cyanamide-induced I-SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter replacement, which simplified the molecular cloning procedure for promoter characterisation in S. cerevisiae. We then characterised three tetracycline-inducible promoters of differential strength, a non-leaky {beta}-estradiol-inducible promoter, cyanamide-inducible DDI2 promoter, bidirectional MAL32/MAL31 promoters, and five pairs of bidirectional GAL1/GAL10 promoters. Overall, alternative regulatory controls for genome engineering tools are important for the construction of complexed genotypes in microbial systems for synthetic biology and metabolic engineering applications.

synthetic biology↗

Functional architecture of intracellular oscillations in hippocampal dendrites

Fast electrical signaling in dendrites is central to neural computations that support adaptive behaviors. Conventional techniques lack temporal and spatial resolution and the ability to track underlying membrane potential dynamics present across the complex three-dimensional dendritic arbor in vivo. Here, we perform fast two-photon imaging of dendritic and somatic membrane potential dynamics in single pyramidal cells in the CA1 region of the mouse hippocampus during awake behavior. We study the dynamics of subthreshold membrane potential and suprathreshold dendritic events throughout the dendritic arbor in vivo by combining voltage imaging with simultaneous local field potential recording, post hoc morphological reconstruction, and a spatial navigation task. We systematically quantify the modulation of local event rates by locomotion in distinct dendritic regions and report an advancing gradient of dendritic theta phase along the basal-tuft axis, then describe a pre-dominant hyperpolarization of the dendritic arbor during sharp-wave ripples. Finally, we find spatial tuning of dendritic representations dynamically reorganizes following place field formation. Our data reveal how the organization of electrical signaling in dendrites maps onto the anatomy of the dendritic tree across behavior, oscillatory network, and functional cell states.

neuroscience↗

The integration of tandem gene repeats via a bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation in Saccharomyces cerevisiae

Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms, like human diseases and microbial productivities of target bioproducts. Here, we develop a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualise the evolutionary trajectories of gene repeats. We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification (ToxAmp) modules, and accidentally re-visited the high-level capacity of multi-fragment co-transformation in S. cerevisiae. This system delivered the multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection. Inducing the toxin (RelE) expressing via a copper (II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin (RelB) module, resulting in [~]40 copies of a green fluorescence reporter (GFP) gene per copy of genome. The copy-number changes, increasing and decreasing, and stable maintenance were visualised using the GFP and blue chromoprotein AeBlue as reporters. Copy-number increasing happened spontaneously not depending on a selection pressure and was quickly enriched through toxin-antitoxin-mediated selection. In summary, the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/578080v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@75d1f3org.highwire.dtl.DTLVardef@12aafeforg.highwire.dtl.DTLVardef@184a1a5org.highwire.dtl.DTLVardef@90586a_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

TRAF2, an innate immune sensor, reciprocally regulates mitophagy and inflammation to maintain cardiac myocyte homeostasis.

Mitochondrial damage triggers cell death signaling with catastrophic consequences in long-lived and irreplaceable cells, such as cardiac myocytes. Sensing of leaked mitochondrial DNA upon mitochondrial damage is also a potent trigger of inflammation. Whether the innate immune response pathways monitor mitochondrial damage in mitochondria-rich cardiac myocytes to prevent inflammation and cell death, remains unknown. TRAF2, an adaptor protein downstream of innate immune receptors, localizes to the mitochondria in the unstressed heart, with increased mitochondrial targeting in cardiomyopathic human hearts and after cardiac ischemia-reperfusion injury in mice. Inducible cardiomyocyte-specific deletion of TRAF2 in young adult mice impairs mitophagy with rapid decline in mitochondrial quality, upregulates TLR9 expression in cardiac myocytes, and results in inflammation and cell death manifesting as a fulminant cardiomyopathy. Preventing TLR9-mediated mitochondrial DNA sensing and resultant inflammation provides a short-term reprieve from cardiomyopathy, but persistence of damaged mitochondria results in long-term recrudescence. Restoration of wild-type TRAF2, but not the E3 ubiquitin ligase deficient mutant, improves mitochondrial quality and rescues cardiomyopathy to restore homeostasis. Thus, the innate immune response acts via TRAF2 as the first line of defense against mitochondrial damage by orchestrating homeostatic mitophagy to dampen myocardial inflammation and prevent cell death.

cell biology↗

Unveiling unexpected complexity and multipotentiality of early heart fields

Complex organs are composed of a multitude of specialized cell types which assemble to form functional biological structures. How these cell types are created and organized remains to be elucidated for many organs including the heart, the first organ to form during embryogenesis. Here, we show the ontogeny of mammalian mesoderm at high-resolution single cell and genetic lineage/clonal analyses, which revealed an unexpected complexity of the contribution and multi-potentiality of mesodermal progenitors to cardiac lineages creating distinct cell types forming specific regions of the heart. Single-cell transcriptomics of Mesp1 lineage-traced cells during embryogenesis and corresponding trajectory analyses uncovered unanticipated developmental relationships between these progenitors and lineages including two mesodermal progenitor sources contributing to the first heart field (FHF), an intraembryonic and a previously uncharacterized extraembryonic-related source, that produce distinct cardiac lineages creating the left ventricle. Lineage-tracing studies revealed that these extraembryonic-related FHF progenitors reside at the extraembryonic-intraembryonic interface in gastrulating embryos and generate cardiac cell types that form the epicardium and the dorsolateral regions of the left ventricle and atrioventricular canal myocardium. Clonal analyses further showed that these progenitors are multi-potent, creating not only cardiomyocytes and epicardial cell types but also extraembryonic mesoderm. Overall, these results reveal unsuspected multiregional origins of the heart fields, and provide new insights into the relationship between intraembryonic cardiac lineages and extraembryonic tissues and the associations between congenital heart disease and placental insufficiency anomalies.

developmental biology↗

Myocardial matrix material supports a proliferative microenvironment for cardiomyocytes

Novel therapeutics have sought to stimulate the endogenous repair mechanisms in the mammalian myocardium as the native regenerative potential of the adult cardiac tissue is limited. In particular, a myocardial matrix derived injectable hydrogel has shown efficacy and safety in various animal myocardial infarction (MI) including evidence of increased myocardium. In this study, investigation on the properties of this myocardial matrix material demonstrated its native capability as an effective reactive oxygen species (ROS) scavenger that can protect against oxidative stress and maintain cardiomyocyte proliferation in vitro. In vivo assessment of of myocardial matrix hydrogel treatment post-MI demonstrated increased thymidine analog uptake in cardiomyocytes compared to saline controls along with co-staining with cell cycle progression marker, phospho-histone H3. Overall, this study provides further evidence that properties of the myocardial matrix hydrogel promote an environment supportive of cardiomyocytes undergoing cell cycle progression.

bioengineering↗

Insights into glycan import by a prominent gut symbiont

In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a "pedal bin" transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the {beta}2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to [~]2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

microbiology↗

Evaluation of Reproducible and Transparent Research Practices in Sports Medicine Research: A Cross-sectional study

BackgroundIn recent years, urgency has been placed on the \"reproducibility crisis\" facing biomedical research. Despite efforts toward improvement, certain elements needed to reproduce a study are often lacking from publications. The current state of reproducibility within the sports medicine research community remains unknown.\n\nPurposeOur study sought to evaluate the presence of eight indicators of reproducibility and transparency to determine the current state of research reporting in sports medicine research.\n\nStudy DesignCross-sectional review\n\nMethodsUsing the National Library of Medicine catalog, we identified 41 MEDLINE-indexed, English language sports medicine journals. From the 41 journals, we randomly sampled 300 publications that were recorded on PubMed as being published between January 1, 2014, and December 31, 2018. Two investigators extracted data in duplicate and blinded fashion.\n\nResultsOf the 300 publications sampled, 280 were accessible and were screened for empirical data. Studies that lack empirical data were excluded from our analysis. Of the remaining 195 with empirical data, 10 (5.13%) publications provided data availability statements, 1 (0.51%) provided a protocol, 0 (0.0%) provided an analysis script, and 9 (4.62%) were pre registered.\n\nConclusionReproducibility and transparency indicators are lacking in sports medicine publications. The majority of publications lack the necessary resources for reproducibility such as material, data, analysis scripts, or protocol availability. While the current state of reproducibility cannot be fixed overnight, we feel combined efforts of data sharing, open access, and verifying disclosure statements can help to improve overall reporting.

scientific communication and education↗

Can Orthopaedics become the Gold Standard for Reproducibility? A Roadmap to Success

BackgroundScientific research is replete with poor accessibility to data, materials, and protocol, which limits the reproducibility of a study. Transparency with regard to materials, protocols, and raw data sets enhances reproducibility by providing the critical information necessary to verify, replicate, and resynthesize research findings. The extent to which transparency and reproducibility exist in the field of orthopaedics is unclear. In our study, we aimed to evaluate transparency and reproducibility-related characteristics of randomly sampled publications in orthopaedic journals.\n\nMethodsWe used the National Library of Medicine catalog to identify English language and MEDLINE-indexed orthopaedic journals. From the 74 journals meeting our inclusion criteria, we randomly sampled 300 publications using a refined PubMed search that were published between January 1, 2014, and December 31, 2018. Two investigators were trained for data extraction and analysis. Both investigators were blinded and independently extracted data from the 300 studies.\n\nResultsOur initial search yielded 68,102 publications, from which we drew a random sample of 300 publications. Of these 300 publications, 286 were screened for empirical data and 14 were inaccessible. For analysis purposes, we excluded publications without empirical data. Of the 182 with empirical data, 13 studies (7.1%) included a data availability statement, 9 (4.9%) reported materials were available, none (0.0%) provided analysis scripts, 2 (1.1%) provided access to the protocol used, 5 (2.7%) were preregistered, and only 2 (1.1%) provided a statement about being a replicated study.\n\nConclusionsComponents necessary for reproducibility are lacking in orthopaedic surgery journals. The vast majority of publications did not provide data or material availability statements, protocols, or analysis scripts, and had no preregistration statements. Intervention is needed to improve reproducibility in the field of orthopaedics. The current state of reproducibility in orthopaedic surgery could be improved by combined efforts from funding agencies, authors, peer reviewers, and journals alike.\n\nLevel of EvidenceN/A

scientific communication and education↗

Evidence for shared conceptual representations for sign and speech

Do different languages evoke different conceptual representations? If so, greatest divergence might be expected between languages that differ most in structure, such as sign and speech. Unlike speech bilinguals, hearing sign-speech bilinguals use languages conveyed in different modalities. We used functional magnetic resonance imaging and representational similarity analysis (RSA) to quantify the similarity of semantic representations elicited by the same concepts presented in spoken British English and British Sign Language in hearing, early sign-speech bilinguals. We found shared representations for semantic categories in left posterior middle and inferior temporal cortex. Despite shared category representations, the same spoken words and signs did not elicit similar neural patterns. Thus, contrary to previous univariate activation-based analyses of speech and sign perception, we show that semantic representations evoked by speech and sign are only partially shared. This demonstrates the unique perspective that sign languages and RSA provide in understanding how language influences conceptual representation.

neuroscience↗

Kilohertz in vivo imaging of neural activity

Understanding information processing in the brain requires us to monitor neural activity in vivo at high spatiotemporal resolution. Using an ultrafast two-photon fluorescence microscope (2PFM) empowered by all-optical laser scanning, we imaged neural activity in vivo at up to 3,000 frames per second and submicron spatial resolution. This ultrafast imaging method enabled monitoring of both supra- and sub-threshold electrical activity down to 345 m below the brain surface in head fixed awake mice.

neuroscience↗

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains

Dynamic restructuring of chromatin architecture has been implicated in cell-type specific gene regulatory programs; yet, how chromatin remodels during lineage specification remains to be elucidated. Through interrogating chromatin reorganization during human cardiomyocyte differentiation, we uncover dynamic chromatin interactions between genes and distal regulatory elements harboring noncoding variants associated with adult and congenital heart diseases. Unexpectedly, we also discover a new class of human pluripotent stem cell (PSC)-specific topologically associating domains (TAD) that are created by the actively transcribed endogenous retrotransposon HERV-H. Deletion or silencing of specific HERV-H elements eliminates corresponding TAD boundaries, while de novo insertion of HERV-H can introduce new chromatin domain boundaries in human PSCs. Furthermore, comparative analysis of chromatin architecture in other species that lack HERV-H sequences supports a role for actively transcribed HERV-H in demarcating human PSC-specific TADs. The biological role of HERV-H is further underscored by the observation that deletion of a specific HERV-H reduces transcription of genes upstream and facilitates cell differentiation. Overall, our results highlight a previously unrecognized role for retrotransposons in restructuring genome architecture in the human genome and delineate dynamic gene regulatory networks during cardiomyocyte development that inform how non-coding genetic variants contribute to human heart diseases.

genomics↗

Repression of Dlx1/2 Signaling by Nolz-1/Znf503 is Essential for Parcellation of the Striatal Complex into Dorsal and Ventral Striatum

The division of the striatum into dorsal and ventral districts is of central clinical importance. The dorsal striatum is differentially affected in Huntingtons disease, dopamine in the ventral striatum is differentially spared in Parkinsons disease, and human brain imaging studies implicate the ventral striatum in addictive disorders. If fits that the dorsal striatum contains the cells of origin of the direct and indirect basal ganglia pathways for motor control. The ventral striatum is a node in neural circuits related to motivation and affect. Despite these striking neurobiologic contrasts, there is almost no information about how the dorsal and ventral divisions of the striatum are set up during development. Here, we demonstrate that interactions between the two key transcription factors Nolz-1 and Dlx1/2 control the migratory paths of developing striatal neurons to the dorsal or ventral striatum. Moreover, these same transcription factors control the cell identity of striatal projection neurons in both the dorsal and ventral striatum including the cell origin of the direct and indirect pathways. We show that Nolz-1 suppresses Dlx1/2 expression. Deletion of Nolz-1 or over-expression of Dlx1/2 can produce a striatal phenotype characterized by withered dorsal striatum and a swollen ventral striatum, and that we can rescue this phenotype by manipulating the interactions between Nolz-1 and Dlx1/2 transcription factors. This evidence suggests that the fundamental basis for divisions of the striatum known to be differentially vulnerable at maturity is already encoded by the time embryonic striatal neurons begin their migrations into the developing striatum.

neuroscience↗