Biology subjects

Oliver, T.

Publications and source records attributed to Oliver, T..

11 recordsLinked to original sources

bioRxiv2026

De Novo Design of Flavoproteins with Controlled Excited State Dynamics

Designing photochemical properties in proteins is a frontier challenge in biomolecular design, which, when realised, will open new avenues in catalysis and biomolecular electronics. Here we demonstrate an integrated computational design framework, supported by ultrafast spectroscopy, combining protein design, quantum mechanical/molecular mechanics molecular dynamics (QM/MM MD) and electronic structure calculations, to control flavin excited states in de novo proteins. Iterative design yields FC-4D2, a flavocytochrome with covalently bound flavin and non-covalently bound heme B and Fl-4D2, where the heme-binding site is removed. Both proteins are highly thermostable, and access all physiologically relevant flavin redox and protonation states, while high-resolution X-ray crystallography confirms the near-[A]ngstrom-level accuracy in design. Incorporating QM/MM MD and linear-response time-dependent density functional theory (LR-TDDFT) into the design workflow enables engineering of a flavin-tryptophan charge-transfer variant, Fl-4D2CT, that modifies the flavin absorption spectrum, substantially alters its redox properties and suppresses fluorescence. Ultrafast studies reveal how protein design reshapes the excited state relaxation timescale and mechanism. Our study establishes a modular strategy for programming flavin photochemistry in designed proteins.

biophysics↗

bioRxiv2026

The builder's legacy: persistent reef structure creates a window for coral recovery after adult loss

Coral reef recovery depends on successful juvenile recruitment, yet which local factors govern early coral demography remains poorly resolved. Adult coral cover and reef structural complexity are widely hypothesized to regulate juvenile success, but their independent and interactive effects have not been mechanistically disentangled, nor has the relative role of living adult tissue versus persisting structural framework been clarified. Here, combining in situ coral size-structure surveys with high resolution photogrammetry across 405 reef segments spanning the main Hawaiian Islands, we quantify how adult cover and three-dimensional reef structure, measured as rugosity and fractal dimension, jointly shape juvenile coral densities. We reveal nonlinear relationships between juvenile density and adult cover, peaking at intermediate (~8%) coral cover, with fine-scale surface complexity and vertical relief exerting opposing influences across the cover gradient. Together, these reveal a structural legacy window in which reduced adult cover relaxes constraints on juvenile establishment while the three-dimensional habitat built by those adults persists. This decoupling of biological loss from structural loss creates a transient opportunity for population renewal, with intermediate-cover reefs supporting juveniles across the broadest range of structural configurations. More generally, our results show how the physical legacy of ecosystem engineers can continue to regulate population recovery after the organisms that create it have declined.

ecology↗

bioRxiv2025

Demographic insights for coral restoration

O_LICoral reef decline has prompted a global surge in reef restoration initiatives. The success of initiatives that aim to sustain coral populations or assemblages will depend on demographic principles. Restoration strategies generally follow two demographic pathways: supplemental approaches, which increase population numbers through the repeated addition of recruits, fragments, or adults, without fundamentally altering long-term population dynamics; and structural approaches, which enhance vital rates-growth, survival, or reproduction- through changes that modify the demographic processes governing population growth on a sustained basis, either extrinsically (e.g., herbivory, habitat protection) or intrinsically (e.g., assisted evolution). Some interventions, such as supplemental feeding, may temporarily improve vital rates but still function as supplemental approaches because benefits persist only while interventions continue. C_LIO_LIWe synthesized 28 coral matrix population models spanning morphologically diverse coral species from the Caribbean, Hawaii, and the Great Barrier Reef to quantify supplemental and structural changes needed to increase population growth. C_LIO_LIResults highlight two consistent demographic leverage points for which population growth was most sensitive: (1) survival of reproductive adults and (2) successful recruitment. Improving adult survival or recruitment by 20% through structural means produced a 5% increase in population growth rate across population on average, assuming the whole population was affected. By contrast through supplemental means, the same increase required [~]100 recruit outplants or 5-10 adult outplants per 1,000 individuals in a population annually. For large populations typical of restoration targets (105-107 individuals), this translates to 103 adult and 104 recruit outplants per year--levels rarely logistically or economically feasible. C_LIO_LIThese findings yield two key implications. First, supplemental interventions are inefficient for large populations and demand sustained, large-scale effort, even when they temporarily enhance growth or survival. Second, strategies enhancing vital rates across broad geographic areas represent the most effective means of boosting coral abundance, including habitat protection, alleviation of environmental stressors, and interventions which promote long-term survival and recruitment. Our demographic framework underscores that if the restoration goal is sustained increases in coral cover, success depends less on repeated supplements and more on interventions that produce lasting improvements in vital rates. C_LI

ecology↗

bioRxiv2025

Mitochondrial instability contributes to IFN-driven heart disease.

AimsType I interferons (IFNs) are linked to an increased risk of cardiovascular disease and are chronically elevated in systemic autoimmune diseases such as systemic lupus erythematosus (SLE). We evaluated the effect of chronic IFNa exposure on cardiac and cardiomyocyte function in order to better understand IFN-driven cardiac disease from the perspective of SLE. Methods and ResultsAdministration of the TLR7/8 agonist, resiquimod, to C57BL6 mice, drove chronic IFN induction and reduced ejection fraction and fractional shortening compared to mice treated with vehicle control. Multiomic analysis demonstrated increased IFN signature in resiquimod treated hearts (transcriptomic and proteomic) and a decrease in genes and proteins representing electron transport chain (ETC) and cytochrome complex assembly. Integration of metabolomics with transcriptomics revealed pathways representing chemokine signaling, Toll-like receptor signaling, HIF-1 signaling and Dilated cardiomyopathy. As our in vivo model of IFN-driven SLE-like heart disease showed both proteomic and transcriptomic changes that reflected changes in mitochondrial and potentially cardiac function, we conducted an in vitro analysis of the effects of acute and chronic IFN on cardiomyocytes, the most energetically demanding cell type in the heart, and the cells most susceptible to stress and inflammation. As with our in vivo findings, proteomic and transcriptomic analysis of AC16 cardiomyocytes exposed to chronic IFN indicated perturbation of mitochondrial pathways. Extracellular flux analysis of chronically exposed AC16 cells showed impaired basal respiration, maximal respiration, ATP production and non-glycolytic acidification, glycolysis and glycolytic capacity, indicating increased mitochondrial stress in response to chronic exposure to IFNa. MitoTracker green staining showed increased fragmentation and perinuclear localization in AC16 chronically exposed to IFN and an increase in mtDNA release and expression of proteins known to contribute to mtDNA release and detection. ConclusionsOur results directly support a role for chronic IFN in driving cardiac dysfunction in both a mouse model of IFN-driven disease that mimics SLE and in cardiomyocytes, though enhanced mitochondrial stress, mtDNA release and potentially exacerbation of cGAS-STING-IFN axis. Translational PerspectivesMany immune features of SLE such as elevated type I interferons, chronic inflammation, and persistent autoantibody production are strongly correlated with increased cardiovascular risk, but it remains difficult to prove direct biological causation. This study demonstrates that chronic IFN exposure induces mitochondrial dysfunction and mtDNA release in cardiomyocytes, directly complementing an in vivo model of SLE-cardiac disease. It suggests that targeting IFNs may reduce CVD risk in IFN-driven autoimmunity.

immunology↗

bioRxiv2024

Cortical Acetylcholine Response to Deep Brain Stimulation of the Basal Forebrain

BackgroundDeep brain stimulation (DBS), the direct electrical stimulation of neuronal tissue in the basal forebrain to enhance release of the neurotransmitter acetylcholine, is under consideration as a method to improve executive function in patients with dementia. While some small studies indicate a positive response in the clinical setting, the relationship between DBS and acetylcholine pharmacokinetics is incompletely understood. ObjectiveWe examined the cortical acetylcholine response to different stimulation parameters of the basal forebrain. Methods2-photon imaging was combined with deep brain stimulation. Stimulating electrodes were implanted in the subpallidal basal forebrain, and the ipsilateral somatosensory cortex was imaged. Acetylcholine activity was determined using the GRABACh-3.0 muscarinic acetylcholine receptor sensor, and blood vessels were imaged with Texas red. ResultsExperiments manipulating pulse train frequency demonstrated that integrated acetylcholine induced fluorescence was insensitive to frequency, and that peak levels were achieved with frequencies from 60 to 130 Hz. Altering pulse train length indicated that longer stimulation resulted in higher peaks and more activation with sublinear summation. The acetylcholinesterase inhibitor donepezil increased the peak response to 10s of stimulation at 60Hz, and the integrated response increased 57% with the 2 mg/kg dose, and 126% with the 4 mg/kg dose. Acetylcholine levels returned to baseline with a time constant of 14 to 18 seconds in all experiments. ConclusionsThese data demonstrate that acetylcholine receptor activation is insensitive to frequency between 60 and 130 Hz. High peak responses are achieved with up to 900 pulses. Donepezil increases total acetylcholine receptor activation associated with DBS but did not change temporal kinetics. The long time constants observed in the cerebral cortex add to the evidence supporting volume in addition to synaptic transmission. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/605828v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@a06bborg.highwire.dtl.DTLVardef@4003f0org.highwire.dtl.DTLVardef@c286d1org.highwire.dtl.DTLVardef@1213d2c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

The ancient evolution of far-red light photoacclimation in cyanobacteria

Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of [~]20 genes, and involves the synthesis of red-shifted chlorophylls f and d, together with paralogues of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to clarify this issue; sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 52 new gene clusters. These data enable high-resolution phylogenetics and - by relying on multiple gene trees, together with gene arrangement conservation - support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and the process may have been associated with microbial mats and stromatolite formation in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing a conserved intergenic regulatory sequence that has been maintained for billions of years. Taken together, our results indicate that oxygenic photosynthesis using far-red light may have played a significant role in Earths early history.

evolutionary biology↗

bioRxiv2023

Rationally seeded computational protein design

Computational protein design is advancing rapidly. Here we describe efficient routes to two families of -helical-barrel proteins with central channels that bind small molecules. The designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides. Adjacent helices are connected using computational loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix-turn-helix-turn-helix motifs that are packed onto the barrels computationally. Throughout these pipelines, residues that define open states of the barrels are maintained. This minimises sequence sampling and accelerates routes to successful designs. For each of 6 targets, just 2 - 6 synthetic genes are made for expression in E. coli. On average, 80% express to give soluble monomeric proteins that are characterized fully, including high-resolution structures for most targets that match the seed structures and design models with high accuracy.

synthetic biology↗

bioRxiv2021

High efficiency excitation energy transfer in biohybrid quantum dot-bacterial reaction center nanoconjugates

Reaction centers (RCs) are the pivotal component of natural photosystems, converting solar energy into the potential difference between separated electrons and holes that is used to power much of biology. RCs from anoxygenic purple photosynthetic bacteria such as Rhodobacter sphaeroides only weakly absorb much of the visible region of the solar spectrum which limits their overall light-harvesting capacity. For in vitro applications such as bio-hybrid photodevices this deficiency can be addressed by effectively coupling RCs with synthetic lightharvesting materials. Here, we studied the time scale and efficiency of Forster resonance energy transfer (FRET) in a nanoconjugate assembled from a synthetic quantum dot (QD) antenna and a tailored RC engineered to be fluorescent. Time-correlated single photon counting spectroscopy of biohybrid conjugates enabled the direct determination of FRET from QDs to attached RCs on a time scale of 26.6 {+/-} 0.1 ns and with a high efficiency of 0.75 {+/-} 0.01.

biophysics↗

bioRxiv2021

Somatic mutations reveal widespread mosaicism and mutagenesis in human placentas

Clinical investigations of human fetuses have revealed that placentas occasionally harbour chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation of the placenta, termed confined placental mosaicism, remains unknown. Here, we investigated the phylogeny of human placentas reconstructed from somatic mutations, using whole genome sequencing of 86 placental biopsies and of 106 microdissections. We found that every placental biopsy represented a clonal expansion that is genetically distinct. Biopsies exhibited a genomic landscape akin to childhood cancer, in terms of mutation burden and mutational imprints. Furthermore, unlike any other human normal tissue studied to date, placental genomes commonly harboured copy number changes. Reconstructing phylogenetic relationships between tissues from the same pregnancy, revealed that developmental bottlenecks confined placental tissues, by separating trophectodermal from inner cell mass-derived lineages. Of particular note were cases in which inner cell mass-derived and placental lineages fully segregated within a few cell divisions of the zygote. Such early embryonic bottlenecks may enable the normalisation of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal cancer-like mutagenesis in placental tissues and portray confined mosaicism as the normal outcome of placental development.

genomics↗

bioRxiv2020

Extensive phylogenies of human development reveal variable embryonic patterns

Starting from the zygote, all cells in the developing and adult human body continuously acquire mutations. A mutation shared between two different cells implies a shared progenitor cell and can thus be used as a naturally occurring marker for lineage tracing. Here, we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissected samples from multiple organs. Early embryonic progenitor cells inferred from the phylogenies often contribute in different proportions to the adult body and the extent of this asymmetry is variable between individuals, with ratios between the first two reconstructed cells ranging from 56:44 to 92:8. Asymmetries also pervade subsequent cell generations and can differ between tissues in the same individual. The phylogenies also resolve the spatial embryonic origins and patterning of tissues, revealing a spatial effect in the development of the human brain. Supplemented by data on eleven men, we timed the split between soma and germline, with the earliest observed segregation occurring at the first cell divisions. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

genomics↗

bioRxiv2020

Origin of photosynthetic water oxidation at the dawn of life

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that relative to the origin of life and bioenergetics, the origin of oxygenic photosynthesis is a late innovation. However, when exactly water oxidation originated remains an unanswered question. Here we use relaxed molecular clocks to compare one of the two ancestral core duplications that are unique to water-oxidizing photosystem II, that leading to CP43 and CP47, with some of the oldest well-described events in the history of life. Namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of cyanobacteria-specific FtsH metalloprotease subunits, of CP43 variants used in a variety of photoacclimation responses, and the speciation events leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on species trees alone.

evolutionary biology↗