Biology subjects

Stuart, A.

Publications and source records attributed to Stuart, A..

8 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

Monotreme transcriptomes shed light on evolution of lactation and placentation

Placentation and lactation are hallmark mammalian reproductive traits and key processes facilitating the transfer of nutrients from the mother to the offspring. The basal mammalian lineage of egg-laying monotremes features a short gestation period supported by a simple placenta and an elongated lactation, similar to marsupials. Eutherian mammals by contrast evolved longer gestation facilitated by extensive placentation and shorter lactation. To understand the gene expression underpinning maternal-foetal nutrient transfer across mammals, we generated transcriptome datasets for the monotreme reproductive tract and mammary gland and compared this to expression in representative species from the other mammalian clades: marsupials (Tammar wallaby) and eutherians (mouse). This revealed extensive overlapping gene expression between the therian placenta and monotreme reproductive tract, including the first observation of retroviral gene expression in the echidna reproductive tract. Interestingly, we discovered that transport and development functions supporting foetal growth are expressed in echidna mammary gland and eutherian placenta, likely a signature of the shift from prolonged lactation to longer placentation. Together, this demonstrates that diverse modes of maternal-foetal nutrient transfer are underpinned by similar gene networks across mammals.

evolutionary biology↗

bioRxiv2026

Conservation rescued the Mauritius kestrel from extinction but not from genomic erosion

Conservation can prevent species extinction via demographic recovery, yet it remains debated whether this translates into genomic recovery and restored fitness. The Mauritius kestrel (Falco punctatus) declined to four known wild birds in 1974 before intensive management recovered the population. Using 130 genomes spanning nearly 200 years, lifetime reproductive success data, and simulations, we reconstructed genomic change across the species collapse and recovery. Long-term small population size had already removed some harmful variation before the crash, a process expected to buffer populations from severe inbreeding depression. Yet the recent bottleneck sharply increased inbreeding, exposed additional harmful variants, and left a signature of genomic erosion associated with reduced reproductive success. The long conservation history of the Mauritius kestrel shows how population collapse and recovery can leave a compounding genetic threat, in which partial genetic purging, continuing genomic erosion, and conservation dependence unfold together in rescued species.

evolutionary biology↗

bioRxiv2024

AMHY and sex determination in egg-laying mammals

The sex chromosomes of egg-laying mammals (monotremes), which lack the sex determining gene SRY1, evolved independently to those of all therian mammals2,3. Here we characterise the candidate monotreme sex determining gene, the Y-localised anti-Mullerian hormone gene (AMHY)4,3 and trace its expression during the period of sexual differentiation. Monotreme AMHX and AMHY gametologues have significant sequence divergence at the promoter, gene and protein level, likely following an original allele inversion in the common monotreme ancestor but retain conserved features of TGF-{beta} molecules. Expression of sexual differentiation genes in the echidna fetal gonad were significantly different from that of therian mammals. AMHY expression was seen exclusively in the male gonad during sexual differentiation, whereas AMHX was expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinise the female urogenital system, a possible result of mammalian specific changes to AMH proteins preventing function in the chicken. Our results provide fundamental insight into the first steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex determination gene.

evolutionary biology↗

bioRxiv2023

Principles of Computation by Competitive Protein Dimerization Networks

Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations, in which the concentrations of monomers (inputs) determine the concentrations of dimers (outputs). Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform (their "expressivity") and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks (3-6 monomers) are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough ([≥]8 proteins), can perform nearly all ([~]90%) potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/564854v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1917f39org.highwire.dtl.DTLVardef@13795bcorg.highwire.dtl.DTLVardef@47913eorg.highwire.dtl.DTLVardef@90bd30_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2021

Naturalistic hyperscanning with wearable magnetoencephalography

The evolution of human cognitive function is reliant on complex social interactions which form the behavioural foundation of who we are. These social capacities are subject to dramatic change in disease and injury; yet their supporting neural substrates remain poorly understood. Hyperscanning employs functional neuroimaging to simultaneously assess brain activity in two individuals and offers the best means to understand the neural basis of social interaction. However, present technologies are limited, either by poor performance (low spatial/temporal precision) or unnatural scanning environment (claustrophobic scanners, with interactions via video). Here, we solve this problem by developing a new form of hyperscanning using wearable magnetoencephalography (MEG). This approach exploits quantum sensors for MEG signal detection, in combination with high-fidelity magnetic field control - afforded by a novel "matrix coil" system - to enable simultaneous scanning of two freely moving participants. We demonstrate our approach in a somatosensory task and an interactive ball game. Despite large and unpredictable subject motion, sensorimotor brain activity was delineated clearly in space and time, and correlation of the envelope of neuronal oscillations between people was demonstrated. In sum, unlike existing modalities, wearable-MEG combines high fidelity data acquisition and a naturalistic setting, which will facilitate a new generation of hyperscanning.

neuroscience↗

bioRxiv2020

Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury

Inflammatory tissue injury such as acute lung injury (ALI) is a disorder that leads to respiratory failure, a major cause of morbidity and mortality worldwide. Excessive neutrophil influx is a critical pathogenic factor in the development of ALI. Here, we identify the subset of neutrophils that is responsible for ALI and lethality in polymicrobial sepsis. The pro-inflammatory neutrophil subpopulation was characterized by its unique ability to endocytose albumin nanoparticles (ANP), upregulation of pro-inflammatory cytokines and chemokines as well as the excessive production of reactive oxygen species (ROS) in models of endotoxemia and septicemia. ANP delivery of the drug piceatannol, a spleen tyrosine kinase (Syk) inhibitor, to the susceptible subset of neutrophils, prevented ALI and mortality in mice subjected to polymicrobial infection. Targeted inhibition of Syk in ANP-susceptible neutrophils had no detrimental effect on neutrophil-dependent host defense because the subset of ANPlow neutrophils effectively controlled polymicrobial infection. The results show that neutrophil heterogeneity can be leveraged therapeutically to prevent ALI without compromising host defense.Competing Interest StatementABM, AS, KB have interests in the biotechnology company Nano Biotherapeutics Inc.View Full Text

immunology↗

bioRxiv2019

A natural antisense to brain-derived neurotrophic factor impairs extinction of drug seeking

BACKGROUNDBrain derived neurotrophic factor (BDNF) is critical for the extinction of drug-seeking. Expression of the Bdnf gene is highly regulated via interactions with non-coding RNA, which themselves are altered following drug exposure. Here we investigate whether a novel long non-coding RNA antisense to Bdnf prevents extinction of drug-seeking. METHODS: Strand-specific RNA sequencing identified a novel long non-coding RNA antisense to exon IV of the Bdnf gene in the ventromedial prefrontal cortex of 8 adult male rats. We then assessed asBdnf-IV expression using strand-specific reverse transcription and quantitative polymerase chain reaction following acquisition, extinction or abstinence from intravenous nicotine self-administration (N = 116). A functional role of the asBdnf-IV in extinction of nicotine-seeking was established by infusing gapmer oligonucleotides into the infralimbic cortex prior to extinction and testing for the effect of these infusions on reinstatement and reacquisition of nicotine-seeking (N = 36). RESULTSRNA sequencing identified the presence of a novel long non-coding RNA antisense to exon IV of the Bdnf gene (asBdnf-IV). Expression of asBdnf-IV was elevated following intravenous nicotine self-administration but not experimenter-administered nicotine. Elevated asBdnf-IV persisted across abstinence and to a greater extent following extinction training, suggesting an interaction between abstinence and extinction learning. In support of this, knockdown of the asBdnf-IV across extinction, but not abstinence, significantly attenuated nicotine-primed reinstatement of nicotine-seeking. CONCLUSIONSasBdnf-IV accumulates in the infralimbic cortex across self-administration training, interferes with the inhibitory learning that underpins extinction of drug-seeking, and predisposes animals to drug relapse.

neuroscience↗