Biology subjects

Phillips, C.

Publications and source records attributed to Phillips, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Development of D-box peptides to inhibit the Anaphase Promoting Complex/Cyclosome

E3 ubiquitin ligases engage their substrates via degrons - short linear motifs typically located within intrinsically disordered regions of substrates. As these enzymes are large, multi-subunit complexes that generally lack natural small-molecule ligands and are hard to drug via conventional means, alternative strategies are needed to target them in diseases, and peptide-based inhibitors derived from degrons represent a promising approach. Here we explore peptide inhibitors of Cdc20, a substrate-recognition subunit and activator of the E3 ubiquitin ligase the anaphase promoting complex/cyclosome (APC/C) that is essential in mitosis and consequently of interest as an anti-cancer target. APC/C engages substrates via degrons that include the Destruction box (D-box) motif. We used a rational design approach to construct binders containing unnatural amino acids aimed at better filling a hydrophobic pocket on the surface of Cdc20. We confirmed binding by thermal-shift assays and surface plasmon resonance and determined the structures of a number of the Cdc20- peptide complexes. Using a cellular thermal shift assay, we confirmed that the D-box peptides also bind to and stabilise Cdc20 in the cell. We found that the D-box peptides inhibit ubiquitination activity of APC/CCdc20 and are more potent than the small molecule inhibitor Apcin. Lastly, these peptides function as portable degrons capable of driving the degradation of a fused fluorescent protein. Interestingly, we find that although inhibitory activity of the peptides correlates with Cdc20-binding affinity, degradation efficacy does not, which may be due to the complex nature of APC/C regulation and effects of degron binding of subunit recruitment and conformational changes. Our study lays the groundwork for the further development of these peptides as molecular therapeutics for blocking APC/C as well as potentially also for harnessing APC/C for targeted protein degradation.

biochemistry↗

bioRxiv2024

Exposure to light supresses the activity of the medial and superior amygdala during emotional processing

The brain mechanisms through which changes in season and light exposure modulate mood may involve different nuclei of the amygdala. We aimed to test this hypothesis using 7 Tesla functional magnetic resonance imaging in 29 healthy young adults. We first considered time-of-year changes in activity that are related to the slow change in photoperiod. We find that the response to emotional stimuli of selected medial and superior nuclei of the amygdala peaked around the start of winter or increased with worse mood status. We further assessed how alternating short exposures to light of different illuminance acutely affected the regional activity of the amygdala. We show that the same areas showed a linear reduction of activity when exposed to increasing light illuminance, specifically when processing emotional stimuli. Importantly, the impact of light on part of these nuclei peaked around the start of summer or decreased with worse mood. These findings provide new evidence that humans show seasonality and that, for mood, it involves parts of the amygdala. The results bring novel insights into the mechanisms that underlie the long-term and acute impact of light on mood and that may contribute to the benefits of light therapy in the treatment of mood disorders.

neuroscience↗

bioRxiv2024

A learnable transition from low temperature to high temperature proteins with neural machine translation

This work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 million protein homologous pairs from organisms adapted to different temperatures, demonstrates promising capability in targeting thermal stability. A designed variant of the Drosophila melanogaster Engrailed Homeodomain shows increased stability at high temperatures, as validated by estimators and molecular dynamics simulations. Furthermore, NOMELT achieves zero-shot predictive capabilities in ranking experimental melting and half-activation temperatures across two protein families. It achieves this without requiring extensive homology data or massive training datasets as do existing zero-shot predictors by specifically learning thermophilicity, as opposed to all natural variation. These findings underscore the potential of leveraging organismal growth temperatures in context-dependent design of proteins for enhanced thermal stability.

bioinformatics↗

bioRxiv2023

Regional response to light illuminance across the human hypothalamus

Light exerts multiple non-image-forming biological effects on physiology including the stimulation of alertness and cognition. However, the subcortical circuitry underlying the stimulating impact of light is not established in humans. We used 7 Tesla functional magnetic resonance imaging to assess the impact of variations in light illuminance on the regional activity of the hypothalamus while healthy young adults (N=26; 16 women; 24.3 {+/-} 2.9y) were completing two auditory cognitive tasks. We find that, during both the executive and emotional tasks, higher illuminance triggered an activity increase over the posterior part of the hypothalamus, which includes part of the tuberomamillary nucleus and the posterior part of the lateral hypothalamus. In contrast, increasing illuminance evoked a decrease in activity over the anterior and ventral parts of the hypothalamus, encompassing notably the suprachiasmatic nucleus and another part of the tuberomammillary nucleus. Critically, the performance of the executive task was improved under higher illuminance and was negatively correlated with the activity of the posterior hypothalamus area. These findings reveal the distinct local dynamics of different hypothalamus regions that underlie the impact of light on cognition.

neuroscience↗

bioRxiv2023

The Origin And Speciation Of Orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and [~]7% (1,921) of the currently 29,524 accepted species. We then use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distribution data through the World Checklist of Vascular Plants. Orchids most recent common ancestor is traced back to the Late Cretaceous in Laurasia. The modern Southeast Asian range of subfamily Apostasioideae is interpreted as relictual, matching the history of numerous clades that went extinct at higher latitudes following the global climate cooled during the Oligocene. Despite their ancient origins, modern orchid species diversity mainly originated over the last 5 Ma, with the fastest speciation rates found in south-eastern Central America. Our results substantially alter our understanding of the geographic origin of orchids, previously proposed as Australian, and further pinpoint the role of Central American as a region of recent and explosive speciation.

evolutionary biology↗

bioRxiv2023

In vivo marker of brainstem myelin is associated to quantitative sleep parameters in healthy young men

Brain structural integrity has been suggested to contribute to the variability in human sleep quality and composition. The associations between sleep parameters and the regional integrity of subcortical structures implicated in sleep-wake regulation remain, however, largely unexplored. The present study aimed at assessing association between quantitative Magnetic Resonance Imaging (qMRI)-derived marker of the myelin content of the brainstem with the variability in the sleep electrophysiology in a large sample of healthy young men (N=321;[~]22y). Generalized Additive Model for Location, Scale and Shape (GAMLSS) was used to seek associations between sleep metrics and Magnetisation Transfer saturation (MTsat) qMRI values, proxy for myelin content. Separate GAMLSS revealed that sleep onset latency and slow wave sleep intensity were significantly associated with MTsat-derived myelin estimates in the brainstem (pcorrected[≤].03), with overall higher MTsat value associated with values reflecting better sleep quality. The association changed with age, however (MTsat-by-age interaction - pcorrected[≤].03), with higher MTsat value linked to better values in the two sleep metrics in the individuals of our sample aged [~]18 to 20y. Similar associations were detected across different parts of the brainstem (pcorrected[≤].03), suggesting that the overall maturation and integrity of the brainstem was associated with both sleep metrics. Our results suggest that myelination of the many reticular nuclei of the brainstem essential to regulation of sleep is associated with inter-individual differences in sleep characteristics during early adulthood. They may have implications for sleep disorders or neurological diseases related to myelin.

neuroscience↗

bioRxiv2023

Light modulates task-dependent thalamo-cortical connectivity during an auditory attentional task

Exposure to blue wavelength light stimulates alertness and performance by modulating a widespread set of task-dependent cortical and subcortical areas. How light affects the crosstalk between brain areas to trigger this stimulating effect is not established. We recorded the brain activity of 19 healthy young participants (24.05{+/-}2.63; 12 women) while they completed an auditory attentional task in darkness or under an active (blue-enriched) or a control (orange) light, in an ultra-high-field 7 Tesla MRI scanner. We tested if light modulated the effective connectivity between an area of the posterior associative thalamus, encompassing the pulvinar, and the intraparietal sulcus (IPS), key areas in the regulation of attention. We found that only the blue-enriched light strengthened the connection from the posterior thalamus to the IPS. Our results provide the first empirical data supporting that blue wavelength light affects ongoing non-visual cognitive activity by modulating task-dependent information flow from subcortical to cortical areas.

neuroscience↗

bioRxiv2023

In vivo Locus Coeruleus activity while awake is associated with REM sleep quality in healthy older individuals

The locus coeruleus (LC) is the primary source of norepinephrine (NE) in the brain, and the LC-NE system is involved in regulating arousal and sleep. It plays key roles in the transition between sleep and wakefulness, and between slow wave sleep (SWS) and rapid eye movement sleep (REMS). However, it is not clear whether the LC activity during the day predicts sleep quality and sleep properties during the night, and how this varies as a function of age. Here, we used 7 Tesla functional Magnetic Resonance Imaging (7T fMRI), sleep electroencephalography (EEG) and a sleep questionnaire to test whether the LC activity during wakefulness was associated with sleep quality in 52 healthy younger (N=33; ~22y; 28 women) and older (N=19; ~61y; 14 women) individuals. We find that, in older, but not in younger participants, higher LC activity, as probed during an auditory mismatch negativity task, is associated with worse subjective sleep quality and with lower power over the EEG theta band during REMS (4-8Hz), which are two sleep parameters significantly correlated in our sample of older individuals. The results remain robust even when accounting for the age-related changes in the integrity of the LC. These findings suggest that the activity of the LC may contribute to the perception of the sleep quality and to an essential oscillatory mode of REMS, and that the LC may be an important target in the treatment of sleep disorders and age-related diseases.

neuroscience↗

bioRxiv2023

MRI-assessed locus coeruleus contrast and functional response are not associated in young and late middle-aged individuals

The brainstem locus coeruleus (LC) influences a broad range of brain processes, including cognition. The so-called LC contrast is an accepted marker of the integrity of the LC that consists of a local hyperintensity on specific Magnetic Resonance Imaging (MRI) structural images. The small size of the LC has, however, rendered its functional characterization difficult in humans, including in aging. A full characterization of the structural and functional characteristics of the LC in healthy young and late middle-aged individuals is needed to determine to potential roles of the LC in different medical conditions. Here, we wanted to determine whether the activation of the LC in a mismatch negativity task changes in aging and whether the LC functional response was associated to the LC contrast. We used Ultra-High Field (UHF) 7-Tesla functional MRI (fMRI) to record brain response during an auditory oddball task in 53 healthy volunteers, including 34 younger (age: 22.15y {+/-} 3.27; 29 women) and 19 late middle-aged (age: 61.05y {+/-} 5.3; 14 women) individuals. Whole-brain analyses confirmed brain responses in the typical cortical and subcortical regions previously associated with mismatch negativity. When focusing on the brainstem, we found a significant response in the rostral part of the LC probability mask generated based on individual LC images. Although bilateral, the activation was more extensive in the left LC. Individual LC activity was not significantly different between young and late middle-aged individuals. Critically, while the LC contrast was higher in older individuals, the functional response of the LC was not associated with its contrast. These findings show that the age-related alterations of the LC structural integrity may not necessarily be related to changes in its functional response. The results further indicate that LC responses could remain stable in healthy individuals aged 20 to 70.

neuroscience↗

bioRxiv2022

Interpreting phytolith assemblages at chimpanzee (Pan troglodytes verus) nut-cracking sites in Bossou Forest, Guinea

The nut-cracking behaviour of the chimpanzees of Bossou Forest has been long documented and studied in order to understand ultimate drivers for this form of durophagy by these apes. At sites in which they break open the nuts of the oil palm (Elaeis guineaeensis) on stone anvils with stone hammers, fragments of the tools as well as remnants of the nuts may be deposited into local sediments; however, they may become less visible at the macroscopic level as these sites are no longer used (become dormant). We build upon work that has been done to document this unique cultural heritage in West African chimpanzees by interpreting phytolith assemblages in sediments at active nut-cracking sites (used within the last two months). We compare these assemblages with those found in sediments of sites that have been dormant for ~10 years and sites where chimpanzees have not been observed to access and crack open oil palm nuts with stone tools. We predicted that larger assemblages of spheroid echinates, a phytolith associated with palms, would be found at active nut-cracking sites, however we found no statistical difference between total spheroid echinates (measured as total number found per gram of dry sediment) assemblages produced across active nut-cracking, dormant, or non-nut-cracking sites. This may have been due to small sample size (N[≤]6 sediment samples for each of the three sites) and so further sample collection and analyses are needed for inter-site comparisons. We also measured 2D area (m2), perimeter and maximum diameter of spheroid echinates found in nut endocarps (shells) and leaflets from an oil palm frond. Intra-specific differences from all three measurements were found with these phytoliths being larger in the nut endocarp than the leaflet. This has implications for (re)interpreting the assemblages of spheroid echinate phytoliths at the three sites to determine if there is a greater productivity larger-sized spheroid echinates that fall within the size range of those measured for the nut endocarp (mean maximum diameter of 14.9 m versus 7.8 m for those found in oil palm leaflet). Finally, we argue for the importance of initialising and continuing the interpretation of phytolith assemblages in local sediments that are located near sites where directed plant input by non-human taxa has occurred, in this case, chimpanzees cracking open oil palm nuts using stone tools. This is important to refine our interpretation of phytolith assemblages where human and non-human taxa who use complex foraging strategies share ecological spaces.

animal behavior and cognition↗

bioRxiv2022

Rigidified Scaffolds for 3-Angstrom Resolution Cryo-EM of Small Therapeutic Protein Targets

Numerous technical advances have made cryo-EM an attractive method for atomic structure determination. Cryo-EM is ideally suited for large macromolecular structures, while problems of low signal-to-noise prevent routine structure determination of proteins smaller than about 50 kDa. This size limitation excludes large numbers of important cellular proteins from structural characterization by this powerful technique, including many cell-signaling proteins of high therapeutic interest. In the present work, we use molecular engineering techniques to rigidify an imaging scaffold, based on a designed protein cage, to the point where 3 [A] resolution can be achieved, even for very small proteins. After optimizing the design of the rigidified scaffold on test proteins, we apply this imaging system to the key oncogenic signaling protein KRAS, which represents an outstanding challenge in the area of structure-based drug design. Despite its 19 kDa size, we show that the structure of KRAS, in multiple mutant forms, and bound to its GDP ligand, can be readily interpreted at a resolution slightly better than 3.0 [A]. This advance further expands the capability of cryo-EM to become an essentially universal method for protein structure determination, including for applications to small therapeutic protein targets.

biochemistry↗

bioRxiv2022

Whole genome assembly and annotation of the lucerne weevil Sitona discoideus

Weevils are a diverse insect group that includes many economically important invasive pest species. Despite their importance and diversity, only nine weevil genomes have been sequenced, representing a tiny fraction of this heterogeneous taxon. The genus Sitona consists of over 100 species, including Sitona discoideus (Coleoptera: Curculionidae: Entiminae), commonly known as lucerne (or alfalfa root) weevil. Sitona discoideus is an important pest of forage crops, particularly Medicago species. Using a dual sequencing approach with Oxford Nanopore MinION long-reads and 10x Genomics linked-read sequencing, we generated a high-quality hybrid genome assembly of S. discoideus. Benchmarks derived from evolutionarily informed expectations of gene content for near-universal single-copy orthologs comparison (BUSCO) scores are above 96% for single-copy orthologs derived from eukaryotes, arthropods, and insects. With a de novo repeat library, Repeatmasker annotated 81.45% of the genome as various repeat elements, of which 22.1% were unclassified. Using the MAKER2 pipeline, we annotated 10,008 protein-coding genes and 13,611 mRNAs. Furthermore, 68.84% of total predicted mRNAs and 67.90% of predicted proteins were functionally annotated to one or more of InterPro, gene ontology, and Pfam databases. This high-quality genome assembly and annotation will enable the development of critical novel genetic pest control technologies and act as an essential reference genome for broader population genetics and weevil comparative genetic studies.

genomics↗

bioRxiv2022

Timely sleep coupling: spindle-slow wave synchrony is linked to early amyloid-β burden and predicts memory decline

Sleep alteration is a hallmark of ageing and emerges as a risk factor for Alzheimers disease (AD). While the fine-tuned coalescence of sleep microstructure elements may influence age-related cognitive trajectories, its association with AD processes is not fully established. Here, we investigated whether the coupling of spindles and slow waves is associated with early amyloid-beta (A{beta}) brain burden, a hallmark of AD neuropathology, and cognitive change over 2 years in 100 healthy individuals in late-midlife (50-70y; 68 women). We found that, in contrast to other sleep metrics, earlier occurrence of spindles on slow-depolarisation slow waves is associated with higher medial prefrontal cortex A{beta} burden (p=0.014, r2{beta}*=0.06), and is predictive of greater longitudinal memory decline (p=0.032, r2{beta}*=0.07). These findings unravel early links between sleep, AD-related processes and cognition and suggest that altered coupling of sleep microstructure elements, key to its mnesic function, contributes to poorer brain and cognitive trajectories in ageing.

neuroscience↗

bioRxiv2021

Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis

The goal of this study is to calibrate a multiscale model of tumor angiogenesis with time-resolved data to allow for systematic testing of mathematical predictions of vascular sprouting. The multi-scale model consists of an agent-based description of tumor and endothelial cell dynamics coupled to a continuum model of vascular endothelial growth factor concentration. First, we calibrate ordinary differential equation models to time-resolved protein expression data to estimate the rates of secretion and consumption of vascular endothelial growth factor by endothelial and tumor cells, respectively. These parameters are then input into the multiscale tumor angiogenesis model, and the remaining model parameters are then calibrated to time resolved confocal microscopy images obtained within a 3D vascularized microfluidic platform. The microfluidic platform mimics a functional blood vessel with a surrounding collagen matrix seeded with inflammatory breast cancer cells, which induce tumor angiogenesis. Once the multi-scale model is fully parameterized, we forecast the spatiotemporal distribution of vascular sprouts at future time points and directly compare the predictions to experimentally measured data. We assess the ability of our model to globally recapitulate angiogenic vasculature density, resulting in an average relative calibration error of 17.7% {+/-} 6.3% and an average prediction error of 20.2% {+/-} 4% and 21.7% {+/-} 3.6% using one and four calibrated parameters, respectively. We then assess the models ability to predict local vessel morphology (individualized vessel structure as opposed to global vascular density), initialized with the first time point and calibrated with two intermediate time points. To the best of our knowledge, this represents the first study to integrate well-controlled, experimental data into a mechanism-based, multiscale, mathematical model of angiogenic sprouting to make specific, testable predictions.

systems biology↗

bioRxiv2021

Auditory word comprehension is less incremental in isolated words

Partial speech input is often understood to trigger rapid and automatic activation of successively higher-level representations of words, from sound to meaning. Here we show evidence from magnetoencephalography that this type of incremental processing is limited when words are heard in isolation as compared to continuous speech. This suggests a less unified and automatic word recognition process than is often assumed. We present evidence from isolated words that neural effects of phoneme probability, quantified by phoneme surprisal, are significantly stronger than (statistically null) effects of phoneme-by-phoneme lexical uncertainty, quantified by cohort entropy. In contrast, we find robust effects of both cohort entropy and phoneme surprisal during perception of connected speech, with a significant interaction between the contexts. This dissociation rules out models of word recognition in which phoneme surprisal and cohort entropy are common indicators of a uniform process, even though these closely related information- theoretic measures both arise from the probability distribution of wordforms consistent with the input. We propose that phoneme surprisal effects reflect automatic access of a lower level of representation of the auditory input (e.g., wordforms) while the occurrence of cohort entropy effects is task-sensitive, driven by a competition process or a higher-level representation that is engaged late (or not at all) during the processing of single words.

neuroscience↗

bioRxiv2021

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets. It serves not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data (PET-BIDS). We describe the PET-BIDS standard in detail and share several open-access datasets curated following PET-BIDS. Additionally, we highlight several tools which are already available for converting, validating and analyzing PET-BIDS datasets.

neuroscience↗

bioRxiv2021

Restoring statistical validity in group analyses of motion-corrupted MRI data

Motion during the acquisition of magnetic resonance imaging (MRI) data degrades image quality, hindering our capacity to characterize disease in patient populations. Quality control procedures allow the exclusion of the most affected images from analysis. However, the criterion for exclusion is difficult to determine objectively and exclusion can lead to a suboptimal compromise between image quality and sample size. We provide an alternative, data-driven solution that assigns weights to each image, computed from an index of image quality using restricted maximum likelihood. We illustrate this method through the analysis of brain MRI data. The proposed method restores the validity of statistical tests, and performs near optimally in all brain regions, despite local effects of head motion. This method is amenable to the analysis of a broad type of MRI data and can accommodate any measure of image quality.

neuroscience↗

bioRxiv2021

Global mismatches between crop distributions and climate suitability

The selection of new crops and the migration of crop areas are two key strategies for agriculture to cope with climate change and ensure food security in the coming years. However, both rely on the assumption that climate is a major factor determining crop distributions worldwide. Here, we show that the current global distributions of nine of twelve major crops strongly diverge from their modelled climatic suitability for yields, after controlling for technology, agricultural management and soil conditions. Comparing the climatic niches of crops and their wild progenitors reveals that climate suitability is higher outside the native climatic range for six of these nine crops while all of them are farmed predominantly in their native ranges. These results show that agricultural strategies coping with climate change will be unsuccessful unless they fully consider the social, cultural, and ecological factors underpinning crop distributions.

ecology↗