Biology subjects

Whittle, S.

Publications and source records attributed to Whittle, S..

16 recordsLinked to original sources

bioRxiv2026

TRF2 mediates force-resistant bridging of distal telomeric DNA repeats

Shelterin binds telomeres, regulates telomere length, and protects chromosome ends from mis-repair, which is essential for genome stability. Telomere end-protection uniquely depends on the TRF2 subunit, which assembles telomeric DNA into a protective T-loop structure in vivo, yet the biochemical mechanism underlying this process remains unresolved. Using single-molecule optical tweezers and atomic force microscopy, we show that the human shelterin complex tethers distal telomeric DNA repeats, looping the intervening DNA. These bridges withstand tens of piconewtons of applied load, rupture at a force that scales with telomeric repeat number and re-form on relaxation. Structure-function analysis demonstrates that this force-resistant tethering is TRF2-dependent under our conditions and depends on multiple interfaces, with the TRFH domain making a major but non-exclusive contribution: introducing the TRF2 TRFH domain into TRF1 is sufficient to confer tethering, whereas its deletion from TRF2 reduces but does not abolish activity. We propose telomeric dsDNA tethering by TRF2 as a candidate first step in T-loop formation, preceding invasion of the telomeric 3' ssDNA overhang.

biophysics↗

bioRxiv2026

Frontolimbic Functional Connectivity Development from Birth to Emerging Adulthood

Frontolimbic circuits connecting the frontal cortex with the amygdala and the hippocampus are critical for emotion and learning. These connections undergo major changes throughout childhood and adolescence, yet the principles guiding their maturation remain unclear. Analyzing large developmental cohorts, we show that fronto-hippocampus connectivity develops rapidly in early childhood and stabilizes thereafter. In contrast, fronto-amygdala connectivity becomes progressively differentiated from fronto-hippocampus connectivity, with development most pronounced during adolescence. This entailed hippocampus and amygdala respectively becoming preferentially tethered to association-related regions and sensorimotor-related regions. Greater adversity exposure was associated with more differentiated fronto-amygdala connectivity for a given age. Higher cognitive ability was associated with less differentiated fronto-hippocampus connectivity. These findings suggest that frontolimbic connectivity development follows a principle of differentiation, with circuit-specific timing and sensitivity to stress and learning. This work provides a foundation for understanding typical and atypical frontolimbic circuitry development from birth to emerging adulthood. Significance StatementThe frontolimbic circuit, especially the fronto-hippocampus and fronto-amygdala circuitry, is integral for cognitive and affective processes. Yet its maturation has been challenging to characterize due to variable connectivity growth across the frontal cortex. Here, we reveal that this variability follows a principle of differentiation, where the hippocampus and the amygdala acquire respectively unique connectivity profiles with the frontal cortex at disparate developmental stages. Deviations from these normative trajectories were linked to cognitive ability and cumulative adversity, respectively. This approach provides a framework to unify inconsistent findings while serving as a foundation for identifying circuit-specific windows of plasticity and vulnerability.

neuroscience↗

bioRxiv2026

Deep Learning-Enhanced TopoStats for the Automated Quantification of DNA and Complex Biomolecular Structures

Atomic force microscopy (AFM) enables nanometre-scale, label-free imaging of biomolecules and surfaces under near-native conditions, yet quantitative analysis of AFM data remains limited compared to other bioimaging modalities. This limitation largely arises from the absence of open, automated tools capable of addressing AFM-specific artefacts, data formats, and topographical outputs. Here, we present the latest version of TopoStats, an open-source Python package for automated and quantitative AFM image analysis, developed as a deep-learning enabled advancement of our original TopoStats software to support more complex samples and richer molecular characterisation. The pipeline integrates all key processing stages, including image flattening and noise correction, object detection and segmentation, morphometric feature extraction, and strand tracing with topological classification. Designed for accessibility and reproducibility, TopoStats adheres to the FAIR for Research Software (FAIR4RS) principles and provides configurable workflows adaptable to diverse biological samples. Combining high-resolution AFM and our analysis pipeline allows the quantification of subtle structural changes within a heterogeneous sample set, revealing properties not accessible with other structural biology techniques. We demonstrate the effectiveness of our pipeline to differentiate between plasmids with both different topology and sequence, by extracting meaningful quantitative descriptors that distinguish the samples with statistical significance. Collectively, these developments establish TopoStats as a versatile framework for high-throughput, quantitative AFM analysis, advancing AFM from a fundamentally qualitative visualisation technique toward a quantitative analytical tool.

biophysics↗

bioRxiv2025

Oestradiol and Progesterone Variability in Adolescent Females: Associations with Brain Structure and Mental Health Problems

ObjectiveAdolescent females are at increased risk for adverse mental health problems, and puberty is thought to be a critical factor. Pubertal onset involves substantial variability in oestradiol (E2) and progesterone (P4), yet the impact of these hormone dynamics remains unclear. We investigated whether within-individual E2 and P4 variability across one month relates to brain structure and mental health problems in adolescent females. MethodsParticipants were 147 females (11-17 years) from the community-based, cross-sectional Puberty and NeuroDevelopment in Adolescents (PANDA) study in Australia. Salivary E2 and P4 were collected weekly for one month, with variability indexed as within-subject standard deviation. Structural MRI was acquired on the final sampling day. Mental health problems were assessed via self- and parent-report. Linear regression and mediation analyses tested associations between hormone variability, brain structure, and mental health, adjusting for demographics. ResultsGreater P4 variability was associated with smaller left thalamus volume (Cohens d = -0.26, pFDR = 0.031). Higher E2 variability was associated with fewer anxiety (d = -0.170, pFDR = 0.043) and depressive symptoms (d = -0.179, pFDR = 0.036), lower emotion dysregulation (d = -0.179, pFDR = 0.036), and smaller right hippocampus volume in pre-menarchal adolescents (d = -0.192, p = 0.02). Weekly reductions in E2 predicted lower positive affect (d = 0.084, p = 0.048). ConclusionThese findings indicate that hormone variability may meaningfully shape brain and behavioural development in adolescent girls differently from hormone-related transitions in adulthood. Larger, replicable, and longer-term studies are needed to confirm these patterns. Oestradiol and Progesterone Variability in Adolescent Females: Associations with Brain Structure and Mental Health Problems. Muskan Khetan 1, Ye Ella Tian 2, Nandita Vijayakumar 3,4, Sarah Whittle 1,4 O_LICentre for Youth Mental Health, University of Melbourne, Australia C_LIO_LIDepartment of Psychiatry, University of Melbourne, Australia C_LIO_LIMurdoch Childrens Research Institute, Australia C_LIO_LISchool of Psychology, Deakin University, Australia C_LI

neuroscience↗

bioRxiv2025

Sex-specific brain structural predictors and outcomes of adolescent depression trajectories

ObjectivesDepressive symptoms often emerge and increase during adolescence, yet the neural predictors and long-term brain outcomes associated with depressive trajectories remain poorly understood. This study adopts a trajectory-based approach to explore the temporal relationship between brain structure and dynamic changes in depressive symptoms across adolescence. MethodsWe used a large longitudinal adolescent neuroimaging sample across five annual waves (n = 11,862; mean age = 9.91 at baseline) from the ABCD study. First, growth mixture models were applied separately for males and females to identify distinct developmental trajectories of depressive symptoms. We then used linear mixed-effects models to identify which baseline brain structural features differentiated trajectory classes, and how these trajectories influenced subsequent brain structure. ResultsWe identified high-decreasing, stable-low, and low-increasing trajectories in females, and relatively stable high, moderate, and low trajectories in males. No baseline brain regions were found to be associated with female trajectories, whereas smaller global brain measures (total subcortical volume, cortical volume, and surface area) predicted the high trajectory in males. Regarding brain outcomes, a low-increasing trajectory in females was associated with smaller global subcortical and cortical volumes, while high and moderate trajectories in males predicted thinner global cortices. Additional trajectory-related regional brain alterations were observed in both sexes. ConclusionsThese findings highlight distinct neurodevelopmental patterns linked to depressive symptom trajectories in males and females, underscoring the importance of a sex-specific and longitudinal approach to identifying neural risk and outcomes in adolescent depression.

neuroscience↗

bioRxiv2025

Neuroanatomical signatures of depression and anxiety in at-risk adolescents: A symptom-oriented perspective

BackgroundMajor depressive disorder (MDD) and generalized anxiety disorder (GAD) often emerge in adolescence. Identifying their symptom structures and neural biomarkers in youth with elevated risk is critical for early detection and developing interventions. This study investigated the central symptoms of MDD and GAD and identified the key brain regions ("brain bridges") linking structural neuroanatomy to symptoms in at-risk adolescents. MethodsA total of 1,568 adolescents at high risk for MDD and 413 adolescents at high risk for GAD were identified from the Adolescent Brain Cognitive Development (ABCD) study. Participants completed MDD and GAD symptom assessments and underwent Magnetic Resonance Imaging scanning. We constructed 10 psychological network models incorporating symptoms and brain structural indices to identify central symptoms and brain bridges. ResultsConcentration difficulties emerged as the shared core symptom, while self-hatred and irritability were the unique central symptoms for MDD and GAD, respectively. Left- and right-pallidum volumes exhibited the highest bridge centrality for MDD symptoms, whereas left-nucleus accumbens volume showed the highest bridge centrality for GAD symptoms. ConclusionOur findings highlight the pallidum and nucleus accumbens as key brain regions linking structural anatomy to symptom networks in high-risk youth. These results provide novel insights into early neurobiological markers of MDD and GAD from a symptom-oriented perspective and may inform targeted interventions.

neuroscience↗

bioRxiv2025

Linking Oestradiol (E2) Timing and Tempo, Brain Development, and Mental Health in Adolescent Females

Background: Earlier timing and faster tempo of puberty have been associated with altered brain development and increased mental health symptoms in adolescents, particularly females. However, the role of oestradiol (E2) in these associations is unclear. Methods: Using longitudinal data from the US-based Adolescent Brain Cognitive Development Study SM (ABCD Study (R), we investigated whether, in females (N ~ 3k), E2 timing (at age 10) and tempo (rate of change from age 10 to 12) were prospectively associated with mental health symptoms at age 13 via structural brain development from age 10 to 12. Linear mixed-effects models and Bayesian mediation models were fitted to investigate the aims of the study. Results: Findings showed that E2 timing was not associated with mental health symptoms. However, earlier E2 timing was associated with a greater reduction in total cortical volume, total surface area, and surface area in the superior and middle temporal cortex over time. Further, a faster E2 tempo was associated with an increase in mental health symptoms, and this association was mediated by a faster reduction in total cortical volume and total surface area over time. Conclusion: Findings suggest that earlier E2 timing and faster E2 tempo contribute to accelerated development of gray matter structure in adolescent females, and for E2 tempo, such associated brain changes may partly contribute to increased mental health risk.

neuroscience↗

bioRxiv2024

Pubertal hormones and the early adolescent female brain: a multimodality brain MRI study

Puberty is a critical developmental process that is associated with changes in steroid hormone levels, which are believed to influence adolescent behaviour via their effects on the developing brain. So far, there are limited and inconsistent findings regarding the relationship between steroid hormones and brain structure and function in adolescent females, with many existing studies employing small sample sizes. Thus, in this study, we explored the association between oestradiol (E2), testosterone (Tes) and dehydroepiandrosterone (DHEA) and brain structure (gray matter volume, sulcal depth, cortical thickness and white matter microstructure) and function (resting-state connectivity, emotional n-back task-related function) in 3024 adolescent females (age 8.92 - 13.33 years, mean age (SD) = 10.37 (0.94) years) from the Adolescent Brain Cognitive DevelopmentSM (ABCD(R)) Study. We used elastic-net regression with cross- validation to investigate associations between hormones and brain phenotypes derived from multiple imaging modalities. We found that structural brain features, including cortical thickness, sulcal depth, and white matter microstructure, were among the most important features associated with hormones. E2 was most strongly associated with prefrontal and premotor regions involved in working memory and emotion processing, while Tes and DHEA were most strongly associated with parietal and occipital regions involved in visuospatial functioning. All three hormones were also associated with prefrontal, temporoparietal junction and insula cortices. Thus, using an advanced methodological approach, this study suggests both unique and overlapping neural correlates of pubertal hormones in adolescent females and sheds light on the mechanisms by which puberty influences adolescent development and behaviour.

neuroscience↗

bioRxiv2024

Multiscale topological analysis of kinetoplast DNA via high-resolution AFM

Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in-vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, selective digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena.

biophysics↗

bioRxiv2024

Under or Over? Tracing Complex DNA Topologies with High-Resolution Atomic Force Microscopy

The topology of DNA plays a crucial role in the regulation of cellular processes and genome stability. Despite its significance, DNA topology remains challenging to determine due to the length and conformational complexity of individual topologically constrained DNA molecules. We demonstrate unparalleled resolution of complex DNA topologies using Atomic Force Microscopy (AFM) in aqueous conditions. We present a new high-throughput automated pipeline to determine DNA topology from raw AFM images, using deep-learning methods to trace the backbone of individual DNA molecules and identify crossing points. Our pipeline efficiently determines which segment passes over which, including the handling of challenging crossings, where the path of each molecule may be harder to resolve. We demonstrate the wider applicability of our tracing method by determining the structure of stalled replication intermediates from Xenopus egg extracts, including theta structures and late replication products. By developing new methodologies to accurately trace the DNA path through every crossing, we determine the topology of plasmids, knots and catenanes from the E. coli Xer recombination system. In doing so we uncover a recurrent depositional effect and reveal its origins using coarse-grained simulations. Our approach is broadly applicable to a range of nucleic acid structures, including those which interact with proteins, and opens avenues for understanding fundamental biological processes which are regulated by or affect DNA topology.

biophysics↗

bioRxiv2023

Loss of Grem1-articular cartilage progenitor cells causes osteoarthritis.

Osteoarthritis (OA), which carries an enormous disease burden across the world, is characterised by irreversible degeneration of articular cartilage (AC), and subsequently bone. The cellular cause of OA is unknown. Here, using lineage tracing in mice, we show that the BMP-antagonist Gremlin 1 (Grem1) marks a novel chondrogenic progenitor (CP) cell population in the articular surface that generates joint cartilage and subchondral bone during development and adulthood. Notably, this CP population is depleted in injury-induced OA, and with age. OA is also induced by toxin-mediated ablation of Grem1 CP cells in young mice. Transcriptomic analysis and functional modelling in mice revealed articular surface Grem1-lineage cells are dependent on Foxo1; ablation of Foxo1 in Grem1-lineage cells led to early OA. This analysis identified FGFR3 signalling as a therapeutic target, and injection of its activator, FGF18, caused proliferation of Grem1-lineage CP cells, increased cartilage thickness, and reduced OA pathology. We propose that OA arises from the loss of CP cells at the articular surface secondary to an imbalance in progenitor cell homeostasis and present a new progenitor population as a locus for OA therapy.

cell biology↗

bioRxiv2023

Corticolimbic connectivity mediates the relationship between pubertal timing and mental health problems

BackgroundUndergoing puberty ahead of peers ("earlier pubertal timing") is an important risk factor for mental health problems during early adolescence. The current study examined pathways between pubertal timing and mental health via connectivity of neural systems implicated in emotional reactivity and regulation (specifically corticolimbic connections) in 9- to 14-year-olds. MethodResearch questions were examined in the Adolescent Brain Cognitive Development (ABCD) Study, a large population representative sample in the United States. Linear mixed models examined associations between pubertal timing and resting-state corticolimbic connectivity. Significant connections were examined as potential mediators of the relationship between pubertal timing and mental health (withdrawn depressed and rule-breaking delinquency) problems. Exploratory analyses interrogated whether the family environment moderated neural risk patterns in those undergoing puberty earlier than their peers. ResultsEarlier pubertal timing was related to decreased connectivity between limbic structures (bilateral amygdala and right hippocampus) and the cingulo-opercular network (CON), as well as between the left hippocampus and ventral attention network (VAN). Corticolimbic connections also mediated the relationship between earlier pubertal timing and increased withdrawn depressed problems (but not rule-breaking delinquency). Finally, parental acceptance buffered against limbic-CON connectivity patterns that were implicated in withdrawn depressed problems in those undergoing puberty earlier than their peers. ConclusionFindings highlight the role of decreased corticolimbic connectivity in mediating pathways between earlier pubertal timing and withdrawn depressed problems, and we present preliminary evidence that the family environment may buffer against these neural risk patterns during early adolescence.

neuroscience↗

bioRxiv2020

A longitudinal analysis of puberty-related cortical development

The brain undergoes extensive structural changes during adolescence, concurrent to puberty-related physical and hormonal changes. While animal research suggests these biological processes are related to one another, our knowledge of brain development in humans is largely based on age-related processes. Thus, the current study characterized puberty-related changes in human brain structure, by combining data from two longitudinal neuroimaging cohorts. Beyond normative changes in cortical thickness, we examined whether individual differences in the rate of pubertal maturation (or "pubertal tempo") was associated with variations in cortical trajectories. Participants (N = 192; scans = 366) completed up to three waves of MRI assessments between 8.5 and 14.5 years of age, as well as questionnaire assessments of pubertal stage at each wave. Generalized additive mixture models were used to characterize trajectories of cortical development. Results revealed widespread linear puberty-related changes across much of the cortex. Many of these changes, particularly within the frontal and parietal cortices, were independent of age-related development. Males exhibiting faster pubertal tempo demonstrated greater thinning in the precuneus and frontal cortices than same-aged and -sex peers. Findings suggest that the unique influence of puberty on cortical development may be more extensive than previously identified, and also emphasize important individual differences in the coupling of these developmental processes.

neuroscience↗

bioRxiv2020

Adolescent rats show estrous cycle-mediated sex differences in extinction of conditioned fear

Anxiety disorders are more prevalent in females than males, and frequently emerge during adolescence. Despite this, preclinical research commonly focuses on adult males. Here we use Pavlovian fear conditioning and extinction in adolescent male and female rats to understand sex- and age-dependent processes relevant to anxiety disorders. In experiment 1, 35-day-old male and female rats were exposed to 6 pairings of a conditioned stimulus (CS, a tone) with an aversive unconditioned stimulus (US, a footshock). The next day they were extinguished in a contextually distinct chamber, via 60 presentations of the CS without the US. Extinction recall was tested 24 hours later in the extinction context. Estrous phase was monitored by cytology on vaginal smears taken 1 hour after each behavioral session. In experiment 2, male and female rats were given sham surgery or gonadectomy at 21 days of age. They were then trained and tested as for experiment 1. We observed that females in proestrus or met/diestrus during extinction showed delayed extinction and impaired extinction recall the next day compared to males. Ovariectomy enhanced extinction for female rats, but orchidectomy delayed extinction for males. Plasma analyses showed that met/di/proestrus phases were associated with high estradiol levels. These findings suggest that high plasma estradiol levels impair extinction for adolescent females. While these results contradict what is observed in adult animals, they are consistent with the prevalence of anxiety disorders observed in females. Our findings have important implications for understanding and treating anxiety in adolescents, particularly where treatment involves extinction-based therapies.

animal behavior and cognition↗

bioRxiv2017

Development of subcortical volumes across adolescence in males and females: A multisample study of longitudinal changes

The developmental patterns of subcortical brain volumes in males and females observed in previous studies have been inconsistent. To help resolve these discrepancies, we examined developmental trajectories using three independent longitudinal samples of participants in the age-span of 8-22 years (total 216 participants and 467 scans). These datasets, including Pittsburgh (PIT; University of Pittsburgh, USA), NeuroCognitive Development (NCD; University of Oslo, Norway), and Orygen Adolescent Development Study (OADS; The University of Melbourne, Australia), span three countries and were analyzed together and in parallel using mixed-effects modeling with both generalized additive models and general linear models. For all regions and across all samples, males were found to have significantly larger volumes as compared to females, and significant sex differences were seen in age trajectories over time. However, direct comparison of sample trajectories and sex differences identified within samples were not consistent. The trajectories for the amygdala, putamen, and nucleus accumbens were most consistent between the three samples. Our results suggest that even after using similar preprocessing and analytic techniques, additional factors, such as image acquisition or sample composition may contribute to some of the discrepancies in sex specific patterns in subcortical brain changes across adolescence, and highlight region-specific variations in congruency of developmental trajectories.

neuroscience↗

bioRxiv2017

Structural brain development: a review of methodological approaches and best practices

Continued advances in neuroimaging technologies and statistical modelling capabilities have improved our knowledge of structural brain development in children and adolescents. While this has provided an increasingly nuanced understanding of brain development, the field is still plagued by inconsistent findings. This review highlights the methodological diversity in existing longitudinal magnetic resonance imaging (MRI) studies on structural brain development during childhood and adolescence, and addresses how such variation might contribute to inconsistencies in the literature. We discuss the impact of method choices at multiple decision points across the research process, from study design and sample selection, to image processing and statistical analysis. We also highlight the extent to which different methodological considerations have been empirically examined, drawing attention to specific areas that would benefit from future investigation. Where appropriate, we recommend certain best practices that would be beneficial for the field to adopt, including greater completeness and transparency in reporting methods, in order to ultimately develop an accurate and detailed understanding of normative child and adolescent brain development.

scientific communication and education↗