Biology subjects

Holland, P.

Publications and source records attributed to Holland, P..

14 recordsLinked to original sources

bioRxiv2026

Chemotherapy-induced transfer of apoptotic machinery in extracellular vesicles between somatic and germ cells of the testis: mechanistic insights into onco-fertility preservation in pre-pubertal boys

Extracellular vesicles (EVs) are increasingly recognized as critical mediators of intercellular communication, not least during cellular stress or therapy. While EV signalling is well-studied in various tissues, its role in the prepubertal testicular environment is not well understood. Chemotherapy, commonly used in paediatric oncology, poses a significant risk to spermatogonial stem cells (SSCs) and may affect long-term fertility in cancer survivors. The role of EVs in chemotherapy-induced testicular damage in these patients is unknown and may be important for developing new fertility preservation methods. Immortalised murine Sertoli (TM4) and spermatogonial (GC1-spg) cell lines were used to investigate cisplatin-induced changes in EV biogenesis, release, and function in an in vitro model of the prepubertal testicular microenvironment. Our findings indicate that cisplatin significantly increases EV secretion and internalisation by recipient cells. Notably, EVs from cisplatin-exposed Sertoli cells exhibit a novel pro-apoptotic phenotype when co-cultured with chemotherapy-naive Sertoli cells. Proteomic profiling of these EVs shows enrichment of apoptosis-regulatory proteins including caspases, activating Caspase-3/7 in recipient Sertoli cells. Conversely, germ cells exposed to Sertoli cell-derived EVs displayed reduced levels of apoptosis as well as a chemoprotective role to germ cells undergoing treatment with cisplatin. These findings indicate a dual role for Sertoli cell-derived EVs in mediating (1) apoptosis in Sertoli cells and (2) protection of germ cells following cisplatin exposure. The presence of pro-apoptotic molecules, especially caspases, in chemotherapy-induced Sertoli cell EVs provides mechanism for the induction of somatic cell apoptosis. Furthermore, their protective effects on germ cells demonstrate the complexity of EV-mediated signalling between testicular cell types. Manipulating EV biogenesis and cargo loading could be a promising approach to reduce chemotherapy-related gonadotoxicity and preserve fertility in childhood cancer patients.

cell biology↗

bioRxiv2025

N-Linked Glycosylation as a Driver of Tau Pathology and Neuronal Transmission

N-Linked glycosylation of Tau is implicated in Alzheimers disease, yet how it influences Tau propagation and neuronal uptake remains unclear. Here, we use chemically defined N-glycoforms of 2N4R Tau and the K18 repeat domain to map how glycan site and structure reprogram Tau-polyanion binding, seeding, and entry into human neurons. Site-specific GlcNAc or high-mannose glycans at Asn359 or Asn410 remodel heparin and RNA binding kinetics in biolayer interferometry assays, revealing avidity-dominated, slow-off heparin interactions that are dampened by N-glycans and faster RNA interactions that can be potentiated by small GlcNAc modifications. Cross-seeding experiments show that N-glycosylation selectively tunes nucleation compatibility between Tau proteoforms; GlcNAc at Asn410 in full-length Tau and small glycans at Asn359 in K18 most strongly accelerate aggregation. In HEK293T FRET biosensor cells and iPSC-derived cortical neurons, N-glycans enhance or suppress seeding and pHrodo-reported uptake in a site- and glycan-dependent manner, with Asn410 glycosylation markedly potentiating cellular seeding. Pharmacological inhibition with atropine, dynasore, and cytochalasin D further indicates that N-glycans rebalance muscarinic, dynamin-dependent, and actin-dependent uptake routes. Together, these data establish N-linked glycosylation as a tunable regulator of Tau trafficking and prion-like spread, coupling extracellular receptor usage to intracellular cofactor engagement, and reveals druggable nodes in uptake.

neuroscience↗

bioRxiv2024

Post-Translational Modifications Control Phase Transitions of Tau

The self-assembly of Tau(297-391) into filaments, which mirror the structures observed in Alzheimers disease (AD) brains, raises questions about the role of AD-specific post-translational modifications (PTMs) in the formation of paired helical filaments (PHFs). To investigate this, we developed a synthetic approach to produce Tau(291-391) featuring N-acetyllysine, phosphoserine, phosphotyrosine, and N-glycosylation at positions commonly modified in post-mortem AD brains, thus facilitating the study of their roles in Tau pathology. Using transmission electron microscopy (TEM), cryo-electron microscopy (cryo-EM), and a range of optical microscopy techniques, we discovered that these modifications generally hinder the in vitro assembly of Tau into PHFs. Interestingly, while acetylations effect on Tau assembly displayed variability, either promoting or inhibiting phase transitions in the context of cofactor free aggregation, heparin-induced aggregation, and RNA-mediated liquid-liquid phase separation (LLPS), phosphorylation uniformly mitigated these processes. Our observations suggest that PTMs, particularly those situated outside the fibrils rigid core are pivotal in the nucleation of PHFs. Moreover, in scenarios involving heparin-induced aggregation leading to the formation of heterogeneous aggregates, most AD-specific PTMs, except for K311, appeared to decelerate the aggregation process. The impact of acetylation on RNA-induced LLPS was notably site-dependent, exhibiting both facilitative and inhibitory effects, whereas phosphorylation consistently reduced LLPS across all proteoforms examined. These insights underscore the complex interplay between site-specific PTMs and environmental factors in modulating Tau aggregation kinetics, enhancing our understanding of the molecular underpinnings of Tau pathology in AD and highlighting the critical role of PTMs located outside the ordered filament core in driving the self-assembly of Tau into PHF structures.

biophysics↗

bioRxiv2023

Dopamine challenge reduces mental state attribution accuracy

Difficulties in reasoning about others mental states (i.e., mentalising / Theory of Mind) are highly prevalent among disorders featuring dopamine dysfunctions (e.g., Parkinsons disease) and significantly affect individuals quality of life. However, due to multiple confounding factors inherent to existing patient studies, currently little is known about whether these socio-cognitive symptoms originate from aberrant dopamine signalling or from psychosocial changes unrelated to dopamine. The present study therefore investigated the role of dopamine in modulating mentalising in a sample of healthy volunteers. We used a double-blind, placebo-controlled procedure to test the effect of the D2 antagonist haloperidol on mental state attribution, using an adaptation of the Heider & Simmel (1944) animations task. On two separate days, once after receiving 2.5mg haloperidol and once after receiving placebo, 33 healthy adult participants viewed and labelled short videos of two triangles depicting mental state (e.g., surprising) and non-mental state (e.g., following) interactions. Using Bayesian mixed effects models we observed that haloperidol decreased accuracy in labelling both mental- and non-mental state animations. Our secondary analyses suggest that dopamine modulates inference from mental- and non-mental state animations via independent mechanisms, pointing towards two putative pathways underlying the dopaminergic modulation of mental state attribution: Action representation and a shared mechanism supporting mentalising and emotion recognition. We conclude that dopamine is causally implicated in Theory of Mind. Our results have implications for the neurochemical basis of socio-cognitive difficulties in patients with dopamine dysfunctions and generate new hypotheses about the specific dopamine-mediated mechanisms underlying social cognition.

neuroscience↗

bioRxiv2023

Calorie restriction brings no benefits to lifespan under stochastic environments

1. Potential immortality is observed in several species (e.g., prickly pear cactus, hydra, flatworms) and is indicative of their negligible or even negative senescence rates. Unlike in senescent species, which experience reduced individual performance with age due to physiological degradation, species with negligible or negative senescence display mortality rates that remain constant or decline with age, respectively. These rates vary across taxa and are correlated with life history traits. Yet, the extent to which variable resource availability, a key driver of variation in life history traits, impacts species that show negligible or negative senescence is currently unknown. 2. Here, we examine whether and how variation in the quantity, quality, and feeding interval of resources impact population structure, population performance, and life history trait trade-offs in two long-lived planaria that do not senesce: Schmidtea mediterranea and Dugesia tahitiensis. In a full factorial design, different combinations of resource quantity (reduced intake, standard intake and high intake) and quality (high and low quality) were provided in two different feeding intervals (7-day and 14-day intervals) for 19 weeks. 3. We show that variability in resource availability, via decreases in quantity, quality, and frequency of resources, does not diminish population viability in either species but does result in suboptimal conditions of stress in S. mediterranea. 4. The high population viability we report can be attributed to two different mechanisms: increased reproduction or increased investment into maintenance at the expense of reproduction. Moreover, which mechanism was responsible for said high population viability was context-dependent and modulated by the specific life history strategy of the two planaria species. 5. We show that suboptimal conditions can cause stress responses that have significant impacts on non-senescent species. The context-dependent response we observe suggests that species that do not senesce but are subject to suboptimal conditions of stress may ultimately exhibit declines in performance and ultimately die. A clearer understanding of the impact of suboptimal conditions of resource availability on non-senescent species is needed to determine the extent of stress experienced and ultimately whether a species can truly be immortal.

ecology↗

bioRxiv2022

Modulation of motor vigour by expectation of reward probability trial-by-trial is preserved in healthy ageing and Parkinson's disease patients

Motor improvements, such as faster movement times or increased velocity, have been consistently associated with reward magnitude in deterministic contexts. Yet whether individual inferences on reward probability influence motor vigour dynamically remains undetermined. Here we investigated how dynamically inferring volatile action-reward contingencies modulated motor performance trial-by-trial in healthy younger (HYA, 37) and older adults (HOA, 37), and in medicated Parkinsons Disease patients (PD, 20). We conducted an online study that coupled a standard one-armed bandit decision-making paradigm with a motor sequence task and used a validated hierarchical Bayesian model to fit trial-by-trial data. Our results showed that stronger predictions about the tendency of the action-reward contingency led to faster performance tempo on a trial-by-trial basis without modulating reaction times (RT). Using Bayesian linear mixed models, we demonstrated in HYA, HOA and PD a similar sensitivity (slope) of execution tempo to inferences about the reward probabilities, despite HOA and PD being generally slower than HYA (intercept). In a second experiment in HYA (39), we additionally showed that subjective inferences about credit assignment - whether lack of reward is associated with an incorrect decision or execution error - led to a similar modulation of motor vigour by reward expectation. Our study is the first to reveal that the dynamic updating of beliefs about volatile action-reward contingencies positively biases motor performance through faster execution tempo, without affecting RT. We also provide novel evidence for a preserved sensitivity of motor vigour to inferences about the action-reward mapping in ageing and medicated PD. SIGNIFICANCE STATEMENTNavigating a world rich in uncertainty relies on updating beliefs about the probability that our actions lead to reward. Here we investigated how inferring the action-reward contingencies in a volatile environment modulated motor vigour trial-by-trial in healthy younger and older adults, and in Parkinsons Disease patients on medication. We found an association between trial- by-trial predictions about the tendency of the action-reward contingency and performance tempo, with stronger expectations speeding performance. We additionally provided evidence for a similar sensitivity of performance tempo to the strength of these predictions in all groups. Thus, dynamic beliefs about the changing relationship between actions and their outcome invigorated motor performance. This positive bias was not compromised by age or Parkinsons disease.

neuroscience↗

bioRxiv2022

Mitotic chromosome condensation resets chromatin to maintain transcriptional homeostasis

Mitotic entry correlates with the condensation of the chromosomes, remodeling of histone modifications, exclusion of transcription factors from DNA and the broad downregulation of transcription. However, whether mitotic condensation influences transcription in the subsequent interphase is unknown. Here, we show that preventing one chromosome to condense during mitosis causes it to fail resetting transcription. Rather it diverted the transcription machinery and underwent unscheduled initiation of gene expression. This caused the activation of inducible transcriptional programs, such as the GAL genes, even in absence of the relevant stimuli. Strikingly, aberrant gene expression persisted into the next interphase. Thus, our study identifies the maintenance of transcriptional homeostasis as an unexpected and yet unexplored function of mitotic chromosome condensation. One-Sentence SummaryMitotic chromatin condensation resets the transcriptome to protect cells from transcriptional drifting after anaphase.

molecular biology↗

bioRxiv2022

Dopaminergic modulation of dynamic emotion perception

Emotion recognition abilities are fundamental to our everyday social interaction. A large number of clinical populations show impairments in this domain, with emotion recognition atypicalities being particularly prevalent among disorders exhibiting a dopamine system disruption (e.g., Parkinsons disease). Although this suggests a role for dopamine in emotion recognition, studies employing dopamine manipulation in healthy volunteers have exhibited mixed neural findings and no behavioural modulation. Interestingly, whilst a dependence of dopaminergic drug effects on individual baseline dopamine function has been well established in other cognitive domains, the emotion recognition literature so far has failed to account for these possible interindividual differences. The present within-subjects study therefore tested the effects of the dopamine D2 antagonist haloperidol on emotion recognition from dynamic, whole-body stimuli while accounting for interindividual differences in baseline dopamine. 33 healthy male and female adults rated emotional point-light walkers (PLWs) once after ingestion of 2.5 mg haloperidol and once after placebo. To evaluate potential mechanistic pathways of the dopaminergic modulation of emotion recognition, participants also performed motoric and counting-based indices of temporal processing. Confirming our hypotheses, effects of haloperidol on emotion recognition depended on baseline dopamine function, where individuals with low baseline dopamine showed enhanced, and those with high baseline dopamine decreased emotion recognition. Drug effects on emotion recognition were related to drug effects on movement-based and explicit timing mechanisms, indicating possible mediating effects of temporal processing. Results highlight the need for future studies to account for baseline dopamine and suggest putative mechanisms underlying the dopaminergic modulation of emotion recognition. Significance statementA high prevalence of emotion recognition difficulties amongst clinical conditions where the dopamine system is affected suggests an involvement of dopamine in emotion recognition processes. However, previous psychopharmacological studies seeking to confirm this role in healthy volunteers thus far have failed to establish whether dopamine affects emotion recognition and lack mechanistic insights. The present study uncovered effects of dopamine on emotion recognition in healthy individuals by controlling for interindividual differences in baseline dopamine function and investigated potential mechanistic pathways via which dopamine may modulate emotion recognition. Our findings suggest that dopamine may influence emotion recognition via its effects on temporal processing, providing new directions for future research on typical and atypical emotion recognition.

neuroscience↗

bioRxiv2022

A role for thalamic projection GABAergic neurons in circadian responses to light

The thalamus is an important hub for sensory information and participates in sensory perception, regulation of attention, arousal and sleep. These functions are executed primarily by glutamatergic thalamocortical neurons that extend axons to the cortex and initiate cortico-thalamocortical connectional loops. However, the thalamus also contains projection GABAergic neurons that do not engage in direct communication with the cortex. Here, we have harnessed recent insight into the development of the intergeniculate (IGL), the ventrolateral geniculate (LGv) and the perihabenula (pHB) to specifically target and manipulate thalamic projection GABAergic neurons in female and male mice. Our results show that thalamic GABAergic neurons of the IGL and LGv receive retinal input from diverse classes of ipRGCs, but not from the M1 ipRGC type, while those in the pHB lack direct retinal input. We describe the synergistic role of the photoreceptor melanopsin and the thalamic neurons of the IGL/LGv in circadian entrainment to dim light. We identify a requirement for the thalamic IGL/LGv in the rapid changes in vigilance states associated with circadian light transitions. Furthermore, we map a previously undescribed thalamic network of developmentally related GABAergic neurons in the IGL/LGv complex and the pHB potentially involved in light-dependent mood regulation. Significance statementThe intergeniculate leaflet and ventral geniculate nucleus are part of the extended circadian system and mediate some non-image-forming visual functions. Here we show that each of these structures has a thalamic (dorsal) as well as prethalamic (ventral) developmental origin. We map the retinal input to thalamus-derived cells in the IGL/LGv complex and discover that while ipRGC input is dominant, this is not likely to originate from M1-ipRGCs. We describe the extent of similarity in synaptic input to developmentally related cells in the IGL/LGv and in the perihabenula nucleus (pHB). We implicate thalamic cells in the IGL/LGv in vigilance state transitions at circadian light changes and in overt behavioural entrainment to dim light, the latter exacerbated by concomitant loss of melanopsin expression.

neuroscience↗

bioRxiv2022

A Methodological Framework to Assess the Accuracy of Virtual Reality Hand-Tracking Systems: A case study with the Oculus Quest 2

Optical marker-less hand-tracking systems incorporated into virtual reality (VR) headsets are transforming the ability to assess motor skills, including hand movements, in VR. This promises to have far-reaching implications for the increased applicability of VR across scientific, industrial and clinical settings. However, so far, there is little data regarding the accuracy, delay and overall performance of these types of hand-tracking systems. Here we present a novel methodological framework which can be easily applied to measure these systems absolute positional error, temporal delay and finger joint-angle accuracy. We used this framework to evaluate the Meta Quest 2 hand-tracking system. Our results showed an average fingertip positional error of 1.1cm, an average finger joint angle error of 9.6o and an average temporal delay of 38.0ms. Finally, a novel approach was developed to correct for these positional errors based on a lens distortion model. This methodological framework provides a powerful tool to ensure the reliability and validity of data originating from VR-based, marker-less hand-tracking systems.

neuroscience↗

bioRxiv2020

Host autophagy mediates organ wasting and nutrient mobilization for tumor growth

During tumor growth - when nutrient and anabolic demands are high - autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling1. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids2-4. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.

cell biology↗

bioRxiv2020

Natural abundance isotope ratios to differentiate sources of carbon used during tumor growth in vivo

BackgroundRadioactive or stable isotopic labeling of metabolites is a strategy that is routinely used to map the cellular fate of a selected labeled metabolite after it is added to cell culture or to the circulation of an animal. However, the transformation of the labeled metabolite by cellular metabolism within organs complicates the use of this experimental strategy to quantify and understand metabolite transfer between organs. These methods are also technically demanding, expensive and potentially toxic. To allow quantification of the bulk movement of metabolites between organs, we have developed a novel application of stable isotope ratio mass spectrometry (SIRMS). ResultsWe exploit natural differences in 13C/12C ratios of plant nutrients for a low-cost and non-toxic carbon labeling, allowing a measurement of bulk carbon transfer between organs in vivo. SIRMS measurements were found to be sufficiently sensitive to measure organs from individual Drosophila melanogaster larvae, giving robust measurements down to 2.5 {micro}g per sample. We apply the method to determine if carbon incorporated into a growing solid tumor is ultimately derived from food or host tissues. ConclusionMeasuring tumor growth in a D.melanogaster larvae tumor model reveals that these tumors derive a majority of carbon from host sources. We believe the low cost and non-toxic nature of this methodology gives it broad applicability to study carbon flows between organs also in other animals and for a range of other biological questions.

cancer biology↗

bioRxiv2018

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

One of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the shape index, a characteristic feature of each TSS describing the spatial distribution of transcription initiation events, has a surprisingly strong negative correlation with the measured expression levels. Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.

systems biology↗

bioRxiv2017

Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. Ss4R), fit such a time-lag model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model called Lineage-specific Ohnologue Resolution (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than older ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear explosively, but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.

genomics↗