Biology subjects

Allen, T.

Publications and source records attributed to Allen, T..

13 recordsLinked to original sources

bioRxiv2026

PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy

Organelles form an interconnected network whose morphology, positioning and interactions reflect cellular state. However, reproducibly quantifying these organelle phenotypes across large cell populations and diverse cell types remains a significant challenge. Here we present PRISM (Plasmid-based Reporter for Intracellular Spectral Microscopy), a PiggyBac-integrable construct encoding five unique fluorescent organelle reporters for spectral microscopy, with an accompanying modular analysis pipeline. PRISM stably labels the Golgi, peroxisomes, endoplasmic reticulum, mitochondria and lysosomes in multiple cell types while remaining compatible with additional molecular or functional probes. The workflow extracts over 500 metrics per cell, describing organelle morphology and distribution alongside pairwise and higher-order contacts. We use PRISM to characterise organelle responses to cytoskeletal perturbation, map PI(4)P redistribution during lysosomal damage, and reveal how Zika virus remodels the organelle landscape during infection. PRISM provides a reproducible approach for investigating organelle network remodelling across biological contexts

cell biology↗

bioRxiv2025

Early developmental neuronal activity inhibits oligodendrocyte differentiation through AMPA receptor activation

Oligodendrocytes produce myelin, a lipid-rich membrane that wraps neuronal axons in the central nervous system to provide metabolic and trophic support and allow for saltatory conduction. Developmental myelination requires precisely timed and localized neuron-oligodendrocyte communication. In the mature brain, neuronal activity promotes oligodendrocyte precursor cell (OPC) proliferation and differentiation, but how OPCs respond to neuronal activity in early brain development, prior to the onset of myelination, is less well characterized. Here, we investigate how sensory-evoked and chemogenetically altered neuronal activity affect oligodendrocyte maturation in the olfactory system, somatosensory cortex, and corpus callosum in mice. We find that early neuronal activity inhibits oligodendrocyte differentiation and that reduced neuronal activity relieves this inhibition, thereby increasing OPC differentiation. Additionally, single-cell RNA sequencing revealed transcriptional changes in oligodendrocytes when neuronal activity was reduced, including upregulation of glutamate receptor gene expression. Finally, we identify AMPAR signaling as a critical regulator of oligodendrocyte differentiation ex vivo.

neuroscience↗

bioRxiv2025

Reproducible autosomal gene expression changes with loss of typical X and Y complement across tumor types

Although there are known sex differences in cancer incidence, severity, and treatment, the sex chromosomes are typically excluded from genomic analyses because of the unique technical challenges associated with assessing their copy number, sequence variation, and expression. Here we assess sex chromosome complement in three widely-used human genomics datasets from normal (non-cancerous) tissues, primary tumors, and cancer cell lines and study the effects on genome-wide gene expression. Expected sex chromosome complements based on reported patient sex were observed in non-cancerous tissues, but about half of tumors and cancer cell lines showed loss of typical sex chromosome gene expression across tissue types with three categories: loss of chromosome Y (LOY), loss of chromosome X (LOX) and reactivation of the inactive X chromosome (XaXa). Genes consistently differentially expressed in tumors with loss of chromosome X, loss of chromosome Y, or loss of X chromosome inactivation are associated with the hallmarks of cancer and include both sex-linked and autosomal genes from nearly all chromosomes, druggable genes, and genes with molecular functions relevant to cancer signaling, such as kinase activity. Strikingly, tumors that are X0, including tumors from female patients that have lost an X chromosome and tumors from male patients that have lost a Y chromosome, cluster together by gene expression profile. Patients with tumors that have LOX or LOY had poorer survival outcomes compared to those with tumors that had maintained their sex chromosome complement. Further, LOX and LOY eliminates nearly all of the differential gene expression between tumors from different patient sexes, affecting sex chromosomal and autosomal gene expression. Going forward, considering patient sex as well as the entire genome, including assessment of the sex chromosome complement, will provide additional insights into personalized tumor etiology, progression, treatment, and patient outcome. TeaserLoss of typical sex chromosome complement is present in primary tumors and cancer cell lines across tissue types. We identify consistent autosomal gene expression changes across multiple cancers when the sex chromosome complement is altered, and show that loss of sex chromosomes reduces tumor gene expression differences between patient sexes. We show that loss of sex chromosomes is also associated with poorer patient survival.

cancer biology↗

bioRxiv2024

Design of linked-domain protein inhibitors of UBE2D as tools to study cellular ubiquitination

Ubiquitin (Ub) is a post-translational modification that largely controls proteostasis through mechanisms spanning transcription, translation, and notably, protein degradation. Ub conjugation occurs through a hierarchical cascade of three enzyme classes (E1, E2, and E3s) involving >1000 proteins that regulate the ubiquitination of proteins. The E2 Ub-conjugating enzymes are the midpoint, yet their cellular roles remain under-characterized, partly due to a lack of inhibitors. For example, the cellular roles of the promiscuous E2 UBE2D/UBCH5 are not well described. Here, we develop a highly selective, multivalent, engineered protein inhibitor for the UBE2D family that simultaneously targets the RING- and backside-binding sites. In HeLa cells, these inhibitors phenocopy knockdown of UBE2D by reducing the IC50 to cisplatin and whole-cell proteomics reveal an increased abundance of [~]20% of the identified proteins, consistent with reduced Ub degradation and proteotoxic stress. These precision tools will enable new studies probing UBE2Ds central role in proteome management.

biochemistry↗

bioRxiv2024

Contribution of Urea to Nitrite Production in Southern Ocean Waters with Contrasting Nitrifying Communities

We compared the contribution of ammonia and urea to nitrite production in >100 samples of Southern Ocean waters with abundant and diverse ammonia-oxidizing archaeal (AOA) communities. Ammonia (AO) and urea (UO) oxidation rates were distributed uniformly within a water mass across coastal and slope waters west of the Antarctic Peninsula; however, rates and AOA community composition displayed strong vertical gradients. Rates in most samples from Antarctic surface and slope water were at or below the limit of detection. Highest mean rates of both processes were in the Winter Water (WW, epipelagic, 21.2 and 1.6 nmol N L-1 d-1), and the Circumpolar Deep Water (CDW, mesopelagic, 7.9 and 2.5 nmol N L-1 d-1), for AO and UO, respectively. However, we also found that the response of AO and UO to substrate amendments varied by water mass. AO rates in WW samples increased by [~]200% with 44 vs 6 nM amendments, but decreased (down to 7%) in CDW samples. UO rates responded similarly, but to a lesser degree. This response suggests that even low NH4+ amendments may inhibit AO by mesopelagic Thaumarchaeota populations. AO and UO rates were not correlated, nor were they correlated with the abundance or ratios of abundance of marker genes, or with the concentrations of ammonium or urea. Our data suggest that while ammonium is the primary substrate, urea-N is responsible for a significant fraction ([~]25% of that from AO alone) of nitrite production in the Southern Ocean, comparable to its contribution at lower latitudes. IMPORTANCESouthern Ocean nitrification fuels denitrification in oxygen depleted zones at higher latitudes, one of the controls of N:P ratios in the global ocean. N2O, a powerful greenhouse gas, is by-product of nitrification. We contrast the contributions of ammonium and urea-N to nitrification in the Southern Ocean. Our work constrains rates and demonstrates that the contribution of urea-N to nitrite production in polar waters is comparable to that in temperate oceans. Correlations between activity and the abundance or ratios of Thaumarchaeota marker genes were weak, questioning their use as indicators of activity. We document differential responses of activity to substrate amendments by water mass: enhanced in epipelagic but inhibited in mesopelagic samples. We interpret this difference in the context of community composition and the production of reactive oxygen species. Our insights into environmental controls of nitrification are relevant to microbial ecologists studying Thaumarchaeota and to modeling the global nitrogen cycle.

microbiology↗

bioRxiv2023

The Dark Side of Mentalizing: Learning Signals in the Default Network During Social Exchanges Support Cooperation and Exploitation

The evolution of human social cognitive capacities such as mentalizing was associated with the expansion of frontoparietal cortical networks, particularly the default network. Mentalizing supports prosocial behaviors, but recent evidence indicates it may also serve a darker side of human social behavior. Using a computational reinforcement learning model of decision-making on a social exchange task, we examined how individuals optimized their approach to social interactions based on a counterparts behavior and prior reputation. We found that learning signals encoded in the default network scaled with reciprocal cooperation and were stronger in individuals who were more exploitative and manipulative, but weaker in those who were more callous and less empathic. These learning signals, which help to update predictions about others behavior, accounted for associations between exploitativeness, callousness, and social reciprocity. Separately, we found that callousness, but not exploitativeness, was associated with a behavioral insensitivity to prior reputation effects. While the entire default network was involved in reciprocal cooperation, sensitivity to reputation was selectively related to the activity of the medial temporal subsystem. Overall, our findings suggest that the emergence of social cognitive capacities associated with the expansion of the default network likely enabled humans to not only cooperate effectively with others, but to exploit and manipulate others as well. SignificanceTo navigate complex social lives, humans must learn from their interactions with others and adjust their own behavior accordingly. Here, we show that humans learn to predict the behavior of social counterparts by integrating reputational information with both observed and counterfactual feedback acquired during social experience. We find that superior learning during social interactions is related to empathy and compassion and associated with activity of the brains default network. Paradoxically however, learning signals in the default network are also associated with manipulativeness and exploitativeness, suggesting that the ability to anticipate others behavior can serve both the light and dark sides of human social behavior.

neuroscience↗

bioRxiv2022

Assessment of ethanol and nicotine interactions using a reinforcer demand modeling with grouped and individual levels of analyses in a long-access self-administration model.

Previous reports have indicated the reciprocal effects of nicotine and ethanol on their rewarding and reinforcing properties, but studies using methodological approaches resembling substance use in vulnerable populations are lacking. In our study, rats first self-administered ethanol, and their sensitivity to ethanols reinforcing effects was assessed using a reinforcer demand modeling approach. Subsequently, rats were equipped with intravenous catheters to self-administer nicotine, and their sensitivity to nicotines reinforcing effects was evaluated using the same approach. In the final phase, rats were allowed to self-administer ethanol and nicotine concurrently, investigating the influence of one substance on the rate of responding for the other substance. Group analyses revealed notable differences in demand among sucrose, sweetened ethanol, and ethanol-alone, with sucrose demonstrating the highest demand and ethanol-alone exhibiting greater sensitivity to changes in cost. At the individual level, our study finds significant correlations between rats demand for sucrose and sweetened ethanol, suggesting parallel efforts for both substances. Our individual data also suggest interconnections in the elasticity of demand for sweetened ethanol and ethanol-alone, as well as a potential relationship in price response patterns between ethanol and nicotine. Furthermore, concurrent self-administration of ethanol and nicotine at the group level displayed reciprocal effects, with reduced responding for nicotine in the presence of ethanol and increased responding for ethanol in the presence of nicotine. This study provides valuable insights into modeling the co-use of ethanol and nicotine and assessing their interaction effects using reinforcer demand modeling and concurrent self-administration or noncontingent administration tests. These findings contribute to our understanding of the complex interplay between ethanol and nicotine and have implications for elucidating the underlying mechanisms involved in polydrug use.

animal behavior and cognition↗

bioRxiv2021

Limited accessibility of nitrogen supplied as amino acids, amides, and amines as energy sources for marine Thaumarchaeota

Genomic and physiological evidence from some strains of ammonia-oxidizing Thaumarchaeota demonstrate their additional ability to oxidize nitrogen (N) supplied as urea or cyanate, fueling conjecture about their ability to conserve energy by directly oxidizing reduced N from other dissolved organic nitrogen (DON) compounds. Similarly, field studies have shown rapid oxidation of polyamine-N in the ocean, but it is unclear whether Thaumarchaeota oxidize polyamine-N directly or whether heterotrophic DON remineralization is required. We tested growth of two marine Nitrosopumilus isolates on DON compounds including polyamines, amino acids, primary amines, and amides as their sole energy source. Though axenic cultures only consumed N supplied as ammonium or urea, there was rapid but inconsistent oxidation of N from the polyamine putrescine when cultures included a heterotrophic bacterium. Surprisingly, axenic cultures oxidized 15N-putrescine during growth on ammonia, suggesting co-metabolism or accelerated breakdown of putrescine by reactive metabolic byproducts. Nitric oxide, hydrogen peroxide, or peroxynitrite did not oxidize putrescine in sterile seawater. These data suggest that the N in common DON molecules is not directly accessible to marine Thaumarchaeota, with thaumarchaeal oxidation (and presumably assimilation) of DON-N requiring initial heterotrophic remineralization. However, reactive byproducts or enzymatic co-metabolism may facilitate limited thaumarchaeal DON-N oxidation.

microbiology↗

bioRxiv2019

Purification, identification, and characterization of two benzophenanthridine alkaloids from Corydalis longicalcarata rhizomes with anti-mitotic and polyploidy-inducing activities

Mitosis has long been a therapeutic target for the treatment of cancer. After conducting a phenotypic screen for anti-mitotic activity in a crude extract library of more than 2000 medicinal plants, we identified the rhizomes of Corydalis longicalcarata. Guided by the bioactivity-based assay, two benzophenanthridine alkaloids were purified and subsequently identified as corynoline and its close analog acetylcorynoline. This study uncovers a previously unknown antimitotic activity for these two phytochemicals, discovers their potential to be developed as anticancer drugs, and highlights their pleiotropic effects on cell division, including prevention of chromosome congression, compromise of spindle checkpoint response, and blockage of cytokinesis.

cancer biology↗

bioRxiv2019

A high-content screen identifies the vulnerability of MYC-overexpressing cells to dimethylfasudil

A synthetic lethal effect arises when a cancer-associated change introduces a unique vulnerability to cancer cells that makes them unusually susceptible to a drugs inhibitory activity. The synthetic lethal approach is attractive because it enables targeting of cancers harboring specific genomic alterations, the products of which may have proven refractory to direct targeting. An example is cancer driven by overexpression of MYC. Here, we conducted a high-content screen for compounds that are synthetic lethal to elevated MYC using a small-molecule library to identify compounds that are closely related to, or are themselves, regulatory-approved drugs. The screen identified dimethylfasudil, a potent and reversible inhibitor of Rho-associated kinases ROCK1 and ROCK2. Close analogs of dimethylfasudil are used clinically to treat neurologic and cardiovascular disorders. The synthetic lethal interaction was conserved in rodent and human cell lines and could be observed with activation of either MYC or its paralog MYCN. The synthetic lethality seems specific to MYC overexpressing cells as it could not be substituted by a variety of oncogenic manipulations and synthetic lethality was diminished by RNAi-mediated depletion of MYC in human cancer cell lines. Collectively, these data support investigation of the use of dimethylfasudil as a drug that is synthetic lethal for malignancies that specifically overexpress MYC.\n\nSignificance StatementSynthetic lethal targeting of tumors overexpressing MYC holds promise for attacking aggressive malignancies. Here we describe a synthetic lethal interaction between dimethylfasudil and overexpression of MYC. Uniquely, this novel synthetic lethal interaction points toward an opportunity for synthetic lethality with a molecule likely to harbor favorable drug-like properties that enable systemic use.

cancer biology↗

bioRxiv2019

Visual acuity performance level is independent of locomotion

Locomotion has a global impact on circuit function throughout the cortex, including regulation of spatiotemporal dynamics in primary visual cortex (V1). The mechanisms driving state-changes in V1 result in a 2-3 fold gain of responsiveness to visual stimuli. To determine whether locomotion-mediated increases in response gain improve the perception of spatial acuity we developed a head-fixed task in which mice were free to run or sit still during acuity testing. Spatial acuity, ranging from 0.1 to 0.7 cycles/{degrees}, was assessed before and after 3-4 weeks of reward-based training in adult mice. Training on vertical orientations once a day improved the average performance across mice by 22.5 {+/-} 0.05%. Improvement transferred to non-trained orientations presented at 45{degrees}, indicating that the improvement in acuity generalized. Furthermore we designed a second closed-loop task in which acuity threshold could be directly assessed in a single session. Using this design, we established that acuity threshold matched the upper limit of the trained spatial frequency; in two mice spatial acuity threshold reached as high as 1.5 cycles/{degrees}. During the 3-4 weeks of training we collected a sufficient number of stimulus trials in which mice performed above chance but below 100% accuracy. Using this subset of stimulus trials, we found that perceptual acuity was not enhanced on trials in which mice were running compared to trials in which mice were still. Our results demonstrate that perception of spatial acuity is not improved by locomotion.

neuroscience↗

bioRxiv2019

The anti-apoptotic proteins Bcl-2 and Bcl-xL suppress Beclin1/Atg6-mediated lethal autophagy in polyploid cells

Inhibition of Aurora-B kinase is a synthetic lethal therapy for tumors that overexpress the MYC oncoprotein. It is currently unclear whether co-occurring oncogenic alterations might influence this synthetic lethality by confering more or less potency in the killing of tumor cells. To identify such modifers, we utilized isogenic cell lines to test a variety of cancer genes that have been previously demonstrated to promote survival under conditions of cellular stress, contribute to chemoresistance and/or suppress MYC-primed apoposis. We found that Bcl-2 and Bcl-xL, two antiapoptotic members of the Bcl-2 family, can partially suppress the synthetic lethality, but not multinucleation, elicited by a panaurora kinase inhibitor, VX-680. We demonstrate that this suppression stems from the rescue of autophagic cell death, specifically of multinucleated cells, rather than a general inhibition of apoptosis. Bcl-2 inhibits VX-680-induced death of polyploid cells by interacting with the autophagy protein Beclin1/Atg6 and rescue requires localization of Bcl-2 to the endoplasmic reticulum. These findings expand on previous conclusions that autophagic death of polyploid cells is mediated by Atg6. Bcl-2 and Bcl-xL negatively modulate MYC-VX-680 synthetic lethality and it is the anti-autophagic activity of these two Bcl-2 family proteins, specifically in multinucleate cells, that contributes to resistance to Aurora kinase-targeting drugs.

cancer biology↗

bioRxiv2017

The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe

Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200-1800 BCE. The mechanism of its expansion is a topic of long-standing debate, with support for both cultural diffusion and human migration. We present new genome-wide ancient DNA data from 170 Neolithic, Copper Age and Bronze Age Europeans, including 100 Beaker-associated individuals. In contrast to the Corded Ware Complex, which has previously been identified as arriving in central Europe following migration from the east, we observe limited genetic affinity between Iberian and central European Beaker Complex-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, human migration did have an important role in the further dissemination of the Beaker Complex, which we document most clearly in Britain using data from 80 newly reported individuals dating to 3900-1200 BCE. British Neolithic farmers were genetically similar to contemporary populations in continental Europe and in particular to Neolithic Iberians, suggesting that a portion of the farmer ancestry in Britain came from the Mediterranean rather than the Danubian route of farming expansion. Beginning with the Beaker period, and continuing through the Bronze Age, all British individuals harboured high proportions of Steppe ancestry and were genetically closely related to Beaker-associated individuals from the Lower Rhine area. We use these observations to show that the spread of the Beaker Complex to Britain was mediated by migration from the continent that replaced >90% of Britains Neolithic gene pool within a few hundred years, continuing the process that brought Steppe ancestry into central and northern Europe 400 years earlier.

genomics↗