Biology subjects

Mann, S.

Publications and source records attributed to Mann, S..

14 recordsLinked to original sources

bioRxiv2026

Dual-stage inhibition of Plasmodium falciparum by a Skeletocutis derived fungal metabolite targeting Pyruvate Kinase II

Plasmodium falciparum resistance to current first line treatments is threatening at-risk populations and underscores the urgent need for novel therapeutic targets and drugs. P. falciparum pyruvate kinases I and II are two essential enzymes with distinct roles and subcellular localizations within the parasite. PfPyrKI is cytosolic, while PfPyrKII is found in the apicoplast, a specific organelle of Apicomplexa, where it is required for the production of (d)NTPs essential for apicoplast maintenance. We identify skeletocutin E, a Basidiomycete-derived metabolite, as a specific inhibitor of PfPyrKII. Skeletocutin E inhibits in vitro the activity of PfPyrKII with an IC50 of 0.52 {+/-} 0.08 {micro}M through a mixed inhibition mechanism and does not affect the activities of three human pyruvate kinases. Structure-activity relationship analyses using synthetic skeletocutin E analogues allowed us to identify the molecular determinants of this inhibition. Furthermore, determination of the quaternary structure of PfPyrKII by mass photometry, showed that this enzyme exists as monomers, dimers, and tetramers in equal proportions, revealing its singularity compared to other pyruvate kinases. Interestingly, skeletocutin E does not alter the distribution of the complexes, indicating that it does not interact at the subunit interfaces. Importantly, skeletocutin E inhibits P. falciparum growth in both blood and liver stages, with IC values of 3.56 {+/-} 0.50 {micro}M in red blood cells and 3.70 {+/-} 0.74 {micro}M in primary human hepatocytes. Together, these findings establish PfPyrKII as a druggable antimalarial target and identify skeletocutin E as a promising lead compound for the rational development of dual-stage antimalarial therapies.

microbiology↗

bioRxiv2026

Altered stem cell properties of human hematopoietic stem and progenitor cells based on bone region location

The bone marrow microenvironment forms a highly specialized niche that houses hematopoietic stem and progenitor cells (HSPCs). Within bone, two anatomically distinct regions, the medullary cavity and the trabecular compartment, differ in their cellular and physical composition, with the potential to differentially regulate influence on resident HSPCs. We hypothesized that HSPCs enriched from the medullary cavity (BM) and trabeculae (TB) represent functionally distinct populations. Contrary to this, functional assessment of HSPCs revealed comparable cellular outputs between BM- and TB-derived HSPCs. To investigate whether microenvironmental signaling contributes to functional regulation, we examined the effects of extracellular vesicles (EVs) isolated from medullary BM and TB. Notably, TB-derived EVs inhibited cell cycle progression, directing HSPCs toward a quiescent state. Together, these findings demonstrate that while isolated BM- and TB-derived HSPCs exhibit similar cell-intrinsic properties, EVs enriched from the TB specifically promote HSPC quiescence, supporting a protective regulatory role for the trabecular microenvironment.

cell biology↗

bioRxiv2025

Social plasticity in reproduction in female Drosophila melanogaster!

The expression of behaviours in individuals are not always fixed and may vary according to the specific environmental conditions encountered by an individual. There is significant evidence that male fruit flies, Drosophila melanogaster, have the capacity to adjust their courtship behaviours depending on the social environment they encounter; however, the extent of plasticity in behavioural responses by females have received much less scrutiny. In this study, we set out to determine whether the presence and/or the types of conspecifics an individual female encounters influences her subsequent reproductive behaviour and patterns of egg production. In our assay, we housed medium-sized adult virgin females in experimental social treatments; either in isolation, or with other conspecific females (that were either of large- or small- body size) to observe how the presence and/or type of social interactions altered later reproductive decisions and outcomes. While in some instances female flies behaved differently depending on their housing treatment, these responses were not particularly consistent between flies obtained from different populations, nor with previously described patterns. Potential contributing factors for these results, and their implications for the future study of female reproductive plasticity are discussed.

evolutionary biology↗

bioRxiv2025

Enriching for Extracellular Vesicles from Human Bone

Extracellular vesicles (EVs) are nano-sized membrane-bound structures thought to be secreted by all cells and increasingly recognized as key mediators of intercellular communication. Established EV isolation protocols for bodily fluids-primarily focus on blood with limited insights into methods optimized for EVs from other hematopoietic regions. In this study, we present a novel protocol for the isolation and enrichment of EVs from human trabecular bone and bone marrow. This method employs a two-step purification strategy, combining iodixanol density cushion (IDC) ultracentrifugation with size exclusion chromatography (SEC), and enables EV recovery from fresh tissue hours after collection. Importantly, this approach facilitates the enrichment of bone-derived EVs without the need for enzymatic digestion or long-term culture, preserving native EV populations. This protocol offers a valuable tool for researchers investigating EVs derived from the diverse cellular constituents of the bone microenvironment.

cell biology↗

bioRxiv2024

Self-assembly of hybrid 3D cultures by integrating living and synthetic cells

Self-assembly, a fundamental property of living matter, drives the interconnected cellular organization of tissues. Synthetic cell models have been developed as bionic materials to mimic inherent cellular features such as self-assembly. Here, we leverage co-assembly of synthetic and natural cells to create hybrid living 3D cancer cultures. We screened synthetic cell models, including giant unilamellar vesicles, coacervates, microdroplet emulsions, proteinosomes, and colloidosomes, for their ability to form hybrid tumoroids. Our results identify the balance of inter- and extracellular adhesion and synthetic cell surface tension as key material properties driving successful co-assembly of hybrids. We further demonstrate that these synthetic cells can establish artificial tumor immune microenvironments (ART-TIMEs), mimicking immunogenic signals within tumoroids. Using the ART-TIME approach, we identify co-signaling mechanisms between PD-1 and CD2 as a driver in immune evasion of pancreatic ductal adenocarcinoma. Our findings demonstrate the 3D bottom-up self-assembly of hybrid cancer microenvironments to replace immune components with defined bionic materials, pushing the boundaries to functionally integrating living and non-living matter.

synthetic biology↗

bioRxiv2024

Corticothalamic modelling of sleep neurophysiology with applications to mobile EEG

AO_SCPLOWBSTRACTC_SCPLOWRecent developments in mathematical modelling of EEG enable the tracking of otherwise-inaccessible neurophysiological parameters throughout sleep. Likewise, advancements in wearable electronics have enabled easy & affordable collection of sleep EEG at home. The convergence of these two advances, namely neurophysiological modelling for mobile sleep EEG, can boost preclinical and clinical assessments of sleep. However, this subject area has received limited attention in existing literature. To address this, we used an established model of the corticothalamic system to analyze EEG power spectra from 5 datasets, spanning from research-grade systems to at-home mobile EEG. In the present work, we compare the convergent and divergent features of the data and the estimated physiological model parameters. While data quality and characteristics differ considerably, key patterns consistent with previous theoretical and empirical work are observed. During the transition from lighter to deeper NREM, i) exponent of the aperiodic (1/f) spectral component is increased, ii) bottom-up thalamocortical drive is reduced, iii) corticocortical connection strengths are increased. This effect is observed in healthy subjects but is interestingly absent when taking SSRI antidepressants, suggesting possible effects of ascending neuromodulation on corticothalamic oscillations. We further show a month-long increase in REM% in one mobile EEG subject, associated with boosted high-frequency activity in spectra and higher thalamothalamic gains in the model, pointing to possible changes of thalamic inhibition in REM parasomnias. Our results provide a proof-of-principle for the utility and feasibility of this physiological modelling-based approach to analyzing mobile EEG data, providing a mechanistic measure of brain physiology during sleep. Statement of significanceWe employ a physiological model of the corticothalamic circuitry to model the EEG power spectra in sleep. We fit this model to 5 EEG datasets, and demonstrate that while mobile and non-mobile EEG recordings differ in their characteristics and quality, they can both robustly represent the changes along sleep stages using the aperiodic (1/f) component. We observe an increased corticocortical connection strength and decreased corticothalamic connection strength as the subject goes into deeper stages of NREM sleep; an effect that is, importantly, not observed in subjects taking SSRIs. This work provides a proof-of-concept for using mathematical modelling, working well for large mobile and non-mobile datasets providing valuable insight into the mechanisms generating sleep EEG.

neuroscience↗

bioRxiv2023

De novo design of drug-binding proteins with predictable binding energy and specificity

The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low M, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles. One Sentence SummaryWe use informatic sampling to design low nM drug-binding proteins, and physics-based calculations to accurately predict affinities.

biophysics↗

bioRxiv2023

Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice

Metabolic dysfunction underlies several chronic diseases. Dietary interventions can reverse metabolic declines and slow aging but remaining compliant is difficult. 17-estradiol (17-E2) treatment improves metabolic parameters and slows aging in male mice without inducing significant feminization. We recently reported that estrogen receptor is required for the majority of 17-E2-mediated benefits in male mice, but that 17-E2 also attenuates fibrogenesis in liver, which is regulated by estrogen receptor {beta} (ER{beta})-expressing hepatic stellate cells (HSC). The current studies sought to determine if 17-E2-mediated benefits on systemic and hepatic metabolism are ER{beta}-dependent. We found that 17-E2 treatment reversed obesity and related systemic metabolic sequela in both male and female mice, but this was partially blocked in female, but not male, ER{beta}KO mice. ER{beta} ablation in male mice attenuated 17-E2-mediated benefits on hepatic stearoyl-coenyzme A desaturase 1 (SCD1) and transforming growth factor {beta}1 (TGF-{beta}1) production, which play critical roles in HSC activation and liver fibrosis. We also found that 17-E2 treatment suppresses SCD1 production in cultured hepatocytes and hepatic stellate cells, indicating that 17-E2 directly signals in both cell-types to suppress drivers of steatosis and fibrosis. We conclude that ER{beta} partially controls 17-E2-mediated benefits on systemic metabolic regulation in female, but not male, mice, and that 17-E2 likely signals through ER{beta} in HSCs to attenuate pro-fibrotic mechanisms.

physiology↗

bioRxiv2023

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Owing to its longevity and extremely high information density, DNA has emerged as an attractive medium for archival data storage. Scalable parallel random access of information is a desirable property of any storage system. For DNA-based storage systems, however, this yet has to be robustly established. Here we develop thermoconfined PCR, a novel method that enables multiplexed, repeated random access of compartmentalized DNA files. Our strategy is based on stable localization of biotin-functionalized oligonucleotides inside microcapsules with temperature-dependent membrane permeability. At low temperatures, microcapsules are permeable to enzymes, primers, and amplified products, while at high temperatures membrane collapse prevents molecular crosstalk during amplification. We demonstrate that our platform outperforms non-compartmentalized DNA storage with respect to repeated random access and reducing amplification bias during multiplex PCR. Using fluorescent sorting, we additionally demonstrate sample pooling and data retrieval by barcoding of microcapsules. Our thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access of archival DNA files.

synthetic biology↗

bioRxiv2022

17α-estradiol, a lifespan-extending compound, attenuates liver fibrosis by modulating collagen turnover rates in male mice

BackgroundEstrogen signaling is protective against chronic liver diseases, although men and a subset of women are contraindicated for chronic treatment with 17{beta}-estradiol (17{beta}-E2) or combination hormone replacement therapies. We sought to determine if 17-estradiol (17-E2), a naturally-occurring diastereomer of 17{beta}-E2, could attenuate liver fibrosis. MethodsWe evaluated the effects of 17-E2 treatment on collagen synthesis and degradation rates using tracer-based labeling approaches in male mice subjected to carbon tetrachloride (CCl4)-induced liver fibrosis. We also assessed the effects of 17-E2 on markers of hepatic stellate cell (HSC) activation, collagen crosslinking, collagen degradation, and liver macrophage content and polarity. FindingsWe found that 17-E2 significantly reduced collagen synthesis rates and increased collagen degradation rates, which was mirrored by declines in transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver. These improvements were associated with increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokines expression in the liver. InterpretationWe conclude that 17-E2 reduces fibrotic burden by suppressing HSC activation and enhancing collagen degradation mechanisms. Future studies will be needed to determine if 17-E2 acts directly in hepatocytes, HSCs, and/or immune cells to elicit these benefits. FundingThis work was supported by the US National Institutes of Health and US Department of Veterans Affairs. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe prevalence and severity of chronic liver diseases are greater in men than women and men are twice as likely to die from chronic liver diseases. However, the prevalence and severity of nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), and liver fibrosis becomes comparable between the sexes following menopause, particularly when hormone replacement therapies (HRT) are not initiated. These observations suggest that estrogen signaling is protective against liver disease onset and progression, which is supported by studies in rodents demonstrating that 17{beta}-estradiol (17{beta}-E2) ameliorates hepatic steatosis and fibrogenesis. However, chronic administration of 17{beta}-E2 or combination HRTs are unrealistic in men due to feminization and increased risk for stroke and prostate cancer, and a subset of the female population are also at an increased risk for breast cancer and cardiovascular events when on HRTs. Therefore, we have begun exploring the therapeutic potential of 17-estradiol (17-E2), a naturally-occurring, nonfeminizing, diastereomer of 17{beta}-E2, for the treatment of liver diseases. Added value of this studyIn this study, using tracer-based labeling approaches in male mice subjected to CCl4-induced liver fibrosis, we show that 17-E2 reduces liver fibrosis by attenuating collagen synthesis and enhancing collagen degradation mechanisms. Both transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver were reduced by 17-E2. We also found that 17-E2 increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokine expression in the liver. Implications of all the available evidenceThis study supports the idea that estrogens are protective against chronic liver diseases and that 17-E2 may have therapeutic utility for the treatment of liver fibrosis.

physiology↗

bioRxiv2020

Light-activated signaling in DNA-encoded sender-receiver architectures

Collective decision making by living cells is facilitated by exchange of diffusible signals where sender cells release a chemical signal that is interpreted by receiver cells. Biologists have started to unravel the underlying physicochemical determinants that control the effective communication distance using genetically modified cells. However, living systems are inherently challenging to manipulate and study systematically and quantitatively. Therefore, the development of generic and tunable abiotic mimics featuring compartmentalized signaling is highly desirable. Here, by adapting a previously reported artificial cell-cell communication system, we engineer DNA-encoded sender-receiver architectures, where protein-polymer microcapsules act as cell mimics and molecular communication occurs through diffusive DNA signals. We prepare spatial distributions of sender and receiver protocells using a microfluidic trapping array, and setup a signaling gradient from a single sender cell using light, which activates surrounding receivers through DNA strand displacement. Our systematic analysis reveals how the effective signal range of a single sender is determined by various factors including the density and permeability of receivers, extracellular signal degradation, signal consumption and catalytic regeneration. In addition, we construct a three-population configuration where two sender cells are embedded in a dense array of receivers that implement Boolean logic and investigate spatial integration of non-identical input cues. The results advance our understanding of diffusion-based sender-receiver topologies and present a strategy for constructing spatially controlled chemical communication systems that have the potential to reconstitute collective cellular behavior.Competing Interest StatementThe authors have declared no competing interest.View Full Text

synthetic biology↗

bioRxiv2020

Health benefits attributed to 17α-estradiol, a lifespan-extending compound, are mediated through estrogen receptor α

Metabolic dysfunction underlies several chronic diseases, many of which are exacerbated by obesity. Dietary interventions can reverse metabolic declines and slow aging, although compliance issues remain paramount. 17-estradiol treatment improves metabolic parameters and slows aging in male mice. The mechanisms by which 17-estradiol elicits these benefits remain unresolved. Herein, we show that 17-estradiol elicits similar genomic binding and transcriptional activation through estrogen receptor (ER) to that of 17{beta}-estradiol. In addition, we show that the ablation of ER completely attenuates the beneficial metabolic effects of 17-E2 in male mice. Our findings suggest that 17-E2 acts primarily through the liver and hypothalamus to improve metabolic parameters in male mice. Lastly, we also determined that 17-E2 improves metabolic parameters in male rats, thereby proving that the beneficial effects of 17-E2 are not limited to mice. Collectively, these studies suggest ER may be a drug target for mitigating chronic diseases in male mammals.

physiology↗

bioRxiv2019

Distributed DNA-based Communication in Populations of Synthetic Protocells

Developing distributed communication platforms based on orthogonal molecular communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled Biomolecular Implementation of Protocellular Communication (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.

synthetic biology↗

bioRxiv2018

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labelled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging. UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2 and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme. As a sensitive, quantitative, flexible and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.

biochemistry↗