Biology subjects

Calvert, M.

Publications and source records attributed to Calvert, M..

12 recordsLinked to original sources

bioRxiv2025

Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator

The androgen receptor (AR) is a critical driver of prostate cancer (PCa). To study regulators of AR protein levels and oncogenic activity, we created the first live cell quantitative endogenous AR fluorescent reporters. Leveraging this novel AR reporter, we performed genome-scale CRISPRi flow cytometry sorting screens to systematically identify genes that modulate AR protein levels. We identified and validated known AR protein regulators including HOXB13 and GATA2 and also unexpected top hits including PTGES3, a poorly characterized gene in PCa. PTGES3 repression resulted in loss of AR protein, cell cycle arrest, and cell death in AR-driven PCa models. PTGES3 is not a commonly essential gene, and our data nominate it as a prime PCa therapeutic target. Clinically, analysis of PCa data demonstrate that PTGES3 expression is associated with AR-directed therapy resistance. Mechanistically, we show PTGES3 binds directly to AR, forms a protein complex with AR in the nucleus, regulates AR protein stability in vitro and in vivo and modulates AR function in the nucleus at AR target genes. PTGES3 represents a novel therapeutic target for overcoming known mechanisms of resistance to existing AR-directed therapies in PCa.

cancer biology↗

bioRxiv2025

Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer

Background: Despite extensive investigation, the factors promoting aggressive prostate cancer are poorly understood. In particular, despite a few prominent examples, the role of long non-coding RNAs (lncRNAs) is largely unknown. Methods: We performed a comprehensive analysis of whole-genome transcriptome data to identify differential expression across 1,567 patients with prostate cancer, then correlated differential expression with risk of metastatic recurrence. We characterized the lncRNA most associated with metastasis in vitro and in vivo to investigate the mechanism by which it promotes aggressive prostate cancer. Results: We have identified a novel lncRNA, Prostate Cancer Associated hnRNPK Interacting Transcript (PCAHIT), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that overexpression/knockdown of PCAHIT in pre-clinical models of prostate cancer modulates proliferation rates and markers of an aggressive phenotype through regulation of steroid biosynthesis and expression of the MHC class I complex, driving increased growth in androgen-depleted conditions and decreased susceptibility to T cell-mediated cytotoxicity. We further find that the heterogeneous nuclear ribonucleoprotein hnRNPK directly binds PCAHIT and is indispensable for its activity. Conclusions: Overall, our findings indicate that PCAHIT is a driver of aggressive prostate cancer phenotypes and poor clinical outcomes through suppression of the immune response and increased androgen-independent cancer growth. PCAHIT is a potential biomarker of aggressive disease.

cancer biology↗

bioRxiv2025

Evidence for balancing selection on loci associated with host use in the genome of a generalist plant parasite

Most research on host-parasite interactions has focused on tightly coevolved species pairs, yet many parasites are generalists that infect a wide range of host taxa. Generalist parasites are subject to highly variable selection pressures across different hosts and the footprints that this heterogeneous selection leaves in the genomes of generalists have been largely unexplored. To address this knowledge gap, we studied patterns of host-associated genetic diversity in the generalist plant parasite, the northern root knot nematode Meloidogyne hapla. By leveraging whole genome amplification, we generated whole genome libraries of individual root-knot nematodes collected from three different host plant species in a spatially replicated design. Despite finding no evidence of host-associated population structure, we did observe several hundred host-associated SNPs putatively under differential host selection. Genomic regions containing these host-associated SNPs were enriched for signals of balancing selection. Additionally, host-associated SNPs were enriched for functions involved in plant pathogenesis, specifically the modification of plant cell walls. Host-associated SNPs were also found in genes with known roles in dampening host plant immune responses to infection. Together, our results suggest a model of balancing selection in which heterogeneous selection by different host taxa maintains adaptive diversity at loci involved in pathogenesis.

evolutionary biology↗

bioRxiv2024

Population-level age effects on the white matter structure subserving cognitive flexibility in the human brain

Cognitive flexibility, a mental process crucial for adaptive behavior, involves multi-scale functioning across several neuronal organization levels. While the neural underpinnings of flexibility have been studied for decades, limited knowledge exists about the structure and age-related differentiation of the white matter subserving brain regions implicated in cognitive flexibility. This study investigated the population-level relationship between cognitive flexibility and properties of white matter across two periods of adulthood, aiming to discern how these associations vary over different life stages and brain tracts. We propose a novel framework to study age effects in brain structure-function associations. First, a meta-analysis was conducted to identify neural regions associated with cognitive flexibility. Next, the white matter projections of these neural regions were traced through the Human Connectome Project tractography template to identify the white matter structure associated with cognitive flexibility. Then, a cohort analysis was performed to characterize myelin-related macromolecular features using a subset of the UK Biobank magnetic resonance imaging (MRI) data, which has a companion functional/behavioral dataset. We found that (1) the wiring of cognitive flexibility is defined by a subset of brain tracts, which present undifferentiated features early in adulthood and significantly differentiated types in later life. (2) These MRI-derived properties are correlated with individual subprocesses of cognition, which are closely related to cognitive flexibility function. (3) In late life, myelin-related homogeneity of specific white matter tracts implicated in cognitive flexibility declines with age, a phenomenon not observed in early life. Our findings support the age-related differentiation of white matter tracts implicated in cognitive flexibility as a natural substrate of adaptive cognitive function. Significance StatementCognitive flexibility function facilitates adaptation to environmental demands. Brain changes affecting structural organization during the lifespan are theorized to impact cognitive flexibility. This study characterizes how the brains connectivity is correlated with cognitive flexibility function throughout adulthood. By analyzing myelin-related properties of white matter, this study found that certain parts of the brains wiring related to cognitive flexibility become more differentiated with advanced age. These age-related features appear as a natural characteristic of the human brain that may impact specific aspects of adaptive thinking, like shifting between tasks or updating information.

neuroscience↗

bioRxiv2023

Toward a trait-based framework for studying mutualism evolution: genotypic variation in benefit and cost traits in the legume-rhizobia mutualism

Mutualisms, reciprocally beneficial interaction between two or more species, are ubiquitous in nature. A common feature of mutualisms is extensive context-dependent variation in fitness outcomes. This context-dependency is hypothesized to stem from the environments mediation of the relative costs and benefits associated with mutualisms. However, traits related to the exchange of goods and services in mutualisms have received little attention in comparison to net fitness outcomes. In this study, we quantified the contribution of host and symbiont genotypes to variation in resource exchange, use, and production traits measured in the host using the model mutualism between legumes and nitrogen-fixing rhizobia. We predicted that plant genotype x rhizobia genotype (GxG) effects would be common to resource exchange traits because resource exchange is hypothesized to be governed by both interacting partners through bargaining. On the other hand, we predicted that plant genotype effects would dominate host resource use and production traits because these traits are only indirectly related to the exchange of resources. Consistent with our prediction for resource exchange traits, but not our prediction for resource use and production traits, we found that rhizobia genotype and GxG effects were the most common sources of variation in the traits that we measured. The results of this study complement the commonly observed phenomenon of GxG effects for fitness by showing that numerous mutualism traits also exhibit GxG variation. Furthermore, our results highlight the possibility that the exchange of resources as well as how partners use and produce traded resources can influence the evolution of mutualistic interactions. Our study lays the groundwork for future work to explore the relationship between resource exchange, use and production traits and fitness (i.e. selection) to test the competing hypotheses proposed to explain the maintenance of fitness variation in mutualisms.

evolutionary biology↗

bioRxiv2022

Increasing the efficacy of exposure using a whole brain approach to real-time fMRI neurofeedback among female victims of interpersonal violence

Individuals who experience interpersonal violence (IPV) and poly-victimization have an increased likelihood of developing Posttraumatic Stress Disorder (PTSD), and statistically, women are more likely than men to be victims of IPV, experience poly-victimization, and develop PTSD. Current gold-standard PTSD treatments utilize exposure, a key mechanism of change; however, exposure-based treatments suffer from moderate remission rates. This outcome underscores the importance of utilizing knowledge of neural mechanisms to increase treatment effectiveness and PTSD remission rates. The current study used a symptom provocation paradigm, which is conceptually similar to exposure, and whole brain multivariate pattern classifiers (MVPC) to provide participants with neurofeedback on their ability to regulate their brain-states. In the MRI scanner, women (N = 21; control n = 11, PTSD n = 10) completed a symptom provocation paradigm. The MVPC was constructed during the first two runs and neurofeedback was given during the third and fourth run. During all four runs, participants were instructed to increase or decrease their emotional engagement with their stress/trauma script and during the last two runs, participants were provided visual feedback indicating their performance in regulating brain states. Skin conductance response was utilized as an independent measure of physiological arousal. Generalized linear models indicated a significant interaction effect of feedback and condition as well as feedback and group. Generalized linear models of skin conductance response largely mirrored these findings. Results indicate neurofeedback of whole brain activation can be utilized to increase engagement with trauma memories. Thus, exposure-based treatments, possibly with refractory cases of PTSD, may be improved with neurofeedback by providing the therapist and patient insight into their brain-state during exposure which may increase the effectiveness of exposure-based treatments.

neuroscience↗

bioRxiv2021

Fibrillar Aβ causes profound microglial metabolic perturbations in a novel APP knock-in mouse model

Microglial dysfunction is believed to play a pathogenic role in Alzheimers disease (AD). Here, we characterize the amyloid-{beta} related pathology and microglial responses in an engineered APP knock-in mouse model of familial AD. This model recapitulates key pathological features of AD such as a progressive accumulation of parenchymal amyloid plaques and vascular amyloid deposits, altered glial responses and neurodegeneration. Leveraging multi-omics approaches, we found lipid accumulation and an exacerbated disease-associated transcriptomic response in methoxy-X04-positive, phagocytic microglia. Together, these findings highlight the potential of this novel, open-access mouse model to investigate AD pathogenesis and demonstrate that fibrillar A{beta} triggers lipid dysregulation and immuno-metabolic perturbations in phagocytic microglia. HighlightsO_LINovel open-access APP KI mouse model shows salient AD pathological features C_LIO_LIDeep phenotyping of sorted microglia reveals profound lipidomic perturbations in line with Alois Alzheimers original descriptions of glial adipose inclusions C_LIO_LIImmunometabolic perturbations are exacerbated in microglia accumulating fibrillar A{beta} C_LI

neuroscience↗

bioRxiv2021

Exo-β-N-acetylmuramidase NamZ of Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidase

Endo-{beta}-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that potentially lyse bacterial cells. They catalyze an endo-lytic cleavage of the peptidoglycan, the structural component of the bacterial cell wall; i.e. they hydrolyze glycosidic N-acetylmuramic acid (MurNAc)-{beta}-1,4-N-acetylglucosamine (GlcNAc)-bonds within the heteroglycan backbone of peptidoglycan. In contrast, little is known about exo-{beta}-N-acetylmuramidases, catalyzing an exo-lytic cleavage of {beta}-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We identified ybbC of B. subtilis, renamed namZ, as encoding the reported exo-{beta}-N-acetylmuramidase. A {Delta}namZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl {beta}-MurNAc and the peptidoglycan-derived disaccharide MurNAc-{beta}-1,4-GlcNAc. Together with the exo-{beta}-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. NamZ is a member of the DUF1343 protein family of unknown function and shows no significant sequence identity with known glycosidases. A structural model of NamZ revealed a putative active site located in a cleft within the interface of two subdomains, one of which constituting a Rossmann-fold-like domain, unusual for glycosidases. On this basis, we propose that NamZ represents the founding member of a novel family of peptidoglycan hexosaminidases, which is mainly present in the phylum Bacteroidetes and, less frequently, within Firmicutes (Bacilli, Clostridia), Actinobacteria and Gammaproteobacteria.

microbiology↗

bioRxiv2020

Breeding Program Optimization for Genomic Selection in Winter Wheat

Developing methodologies in the fields of phenomics and genomic prediction have the potential to increase the production of crop species by accelerating germplasm improvement. The integration of these technologies into germplasm improvement and breeding programs requires evidence that there will be a direct economic benefit to the program. We determined a basic set of parameters, such as prediction accuracy greater than 0.3, the ability to genotype over 7 lines for the cost of one phenotypic evaluation, and heritability levels below 0.4, at which the use of genomic selection would be of economic benefit in terms of genetic gain and operational costs to the Kansas State University (KSU) winter wheat breeding program. The breeding program was then examined to determine whether the parameters benefitting genomic selection were observed or achievable in a practical sense. Our results show that the KSU winter wheat breeding program is at a decision point with regards to their primary means of selection. A few operational changes to increase prediction accuracy would place the program in the parameter space where genomic selection is expected to outpace the current phenotypic selection methodology at a parity of the operation cost and would be of greatest benefit to the program.

genomics↗

bioRxiv2020

A Molecular Mechanism for Probabilistic Bet-hedging and its Role in Viral Latency

Probabilistic bet hedging, a strategy to maximize fitness in unpredictable environments by matching phenotypic variability to environmental variability, is theorized to account for the evolution of various fate-specification decisions, including viral latency. However, the molecular mechanisms underlying bet-hedging remain unclear. Here, we report that large variability in protein abundance within individual herpesvirus virion particles enables probabilistic bet hedging between viral replication and latency. Super-resolution imaging of individual virions of the human herpesvirus cytomegalovirus (CMV) showed that virion-to-virion levels of pp71 tegument protein--the major viral transactivator protein--exhibit extreme variability. This super-Poissonian tegument variability promoted alternate replicative strategies: high virion pp71 levels enhance viral replicative fitness but, strikingly, impede silencing, whereas low virion pp71 levels reduce fitness but promote silencing. Overall, the results indicate that stochastic tegument packaging provides a mechanism enabling probabilistic bet hedging between viral replication and latency. SIGNIFICANCEProbabilistic bet hedging is a generalized diversification strategy to maximize fitness in unpredictable environments, and has been proposed as an evolutionary basis for herpesvirus latency. However, the molecular mechanisms enabling probabilistic bet hedging have remained elusive. Here, we find that the human herpesvirus cytomegalovirus--a major cause of birth defects and transplant failures--utilizes stochastic variability in the abundance of a protein packaged into individual viral particles to enable probabilistic bet hedging between alternate viral states.

molecular biology↗

bioRxiv2020

Mitochondrial fission is a critical modulator of mutant APP-induced neural toxicity

Alterations in mitochondrial fission may contribute to the pathophysiology of several neurodegenerative diseases, including Alzheimers disease (AD). However, we understand very little about the normal functions of fission, or how fission disruption may interact with AD-associated proteins to modulate pathogenesis. Here we show that loss of the central mitochondrial fission protein dynamin-related 1 (Drp1) in CA1 and other forebrain neurons markedly worsens the learning and memory of mice expressing mutant human amyloid-precursor protein (hAPP) in neurons. In cultured neurons, Drp1KO and hAPP converge to produce mitochondrial Ca2+ (mitoCa2+) overload, despite decreasing mitochondria-associated ER membranes (MAMs) and cytosolic Ca2+. This mitoCa2+ overload occurs independently of ATP levels. These findings reveal a potential mechanism by which mitochondrial fission protects against hAPP-driven pathology.

neuroscience↗

bioRxiv2020

Single cell determination of cardiac microtissue structure and function using light sheet microscopy

Native cardiac tissue is comprised of heterogeneous cell populations that work cooperatively for proper tissue function; thus, engineered tissue models have moved toward incorporating multiple cardiac cell types in an effort to recapitulate native multicellular composition and organization. Cardiac tissue models comprised of stem cell-derived cardiomyocytes require inclusion of non-myocytes to promote stable tissue formation, yet the specific contributions of the supporting non-myocyte population on the parenchymal cardiomyocytes and cardiac microtissues have yet to be fully dissected. This gap can be partly attributed to limitations in technologies able to accurately study the individual cellular structure and function that comprise intact 3D tissues. The ability to interrogate the cell-cell interactions in 3D tissue constructs has been restricted by conventional optical imaging techniques that fail to adequately penetrate multicellular microtissues with sufficient spatial resolution. Light sheet fluorescence microscopy overcomes these constraints to enable single cell-resolution structural and functional imaging of intact cardiac microtissues. Multicellular spatial distribution analysis of heterotypic cardiac cell populations revealed that cardiomyocytes and cardiac fibroblasts were randomly distributed throughout 3D microtissues. Furthermore, calcium imaging of live cardiac microtissues enabled single-cell detection of cardiomyocyte calcium activity, which showed that functional heterogeneity correlated with spatial location within the tissues. This study demonstrates that light sheet fluorescence microscopy can be utilized to determine single-cell spatial and functional interactions of multiple cell types within intact 3D engineered microtissues, thereby facilitating the determination of structure-function relationships at both tissue-level and single-cell resolution. Impact StatementThe ability to achieve single-cell resolution by advanced 3D light imaging techniques enables exquisite new investigation of multicellular analyses in native and engineered tissues. In this study, light sheet fluorescence microscopy was used to define structure-function relationships of distinct cell types in engineered cardiac microtissues by determining heterotypic cell distributions and interactions throughout the tissues as well as by assessing regional differences in calcium handing functional properties at the individual cardiomyocyte level.

bioengineering↗