Biology subjects

Wells, M.

Publications and source records attributed to Wells, M..

13 recordsLinked to original sources

bioRxiv2026

Functional importance and paralog-specificity of the intrinsically disordered RsmE C-terminus region in Pseudomonas fluorescens Pf0-1

RsmE and its homologs function as RNA-binding post-transcriptional regulators that control the production of diverse secondary metabolites. Pseudomonads harbor varying numbers of RsmE paralogs that are often generalized to overlap in function. However, recent studies indicate that these paralogs bind to both overlapping and unique sets of mRNA. In Pseudomonas fluorescens Pf0-1, RsmE exclusively regulates the production of multiple extracellular secretions, distinguishing it from its paralogs, RsmA and RsmI. While the majority of the three paralogs core sequences are highly conserved, each possesses a vastly different C-terminus region. The C-terminus tails are generalized to be functionless, as they are intrinsically disordered and devoid of known mRNA binding sites. Here, we challenge this notion through analyses of various naturally emergent RsmE variants that differentially impact repressive function solely from changes in the C-terminus tail. Engineered Rsm chimeras containing the various paralog cores and tails further confirmed the functional importance of the C-terminus tail, as neither replacing the RsmE tail with the RsmA tail nor attaching the RsmE tail to a different paralog core restored repression. However, the RsmI tail complemented function in the presence of the RsmE core, indicating that RsmEs functional specificity lies within the core despite the essentiality of the C-terminus. Bioinformatic analyses also revealed that the C-terminus tail composition of RsmA to be the most unique among the paralogs and each tail sequence is uniquely and highly conserved across diverse proteins, not only in bacteria, but also in eukaryotic species.

microbiology↗

bioRxiv2026

Functional impact of a type VI secretion system on RsmE-mediated spatial structure formation in Pseudomonas fluorescens Pf0-1

Bacteria naturally form densely structured populations wherein both space and nutrients become locally limited. In densely populated Pseudomonas fluorescens Pf0-1 colonies, spatiogenetic patches with drastically reduced cellular density naturally emerge through spontaneous mutations in rsmE. RsmE is a posttranscriptional regulator that binds to specific mRNAs, including those that consequently repress the production of extracellular secretions. We have previously shown that {Delta}rsmE produces an extracellular polysaccharide (EPS) and biosurfactant that collectively function to define the spatiogenetic structure and locally outcompete the WT. Here, we identify additional RsmE-regulated secretions through a combination of RNA-sequencing and LC-MS/MS. In particular, a type VI secretion system (T6SS) was exclusively produced by {Delta}rsmE. Confocal microscopy imaging of WT and genetically modified {Delta}rsmE cocultures showed that the T6SS kills WT cells that invade the low- density spatiogenetic structure. However, its impact on competition with the WT was both quantifiably and spatially limited in the absence of the normally co-produced EPS and biosurfactant, largely due to the consequently altered spatial structure. These results highlight the importance of understanding both the individual and collective spatial functions of extracellular secretions, especially in the ecological context of densely structured microbial populations. IMPORTANCEIn crowded wild type (WT) Pseudomonas fluorescens Pf0-1 colonies, rsmE mutants spontaneously emerge by forming a low cellular density spatial structure that is devoid of WT cells. RsmE functions primarily to repress the production of various extracellular secretions, including an extracellular polysaccharide and biosurfactant, that collectively form the unique spatial structure. Here, we describe an RsmE-regulated type VI secretion system that kills the invading WT cells and protect the low-density structure. Importantly, individual RsmE-regulated secretions carry out unique functions, but their efficacies largely depend on other co-regulated products. Extracellular secretions that are mechanistically similar to those described here are co- produced across diverse biofilm-forming and virulent bacterial species, where they also likely play complex molecular and ecological roles.

microbiology↗

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↗

bioRxiv2025

Oncogene SETDB1s Dual Role in Endometrial Cancer: Driving Tumor Progression and Immune Escape

Oncogene SETDB1, an H3K9 methyltransferase, drives tumorigenesis in various cancers. Using endometrial cancer (EC) as a model, we discovered SETDB1s dual mechanisms in driving EC tumorigenesis and mediating immune evasion. SETDB1 knockout (SETDB1-/-) tumor-bearing mice exhibited prolonged survival of up to 100 days. Transcriptomic profiling of SETDB1-/- EC cells revealed decreased expression of oncogenes (POLR2A, MSH6, FLNA) and increased expression of tumor suppressor genes (PGR, RERG, ZNF582), which indicates that SETDB1 intrinsically promotes EC tumor proliferation by regulating these downstream genes. SETDB1 repressed repeat elements and the interferon pathway, mediating immune evasion extrinsically by inhibiting anti-tumor macrophage infiltration. ChIP-seq analysis showed SETDB1 binding at pericentromeric regions on many chromosomes and numerous ZNFs. Loss of SETDB1 resulted in abnormal cell division. SETDB1-/- tumors displayed reduced proliferation markers (Ki67, pHH3) and increased macrophage infiltration. Mechanistically, SETDB1 promotes CD47 (a dont-eat-me signal) and represses CCL5 and CXCL9 (macrophage and T-cell recruiting chemokines), contributing to immune evasion. M1-like macrophages killed more SETDB1-/- cells in co-culture. Additionally, SETDB1 knockout in mouse EC cells reduced tumor growth in C57BL/6 mice, with increased macrophage and CD4+ T-cell infiltration. Our results indicates that elevated SETDB1 and its target genes can predict higher tumor grade and worse survival, suggesting that targeting SETDB1 could be a promising therapeutic strategy for EC.

cancer biology↗

bioRxiv2025

The Stop Signal Stepping Task: how action cancellation commands disrupt step initiation in young and healthy older adults

Action cancellation - the ability to rapidly cancel an initiated movement in response to unexpected events - has been extensively studied in the upper limb using the stop signal task (SST). During gait, action cancellation is needed to stop and modify steps to avoid hazards and prevent falls. By adapting the SST to step initiation, this study investigated how the anticipatory postural adjustment (APA) and foot-lift phases of forward stepping were affected by action cancellation commands, and whether this changed with healthy ageing. The SST was performed in stepping, foot tap, and finger button conditions in 27 young (Mage = 28.7 years) and 29 healthy older adults (Mage = 70.1 years). Across conditions, older adults exhibited slower response speed compared to young adults and greater proactive slowing of responses when stop cues were anticipated. However, there was no significant difference in stopping speed between young and older adults. Stopping speed was fastest in the finger tap condition, and slowest in the step condition. When an APA was initiated in a step cancellation trial, the magnitude of the weight shift toward the step leg did not differ between successful and unsuccessful foot-lift cancellations. Foot-lift could be cancelled when stop cues were presented at similar phases of step preparation for young and older adults. These results suggest that the initial loading of the step leg is a ballistic process, however as weight is shifted toward the stance leg, action cancellation commands responding to external stimuli can decouple the APA and foot-lift step phases. Key PointsO_LIThe stop signal task (SST) - which allows an estimation of stopping speed independently of response speed - was applied to voluntary stepping in young and older adults. C_LIO_LIWhile response speed was slower for older than young adults, stopping speed was not significantly different between age groups in the upper limb, lower limb when seated, and during forward stepping. C_LIO_LIWhen stop cues were introduced, response speed slowed more in older than young adults, and more in the upper than the lower limb (i.e., Foot Tap and Step conditions). C_LIO_LIThe initial preparatory weight shift toward the stepping foot was not significantly different between successfully cancelled steps and normal steps, highlighting the ballistic nature of the early phase of step preparation. C_LIO_LIPrior to foot-lift, action cancellation commands could decouple the preparatory weight shift phase from foot-lift at similar stages of step initiation in young and healthy older adults. C_LI

neuroscience↗

bioRxiv2023

Efficacy of Drpitor1a, a Dynamin-Related Protein 1 inhibitor, in Pulmonary Arterial Hypertension

RationaleDynamin-related protein 1 (Drp1), a large GTPase, mediates mitochondrial fission. Increased Drp1-mediated fission permits accelerated mitosis, contributing to hyperproliferation of pulmonary artery smooth muscle cells (PASMC), which characterizes pulmonary arterial hypertension (PAH). We developed a Drp1 inhibitor, Drpitor1a, and tested its ability to regress PAH. ObjectivesAssess Drpitor1as efficacy and toxicity in: a)normal and PAH human PASMC (hPASMC); b)normal rats versus rats with established monocrotaline (MCT)-induced PAH. MethodsDrpitor1as effects on recombinant and endogenous Drp1-GTPase activity, mitochondrial fission, and cell proliferation were studied in hPASMCs (normal=3; PAH=5). Drpitor1as pharmacokinetics and tissue concentrations were measured (n=3 rats/sex). In a pilot study (n=3-4/sex/dose), Drpitor1a (1mg/kg/48-hours, intravenous) reduced adverse PA remodeling only in females. Consequently, we compared Drpitor1a to vehicle in normal (n=6 versus 8) and MCT-PAH (n=9 and 11) females, respectively. Drpitor1a treatment began 17-days post-MCT with echocardiography and cardiac catheterization performed 28-29 days post-MCT. ResultsDrpitor1a inhibited recombinant and endogenous Drp1 GTPase activity, which was increased in PAH hPASMC. Drpitor1a inhibited mitochondrial fission and proliferation and induced apoptosis, in PAH hPASMC but not normal hPASMC. Drpitor1a tissue levels were higher in female versus male RVs. In MCT-PAH females, Drpitor1a regressed PA obstruction, lowered pulmonary vascular resistance, and improved RV function, without hematologic, renal, or hepatic toxicity. ConclusionsDrpitor1a inhibits Drp1 GTPase, reduces mitochondrial fission, and inhibits cell proliferation in PAH hPASMC. Drpitor1a caused no toxicity in MCT-PAH and had no significant effect on normal rats or hPASMCs. Drpitor1a is a potential PAH therapeutic which displays an interesting therapeutic sexual dimorphism.

pharmacology and toxicology↗

bioRxiv2023

Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria

Four distinct lineages of ammonia-oxidizing microorganisms (AOM) collectively contribute to one of the largest nitrogen fluxes in the global nitrogen budget. AOM possess widely different specific affinities for ammonia, thought to determine their niche differentiation. Nevertheless, ammonia-oxidizing archaea and bacteria (AOA, AOB), and complete ammonia oxidizers (comammox) co-occur in soils, freshwater sediments, and aquifers, suggesting that other factors must drive their coexistence. Here, we show that representatives of four AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct competition for either substrate. The tested AOA and comammox species preferentially used ammonia over urea, while beta-proteobacterial AOB favored urea utilization, repressed ammonia transport in the presence of urea, and showed higher affinity for urea than ammonia, whereas gamma-proteobacterial AOB co-utilized both substrates. Stable isotope tracing, kinetics, and transcriptomics experiments revealed that both assimilation and oxidation of ammonia are transport-dependent. These results reveal novel mechanisms of nitrogen metabolism regulation and transporter-based affinity underlying the contrasting niche adaptation and coexistence patterns among the major AOM lineages.

microbiology↗

bioRxiv2022

The City Nature Challenge - A global citizen science phenomenon contributing to biodiversity knowledge and informing local government practices

The bioblitz phenomenon has recently branched into cities, presenting exciting opportunities for local governments to channel participants efforts toward local issues. The City Nature Challenge (CNC) is one such initiative that has been quickly uptaken by hundreds of municipalities worldwide. Despite high participation, we still lack a framework for evaluating how the CNC contributes to local biodiversity knowledge and to inform local government practices. Here, we develop such a tool and present a case study that illustrates its applicability. We demonstrate that the collected records contributed to a better understanding of contemporary, local biodiversity patterns and provided a more realistic representation of understudied groups such as insects and fungi. Importantly, we show that the CNC presented local governments with a cost-effective tool to make informed, evidence-based management and policy decisions, improve education and engagement programs, foster cross-council collaborations, and support a stronger sense of environmental stewardship within the local community.

scientific communication and education↗

bioRxiv2022

Spatial structure formation by RsmE-regulated extracellular secretions in Pseudomonas fluorescens Pf0-1

Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures manifest through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene are repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmEs primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identify the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses show that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community. IMPORTANCEIn densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces, however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmEs paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.

microbiology↗

bioRxiv2020

DNA Methylation-based Signatures Classify Sporadic Pituitary Tumors According to Clinicopathological Features.

BackgroundDistinct genome-wide methylation patterns have consistently clustered pituitary neuroendocrine tumors (PT) into molecular groups associated with specific clinicopathological features. Here we aim to identify, characterize and validate the methylation signatures that objectively classify PT into those molecular groups. MethodsCombining in-house and publicly available data, we conducted an analysis of the methylome profile of a comprehensive cohort of 177 tumor and 20 non-tumor specimens from the pituitary gland. We also retrieved methylome data from an independent pituitary tumor (PT) cohort (N=86) to validate our findings. ResultsWe identified three methylation clusters associated with functional status and adenohypophyseal cell lineages using an unsupervised approach. We also identified signatures based on differentially methylated CpG probes (DMP), some of which overlapped with pituitary-specific transcription factors genes (SF1 and Tpit), that significantly distinguished pairs of clusters related to functional status and adenohypophyseal cell lineage. These findings were reproduced in an independent cohort, validating these methylation signatures. The DMPs were mainly annotated in enhancer regions associated with pathways and genes involved in cell identity and tumorigenesis. ConclusionsWe identified and validated methylation signatures that distinguished PT by distinct functional status and adenohypophyseal cell lineages. These signatures, annotated in enhancer regions, indicate the importance of these elements in pituitary tumorigenesis. They also provide an unbiased approach to classify pituitary tumors according to the most recent classification recommended by the WHO 2017 using methylation profiling. Key-pointsO_LIDistinct methylation landscapes define PT groups with specific functional status/subtypes and adenohypophyseal lineages subtypes. C_LIO_LIMethylation abnormalities in each cluster mainly occur in CpG annotated in distal regions overlapping predicted enhancers regions associated with pathways and genes involved in cell identity and tumorigenesis. C_LIO_LIDNA methylation signatures provide an unbiased approach to classify PT. C_LI Importance of the studyThis study harnessed the largest methylome data to date from a comprehensive cohort of pituitary specimens obtained from four different institutions. We identified and validated methylation signatures that distinguished pituitary tumors into molecular groups that reflect the functionality and adenohypophyseal cell lineages of these tumors. These signatures, mainly located in enhancers, are associated with pathways and genes involved in cell identity and tumorigenesis. Our results show that methylome profiling provides an objective approach to classify PT according to the most recent classification of PT recommended by the 2017 WHO.

cancer biology↗

bioRxiv2020

A standardized and reproducible method to measure decision-making in mice

Progress in science requires standardized assays whose results can be readily shared, compared, and reproduced across laboratories. Reproducibility, however, has been a concern in neuroscience, particularly for measurements of mouse behavior. Here we show that a standardized task to probe decision-making in mice produces reproducible results across multiple laboratories. We designed a task for head-fixed mice that combines established assays of perceptual and value-based decision making, and we standardized training protocol and experimental hardware, software, and procedures. We trained 140 mice across seven laboratories in three countries, and we collected 5 million mouse choices into a publicly available database. Learning speed was variable across mice and laboratories, but once training was complete there were no significant differences in behavior across laboratories. Mice in different laboratories adopted similar reliance on visual stimuli, on past successes and failures, and on estimates of stimulus prior probability to guide their choices. These results reveal that a complex mouse behavior can be successfully reproduced across multiple laboratories. They establish a standard for reproducible rodent behavior, and provide an unprecedented dataset and open-access tools to study decision-making in mice. More generally, they indicate a path towards achieving reproducibility in neuroscience through collaborative open-science approaches.

neuroscience↗

bioRxiv2019

Data architecture and visualization for a large-scale neuroscience collaboration

Effective data management is a major challenge for neuroscience labs, and even greater for collaborative projects. In the International Brain laboratory (IBL), ten experimental labs spanning 7 geographically distributed sites measure neural activity across the brains of mice making perceptual decisions. Here, we report a novel, modular architecture that allows users to contribute, access, and analyze data across this collaboration. Users contribute data using a web-based electronic lab notebook (Alyx), which automatically registers recorded data files and uploads them to a central server. Users access data with a lightweight interface, the Open Neurophysiology Environment (ONE), which searches data from all labs and loads it into MATLAB or Python. To analyze data, we have developed pipelines based on DataJoint, which automatically populate a website displaying a graphical summary of results to date. This architecture provides a new framework to contribute, access and analyze data, surmounting many challenges currently faced by neuroscientists.

neuroscience↗

bioRxiv2019

Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers

Genome-wide DNA methylation profiling has shown that epigenetic abnormalities are biologically important in glioma and can be used to classify these tumors into distinct prognostic groups. Thus far, DNA profiling has required surgically resected glioma tissue; however, gliomas release tumoral material into biofluids, such as blood and cerebrospinal fluid, providing an opportunity for a minimally invasive testing. While prior studies have shown that genetic and epigenetic markers can be detected in blood or cerebrospinal fluid (e.g., liquid biopsy [LB]), there has been low sensitivity for tumor-specific markers. We hypothesize that the low sensitivity is due to the targeted assay methods. Therefore, we profiled the genome-wide CpG methylation levels in DNA of tumor tissue and cell-free DNA in serum of glioma patients, to identify non-invasive epigenetic LB (eLB) markers in the serum that reflect the characteristics of the tumor tissue. From the epigenetic profiles of serum from patients diagnosed with glioma (N=15 IDH mutant and N=7 IDH wildtype) and with epilepsy (N=3), we defined glioma-specific and IDH-specific eLB signatures (Glioma-eLB and IDH-eLB, respectively). The epigenetic profiles of the matched tissue demonstrate that these eLB signatures reflected the signature of the tumor. Through cross-validation we show that Glioma-eLB can accurately predict a patients glioma from those with other neoplasias (N=6 Colon; N=14 Pituitary; N=3 Breast; N=4 Lung), non-neoplastic immunological conditions (N=22 sepsis; N=9 pancreatic islet transplantation), and from healthy individuals (sensitivity: 98%; specificity: 99%). Finally, IDH-eLB includes promoter methylated markers associated with genes known to be involved in glioma tumorigenesis (PVT1 and CXCR6). The application of the non-invasive eLB signature discovered in this study has the potential to complement the standard of care for patients harboring glioma.

cancer biology↗