Biology subjects

Gill, B.

Publications and source records attributed to Gill, B..

9 recordsLinked to original sources

bioRxiv2026

A Purpose-Built Open Source Liquid Handler for Industry-Class Automated Experiments

The expanding scope of laboratory automation increasingly demands systems that can be tailored to specific experimental constraints, including footprint, timing, cost, and control. While open-source software has improved protocol flexibility, liquid-handling hardware itself remains largely closed, limiting the ability of academic and startup laboratories to build instruments around biological requirements rather than vendor defaults. Here, we present a fully open-source, purpose-built liquid-handling robot assembled from commercially available components and developed entirely in a research setting. The platform integrates open hardware, electronics, and a Python-based control stack compatible with PyLabRobot, exposing low-level motion dynamics and liquid-handling behaviors directly to experiment code. We validate the system using a high-throughput turbidostat workflow that requires rapid, closed-loop measurement and actuation to maintain microbial cultures at defined density setpoints. The robot sustains stable steady-state growth across approximately 200 cultures with heterogeneous growth dynamics. A replica build completed by two lab members in approximately one week confirms that the platform can be reproduced from its bill of materials and assembly guide. Its compact footprint and use of off-the-shelf components make it suitable for rapid, parallel deployment in settings such as public health emergencies or by distributed laboratories. Together, these results demonstrate that industry-class liquid handlers can be custom-built for specific experimental goals, establishing a blueprint for open, purpose-driven hardware development across research and industrial automation contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/709168v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1b2cb4eorg.highwire.dtl.DTLVardef@1418e8dorg.highwire.dtl.DTLVardef@f60618org.highwire.dtl.DTLVardef@a3d3b_HPS_FORMAT_FIGEXP M_FIG Open Liquid Handler (OLH) Design Goals. Left: Design goals for a purpose-built platform for time-sensitive, closed-loop biological workflows, emphasizing high-accuracy dosing (low variability liquid handling), rapid integrated measurement (plate deck and isolated workspace), customizable deck and peripheral options, compact footprint with high throughput, containment via an enclosed wet workspace for biosafety and sterility, and a replicable build using off-the-shelf OEM components with open design files. Right: Open Liquid Handler design and physical implementation, with aerial and front views highlighting the enclosed cabinet and the working envelope over a compact deck. C_FIG

bioengineering↗

bioRxiv2026

IDH-mutant inhibitors enhance the sensitivity of IDH1-mutant gliomas to cysteine-methionine deprivation and ferroptosis

Cysteine is essential for synthesizing glutathione, the brains main antioxidant, and cysteine deprivation can trigger ferroptosis. Here, using a new mouse model of IDH1-mutant glioma that recapitulates the characteristics of human IDH1-mutant low-grade gliomas, we demonstrate that IDH1-mutant glioma cells are significantly more vulnerable to cysteine deprivation alone or in combination with the ferroptosis inducer RSL3, compared to IDH1-wildtype glioma cells. In addition, treatments with the IDH-mutant inhibitors vorasidenib and ivosidenib further sensitize the cells to ferroptosis. Metabolomics analysis reveals that IDH1-mutant cells have altered cysteine and methionine metabolism with deficiency in transsulfuration, which is further exacerbated by cysteine-methionine deprivation and IDH-mutant inhibitors. Furthermore, dietary cysteine-methionine deprivation alone or in combination with convection-enhanced delivery of RSL3 or ivosidenib in vivo significantly prolongs survival of IDH1-mutant tumor-bearing mice. Our findings suggest that targeting cysteine and methionine metabolism in combination with IDH-mutant inhibition provides promising therapeutic strategies for IDH1-mutant gliomas.

cancer biology↗

bioRxiv2025

Suppressing cortical glutamatergic neurons produces paradoxical interictal discharges and seizures

IntroductionSeizures are traditionally attributed to excessive excitation or deficient inhibition, yet recent clinical and slice data show they can also paradoxically arise when inhibition outweighs excitation. We chemogenetically suppressed neocortical glutamatergic neurons to test whether such suppression elicits epileptic activity in vivo. MethodsCaMKII-driven Gi-coupled hM4Di or Gq-coupled hM3Dq Designer Receptor Exclusively Activated by Designer Drug (DREADDs) were expressed in cortical glutamatergic neurons of Rasgrf2-jGCaMP8m and wildtype C57BL/6J mice. Widefield calcium imaging and 32-channel transparent electrocorticography were performed before and after systemic clozapine-N-oxide (CNO; 1.25-5 mg kg {superscript 1}). ResultsDREADD activation induced intermittent, large-amplitude, synchronized calcium transients confined to the CaMKII-hM4Di focus, accompanied by focal ECoG spikes that persisted for >3 h and sometimes evolved into seizures. By contrast, CNO activation of excitatory neurons via CaMKII-hM3Dq DREADDs desynchronized activity without epileptiform discharges. The same process duplicated in wild-type animals provoked similar epileptiform discharges. ConclusionSelective suppression of excitation can paradoxically drive cortical networks into hypersynchronous, epileptic states, challenging the simple excess-excitation model of ictogenesis. These findings highlight that seizures may result from relative inhibitory dominance, and that considering this excess inhibition mechanism could inspire new therapeutic approaches.

neuroscience↗

bioRxiv2025

Exogenous BMP9 therapy ameliorates primary graft dysfunction post lung transplantation

Primary graft dysfunction (PGD) is a leading cause of early mortality after lung transplantation and is driven by ischemia-reperfusion injury (IRI), which destabilizes the pulmonary endothelium. Bone morphogenetic protein 9 (BMP9), a vascular quiescence factor of the TGF superfamily, maintains endothelial homeostasis through ALK-1/BMPR2-mediated signaling. Herein, this work identified a previously unrecognized suppression of BMP9 signaling during early reperfusion in a murine orthotopic lung transplant model. Allograft transcriptomic profiling revealed rapid downregulation of BMP9 pathway components, including Bmpr2, Acvrl1, Smad5, and Eng. Recombinant BMP9 administered at reperfusion enhanced Id1 expression in pulmonary endothelium, reduced neutrophil infiltration, preserved vascular barrier function, and improved oxygenation. In vitro, BMP9 attenuated proinflammatory cytokine release following simulated cold ischemia-reperfusion injury in human lung endothelial cells. Plasma from lung transplant recipients, regardless of PGD status, had impaired BMP9-induced ID1 expression in endothelial cells, with the most profound suppression observed in patients with interstitial lung disease. These findings implicate transient loss of BMP9 signaling as a key feature of transplant-induced vascular injury and support the therapeutic potential of BMP9 supplementation to restore endothelial homeostasis and improve early graft outcomes.

immunology↗

bioRxiv2025

TaWUS2D regulates the number of grains per spikelet by enhancing the number of fertile ovaries in Multi-Ovary Wheat

Innovative genetic improvements in the staple crop Triticum aestivum (bread wheat) are urgently needed to address the growing global food security crisis. Here, we report the map-based cloning of TaWUS2D, the gene responsible for the dominant multi-ovary phenotype in wheat. Multi-ovary lines are characterized by the development of three fertile ovaries per floret that results in three grains, as opposed to wildtype single ovary wheat. We used HiFi long-reads to assemble a 14.48 Gbp genome scaffold assembly in the background of mutli-ovary wheat line MOV. Using high-resolution genetic mapping, combined with additional genomic resources, we defined the Mov-1 locus to a 135 Kbp region containing two genes. Using five independent deletion mutants and eight TILLING mutants, we demonstrate that a functional WUSCHEL-like protein, TaWUS2D, is required for the multi-ovary phenotype. TaWUS2D is upregulated in the MOV genetic background. This research lays the groundwork for developing new approaches to improve wheat production potential and sustainability in the face of current and future global food challenges.

plant biology↗

bioRxiv2024

Peripheral Blood Immune Cells from Individuals with Parkinson's Disease or Inflammatory Bowel Disease Share Deficits in Iron Storage and Transport that are Modulated by Non-Steroidal Anti-Inflammatory Drugs

Parkinsons Disease (PD) is a multisystem disorder in which dysregulated neuroimmune crosstalk and inflammatory relay via the gut-blood-brain axis have been implicated in PD pathogenesis. Although alterations in circulating inflammatory cytokines and reactive oxygen species (ROS) have been associated with PD, no biomarkers have been identified that predict clinical progression or disease outcome. Gastrointestinal (GI) dysfunction, which involves perturbation of the underlying immune system, is an early and often-overlooked symptom that affects up to 80% of individuals living with PD. Interestingly, 50-70% of individuals with inflammatory bowel disease (IBD), a GI condition that has been epidemiologically linked to PD, display chronic illness-induced anemia -- which drives toxic accumulation of iron in the gut. Ferroptotic (or iron loaded) cells have small and dysmorphic mitochondria--suggesting that mitochondrial dysfunction is a consequence of iron accumulation. In pro-inflammatory environments, iron accumulates in immune cells, suggesting a possible connection and/or synergy between iron dysregulation and immune cell dysfunction. Peripheral blood mononuclear cells (PBMCs) recapitulate certain PD-associated neuropathological and inflammatory signatures and can act as communicating messengers in the gut-brain axis. Additionally, this communication can be modulated by several environmental factors; specifically, our data further support existing literature demonstrating a role for non-steroidal anti-inflammatory drugs (NSAIDs) in modulating immune transcriptional states in inflamed individuals. A mechanism linking chronic gut inflammation to iron dysregulation and mitochondrial function within peripheral immune cells has yet to be identified in conferring risk for PD. To that end, we isolated PBMCs and simultaneously evaluated their directed transcriptome and bioenergetic status, to investigate if iron dysregulation and mitochondrial sensitization are linked in individuals living with PD or IBD because of chronic underlying remittent immune activation. We have identified shared features of peripheral inflammation and immunometabolism in individuals living with IBD or PD that may contribute to the epidemiological association reported between IBD and risk for PD.

neuroscience↗

bioRxiv2024

Predicting Primary Graft Dysfunction in Lung Transplantation: Machine Learning-Guided Biomarker Discovery

BACKGROUNDThere is an urgent need to better understand the pathophysiology of primary graft dysfunction (PGD) so that point-of-care methods can be developed to predict those at risk. Here we utilize a multiplex multivariable approach to define cytokine, chemokines, and growth factors in patient-matched biospecimens from multiple biological sites to identify factors predictive of PGD. METHODSBiospecimens were collected from patients undergoing bilateral LTx from three distinct sites: donor lung perfusate, post-transplant bronchoalveolar lavage (BAL) fluid (2h), and plasma (2h and 24h). A 71-multiplex panel was performed on each biospecimen. Cross-validated logistic regression (LR) and random forest (RF) machine learning models were used to determine whether analytes in each site or from combination of sites, with or without clinical data, could discriminate between PGD grade 0 (n = 9) and 3 (n = 8). RESULTSUsing optimal AUROC, BAL fluid at 2h was the most predictive of PGD (LR, 0.825; RF, 0.919), followed by multi-timepoint plasma (LR, 0.841; RF, 0.653), then perfusate (LR, 0.565; RF, 0.448). Combined clinical, BAL, and plasma data yielded strongest performance (LR, 1.000; RF, 1.000). Using a LASSO of the predictors obtained using LR, we selected IL-1RA, BCA-1, and Fractalkine, as most predictive of severe PGD. CONCLUSIONSBAL samples collected 2h post-transplant were the strongest predictors of severe PGD. Our machine learning approach not only identified novel cytokines not previously associated with PGD, but identified analytes that could be used as a point-of-care cytokine panel aimed at identifying those at risk for developing severe PGD.

immunology↗

bioRxiv2018

Drought frequency predicts life history strategies in Heliophila

Explaining variation in life history strategies is a long-standing goal of evolutionary biology. For plants, annual and perennial life histories are thought to reflect adaptation to environments that differ in the frequency of stress events such as drought. Here we test this hypothesis in Heliophila (Brassicaceae), a diverse genus of flowering plants native to Africa, by integrating 34 years of satellite-based drought measurements with 2192 herbaria occurrence records. Consistent with predictions from classic life history theory, we find that perennial Heliophila species occur in environments where droughts are significantly less frequent compared to annuals. These associations are predictive while controlling for phylogeny, lending support to the hypothesis that drought related natural selection has influenced the distributions of these strategies. Additionally, the collection dates of annual and perennial species indicate that annuals escape drought prone seasons during the seed phase of their life cycle. Together, these findings provide empirical support for classic hypotheses about the drivers of life history strategy in plants - that perennials out compete annuals in environments with less frequent drought and that annuals are adapted to environments with more frequent drought by escaping drought prone seasons as seeds.

evolutionary biology↗

bioRxiv2018

Efficient curation of genebanks using next-generation sequencing reveals substantial duplication of germplasm accessions

Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

genomics↗