Biology subjects

Barry, R.

Publications and source records attributed to Barry, R..

5 recordsLinked to original sources

bioRxiv2024

Accelerating Cell Culture Media Development Using Bayesian Optimization-Based Iterative Experimental Design

Optimizing operational conditions for complex biological systems used in life sciences research and biotechnology is an arduous task. Here, we have applied a Bayesian Optimization-based iterative framework for experimental design to accelerate cell culture media development for two applications. First, we show this approach yields new compositions of media with cytokine supplementation to maintain the viability and distribution of PBMCs in culture. Second, we applied this framework to optimize the production of three recombinant proteins in K.phaffii cultivations. For both applications, we identified conditions with improved outcomes compared to the initial standard media using 3 to 30 times fewer experiments than other methods such as the Design of Experiments. Subsequently, we also demonstrated the extensibility of our approach to efficiently account for additional design factors through transfer learning. These examples demonstrate how coupling data collection, modeling, and optimization in this iterative paradigm, while using an exploration-exploitation tradeoff in each iteration, can reduce the time and resources for these types of optimizations.

bioengineering↗

bioRxiv2024

Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome

Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as lipids, by intestinal epithelial cells. However, whether protein absorption is also affected by the gut microbiome is poorly understood. Here, we investigate connections between protein absorption and microbes in the zebrafish gut. Using live microscopy-based quantitative assays, we find that microbes slow the pace of protein uptake and degradation in LREs. While microbes do not affect the number of absorbing LRE cells, microbes lower the expression of endocytic and protein digestion machinery in LREs. Using transgene assisted cell isolation and single cell RNA-sequencing, we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria-sensing and metabolic pathways in LREs, and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs. Using custom-formulated diets, we investigated the influence of diet and LRE activity on the gut microbiome. Impaired protein uptake activity in LREs, along with a protein-deficient diet, alters the microbial community and leads to increased abundance of bacterial genera that have the capacity to reduce protein uptake in LREs. Together, these results reveal that diet-dependent reciprocal interactions between LREs and the gut microbiome regulate protein absorption.

cell biology↗

bioRxiv2021

RAP1 regulates TIP60 function during fate transition between 2 cell-like and pluripotent states

In mammals, the conserved telomere binding protein RAP1 serves a diverse set of non- telomeric functions including activation of the NF-kB signaling pathway, maintenance of metabolic function in vivo, and transcriptional regulation. Here, we uncover the mechanism by which RAP1 modulates gene expression. Using a separation-of-function allele, we show that RAP1 transcriptional regulation is independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci. Instead, RAP1 interacts with the TIP60/p400 complex and modulates its histone acetyltransferase activity. Notably, we show that deletion of RAP1 in mouse embryonic stem cells increases the fraction of 2-cell-like cells. Specifically, RAP1 enhances the repressive activity of Tip60/p400 across a subset of 2-cell-stage genes, including Zscan4 and the endogenous retrovirus MERVL. Preferential upregulation of genes proximal to MERVL elements in Rap1 deficient settings implicate these endogenous retroviral elements in the de- repression of proximal genes. Altogether, our study reveals an unprecedented link between RAP1 and TIP60/p400 complex in the regulation of totipotency.

molecular biology↗

bioRxiv2020

Ultra-high field (7T) functional magnetic resonance imaging in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of the central nervous system that results in a progressive loss of motor function and ultimately death. It is critical, yet also challenging, to develop non-invasive biomarkers to identify, localize, measure and/or track biological mechanisms implicated in ALS. Such biomarkers may also provide clues to identify potential molecular targets for future therapeutic trials. Herein we report on a pilot study involving twelve participants with ALS and nine age-matched healthy controls who underwent high-resolution resting state functional magnetic resonance imaging at an ultra-high field of 7 Tesla. A group-level whole-brain analysis revealed a disruption in long-range functional connectivity between the superior sensorimotor cortex (in the precentral gyrus) and bilateral cerebellar lobule VI. Post hoc analyses using atlas-derived left and right cerebellar lobule VI revealed decreased functional connectivity in ALS participants that predominantly mapped to bilateral postcentral and precentral gyri. Cerebellar lobule VI is a transition zone between anterior motor networks and posterior non-motor networks in the cerebellum, and is associated with a wide range of key functions including complex motor and cognitive processing tasks. Our observation of the involvement of cerebellar lobule VI adds to the growing number of studies implicating the cerebellum in ALS. Future avenues of scientific investigation should consider how high-resolution imaging at 7T may be leveraged to visualize differences in functional connectivity disturbances in various genotypes and phenotypes of ALS along the ALS-frontotemporal dementia spectrum.

neuroscience↗

bioRxiv2019

Direct readout of neural stem cell transgenesis with an integration-coupled gene expression switch

SUMMARYStable genomic integration of exogenous transgenes is critical for neurodevelopmental and neural stem cell studies. Despite the emergence of tools driving genomic insertion at high rates with DNA vectors, transgenesis procedures remain fundamentally hindered by the impossibility to distinguish integrated transgenes from residual episomes. Here, we introduce a novel genetic switch termed iOn that triggers gene expression upon insertion in the host genome, enabling simple, rapid and faithful identification of integration events following transfection with naked plasmids accepting large cargoes. In vitro, iOn permits rapid drug-free stable transgenesis of mouse and human pluripotent stem cells with multiple vectors. In vivo, we demonstrate accurate cell lineage tracing, assessment of regulatory elements and mosaic analysis of gene function in somatic transgenesis experiments that reveal new aspects of neural progenitor potentialities and interactions. These results establish iOn as an efficient and widely applicable strategy to report transgenesis and accelerate genetic engineering in cultured systems and model organisms.

developmental biology↗