Biology subjects

Ellison, M. A.

Publications and source records attributed to Ellison, M. A..

9 recordsLinked to original sources

bioRxiv2026

The Microglia Forebrain Assembloid Model Recapitulates Human Brain Development and Neuroimmune Biology.

Microglia are innate immune cells of the CNS whose dysfunction contributes to inflammation and metabolic changes across neurodegenerative and CNS disorders. Across all stages of life, microglia are essential for immune surveillance, neural homeostasis, and synaptic pruning; however, their role in neurodevelopment is less understood. Microglia invade the brain during early neurogenesis, prior to neuronal/glial differentiation, but their potential role at this stage remains undescribed. To model neuroimmune interactions during human cortical development, we created an "assembloid" of human ESC-derived forebrain organoids combined with developmentally matched microglia during cortex formation. Functional contributions of microglia were compared to control organoids using histology and metabolomics.

neuroscience↗

bioRxiv2025

Photoacoustic imaging assessment of acute kidney injury associated with experimental necrotizing enterocolitis

BackgroundNecrotizing enterocolitis (NEC) is a devastating gastrointestinal condition increasingly recognized to cause systemic complications, including acute kidney injury (AKI). However, the underlying mechanisms and variations in renal impairment remain largely unknown, and there is a lack of non-invasive imaging methods for detecting early kidney injury. MethodsWe evaluated kidney injury through a multimodal approach, using a neonatal rat model of experimental NEC. Plasma and renal tissue were analyzed for pro-inflammatory cytokines (TNF-, IL-6, IL-1{beta}) by ELISA. Histological analysis and immunofluorescence staining were used to identify renal abnormalities and expressions of KIM-1 and NGAL. Photoacoustic imaging (PAI) was used to assess renal oxygenation and total hemoglobin as functional imaging biomarkers of kidney injury. ResultsNEC pups showed significant elevations of systemic and renal cytokines, as well as increased expression of KIM-1, NGAL and CD31 in proximal tubules of the kidney. Histological examination further confirms renal injury in the NEC cohort. PAI demonstrated reduction in renal oxygen saturation, offering non-invasive assessment of physiological kidney damage. ConclusionThis study characterizes AKI associated with NEC as an inflammatory and hypoxic response in the neonatal rat NEC model and introduces PAI as a promising imaging modality for non-invasive evaluation of renal injury in NEC.

bioengineering↗

bioRxiv2023

Photoacoustic Imaging for Non-Invasive Assessment of Physiological Biomarkers of Intestinal Injury in Experimental Necrotizing Enterocolitis

BackgroundNecrotizing enterocolitis (NEC) is an often-lethal disease of the premature infants intestinal tract that is exacerbated by significant difficulties in early and accurate diagnosis. In NEC disease, the intestine often exhibits hypoperfusion and dysmotility, which contributes to advanced disease pathogenesis. However, these physiological features cannot be accurately and quantitively assessed within the current constraints of imaging modalities frequently used in the clinic (plain film X-ray and ultrasound). We have previously demonstrated the ability of photoacoustic imaging (PAI) to non-invasively and quantitively assess intestinal tissue oxygenation and motility in a healthy neonatal rat model. As a first-in-disease application, we evaluated NEC pathogenesis using PAI to assess intestinal health biomarkers in a preclinical neonatal rat experimental model of NEC. MethodsNEC was induced in neonatal rat pups from birth to 4 days old via hypertonic formula feeding, full-body hypoxic stress, and lipopolysaccharide administration to mimic bacterial colonization. Healthy breastfed (BF) controls and NEC rat pups were imaged at 2- and 4-days old. Intestinal tissue oxygen saturation was measured with PAI imaging for oxy- and deoxyhemoglobin levels. To measure intestinal motility, ultrasound and co-registered PAI cine recordings were used to capture intestinal peristalsis motion and contrast agent (indocyanine green) transit within the intestinal lumen. Additionally, both midplane two-dimensional and volumetric three-dimensional imaging acquisitions were assessed for oxygenation and motility. ResultsNEC pups showed a significant decrease of intestinal tissue oxygenation as compared to healthy BF controls at both ages (2-days old: 55.90% +/-3.77% vs 44.12% +/-7.18%; 4-days old: 56.13% +/-3.52% vs 38.86% +/-8.33%). Intestinal motility, assessed using a computational intestinal deformation analysis, demonstrated a significant reduction in the intestinal motility index in both early (2-day) and established (4-day) NEC. Extensive NEC damage was confirmed with histology and dysmotility was confirmed by small intestinal transit assay. ConclusionsThis study presents PAI as a successful emerging diagnostic imaging modality for both intestinal tissue oxygenation and intestinal motility disease hallmarks in a rat NEC model. PAI presents enormous significance and potential for fundamentally changing current clinical paradigms for detecting and monitoring intestinal pathologies in the premature infant.

bioengineering↗

bioRxiv2023

Photoacoustic Imaging as a Novel Non-Invasive Biomarker to Assess Intestinal Tissue Oxygenation and Motility in Neonatal Rats

BackgroundWithin the premature infant intestine, oxygenation and motility play key physiological roles in healthy development and disease such as necrotizing enterocolitis. To date, there are limited techniques to reliably assess these physiological functions that are also clinically feasible for critically ill infants. To address this clinical need, we hypothesized that photoacoustic imaging (PAI) can provide non-invasive assessment of intestinal tissue oxygenation and motility to characterize intestinal physiology and health. MethodsUltrasound and photoacoustic images were acquired in 2-day and 4-day old neonatal rats. For PAI assessment of intestinal tissue oxygenation, an inspired gas challenge was performed using hypoxic, normoxic, and hyperoxic inspired oxygen (FiO2). For intestinal motility, oral administration of ICG contrast agent was used to compare control animals to an experimental model of loperamide-induced intestinal motility inhibition. ResultsPAI demonstrated progressive increases in oxygen saturation (sO2) as FiO2 increased, while the pattern of oxygen localization remained relatively consistent in both 2-day and 4-day old neonatal rats. Analysis of intraluminal ICG contrast enhanced PAI images yielded a map of the motility index in control and loperamide treated rats. From PAI analysis, loperamide significantly inhibited intestinal motility, with a 32.6% decrease in intestinal motility index scores in 4-day old rats. ConclusionThese data establish the feasibility and application of PAI to non-invasively and quantitatively measure intestinal tissue oxygenation and motility. This proof-of-concept study is an important first step in developing and optimizing photoacoustic imaging to provide valuable insight into intestinal health and disease to improve the care of premature infants. HighlightsO_LIIntestinal tissue oxygenation and intestinal motility are important biomarkers of intestinal physiology in health and disease of premature infants. C_LIO_LIThis proof-of-concept preclinical rat study is the first to report application of photoacoustic imaging for the neonatal intestine. C_LIO_LIPhotoacoustic imaging is demonstrated as a promising non-invasive diagnostic imaging method for quantifying intestinal tissue oxygenation and intestinal motility in premature infants. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=145 HEIGHT=200 SRC="FIGDIR/small/545971v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@585d0forg.highwire.dtl.DTLVardef@145a2bcorg.highwire.dtl.DTLVardef@bf0c46org.highwire.dtl.DTLVardef@bed354_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Spt6 directly interacts with Cdc73 and is required for Paf1C recruitment to active genes

Paf1C is a conserved transcription elongation factor that regulates transcription elongation efficiency, facilitates co-transcriptional histone modifications, and impacts molecular processes linked to RNA synthesis, such as polyA site selection. Coupling of the activities of Paf1C to transcription elongation requires its association with RNA polymerase II (Pol II). Mutational studies in yeast identified Paf1C subunits Cdc73 and Rtf1 as important mediators of Paf1C recruitment to Pol II on active genes. While the interaction between Rtf1 and the general elongation factor Spt5 is relatively well-understood, the interactions involving Cdc73 remain to be elucidated. Using an in vivo site-specific protein cross-linking strategy, we identified direct interactions between Cdc73 and two components of the elongation complex, the elongation factor Spt6 and the largest subunit of Pol II. Through in vitro protein binding assays and crosslinking/mass spectrometry, we show that Cdc73 and Spt6 can interact in the absence of additional factors and propose a binding interface. Rapid depletion of Spt6 dissociated Paf1 from chromatin and altered patterns of Paf1C-dependent histone modifications genome-wide. These results reveal previously unrecognized interactions between Cdc73 and the Pol II elongation complex and identify Spt6 as a key factor contributing to Paf1C recruitment to active genes in Saccharomyces cerevisiae.

molecular biology↗

bioRxiv2020

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription initiation in Saccharomyces cerevisiae

Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous chromatin regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within a coding gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified a mutation in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase, as a suppressor of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other histone deacetylases does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, we find that deletion of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest a coordination between two epigenetic modifiers, the H2B ubiquitylation pathway and Hda1C, in regulating chromatin structure during transcription elongation and reveal an unexpected role for a histone deacetylase in supporting chromatin accessibility.

molecular biology↗

bioRxiv2020

MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

MutantHuntWGS is a user-friendly pipeline for analyzing Saccharomyces cerevisiae whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files. To demonstrate its utility, we use MutantHuntWGS to assess multiple published datasets; in all cases, it detects the same causal variants reported in the literature. To encourage broad adoption and promote reproducibility, we distribute a containerized version of the MutantHuntWGS pipeline that allows users to install and analyze data with only two commands. The MutantHuntWGS software and documentation can be downloaded free of charge from https://github.com/mae92/MutantHuntWGS.

genetics↗

bioRxiv2020

The nucleosome DNA entry-exit site is important for transcription termination in Saccharomyces cerevisiae

Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. Through a genetic screen, we identified histone mutant strains that exhibit transcriptional readthrough of terminators in vivo. Amino acid subtitutions map to the nucleosome DNA entry-exit site. On a genome-wide scale, the strongest H3 mutants revealed increased sense-strand transcription upstream and downstream of Pol II transcribed genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3 ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase II progression and highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome.

molecular biology↗

bioRxiv2019

The Paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here we took advantage of a genetic background that enriches for unstable transcripts and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs. By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 tri-methylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

genomics↗