Biology subjects

Bennett, M. E.

Publications and source records attributed to Bennett, M. E..

3 recordsLinked to original sources

bioRxiv2026

The effect of minocycline on the gut microbiome in individuals with alcohol use disorder and healthy controls

Alcohol Use Disorder (AUD) is associated with altered gut microbial composition. Yet, many microbiome studies have included AUD populations with co-occurring conditions (e.g., alcohol associated liver disease; ALD), limiting insight into unique contributions of AUD to gut dysbiosis. Further, preclinical studies show that gut microbiome composition can mediate the behavioral effects of minocycline, including alcohol-related and affective behaviors, but no studies have tested these effects in humans with AUD. This study aimed to 1) compare gut microbiome features between healthy controls (HCs) and individuals with AUD, without ALD, and 2) determine the effects of minocycline on the human gut microbiome. We conducted a four-week randomized, double-blind, placebo-controlled trial of minocycline (100-200 mg/day) in adults with AUD (n=31) and HCs (n=26). We collected fecal samples (n=244) at baseline and each weekly visit for 16S rRNA gene sequencing. Alpha diversity (richness and evenness of taxa within a sample) did not differ by diagnostic group, treatment, or time. In contrast, beta diversity (microbiome composition differences between samples) differed between AUD and controls and was shifted by minocycline over time. AUD, vs. controls, was associated with differences in several taxa prevalences, including reduced Dialister and Subdoligranulum and increased Collinsella, Streptococcus, and Phascolarctobacterium. Minocycline, vs. placebo, rapidly and robustly restructured the microbiome, altering numerous taxa, including Lachnospira, Ruminococcaceae, Clostridium sensu stricto, and Christensenellaceae, and metabolic pathways (e.g., ubiquinol biosynthesis and methylphosphonate degradation). AUD is associated with a distinct gut microbial composition, whereas minocycline produces rapid, sustained, diagnosis-independent gut microbiome restructuring, without altering alpha diversity.

genomics↗

bioRxiv2024

Multiplexed ultrasound imaging of gene expression

Acoustic reporter genes (ARGs) have enabled the imaging of gene expression with ultrasound, which provides high-resolution access to deep, optically opaque living tissues. However, unlike their fluorescent counterparts, ARGs have so far been limited to a single "color," preventing multiplexed imaging of cellular states or populations. Here, we use rational protein design and directed evolution to develop two novel ARGs that can be distinguished from each other based on their acoustic pressure response profiles, enabling "two-color" ultrasound imaging of gene expression. We demonstrate the utility of multiplexed ARGs for delineating bacterial cell species and cell states in vitro, and then apply them towards imaging distinct subpopulations of probiotics in the mouse gastrointestinal tract and in tumor-colonizing bacterial agents in vivo. Just as the first wavelength-shifted derivatives of fluorescent proteins opened a vivid world for optical microscopy, our next-generation acoustic proteins set the stage for a richer symphony of ultrasound signals from living subjects.

bioengineering↗

bioRxiv2018

Elongated cells drive morphogenesis in a surface-wrapped finite element model of germband retraction

During Drosophila embryogenesis, the germband first extends to curl around the posterior end of the embryo, and then retracts back; however, retraction is not simply the reversal of extension. At a tissue level, extension is coincident with ventral furrow formation, and at a cellular level, extension occurs via convergent cell neighbor exchanges in the germband while retraction involves only changes in cell shape. To understand how cell shapes, tissue organization and cellular forces drive germband retraction, we investigate this process using a whole-embryo, surface-wrapped cellular finite element model. This model represents two key epithelial tissues - amnioserosa and germband - as adjacent sheets of 2D cellular finite elements that are wrapped around an ellipsoidal 3D approximation of an embryo. The model reproduces the detailed kinematics of in vivo retraction by fitting just one free model parameter, the tension along germband cell interfaces; all other cellular forces are constrained to follow ratios inferred from experimental observations. With no additional parameter adjustments, the model also reproduces failures of retraction when amnioserosa cells are removed to mimic U-shaped mutants or laser-microsurgery experiments. Surprisingly, retraction in the model is robust to changes in cellular force values, but is critically dependent on starting from a configuration with highly elongated amnioserosa cells. Their extreme cellular elongation is established during the prior process of germband extension and is then used to drive retraction. The amnioserosa is the one tissue whose cellular morphogenesis is reversed in germband extension and retraction - serving as a store of morphological information that coordinates the forces needed to retract the germband back to its pre-extension position and shape. In this case, and perhaps more generally, cellular force strengths are less important than the carefully established cell shapes that direct them.

biophysics↗