Biology subjects

Booth, J. G.

Publications and source records attributed to Booth, J. G..

3 recordsLinked to original sources

bioRxiv2020

Food waste as a resource: grinding, dilution, and storage as a pretreatment strategy to produce fermentation intermediates

In several states of the U.S., one measure to mitigate greenhouse-gas emissions has been to ban food wastes from landfills. As a result, U.S.-based companies are now providing decentralized food-waste management systems for supermarkets and restaurants, which include storage as a slurry. It is unclear, however, which storage conditions (factors) would affect the spontaneous microbial activity, resulting in a different fermentation product spectra, and how this would affect further post-treatment. Here, we performed two experiments to mimic: 1) storage and 2) subsequent anaerobic digestion. For the food-waste storage system, we designed a mixed-level fractional factorial analysis with 12 experimental combinations, including separating food waste into: carbohydrate-rich, lipid-rich, and protein-rich food waste. We found that all factors that we tested correlated with the fermentation product spectra, but that especially the factors: i) storage temperature; ii) food-waste composition; and iii) storage time affected the fermentation outcome. We observed that relatively low pH levels of 3-4, which were achieved due to rapid lactic acid accumulation by microbial activity during storage, coincided with greater lactate production at a maximum chemical oxygen demand (COD) selectivity of 90%. This provides an opportunity to optimize lactate production, which is ideal for subsequent methane or chemical production. TOC/Abstract graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioengineering↗

bioRxiv2019

Transcription imparts architecture, function, and logic to enhancer units

Distal enhancers remain one of the least understood regulatory elements with pivotal roles in development and disease. We used massively parallel reporter assays to perform functional comparisons of two leading enhancer models and find that gene-distal transcription start sites (TSSs) are robust predictors of enhancer activity with higher resolution and specificity than histone modifications. We show that active enhancer units are precisely delineated by active TSSs, validate that these boundaries are sufficient to capture enhancer function, and confirm that core promoter sequences are required for this activity. Finally, we assay pairs of adjacent units and find that their cumulative activity is best predicted by the strongest unit within the pair. Synthetic fusions of enhancer units demonstrate that adjacency imposes winner-takes-all logic, revealing a simple design for a maximum-activity filter of enhancer unit outputs. Together, our results define fundamental enhancer units and a principle of non-cooperativity between adjacent units.

genomics↗

bioRxiv2018

Human salivary amylase gene copy number impacts oral and gut microbiomes

Host genetic variation influences the composition of the human microbiome. While studies have focused on associations between the microbiome and single nucleotide polymorphisms in genes, their copy number (CN) can also vary. Here, in a study of human subjects including a 2-week standard diet, we relate oral and gut microbiome to CN at the AMY1 locus, which encodes the gene for salivary amylase, active in starch degradation. We show that although diet standardization drove gut microbiome convergence, AMY1-CN influenced oral and gut microbiome composition and function. The gut microbiomes of low-AMY1-CN subjects had an enhanced capacity for breakdown of complex carbohydrates. Those of high-AMY1 subjects were enriched in microbiota linked to resistant starch fermentation, had higher fecal SCFAs, and drove higher adiposity when transferred to germfree mice. Gut microbiota results were validated in a larger separate population. This study establishes AMY1-CN as a genetic factor patterning microbiome composition and function.

genetics↗