Biology subjects

Lett, S.

Publications and source records attributed to Lett, S..

3 recordsLinked to original sources

bioRxiv2024

Hydrothermal pretreatment renders peat susceptible to enzymatic saccharification

Sphagnum peat bogs store a large fraction of biologically-bound carbon, due to a steady accumulation of plant material over millennia. The resistance of Sphagnum biomass to decay is poorly understood but of high importance for preservation efforts and climate models. It is shown that peat cellulose and other glucose-rich polysaccharides are readily degradable by a commercial enzyme cocktail designed for the industrial saccharification of lignocellulose of vascular plants. However, prior hydrothermal pretreatment of peat was required for the enzymes to gain access to the polysaccharides. The pretreatment itself released monosaccharides and glucose-containing soluble oligosaccharides. The monosaccharide profile released from hydrothermal pretreatment was consistent with the expected hemicellulose content of Sphagnum and was clearly different from that seen for pretreated tissue from vascular plants, such as pretreated wheat straw. Cellulose retained in the insoluble part of peat was cleaved at a similar or higher rate compared to cellulose from vascular plant tissues. Confocal laser scanning microscopy showed that the hydrothermal pretreatment disrupted the cells and relocated lignin-like compounds. Peat contains a high concentration of iron, which likely explains the pronounced acidification observed for the pretreated peat slurry at ambient conditions during saccharification assays. The acidification is due to abiotic oxidative reactions that also inactivate the enzymes. Adding catalase to the reactions alleviated enzyme inactivation and essentially stopped acidification during saccharification. This study confirms the importance of considering those abiotic oxidative reactions that take place in drained peat material.

plant biology↗

bioRxiv2023

Controlling biases in targeted plant removal experiments

O_LITargeted removal experiments are a powerful tool to assess the effects of plant species or (functional) groups on ecosystem functions. However, removing plant biomass in itself can bias the observed responses. This bias is commonly addressed by waiting until ecosystem recovery, but this is inherently based on unverified proxies or anecdotal evidence. Statistical control methods are efficient, but restricted in scope by underlying assumptions. C_LIO_LIWe propose accounting for such biases within the experimental design, using a gradient of biomass removal controls. We demonstrate the relevance of this design by presenting i) conceptual examples of suspected biases and ii) how to observe and control for these biases. C_LIO_LIUsing data from a mycorrhizal association-based removal experiment we show that ignoring biomass removal biases (including by assuming ecosystem recovery) can lead to incorrect, or even contrary conclusions (e.g., false positive and false negative). Our gradient design can prevent such incorrect interpretations, whether aboveground biomass has fully recovered or not. C_LIO_LIOur approach provides more objective and quantitative insights, independently assessed for each variable, than using a proxy to assume ecosystem recovery. Our approach circumvents the strict statistical assumptions of e.g. ANCOVA and thus offers greater flexibility in data analysis. C_LI

ecology↗

bioRxiv2018

Co-circulating mumps lineages at multiple geographic scales

Despite widespread vaccination, eleven thousand mumps cases were reported in the United States (US) in 2016-17, including hundreds in Massachusetts, primarily in college settings. We generated 203 whole genome mumps virus (MuV) sequences from Massachusetts and 15 other states to understand the dynamics of mumps spread locally and nationally, as well as to search for variants potentially related to vaccination. We observed multiple MuV lineages circulating within Massachusetts during 2016-17, evidence for multiple introductions of the virus to the state, and extensive geographic movement of MuV within the US on short time scales. We found no evidence that variants arising during this outbreak contributed to vaccine escape. Combining epidemiological and genomic data, we observed multiple co-circulating clades within individual universities as well as spillover into the local community. Detailed data from one well-sampled university allowed us to estimate an effective reproductive number within that university significantly greater than one. We also used publicly available small hydrophobic (SH) gene sequences to estimate migration between world regions and to place this outbreak in a global context, but demonstrate that these short sequences, historically used for MuV genotyping, are inadequate for tracing detailed transmission. Our findings suggest continuous, often undetected, circulation of mumps both locally and nationally, and highlight the value of combining genomic and epidemiological data to track viral disease transmission at high resolution.

genomics↗