Biology subjects

Dawson, A.

Publications and source records attributed to Dawson, A..

21 records · Page 2Linked to original sources

bioRxiv2019

Statistically-estimated tree biomass, stem density, and basal area for the upper Midwestern United States at the time of Euro-American settlement

We present gridded 8 km-resolution data products of the estimated biomass, basal area, and stem density of tree taxa at the time of Euro-American settlement of the midwestern United States for the states of Minnesota, Wisconsin, Michigan, Illinois, and Indiana. The data come from settlement-era Public Land Survey (PLS) data (ca. 0.8-km resolution) of trees recorded by land surveyors. The surveyor notes have been transcribed, cleaned, and processed to estimate biomass, basal area, and stem density at individual points on the landscape. The point-level data are then aggregated within grid cells and statistically smoothed using a statistical model that accounts for zero-inflated continuous data with smoothing based on generalized additive modeling techniques and approximate Bayesian uncertainty estimates. We expect this data product to be useful for understanding the state of vegetation in the midwestern United States prior to large-scale Euro-American settlement. In addition to specific regional questions, the data product can serve as a baseline against which to investigate how forests and ecosystems change after intensive settlement. The data products (including both raw and statistically smoothed estimates at the 8-km scale) are being made available at the LTER network data portal as version 1.0.

ecology↗

bioRxiv2019

A roadblock-and-kill model explains the action of the DNA-targeting antibiotic ciprofloxacin

Fluoroquinolones - antibiotics that cause DNA damage by inhibiting DNA topoisomerases - are clinically important, but their mechanism of action is not yet fully understood. In particular, the dynamical response of bacterial cells to fluoroquinolone exposure has hardly been investigated, although the SOS response, triggered by DNA damage, is often thought to play a key role. Here we investigate growth inhibition of the bacterium Escherichia coli by the fluoroquinolone ciprofloxacin at low doses (up to 5x the minimum inhibitory concentration). We measure the long-term and short-term (dynamic) response of the growth rate and DNA production rate to ciprofloxacin, at both population- and single-cell level. We show that despite the molecular complexity of DNA metabolism, a simple `roadblock-and-kill model focusing on replication fork blockage and DNA damage by ciprofloxacin-poisoned DNA topoisomerase II (gyrase) quantitatively reproduces long-term growth rates. The model also predicts dynamical changes in DNA production rate in wild type E. coli and in an SOS-deficient mutant, following a step-up of ciprofloxacin. Our work reveals new insights into the dynamics of fluoroquinolone action, with important implications for predicting the rate of resistance evolution. Most importantly, our model explains why the response is delayed: it takes many doubling times to fragment the DNA sufficiently to inhibit gene expression. Our model also challenges the view that the SOS response plays a central role: the dynamical response is controlled by the timescale of DNA replication and gyrase binding/unbinding to the DNA rather than by the SOS response. More generally, our work highlights the importance of including biophysical processes in biochemical-systems models to fully understand bacterial response to antibiotics.

systems biology↗

bioRxiv2018

Repetition of deliberate self-poisoning in rural Sri Lanka

Repetition of deliberate self harm is an important predictor of subsequent suicide. Repetition rates in Asian countries appear to be significantly lower than in western high income countries. The reason for these reported differences is not clear and has been suggested to due methodological differences or the impact of access to more lethal means of self harm. This prospective study determines the rates and demographic pattern of deliberate self-poisoning, suicide and fatal and non fatal repeated deliberate self-poisoning in rural Sri Lanka.\n\nDetails of deliberate self poisoning admission in all hospitals (n=46) and suicides reported to all the police stations (n=28) of a rural district were collected for 3 years, 2011-2013. Demographic details of the cohort of deliberate self-poisoning patients admitted to all hospitals in 2011 (N=4022), were screened to link with patient records and police reports of successive two years with high sensitivity using a computer program and manual matching was performed with higher specificity. Life time repetition was assessed in a randomly selected subset of DSP patients (n=438).\n\nThere were 15,914 DSP admissions and 1078 suicides during the study period. Within the study area the deliberate self poisoning and suicide population incidences were, 248.3/100,000 and 20.7/100,000 in 2012. Repetition rate for four weeks, one-year and two-years were 1.9% (95% CI 1.5-2.3%), 5.7% (95% CI 5.0 to 6.4) and 7.9% (95% CI 7.1 to 8.8) respectively. The median interval between two attempts were 92 (IQR 10 - 238) and 191 (IQR 29 - 419.5) days for the one and two-year repetition groups. The majority of patients used the same poison in the repeat attempt. Age and hospital stay of individuals with repetitive events were not significantly different from those who had no repetitive events. The two-year rate for suicide following DSP was 0.7% (95% CI 0.4-0.9%). Reported life time history of deliberate self harm attempts was 9.5% (95% CI 6.7-12.2%).\n\nThe low comparative repetition rates in rural Sri Lanka was not explained by higher rates of suicide or access to more lethal means or differences in methodology.

epidemiology↗