Ortega, A. C. | Search bioRxiv

bioRxiv2023

IDENTIFICATION OF PROMOTER ACTIVITY IN GENE-LESS CASSETTES FROM VIBRIONACEAE SUPERINTEGRONS

Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encode promoterless genes, whose expression relies on the platform-associated Pc promoter, with the cassette array functioning as an operon-like structure regulated by the distance to the Pc. This is relevant in large sedentary chromosomal integrons (SCIs) carrying hundreds of ICs, like those in Vibrio species. We selected 29 gene-less cassettes in four Vibrio SCIs, and explored whether their function could be related to the transcription regulation of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Additionally, we identified the transcription start sites of gene-less ICs through 5-RACE. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Furthermore, one cassette with an antisense promoter can reduce trimethoprim resistance when cloned downstream. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in SCIs and their clinical importance if captured by mobile integrons.

microbiology↗

bioRxiv2023

Assessing bias and robustness of social network metrics using GPS based radio-telemetry data

O_LISocial network analysis of animal societies allows scientists to test hypotheses about social evolution, behaviour, dynamical processes, and transmission events such as the spread of disease. However, the accuracy of estimated social network metrics depends on the proportion of individuals sampled, actual sample size, and frequency of observations. Robustness of network metrics derived from a sample has thus far been examined through various simulation studies. However, simulated data do not necessarily reflect the nuances of real empirical data. C_LIO_LIWe used some of the largest available GPS telemetry relocation datasets from five species of ungulates characterised by different behavioural and ecological traits and living in distinct environmental contexts to study the bias and robustness of social network metrics. We introduced novel statistical methods to quantify the uncertainty in network metrics obtained from a partial population suited to autocorrelated data such as telemetry relocations. We analysed how social network metrics respond to down-sampling from the observed data and applied pre-network data permutation techniques, a bootstrapping approach, correlation, and regression analyses to assess the stability of network metrics when based on samples of a population. C_LIO_LIWe found that global network metrics like density remain robust when the sample size is lowered, whereas some local network metrics, such as eigenvector centrality, are entirely unreliable when a large proportion of the population is not monitored. We show how to construct confidence intervals around the point estimates of these metrics representing the uncertainty as a function of the number of nodes in the network. C_LIO_LIOur uncertainty estimates enable the statistical comparison of social network metrics under different conditions, such as analysing daily and seasonal changes in the density of a network. Despite the striking differences in the ecology and sociality among the five different ungulate species, the various social network metrics behave similarly under downsampling, suggesting that our approach can be applied to a wider range of species across vertebrates. Our methods can guide methodological decisions about animal social network research (e.g., sampling design and sample sizes) and allow more accurate ecological inferences from the available data. C_LI

animal behavior and cognition↗