Non-lethal control of the cariogenic potential of an agent-based model for dental plaque

Dental caries or tooth decay is a prevalent global disease whose causative agent is the oral biofilm known as plaque. According to the ecological plaque hypothesis, this biofilm becomes pathogenic when external challenges drive it towards a state with a high proportion of acid-producing bacteria. Determining which factors control biofilm composition is therefore desirable when developing novel clinical treatments to combat caries, but is also challenging due to the system complexity and the existence of multiple bacterial species performing similar functions. Here we employ agent-based mathematical modelling to simulate a biofilm consisting of two competing, distinct types of bacterial populations, each parameterised by their nutrient uptake and aciduricity, periodically subjected to an acid challenge resulting from the metabolism of dietary carbohydrates. It was found that one population was progressively eliminated from the system to give either a benign or a pathogenic biofilm, with a tipping point between these two fates depending on a multiplicity of factors relating to microbial physiology and biofilm geometry. Parameter sensitivity was quantified by individually varying the model parameters against putative experimental measures, suggesting non-lethal interventions that can favourably modulate biofilm composition. We discuss how the same parameter sensitivity data can be used to guide the design of validation experiments, and argue for the benefits of in silico modelling in providing an additional predictive capability upstream from in vitro experiments

Threatened North African seagrass meadows have supported green turtle populations for millennia

"Protect and restore ecosystems and biodiversity" is the second official aim of the current UN Ocean Decade (2021 to 2030) calling for the identification and protection of critical marine habitats. However, data to inform policy are often lacking altogether or confined to recent times, preventing the establishment of long-term baselines. The unique insights gained from combining bioarchaeology (palaeoproteomics, stable isotope analysis) with contemporary data (from satellite tracking) identified habitats which sea turtles have been using in the Eastern Mediterranean over five millennia. Specifically, our analysis of archaeological green turtle (Chelonia mydas) bones revealed that they likely foraged on the same North African seagrass meadows as their modern-day counterparts. Here, millennia-long foraging habitat fidelity has been directly demonstrated, highlighting the significance (and long-term dividends) of protecting these critical coastal habitats that are especially vulnerable to global warming. We highlight the potential for historical ecology to inform policy in safeguarding critical marine habitats

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Data from: Defining conservation units with enhanced molecular tools to reveal fine scale structuring among Mediterranean green turtle rookeries

Understanding the connectivity among populations is a key research priority for species of conservation concern. Genetic tools are widely used for this purpose, but the results can be limited by the resolution of the genetic markers in relation to the species and geographic scale. Here, we investigate natal philopatry in green turtles (Chelonia mydas) from four rookeries within close geographic proximity (~ 200km) on the Mediterranean island of Cyprus. We genotyped hypervariable mtSTRs, a mtDNA control region sequence (CR) and 13 microsatellite loci to genetically characterise 479 green turtles using markers with different modes of inheritance. We demonstrated matrilineal stock structure for the first time among Mediterranean green turtle rookeries. This result contradicts previous regional assessments and supports a growing body of evidence that green turtles exhibit a more precise level of natal site fidelity than has commonly been recognised. The microsatellites detected weak male philopatry with significant stock structure among three of the six pairwise comparisons. The absence of Atlantic CR haplotypes and mtSTRs among these robust sample sizes reaffirm the reproductive isolation of Mediterranean green turtles and supports their status as a subpopulation. A power analysis effectively demonstrated that the mtDNA genetic markers previously employed to evaluate regional stock identity were confounded by an insufficient resolution considering the recent colonisation of this region. These findings improve the regional understanding of stock connectivity and illustrate the importance of using suitable genetic markers to define appropriate units for management and conservation

POWSIM_input_sample_size_frequencies

The Excel file ‘POWSIM_input_sample_size_frequencies.xlsx’ contains the input data used for the power analysis of the genetic markers conducted in POWSIM v4.1 (Ryman & Palm 2006). The file contains two tables, one table entitled ‘Cyprus’ which contains the sample sizes and the CR, HR haplotype and microsatellite allele frequencies pertaining to this study. The second table entitled ‘Roberts (2004)’ contains the sample sizes and approximate allele frequencies used in the global assessment of green turtle genetic structure (Roberts et al. 2004)

Satellite tracking and stable isotope analysis highlight differential recruitment among foraging areas in green turtles

Identifying links between breeding and non-breeding sites in migratory animals is an important step in understanding their ecology. Recognising the relative importance of foraging areas and ascertaining site-specific levels of recruitment can provide fundamental and applied insights. Here, satellite telemetry and the stable isotope ratios (δ13C, δ15N and δ34S) of 230 green turtles Chelonia mydas from a regionally important rookery in northern Cyprus were employed to evaluate the relative importance of 4 foraging areas. A preliminary analysis of stable isotope ratios suggested that a major foraging area had been missed through satellite telemetry as a large proportion of turtles had isotope ratios that did not correspond to sites previously identified. Stable isotope ratios were then employed to select 5 turtles to be fitted with platform terminal transmitters in 2015. All 5 turtles were subsequently tracked to the same location, Lake Bardawil in Egypt. Serially collected tissue samples from 45 females, ranging over 2 to 4 breeding seasons, suggested that foraging site fidelity was very common, with 82% of females exhibiting extremely high temporal consistency in isotope ratios. Quantifying fidelity allowed an evaluation of foraging area - specific contributions to each breeding cohort over the past 2 decades and demonstrated that recruitment was unequal among sites, and dynamic over time, with Egypt now currently the major contributor to the nesting aggregation. This work demonstrates the utility of stable isotope analysis to elucidate the spatial ecology of cryptic taxa and illustrates how more robust baselines can be assembled against which to measure the success of future marine conservation initiatives

Satellite tracking and stable isotope analysis highlight differential recruitment among foraging areas in green turtles

Identifying links between breeding and non-breeding sites in migratory animals is an important step in understanding their ecology. Recognising the relative importance of foraging areas and ascertaining site-specific levels of recruitment can provide fundamental and applied insights. Here, satellite telemetry and the stable isotope ratios (δ13C, δ15N and δ34S) of 230 green turtles Chelonia mydas from a regionally important rookery in northern Cyprus were employed to evaluate the relative importance of 4 foraging areas. A preliminary analysis of stable isotope ratios suggested that a major foraging area had been missed through satellite telemetry as a large proportion of turtles had isotope ratios that did not correspond to sites previously identified. Stable isotope ratios were then employed to select 5 turtles to be fitted with platform terminal transmitters in 2015. All 5 turtles were subsequently tracked to the same location, Lake Bardawil in Egypt. Serially collected tissue samples from 45 females, ranging over 2 to 4 breeding seasons, suggested that foraging site fidelity was very common, with 82% of females exhibiting extremely high temporal consistency in isotope ratios. Quantifying fidelity allowed an evaluation of foraging area - specific contributions to each breeding cohort over the past 2 decades and demonstrated that recruitment was unequal among sites, and dynamic over time, with Egypt now currently the major contributor to the nesting aggregation. This work demonstrates the utility of stable isotope analysis to elucidate the spatial ecology of cryptic taxa and illustrates how more robust baselines can be assembled against which to measure the success of future marine conservation initiatives

Satellite tracking and stable isotope analysis highlight differential recruitment among foraging areas in green turtles

Identifying links between breeding and non-breeding sites in migratory animals is an important step in understanding their ecology. Recognising the relative importance of foraging areas and ascertaining site-specific levels of recruitment can provide fundamental and applied insights. Here, satellite telemetry and the stable isotope ratios (δ13C, δ15N and δ34S) of 230 green turtles Chelonia mydas from a regionally important rookery in northern Cyprus were employed to evaluate the relative importance of 4 foraging areas. A preliminary analysis of stable isotope ratios suggested that a major foraging area had been missed through satellite telemetry as a large proportion of turtles had isotope ratios that did not correspond to sites previously identified. Stable isotope ratios were then employed to select 5 turtles to be fitted with platform terminal transmitters in 2015. All 5 turtles were subsequently tracked to the same location, Lake Bardawil in Egypt. Serially collected tissue samples from 45 females, ranging over 2 to 4 breeding seasons, suggested that foraging site fidelity was very common, with 82% of females exhibiting extremely high temporal consistency in isotope ratios. Quantifying fidelity allowed an evaluation of foraging area - specific contributions to each breeding cohort over the past 2 decades and demonstrated that recruitment was unequal among sites, and dynamic over time, with Egypt now currently the major contributor to the nesting aggregation. This work demonstrates the utility of stable isotope analysis to elucidate the spatial ecology of cryptic taxa and illustrates how more robust baselines can be assembled against which to measure the success of future marine conservation initiatives

Unfiltered_microsatellite_genotypes_CR_mtSTRs_HR_haplotypes

The Excel file ‘Unfiltered_Microsatellite_genotypes_CR_mtSTRs_HR_haplotypes.xlsx’ contains the CR haplotypes, the mtSTRs, the HR haplotypes and genotypes at 13 microsatellite loci of all individuals used in the COLONY2 (Wang 2004, Jones & Wang 2010) analyses to remove putative relatives before the analysis of genetic structur