Twin Studies: Research in Genes, Teeth and Faces

This volume is about an ongoing long-term research initiative led by researchers from the School of Dentistry at the University of Adelaide. The aim of this book is to provide an overview of the studies of the teeth and faces of Australian twins and their families that have extended over more than thirty years

Phylogenetic relationships of Chanidae (Teleostei: Gonorynchiformes) as impacted by Dastilbe moraesi, from the Sanfranciscana basin, Early Cretaceous of Brazil

Fossil gonorynchiform fishes range from the Lower Cretaceous to the early Miocene, and are represented by a few dozen living species. The order is currently divided into two major clades: Gonorynchoidei, which includes the families Gonorynchidae and Kneriidae, and Chanoidei, encompassing a single family, Chanidae, with a single recent species, the Indo-Pacific Chanos chanos, and several fossil taxa. Chanidae includes some poorly known taxa, such as Dastilbe moraesi, described from the Aptian (Lower Cretaceous) of the Areado Formation, Sanfranciscana basin, Brazil. This species is currently considered to be a junior synonym of the type species of its genus, Dastilbe crandalli, from Santana Formation, Aptian, northeastern Brazil. The analysis of abundant D. moraesi specimens revealed several new morphological features, many of which had previously been misinterpreted. Dastilbe moraesi was incorporated into a gonorynchiform character matrix as revised and modified for the Chanidae. We obtained a single most parsimonious tree in which D. moraesi is distinct and phylogenetically apart from D. crandalli. According our analysis, D. moraesi forms a sister pair with Chanos, a clade which is closely related to Tharrhias, all composing the tribe ChaniniGonorynchiformes fósseis ocorrem desde do Cretáceo inferior ao Mioceno inferior, e são representados por alguns representantes viventes. A ordem está dividida atualmente em dois clados principais: Gonorynchoidei, que inclui as famílias Gonorynchidae e Kneriidae, e Chanoidei, compreendendo uma única família, Chanidae, com uma única espécie vivente, Chanos chanos, do Indo-Pacífico, além de vários representantes fósseis. Chanidae inclui alguns táxons problemáticos, tais como Dastilbe moraesi, descrito do Aptiano (Cretáceo Inferior) da Formação Areado, bacia Sanfranciscana, Brasil. Esta espécie é atualmente considerada um sinônimo júnior da espécie-tipo de seu gênero, Dastilbe crandalli, da Formação Santana, Aptiano do nordeste do Brasil. A análise de abundante material de D. moraesi revelou várias novas características anatômicas, muitas das quais haviam sido previamente mal interpretadas. Dastilbe moraesi foi incorporado em uma matriz revisada de caracteres da família Chanidae. Nós obtivemos uma única árvore mais parcimoniosa na qual D. moraesi é distinto e filogeneticamente distante de D. crandalli. De acordo com nossa análise, D. moraesi é o grupo-irmão de Chanos, um clado intimamente relacionado a Tharrhias, com todos compondo a tribo ChaniniThis study was supported by CNPq (process # 401818/2010-1) and project CGL2013-42643P, Ministerio de Ciencia e Innovación de Españ

Timing of Colonization of Caries-Producing Bacteria: An Approach Based on Studying Monozygotic Twin Pairs

Findings are presented from a prospective cohort study of timing of primary tooth emergence and timing of oral colonization of Streptococcus mutans (S. mutans) in Australian twins. The paper focuses on differences in colonization timing in genetically identical monozygotic (MZ) twins. Timing of tooth emergence was based on parental report. Colonization timing of S. mutans were established by plating samples of plaque and saliva on selective media at 3 monthly intervals and assessing colony morphology. In 25% of individuals colonization occurred prior to emergence of the first tooth. A significant proportion of MZ pairs (21%) was discordant for colonization occurring before or after first tooth emergence, suggesting a role of environmental or epigenetic factors in timing of tooth emergence, colonization by S. mutans, or both. These findings and further application of the MZ co-twin model should assist in development of strategies to prevent or delay infection with S. mutans in children

Identification of Melatonin-Regulated Genes in the Ovine Pituitary Pars Tuberalis, a Target Site for Seasonal Hormone Control

The pars tuberalis (PT) of the pituitary gland expresses a high density of melatonin (MEL) receptors and is believed to regulate seasonal physiology by decoding changes in nocturnal melatonin secretion. Circadian clock genes are known to be expressed in the PT in response to the decline (Per1) and onset (Cry1) of MEL secretion, but to date little is known of other molecular changes in this key MEL target site. To identify transcriptional pathways that may be involved in the diurnal and photoperiod-transduction mechanism, we performed a whole genome transcriptome analysis using PT RNA isolated from sheep culled at three time points over the 24-h cycle under either long or short photoperiods. Our results reveal 153 transcripts where expression differs between photoperiods at the light-dark transition and 54 transcripts where expression level was more globally altered by photoperiod (all time points combined). Cry1 induction at night was associated with up-regulation of genes coding for NeuroD1 (neurogenic differentiation factor 1), Pbef / Nampt (nicotinamide phosphoribosyltransferase) , Hif1α (hypoxia-inducible factor-1α), and Kcnq5 (K channel) and down-regulation of Rorβ, a key clock gene regulator. Using in situ hybridization, we confirmed day-night differences in expression for Pbef / Nampt, NeuroD1, and Rorβ in the PT. Treatment of sheep with MEL increased PT expression for Cry1, Pbef / Nampt, NeuroD1, and Hif1α, but not Kcnq5. Our data thus reveal a cluster of Cry1-associated genes that are acutely responsive to MEL and novel transcriptional pathways involved in MEL action in the PT

Developing a Collaborative Strategy to Manage and Preserve Cultural Heritage During the Libyan Conflict. The Case of the Gebel Nafusa

The paper discusses the potential of a collaborative scheme for the development of a protocol for recording and managing the cultural heritage in Libya. The critical political situation in the country urges the development of cultural heritage management policies in order to protect it more thoroughly and consistently. Moving on from the numerous international initiatives and projects dealing with a mostly “remote” approach to the issue, the project here presented to engages with staff members of the Department of Antiquities (DoA) in the development of a joint strategy for the application of remote sensing and geographical information systems (GIS) to the preservation and monitoring of Libyan cultural heritage. A series of training courses resulted in an initial development of new ways of recording and analysing field data for a better awareness of the full range of threats that the archaeology of the country is subject to. Focussing on the case of the Jebel Nafusa, the training involved the assessment of site visibility on satellite imagery, the analysis of high-resolution satellite datasets for archaeological mapping, the creation of a GIS spatial database of field data, and the mapping of risks and threats to archaeology from remote sensing data. This led to the creation of of a risk map showing the areas that are affected by a number of threats, thus giving the DoA a tool to prioritise future fieldwork to keep the assessment of site damage up to date. Only a collaborative approach can lead to a sustainable strategy for the protection of the invaluable cultural heritage of Libya

Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries

Advance access publication date: 18 October 2022Dental caries is a microbial disease and the most common chronic health condition, affecting nearly 3.5 billion people worldwide. In this study, we used a multiomics approach to characterize the supragingival plaque microbiome of 91 Australian children, generating 658 bacterial and 189 viral metagenome-assembled genomes with transcriptional profiling and gene-expression network analysis. We developed a reproducible pipeline for clustering sample-specific genomes to integrate metagenomics and metatranscriptomics analyses regardless of biosample overlap. We introduce novel feature engineering and compositionally-aware ensemble network frameworks while demonstrating their utility for investigating regime shifts associated with caries dysbiosis. These methods can be applied when differential abundance modeling does not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a coexpression network as well as how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core bacterial microbiome that was transcriptionally active in the supragingival plaque of all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.Josh L. Espinoza, Manolito Torralba, Pamela Leong, Richard Saffery, Michelle Bockmann, Claire Kuelbs, Suren Singh, Toby Hughes, Jeffrey M. Craig, Karen E. Nelson and Chris L. Dupon

Baryon masses from lattice QCD: Beyond the perturbative chiral regime

Consideration of the analytic properties of pion-induced baryon self-energies leads to new functional forms for the extrapolation of light baryon masses. These functional forms reproduce the leading non-analytic behavior of chiral perturbation theory, the correct non-analytic behavior at the $N \pi$ threshold and the appropriate heavy-quark limit. They involve only three unknown parameters, which may be obtained by fitting to lattice data. Recent dynamical fermion results from CP-PACS and UKQCD are extrapolated using these new functional forms. We also use these functions to probe the limit of applicability of chiral perturbation theory to the extrapolation of lattice QCD results.Derek B. Leinweber, Anthony W. Thomas, Kazuo Tsushima, and Stewart V. Wrigh

CHARMM: The biomolecular simulation program

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63074/1/21287_ftp.pd

Development of the oral resistome during the first decade of life

Published online: 09 March 2023Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Genome sequencing reveals the widespread presence of antimicrobial resistance genes (ARGs) in diverse microbial environments. Hence, surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. Here, we characterise the development of the paediatric oral resistome and investigate its role in dental caries in 221 twin children (124 females and 97 males) sampled at three time points over the first decade of life. From 530 oral metagenomes, we identify 309 ARGs, which significantly cluster by age, with host genetic effects detected from infancy onwards. Our results suggest potential mobilisation of ARGs increases with age as the AMR associated mobile genetic element, Tn916 transposase was co-located with more species and ARGs in older children. We find a depletion of ARGs and species in dental caries compared to health. This trend reverses in restored teeth. Here we show the paediatric oral resistome is an inherent and dynamic component of the oral microbiome, with a potential role in transmission of AMR and dysbiosis.Smitha Sukumar, FangWang, Carra A. Simpson, Cali E. Willet, Tracy Chew, Toby E. Hughes, Michelle R. Bockmann, Rosemarie Sadsad, F. ElizabethMartin, Henry W. Lydecker, Gina V. Browne, KylieM. Davis, Minh Bui, ElenaMartinez, Christina J. Adle