The experimental degradation of archaeological human bone by anaerobic bacteria and the implications for recovery of ancient DNA

DNA recovery from human bone has been key to the developing science and technology of ancient DNA studies. The recovery of macromolecules from bone however, does not correlate well with recognisable parameters of preservation and predicting DNA recovery rates from ancient bone can be very difficult. The extent of degradation of buried bones often depends on environmental taphonomy and can vary from virtually none to complete and rapid destruction. Although soil or related microbes are undoubtedly responsible for the majority of this structural degradation over time, exceptionally little is known of the mechanisms or specific bacteria involved. Fungi were previously thought to be responsible for destructive processes (tunnelling) within bone but over the last 30 years the role of bacteria has been increasingly recognised. Our aim was to develop a less complex in vitro model of the destructive effects of microbes on bone which might allow a better understanding of the recovery of mitochondrial or pathogen DNA over time

16-03 The Effects of High Visibility Enforcement on Driver Compliance to Pedestrian Stop Right-of-Way Laws in Ann Arbor, MI

The purpose of this study was to replicate the findings of Van Houten et. al. (2013) demonstrating that a multifaceted program could increase the percentage of motorist’s yielding to pedestrians in crosswalks on a community basis in Gainesville, FL, and that these changes actually improved further over a four year follow-up period (Van Houten et. al. (2017). The current study replicated the original findings in a similar sized city in a different region of the US (Ann Arbor, MI). Stopping for pedestrians in Ann Arbor increased from a mean of 28.5% to 65.2% at the treatment sites, which also received police enforcement, and from 34.2% to 53% at the generalization sites that did not receive police enforcement. These changes were very similar to those observed in the city of Gainesville Florida. The finding indicated that the use of the feedback signs showing the percentage of motorists stopping for pedestrians each week along with the record level of compliance with the ordinance was a key element contributing to the success of the package. Follow-up data should be collected after 4 years to determine whether further improvements in driver compliance occur

Ichnology of the Palaeogene Richmond Formation of eastern Jamaica - the final chapter?

Previously unrecorded ichnotaxa from the Palaeogene Richmond Formation of eastern Jamaica, namely Cos-morhaphe cf. gracilis, Helminthoida crassa, Paleodictyon? isp. and Taenidium cameronensis, are described. The ichnotaxa are assigned to a previously defined deep-water Scolicia ichnocoenosis characteristic of turbidilic strata. The general exclusion of graphoglyptids in these strata is believed to reflect a combination of the relatively shallow-water depths in which the turbidilic strata accumulated, the abundant organic matter available for biological consumption, and the existence of fluctuating dysaerobic/anoxic and oxygenated conditions at, or immediately below, the sediment-water interface. RÉSUMÉ Les ichnofossiles auparavant non enregistrés provenant de la Formation paleogène de Richmond de Test de la Jamaique, soil Cosmorhaphe cf. gracilis, Helminthoida crassa, Paleodictyon? isp. et Taenidium cameronensis, sont décrits. Ces ichnofossiles sont assigned à l’assemblage d'eau profonde Scolicia anterieurement défini, caractérislique des strates de turbidites. L'absence générate de graphoglyplides dans ces couches est considérée comme refletant une combinaison de la faible profondeur relative à laquelle les strates de turbidites se sont accumulées, l'abondance de matière organique disponible pour la consommation biologique et l’existence de conditions anoxiques et oxygénées fluctuantes è l'interface eau-sédiment ou immédiatement en-dessous. [Traduit par la rédaction

Investigation into the changing colonisation of skin bacteria during isotretinoin treatment for acne vulgaris

Poster presentatio

A metagenomic analysis of the bacterial microbiome of limestone, and the role of associated biofilms in the biodeterioration of heritage stone surfaces.

There is growing concern surrounding the aesthetic and physical effects of microbial biofilms on heritage buildings and monuments. Carboniferous stones, such as limestone and marble, are soluble in weak acid solutions and therefore particularly vulnerable to biocorrosion. This paper aims to determine the differences and commonalities between the microbiome of physically damaged and undamaged Lincolnshire limestone, an area of research which has not been previously studied. A lack of information about the core microbiome has resulted in conflicting claims in the literature regarding the biodeteriorative potential of many microorganisms. To address this, we used metagenomics alongside traditional microbiological techniques to produce an in-depth analysis of differences between the bacterial microbiomes found on deteriorated and undamaged external limestone surfaces. We demonstrate there is a core microbiome on Lincolnshire limestone present on both damaged and undamaged surfaces. In addition to the core microbiome, significant differences were found between species isolated from undamaged compared to damaged surfaces. Isolated species were characterised for biofilm formation and biodeteriorative processes, resulting in the association of species with biodeterioration that had not been previously described. Additionally, we have identified a previously undescribed method of biofilm-associated biomechanical damage. This research adds significant new understanding to the field, aiding decision making in conservation of stone surface

Population genetic data for 17 Y STR markers from Benghazi (East Libya)

The seventeen Y-STR loci included in the AmpF‘STR1 YfilerTM PCR Amplification kit (DYS19, DYS389I,DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS438, DYS439, DYS437, DYS448, DYS458,DYS456, DYS635, and Y-GATA-H4) were used to type a sample population of 238 males from eastern Libya (Benghazi region). Of 238 observed haplotypes, 214 were unique (90%) and 24 (10%) were found more than once. The 17 loci gave a discriminating power of 0.999. DYS458 showed the highest diversity as a single-locus marker (0.73). Allelic frequencies and gene diversities for each Y-STR locus were determined. The high haplotype diversity and discrimination capacity (0.996) demonstrate the utility of these loci for human identification in forensic applications. Comparative analysis with Y-STR datasets of relevant populations and submission of the haplotypes to the Y-STR Haplotype Reference Database (YHRD) was undertaken

Foodborne Outbreaks of Microbial Infection from Fresh Produce in Europe And North America: A Systematic Review of Data from This Millennium

This study focuses on foodborne outbreaks of microbial infection associated with fresh produce in Europe and North America from this millennium. A total of 277 outbreaks with 44,524 individual cases were identified. Foodborne pathogens associated with the most outbreak frequency include Cryptosporidium (20.5%) in Europe and Salmonella (52.2%) in North America although Norovirus (54.3%) and Salmonella (61.3%) were associated with the number of cases in Europe and North America respectively. Vegetables were the most implicated fresh produce category with outbreak frequencies of 34.1% in Europe and 47.4% in North America. Increased consumption of fresh produce in Europe and North America, as measures to improve diets correlates with the increased fresh produce related outbreaks of microbial infection. This systematic review suggests the need for more rapid methodologies for traceback investigations in order to determine trends and epicentres of foodborne infections related to fresh produce

On orbifolds and free fermion constructions

This work develops the correspondence between orbifolds and free fermion models. A complete classification is obtained for orbifolds X/G with X the product of three elliptic curves and G an abelian extension of a group (Z_2)^2 of twists acting on X. Each such quotient X/G is shown to give a geometric interpretation to an appropriate free fermion model, including the geometric NAHE+ model. However, the semi-realistic NAHE free fermion model is proved to be non-geometric: its Hodge numbers are not reproduced by any orbifold X/G. In particular cases it is shown that X/G can agree with some Borcea-Voisin threefolds, an orbifold limit of the Schoen threefold, and several further orbifolds thereof. This yields free fermion models with geometric interpretations on such special threefolds.Comment: 46 pages; typos corrected and references adde

Assessing the impact of heat treatment of food on antimicrobial resistance genes and their potential uptake by other bacteria - A critical review

The dissemination of antibiotic resistance genes (ARGs) is a global health concern. This study identifies and critically reviews the published evidence on whether cooking (heating) food to eliminate bacterial contamination induces sufficient damage to the functionality of ARGs. Overall, the review found that there is evidence in the literature that Antimicrobial Resistant (AMR) bacteria are no more heat resistant than non-AMR bacteria. Consequently, recommended heat treatments sufficient to kill non-AMR bacteria in food (70 °C for at least 2 min, or equivalent) should be equally effective in killing AMR bacteria. The literature shows there are several mechanisms through which functional genes from AMR bacteria could theoretically persist in heat-treated food and be trans-ferred to other bacteria. The literature search found sparce published evidence on whether ARGs may actually persist in food after effective heat treatments, and whether functional genes can be transferred to other bacteria. However, three publications have demonstrated that functional ARGs in plasmids may be capable of persisting in foods after effective heat treatments. Given the global impact of AMR, there is clearly a need for further practical research on this topic to provide suffi-cient evidence to fully assess whether there is a risk to human health from the persistence of func-tional ARGs in heat-treated and cooked foods

Assessing the impact of heat treatment on antimicrobial resistance genes and their potential uptake by other ‘live’ bacteria

Antimicrobial resistance (AMR) is a complex issue driven by a variety of interconnected factors enabling microorganisms to withstand the killing or microstatic effects of antimicrobial treatments, such as antibiotics, antifungals, disinfectants, preservatives. Microorganisms may be inherently resistant to such treatments or can change and adapt to overcome the effects of such treatments. Microorganisms can acquire antimicrobial resistance genes (ARGs) because of mutation or from other microorganisms through a range of mechanisms. The widespread use of antimicrobial treatments is known to result in selection for AMR in microorganisms. AMR and ARGs are a major public health issue worldwide and it is estimated that unless action is taken now to tackle AMR the global impact of AMR could be 10 million deaths annually by 2050 and cost up to US $100 trillion in cumulative lost economic output (O’Neill Report, 2014). It is recognised that anthropogenic, commensal, and environmental microorganisms all contribute to the reservoir of ARGs, collectively forming the antimicrobial resistome (Wright, 2007). Relatively little is known regarding the role of heat�treated/cooked food in disseminating AMR, and whether heating/cooking is sufficient to inactivate ARGs to the extent that resistance is not passed onto other ‘live’ bacteria. This study was undertaken to critically review the available scientific literature for assessing the impact of heat treatment of food on ARGs, and the potential uptake of such ARGs by surrounding viable bacterial communities resident in other foods and the human gut. For the purpose of this review, heat treatments were regarded as any thermal processes that are undertaken during the processing or prior to consumption of any foods. The review focused particularly, but not exclusively, on what scientific evidence exists that provides an understanding on whether cooking (heating) food to eliminate bacterial contamination can also induce sufficient damage to ARGs to 8 of 91 prevent their uptake by surrounding viable bacteria present in other settings, including other foods and the human gut. The review question was defined as: “Do different heat treatments applied to eliminate bacterial contamination in foods also induce sufficient damage to ARGs to prevent or inhibit their uptake by surrounding viable bacteria present in other settings, including the human gut and other foods?” Systemic searching of two literature databases (Web of Science, and PubMed) was undertaken, supplemented by additional records identified through other sources. A total of 2681 of publications were identified between 1990 and May 2021, which were reduced to 247 after screening the titles and abstracts. This total was further reduced to 53, from which some data were extracted after appraising the full publications. This clearly indicated that literature relating to AMR bacteria and ARGs and heat treatments was sparse. Of these 53 publications identified that were considered eligible for some data extraction, only four were found that had studied the impact of heat treatments on ARGs. The majority of publications identified related to the relative heat resistance of various AMR bacteria in comparison to non-AMR strains and serotypes/serovars. Nine publications were reviews with some mention of the impact of heat on AMR bacteria, while 17 had evidence on the relative heat resistance of AMR bacteria in comparison to non-AMR bacteria. These publications provide evidence that AMR bacteria are likely to be no more heat-resistant than non-AMR bacteria. There is therefore evidence that heat treatments sufficient to kill non-AMR bacteria (such as 70°C for at least 2 min, or the equivalent) will be equally effective in killing AMR bacteria. 9 of 91 Most of these publications have not considered whether ARGs may persist after such heat treatments, and whether these genes could be transferred to other bacteria. Only four publications were identified that provide some evidence on the fate of ARGs after heat treatments. Due to the small number of publications identified and different laboratory methodologies used in the studies no statistical analysis was possible. Three of the four studies provided evidence that ARGs can at least be identified after heat treatments that are effective at inactivating AMR bacteria, but there is no certainty that such ARGs are intact and functional. Of the four studies identified, one (Koncan et al., 2007) used in vitro experiments to mimic cooking processes. Another in vitro study (Taher et al., 2020a) mimicked commercial milk pasteurisation, whilst the third (Le Devendec et al., 2018) was not designed to mimic any particular heat treatment but did use strains originating from animal sources and temperatures and times similar to thermal processes used to treat and cook food. A further study on autoclaving (Masters et al., 1998) was considered relevant, but was not applied to food. The in vitro mimic of cooking processes study (Koncan et al., 2007) detected the presence of ARGs after cooking but did not demonstrate that these genes were transferable to other bacteria. The other three studies did demonstrate that plasmid�encoded ARGs could be transferred to other bacteria following heat treatments under laboratory conditions. The ARG considered by Koncan et al. (2007) was aac(6’)-Ie-aph(2’’)-Ia, while Taher et al. (2020a) considered blaZ, mecC, tetK, and Le Devendec et al. (2018) considered blaCTX-M-1, blaCMY-2, tetA, strA. Masters et al. (1998) did not give any details of the gene considered. 10 of 91 These studies did not establish how likely was the occurrence of such transfer in the field. One of the studies (Le Devendec et al., 2018) theorised that natural transfer is probably rare. None of the studies demonstrated whether ARGs from heat-treated AMR bacteria could be taken up by other live bacteria in the human gut after ingestion. In conclusion, only a small number of studies were identified on the persistence of ARGs in heat-treated foods and their possible uptake by surrounding viable bacteria present in other settings, such as the human gut and other foods. Because of differences in conditions, these studies were not directly comparable. While the literature suggests that adequate heat treatment / cooking (e.g., cooking until the middle of the food commodity reaches 70°C for at least 2 min, or the equivalent) should be effective in ‘killing’ AMR bacteria in food, there is very little evidence if intact and functional ARGs are released from AMR bacteria following such heat treatments. Similarly, there does not appear to be any convincing data for the ready transfer of ARGs to the commensal bacteria of the mammalian gastrointestinal tract following cooking. Evidence to determine if there is a risk of transfer is sparse. We would therefore recommend further focused practical research be undertaken to provide evidence for a full assessment of risk in relation to transfer of ARGs from heat-treated foods to bacteria in other matrices