The millennial dynamics of malaria in the mediterranean basin: documenting Plasmodium spp. on the medieval island of Corsica.

Introduction: The lack of well-preserved material upon which to base the paleo-microbiological detection of Plasmodium parasites has prevented extensive documentation of past outbreaks of malaria in Europe. By trapping intact erythrocytes at the time of death, dental pulp has been shown to be a suitable tissue for documenting ancient intraerythrocytic pathogens such as Plasmodium parasites. Methods: Total DNA and proteins extracted from 23 dental pulp specimens collected from individuals exhumed from the 9th to 13th century archaeological site in Mariana, Corsica, were analyzed using open-mind paleo-auto-immunohistochemistry and direct metagenomics, Plasmodium-targeting immunochromatography assays. All experiments incorporated appropriate negative controls. Results: Paleo-auto-immunohistochemistry revealed the presence of parasites Plasmodium spp. in the dental pulp of nine teeth. A further immunochromatography assay identified the presence of at least one Plasmodium antigen in nine individuals. The nine teeth, for which the PfHRP-2 antigen specific of P. falciparum was detected, were also positive using paleo-autoimmunohistochemistry and metagenomics. Conclusion: Dental pulp erythrocytes proved to be suitable for the direct paleomicrobiology documentation of malaria in nine individuals buried in medieval Corsica, in agreement with historical data. This provides additional information on the millennial dynamics of Plasmodium spp. in the Mediterranean basin.

Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.

Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.

Surnames in south-eastern France: structure of the rural population during the 19th century through isonymy.

An analysis of the distribution of surnames through time and space allows us to understand the structure of human groups, their exchanges or even their possible isolation. The French population has already been studied through surnames and it has been shown that the Sud-Provence-Alpes-Côte d'Azur region differed from the rest of France in both the 20th and 21st centuries (Mourrieras et al., ; Scapoli et al., ). The objective of this study was to understand the population evolution and particularities of the Sud-Provence-Alpes-Côte d'Azur region through an analysis of the distribution of surnames over an earlier period: the 19th century. For this work, 806,069 birth records from 521 communes between 1810 and 1890 were recorded and a total of 23,340 surnames were collected. The estimation of various isonymic parameters has allowed a description of this corpus never exploited before. In order to appreciate the population evolution, the data set was divided into three periods of 25 years. The canton was the geographical unit of this study, and similarities and differences between each of them were evaluated using Lasker distances, which allow the construction of dendrograms. A positive and significant correlation (p<0.0001) was found between Lasker distances and geographical distances using the Mantel test. The lowest inbreeding estimates were found in the Durance Valley. Migration, estimated from the v-index of Karlin and McGregor (), showed higher values in the south-western quarter of the region. The decrease in Rst values across the three periods is consistent with a homogenization of the patronymic between the cantons. This three-period approach showed a population evolution influenced by linguistic, cultural, historical and migratory phenomena since the Middle Ages, disrupted by the socioeconomic changes of the 19th century.

History of the plague of 1720-1722, in Marseille.

The plague epidemic of 1720-1722 had a profound effect on the history of the city of Marseille. A subject of numerous scientific studies and a source of inspiration for novels, one of the last great European epidemics is well-documented. In this article, we have sought to draw on the numerous documents left by the administrative services of the time or by the writings of survivors recounting their vision of the situation. We have completed this historical approach by referring to the study of mass graves of plague victims and will show how the simultaneous reading of two types of archives (historical and biological) can provide better anthropological knowledge of epidemic phenomena. The perspectives of interdisciplinary approaches to past infectious diseases are numerous, notably with the contributions of paleomicrobiology and genomics, and are particularly relevant today's health context.

Post-traumatic growth 5 years after cancer: identification of associated actionable factors.

BACKGROUND: The number of cancer survivors is growing increasingly worldwide. The long-term negative consequences of the disease are now better known. Cancer may also foster positive outcomes. Some survivors consider life after cancer as the start of a new life and experience positive changes called post-traumatic growth (PTG) measured by a scale developed by Tedeschi and Calhoun. OBJECTIVE: The purpose of this article was to explore actionable factors affecting PTG, particularly those in relation with health care management and those that reflected health behavior changes. METHODS: This study included the 1,982 participants in the VICAN cohort who responded to the questionnaire on living conditions 2 and 5 years after diagnosis. Factors associated with a moderate or high PTG (score ≥ 63) were identified using logistic regressions. RESULTS: Factors positively associated with moderate or high PTG were being satisfied with the time spent by health care team on information (OR:1.35 [1.08;1.70]), increased physical activity (OR:1.42 [1.04;1.95]) and healthier diet (OR:1.85 [1.44;2.36]) since diagnosis, and having benefited from psychological support at diagnosis (OR:1.53 [1.16;2.01]). CONCLUSION: High PTG is positively associated with health behavior and time spent on information. Our findings suggest that appropriate clinical and educational interventions can help foster growth after the experience of cancer. Even if we do not know what causes what, it is admitted that the interventions leading to an increase of physical activity, for example, are good from all points of view.

Differential word expression analyses highlight plague dynamics during the second pandemic.

Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools routinely used in biology, we developed a quantitative lexicography of 32 texts describing two major plague outbreaks, using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome, comprising overrepresented terms in plague-related texts, indicated that 'buboes' and 'carbuncles' are words that were significantly associated with the plague and signalled an ectoparasite-borne plague. Moreover, plague-related words were associated with the terms 'merchandise', 'movable', 'tatters', 'bed' and 'clothes'. Analysing ancient texts using the method reported in this paper can certify plague-related historical records and indicate the particularities of each plague outbreak, which can inform on the potential sources for the causative Yersinia pestis.

African Gene Flow Reduces Beta-Ionone Anosmia/Hyposmia Prevalence in Admixed Malagasy Populations.

While recent advances in genetics make it possible to follow the genetic exchanges between populations and their phenotypic consequences, the impact of the genetic exchanges on the sensory perception of populations has yet to be explored. From this perspective, the present study investigated the consequences of African gene flow on odor perception in a Malagasy population with a predominantly East Asian genetic background. To this end, we combined psychophysical tests with genotype data of 235 individuals who were asked to smell the odorant molecule beta-ionone (ßI). Results showed that in this population the ancestry of the OR5A1 gene significantly influences the ability to detect ßI. At the individual level, African ancestry significantly protects against specific anosmia/hyposmia due to the higher frequency of the functional gene (OR ratios = 14, CI: 1.8-110, p-value = 0.012). At the population level, African introgression decreased the prevalence of specific anosmia/hyposmia to this odorous compound. Taken together, these findings validate the conjecture that in addition to cultural exchanges, genetic transfer may also influence the sensory perception of the population in contact.

No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy.

The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.

French soldiers who died during both World Wars: from recovery to repatriation.

The study of human remains from the first and the second World War is important for enhancing our understanding of that historical period. Despite the fact that the period has been well-documented previously, gaps remain, particularly as a result of the destruction of archives. In fact, for just WWI, more than 700,000 soldiers from both sides remain missing. Scientific and political collaborations established in hopes of recovering and identifying soldiers will allow many families understand "what happened" to their loved ones and facilitate the return of the soldiers their homes. In this paper, the recovery of the human remains of French soldiers WWI and WWII will be described through the lens of the legislation in place governing the retrieval and identification of the remains, protocols established for recovery, excavation and analysis, and the dissemination data. These features will be illustrated using three case studies that involve French soldiers who died during WWI. Research of this type is the result of true interdisciplinary and sometimes international, depending on the context, collaboration. The public and academic the dissemination of these archaeological discoveries, both to academics and the public, is crucial and a type of remembrance.

An outbreak of relapsing fever unmasked by microbial paleoserology, 16th century, France.

OBJECTIVES: Depicting past epidemics currently relies on DNA-based detection of pathogens, an approach limited to pathogens with well-preserved DNA sequences. We used paleoserology as a complementary approach detecting specific antibodies under a mini line-blot format including positive and negative control antigens. METHODS: Mini line blot assay incorporated skim milk as negative control, Staphylococcus aureus as positive control, and antigens prepared from lice-borne pathogens Rickettsia prowazekii, Borrelia recurrentis, Bartonella quintana, and Yersinia pestis. Paleoserums were extracted from rehydrated dental pulp recovered from buried individuals. Mini line blots observed with the naked eye, were quantified using a scanner and appropriate software. Paleoserology was applied to the indirect detection of lice-borne pathogens in seven skeletons exhumed from a 16th-17th century suspected military burial site (Auxi-le-Château); and 14 civils exhumed from a 5th-13th century burial site (Saint-Mont). Direct detection of pathogens was performed using quantitative real-time PCR. RESULTS: In Auxi-le-Château, paleoserology yielded 7/7 interpretable paleoserums including 7/7 positives for B. recurrentis including one also positive for B. quintana. In Saint-Mont, paleoserology yielded 8/14 interpretable paleoserums and none reacted against any of the four pathogens. Antibodies against R. prowazekii and Y. pestis were not detected. The seroprevalence was significantly higher in the military burial site of Auxi-le-Château than in the civil burial site of Saint-Mont. Real-time PCR detection of B. quintana yielded 5/21 positive (3 at Saint-Mont and 2 at Auxi-le-Château) whereas B. recurrentis was not detected. CONCLUSIONS: Paleoserology unmasked an outbreak of relapsing B. recurrentis fever in one 16th - 17th century military garrison, missed by real-time PCR. Paleoserology offers a new tool for investigating past epidemics, in complement to DNA sequence-based approaches.

When a lost "Petit Prince" meets Antoine de Saint Exupéry: An anthropological case report.

This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on "The Fountain of the Greeks" square on Riou Island occurred in the 1960's and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was "closed" and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis fürst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.

Developmental stability and environmental stress: A geometric morphometrics analysis of asymmetry in the human femur.

OBJECTIVES: The evaluation of developmental stability (DS) by measuring fluctuating asymmetry (FA), a bioindicator of general cumulative stress, is an approach that has often been used to characterize health status in past populations. New techniques of geometric morphometrics now enable a better appreciation of FA than before, with a more refined quantification of variation. The aim of our study is to determine the effectiveness of geometric morphometrics analyses of asymmetry in the human femur for the study of individual DS and inferring health status of human populations. MATERIALS AND METHODS: We conducted a comparative analysis between two diachronic populations of distinct and known health status. Two samples of 70 pairs of adult femurs from individuals of comparable age range and sex were selected and CT-scanned. For each 3D reconstruction, two sets of 27 landmarks were digitized to quantify and minimize the effect of measurement error on the evaluation of FA. RESULTS: While the measurement of FA in femoral centroid size seemed comparable between the samples, the amount of FA in femoral shape differed. Individuals who experienced high levels of environmental stress presented higher intra-individual variation. In parallel, results did not reveal any significant differences in DS between sexes or age groups. DISCUSSION: The geometric morphometrics analysis of femoral asymmetry was effective for distinguishing two populations. After considering various factors of influence, genetics and biomechanics seem to have a limited impact on the results. Expressing FA appears to be normal but dependent on the disturbances of DS produced by environmental stress.

Paleoproteomics of the Dental Pulp: The plague paradigm.

Chemical decomposition and fragmentation may limit the detection of ancient host and microbial DNA while some proteins can be detected for extended periods of time. We applied paleoproteomics on 300-year-old dental pulp specimens recovered from 16 individuals in two archeological funeral sites in France, comprising one documented plague site and one documented plague-negative site. The dental pulp paleoproteome of the 16 teeth comprised 439 peptides representative of 30 proteins of human origin and 211 peptides representative of 27 proteins of non-human origin. Human proteins consisted of conjunctive tissue and blood proteins including IgA immunoglobulins. Four peptides were indicative of three presumable Yersinia pestis proteins detected in 3/8 dental pulp specimens from the plague-positive site but not in the eight dental pulp specimens collected in the plague-negative site. Paleoproteomics applied to the dental pulp is a new and innovative approach to screen ancient individuals for the detection of blood-borne pathogens and host inflammatory response.

Analysis of Anelloviridae sequences characterized from serial human and animal biological samples.

Rolling-circle amplification-sequence-independent single primer amplifications (RCA-SISPA) and/or RCA-PCR-based approaches were applied to serial human plasma and animal (domestic cat) saliva samples. Complete SENV-H-related and PRA4 Anelloviridae genomes were characterized and analysed over time (~16 and 6.5years for human and animal samples, respectively). Genomic sequences and deduced putative coding regions were compared. Comparable values, i.e. ~2×10-4subs/site/year, were obtained for estimated rates of non-synonymous substitutions. A "hot-spot" of mutations located on the SENV-H-related ORF1 was identified. These results are first data concerning Anelloviridae evolution in a human and an animal host based on the analysis of complete sequences.

Characterization of the Funeral Groups Associated with Plague Epidemics.

There are several scenarios regarding how burial sites in archaeological contexts are discovered. We will focus on two scenarios according to the degree of historical knowledge regarding the studied sector. The excavation may be performed in a known funeral place or a highly suspected place (e.g., the interior or immediate exterior space in a religious monument or a parish cemetery). Also, the excavation of unexpected graves or graves discovered by chance may occur in places that had unknown or forgotten funeral purposes.

Restricted diversity of dental calculus methanogens over five centuries, France.

Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus.

Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth.

Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities present in dental pulps. Here, we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by distinct microbial communities, which can be differentiated from other oral cavity samples. We found that despite the presence of environmental bacteria, ancient dental pulps conserve a clear and well-conserved record of oral microbes. We were able to detect several different oral pathogens in ancient and modern dental pulps, which are commonly associated with periodontal diseases. We thus showed that ancient dental pulps are not only valuable sources of DNA from humans and systemic infections, but also an open window for the study of ancient oral microbiomes.

Immuno-PCR--a new tool for paleomicrobiology: the plague paradigm.

BACKGROUND: The cause of past plague pandemics was controversial but several research teams used PCR techniques and dental pulp as the primary material to reveal that they were caused by Yersinia pestis. However, the degradation of DNA limits the ability to detect ancient infections. METHODS: We used for the first time immuno-PCR to detect Yersinia pestis antigens; it can detect protein concentrations 70 times lower than the standard ELISA. After determining the cut-off value, we tested 34 teeth that were obtained from mass graves of plague, and compared previous PCR results with ELISA and immuno-PCR results. RESULTS: The immuno-PCR technique was the most sensitive (14 out of 34) followed by the PCR technique (10 out of 34) and ELISA (3 out of 34). The combination of these three methods identified 18 out of 34 (53%) teeth as presumably being from people with the plague. CONCLUSION: Immuno-PCR is specific (no false-positive samples were found) and more sensitive than the currently used method to detect antigens of ancient infections in dental pulp. The combination of three methods, ELISA, PCR and immuno-PCR, increased the capacity to identify ancient pathogens in dental pulp.