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1.
Tuberculosis (Edinb) ; 125: 101995, 2020 12.
Article in English | MEDLINE | ID: mdl-32979676

ABSTRACT

The Mycobacterium tuberculosis complex (MTC) has affected South American populations since ca. 200 years BCE. In Argentina, possible cases date from ca. 1000-1400 Common Era (CE). This paper describes the oldest (905-1030 CE) confirmed case of tuberculosis (TB) in a young adult male from Lomitas de Saujil (Tinogasta, Catamarca, Argentina). Osteolytic lesions on the bodies of the lower spine were macroscopically and radiographically identified. Bilateral new bone formation was seen on the visceral vertebral third of several ribs and in long bones, compatible with hypertrophic osteoarthropathy. Representative rib and hand bones gave profiles for MTC-specific C27-C32 mycocerosic acid lipid biomarkers; these were strongest in one heavily-lesioned lower rib, which also had MTC-diagnostic C76-C89 mycolic acids and positive amplification of MTC-typical IS6110 aDNA fragments. During the first millennium CE, the intense social interaction, the spatial circumscription of villages among the pre-Hispanic societies in the mesothermal valleys of Catamarca and the fluid contacts with the Eastern lowlands, valleys and puna, were factors likely to favor disease transmission. It is proposed that TB arrived from northern Chile and dispersed towards the northeast into the Yocavil valley, where several cases of TB infection were macroscopically identified for a later chronology.


Subject(s)
Bone and Bones/diagnostic imaging , DNA, Bacterial/history , Mycobacterium tuberculosis/genetics , Paleopathology/methods , Tuberculosis, Osteoarticular/history , Adult , Argentina/epidemiology , Bone and Bones/microbiology , DNA, Bacterial/analysis , History, 15th Century , History, 16th Century , History, Ancient , History, Medieval , Humans , Incidence , Male , Mycobacterium tuberculosis/isolation & purification , Tuberculosis, Osteoarticular/diagnosis , Tuberculosis, Osteoarticular/epidemiology
2.
Int J Paleopathol ; 29: 128-140, 2020 06.
Article in English | MEDLINE | ID: mdl-31964606

ABSTRACT

Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.


Subject(s)
DNA, Bacterial/history , Mycobacterium tuberculosis , Paleopathology , Research Design , Sequence Analysis, DNA/trends , Tuberculosis/history , DNA, Bacterial/genetics , Diffusion of Innovation , Forecasting , High-Throughput Nucleotide Sequencing/trends , History, Ancient , Humans , Metagenomics/trends , Mycobacterium tuberculosis/genetics , Paleopathology/trends , Research Design/trends , South America , Tuberculosis/genetics , Tuberculosis/microbiology
3.
Int J Paleopathol ; 27: 1-8, 2019 12.
Article in English | MEDLINE | ID: mdl-31430635

ABSTRACT

OBJECTIVE: We assessed whether Petrus Donders (died 1887), a Dutch priest who for 27 years cared for people with leprosy in the leprosarium Batavia, Suriname, had evidence of Mycobacterium (M.) leprae infection. A positive finding of M. leprae ancient (a)DNA would contribute to the origin of leprosy in Suriname. MATERIALS: Skeletal remains of Father Petrus Donders; two additional skeletons excavated from the Batavia cemetery were used as controls. METHODS: Archival research, paleopathological evaluation and aDNA-based testing of skeletal remains. RESULTS: Neither archives nor inspection of Donders skeletal remains revealed evidence of leprosy, and aDNA-based testing for M. leprae was negative. We detected M. leprae aDNA by RLEP PCR in one control skeleton, which also displayed pathological lesions compatible with leprosy. The M. leprae aDNA was genotyped by Sanger sequencing as SNP type 4; the skeleton displayed mitochondrial haplogroup L3. CONCLUSION: We found no evidence that Donders contracted leprosy despite years of intense leprosy contact, but we successfully isolated an archaeological M. leprae aDNA sample from a control skeleton from South America. SIGNIFICANCE: We successfully genotyped recovered aDNA to a M. leprae strain that likely originated in West Africa. The detected human mitochondrial haplogroup L3 is also associated with this geographical region. This suggests that slave trade contributed to leprosy in Suriname. LIMITATIONS: A limited number of skeletons was examined. SUGGESTIONS FOR FURTHER RESEARCH: Broader review of skeletal collections is advised to expand on diversity of the M. leprae aDNA database.


Subject(s)
Cemeteries/history , DNA, Bacterial/genetics , Genome, Bacterial/genetics , Mycobacterium leprae/pathogenicity , Skeleton/microbiology , DNA, Bacterial/history , Genotype , History, 19th Century , Humans , Paleopathology/methods , Suriname
5.
PLoS One ; 13(5): e0196482, 2018.
Article in English | MEDLINE | ID: mdl-29768437

ABSTRACT

Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.


Subject(s)
Oral Health/history , DNA, Ancient/isolation & purification , DNA, Bacterial/genetics , DNA, Bacterial/history , DNA, Bacterial/isolation & purification , Dental Caries/history , Dental Caries/microbiology , Dental Caries/pathology , Female , France , Health Status , History, 18th Century , Humans , Male , Metagenomics , Microbiota/genetics , Paleodontology , Periodontitis/history , Periodontitis/microbiology , Periodontitis/pathology , Rural Population/history
6.
PLoS Pathog ; 14(5): e1006997, 2018 05.
Article in English | MEDLINE | ID: mdl-29746563

ABSTRACT

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.


Subject(s)
Leprosy/history , Mycobacterium leprae/genetics , DNA, Bacterial/genetics , DNA, Bacterial/history , Europe/epidemiology , Evolution, Molecular , Genetic Variation , Genome, Bacterial , History, Medieval , Host-Pathogen Interactions/genetics , Humans , Leprosy/epidemiology , Leprosy/microbiology , Mycobacterium leprae/classification , Mycobacterium leprae/pathogenicity , Phylogeny , Phylogeography , Polymorphism, Single Nucleotide
8.
Postepy Biochem ; 61(3): 256-9, 2015.
Article in Polish | MEDLINE | ID: mdl-26677572

ABSTRACT

Secretion of a metabolite enabling Streptococci to undergo genetic transformation was discovered. The metabolite combined with an optimization process were applied to increase the transformation yield about 20-fold. It was observed that large amounts of DNA exert a bactericidal effect, indicating the ability of at least 70% of cells to uptake the polymer. While studying the molecular mechanism of transformation of Bacillus subtilis it was shown that the uptaken DNA forms complexes with bacterial proteins, which hinders determination of its structure. A method was found to dissociate these complexes which enabled to determine the single-stranded structure of the uptaken DNA. Donor DNA fragments incorporated into the host DNA were of about 10 Da. Non-transforming DNA can be uptaken similarly but does not undergo incorporation into the host DNA. The selectivity of Bacillus subtilis receptors was determined towards DNA of phages containing modified bases: uracil, putrescinyl-thymine and its acetylated derivative, 5'-hydroxymethylcytosine and its glycosylated derivative and also towards double-stranded RNA of f2 phage. All these modifications were tolerated by the cellular receptors, with the exception of glycosylation and the 2'-OH group in RNA.


Subject(s)
DNA, Bacterial/history , Genetics/history , Transformation, Genetic , Bacillus/genetics , Bacteriophages/genetics , History, 20th Century , Poland , Streptococcus/genetics
9.
J Contemp Dent Pract ; 16(7): 588-94, 2015 07 01.
Article in English | MEDLINE | ID: mdl-26329415

ABSTRACT

BACKGROUND: Paleomicrobiology is a special branch of micropaleontology concerned with the study of bacterial fossils. We have used the term 'oral paleomicrobiology', as in this review we have focused on the ancient oral microflora. Recently, dental calculus and dental pulp have been identified as rich sources of ancient microbial DNA. Study of this ancient genetic material opens a new door to the ancient world. This review gives an overview of history of ancient DNA research, various techniques of analyzing ancient DNA in dental calculus and dental pulp, and the implications of the oral paleomicrobiology. MATERIALS AND METHODS: A comprehensive literature search was performed in the following databases-pubmed, medline and google scholar for studies published before 10 April, 2015. The following keywords were used- 'ancient DNA', 'ancient oral flora, 'oral paleomicrobiology' and 'oral microbiome', '16S rRNA sequencing'. To obtain additional data, a manual search was performed using the reference lists of selected articles. RESULT: As a result of literature search, 27 articles were found in pubmed, 12 in google scholar and one in medline. Eight more articles were selected from the reference list of selected articles. CONCLUSION: The combination of microbiology and paleontology has brought a revolution in the study of human evolution and microbial communities. The naturally well-preserved samples of microbial DNA from dental pulp and microbial colonies trapped in dental calculus are a potential source of microbial genetic material, which will prove invaluable in resolving mysteries of the past. This may be a beginning of a new era of oral paleomicrobiology, which will contribute in our studies about prevention of disease by establishing symbiosis between human beings and their microbiome.


Subject(s)
Dental Calculus/history , Microbiota , Paleodontology , DNA, Bacterial/history , Dental Calculus/microbiology , Dental Pulp/microbiology , History, Ancient , Humans , Paleontology
10.
Wien Med Wochenschr ; 165(7-8): 133-9, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25994097

ABSTRACT

Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable.


Subject(s)
Bone and Bones/microbiology , Bone and Bones/pathology , DNA, Bacterial/genetics , DNA, Bacterial/history , Museums/history , Paleopathology/history , Treponema pallidum/genetics , Treponemal Infections/genetics , Treponemal Infections/history , Austria , History, Ancient , Humans
11.
Infez Med ; 23(1): 83-93, 2015 Mar.
Article in Italian | MEDLINE | ID: mdl-25819058

ABSTRACT

The introduction of agriculture and animal husbandry at the end of the Mesolithic era, despite enabling a significant demographic growth through an increase in food storage and availability, caused new infectious noxae to enter the pathocoenosis. However in the Palaeolithic era, hunter-gatherers were already in contact with infectious diseases of animal origin, albeit episodically. Modern biomedical technologies allow us to estimate, with better approximation, how long mankind has been in contact with Mycobacterium tuberculosis. Archaeological finds, including human and animal remains (especially the aurochs), are particularly studied by palaeopathologists, as mycobacteria frequently cause bone involvement and this characteristic is of particular interest for palaeopathological (even macroscopic) studies; the interest is to detect the ancient DNA of MT, which is the cause of bone tuberculosis in skeletal remains as well as in mummies. According to our present knowledge, palaeopathological findings, confirmed by molecular techniques, suggest that tuberculosis in human skeletons goes back at most to 9000 years ago, while, in a veterinary environment, the most ancient DNA of MTBC to be detected in an American bison dates back about 17,000 years. The possibility of discovering archaeological finds making even more ancient human remains available leaves opens up the possibility of dating back to previous eras the transmission of MTBC infection to mankind. Phylogenetic works examining the available materials (DNAa) suggest that Mycobacterium tuberculosis, the cause of tuberculosis infection in humans and cattle (Aurochs), would have had a co-evolutionary process. On the basis of recent phylogenetic studies, the MTBC genome would have had a wide span of time to reach a suitable adjustment, co-evolving in geographical environments both at high and low host density. It is likely that the strains that did not show this strong "flexibility" underwent extinction, in favour of more versatile, adaptable strains, that are able to infect susceptible hosts "always" and in any environmental condition.


Subject(s)
Cattle Diseases/history , DNA, Bacterial/history , Emigration and Immigration/history , Genome, Bacterial , Medical Illustration/history , Mycobacterium tuberculosis , Tuberculosis/history , Africa , Ancient Lands , Animal Husbandry/history , Animals , Cattle , Cattle Diseases/microbiology , Cultural Evolution/history , History, 17th Century , History, 18th Century , History, 19th Century , History, 20th Century , History, 21st Century , History, Ancient , History, Medieval , Humans , Mycobacterium tuberculosis/genetics , North America , Paleopathology/history , Paleopathology/methods , Phylogeny , Phylogeography
12.
Philos Trans R Soc Lond B Biol Sci ; 370(1660): 20130622, 2015 Jan 19.
Article in English | MEDLINE | ID: mdl-25487341

ABSTRACT

The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.


Subject(s)
Bone and Bones/chemistry , DNA, Bacterial/genetics , Fossils , Mycobacterium tuberculosis/genetics , Paleopathology/methods , Real-Time Polymerase Chain Reaction/methods , DNA Primers/genetics , DNA, Bacterial/history , History, Ancient , Humans , Paleopathology/trends
13.
Wien Med Wochenschr ; 165(7-8): 126-32, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25007893

ABSTRACT

Leprosy used to be a widespread, dreaded disease in Europe during the middle ages, and it still remains an important health problem in some parts of the world today. Herein, we present data on the earliest 'Austrian' (an adult female from the early medieval period) proven to have suffered from leprosy. Manifestations of the disease were first identified during a systematic screening of pathological changes in skeletons recovered from an archaeological site in Pottenbrunn (Lower Austria). In the present study, DNA extracts from selected cranial and postcranial bone samples were investigated using polymerase chain reaction primers specific to the Mycobacterium leprae (M. leprae) repetitive element (RLEP). M. leprae traces were detected in extracts from nasal and palatine bones. Sequence analysis of informative polymorphic sites supports previous reports indicating that European M. leprae strains fall into single nucleotide polymorphism group 3. In summary, these findings put Austria on the map of confirmed leprosy cases in ancient Europe.


Subject(s)
DNA, Bacterial/history , Leprosy/genetics , Leprosy/history , Mycobacterium leprae/genetics , Polymorphism, Single Nucleotide/genetics , Adult , Australia , Female , History, Medieval , Humans
15.
Environ Microbiol ; 14(12): 3069-80, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22497633

ABSTRACT

In 1998, a cultivation-independent survey of the microbial community in Obsidian Pool, Yellowstone National Park, detected 12 new phyla within the Domain Bacteria. These were dubbed 'candidate divisions' OP1 to OP12. Since that time the OP10 candidate division has been commonly detected in various environments, usually as part of the rare biosphere, but occasionally as a predominant community component. Based on 16S rRNA gene phylogeny, OP10 comprises at least 12 class-level subdivisions. However, despite this broad ecological and evolutionary diversity, all OP10 bacteria have eluded cultivation until recently. In 2011, two reference species of OP10 were taxonomically validated, removing the phylum from its 'candidate' status. Construction of a highly resolved phylogeny based on 29 universally conserved genes verifies its standing as a unique bacterial phylum. In the following paper we summarize what is known and what is suspected about the newest described bacterial phylum, the Armatimonadetes.


Subject(s)
Bacteria, Anaerobic/classification , Phylogeny , RNA, Ribosomal, 16S/isolation & purification , Bacteria, Anaerobic/genetics , Bacteria, Anaerobic/isolation & purification , DNA, Bacterial/genetics , DNA, Bacterial/history , Genes, Bacterial/genetics , History, 20th Century , Hot Temperature , Hydrobiology/history , Sequence Analysis, DNA , Species Specificity , Water Microbiology , Wyoming
16.
Infect Genet Evol ; 12(4): 642-8, 2012 Jun.
Article in English | MEDLINE | ID: mdl-21896337

ABSTRACT

Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World.


Subject(s)
Tuberculosis/history , Brazil/epidemiology , DNA, Bacterial/history , DNA, Mitochondrial/history , History, 17th Century , Humans , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Nucleic Acid Hybridization , Tuberculosis/epidemiology
17.
Hist Philos Life Sci ; 33(1): 105-27, 2011.
Article in English | MEDLINE | ID: mdl-21789957

ABSTRACT

The chemical characterization of the substance responsible for the phenomenon of "transformation" of pneumococci was presented in the now famous 1944 paper by Avery, MacLeod, and McCarty. Reception of this work was mixed. Although interpreting their results as evidence that deoxyribonucleic acid (DNA) is the molecule responsible for genetic changes was, at the time, controversial, this paper has been retrospectively celebrated as providing such evidence. The mixed and changing assessment of the evidence presented in the paper was due to the work's interpretive flexibility--the evidence was interpreted in various ways, and such interpretations were justified given the neophytic state of molecular biology and methodological limitations of Avery's transformation studies. I argue that the changing context in which the evidence presented by Avery's group was interpreted partly explains the vicissitudes of the assessments of the evidence. Two less compelling explanations of the reception are a myth-making account and an appeal to the wartime historical context of its publication.


Subject(s)
DNA/history , Genetics/history , Bacteriology/history , DNA, Bacterial/history , History, 20th Century , Streptococcus pneumoniae/genetics , Transformation, Bacterial , United States
18.
Homo ; 62(3): 165-83, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21530965

ABSTRACT

The distribution, antiquity and epidemiology of tuberculosis (TB) have previously been studied in osteoarchaeological material in the eastern part of Hungary, mainly on the Great Plain. The purpose of this study is to map the occurrence of skeletal TB in different centuries in the western part of Hungary, Transdanubia, and to present new cases we have found. Palaeopathological analysis was carried out using macroscopic observation supported by radiographic and molecular methods. A large human osteoarchaeological sample (n=5684) from Transdanubian archaeological sites ranging from the 2nd to the 18th centuries served as a source of material. Spinal TB was observed in seven individuals (in three specimens with Pott's disease two of which also had cold abscess) and hip TB was assumed in one case. The results of DNA for Mycobacterium tuberculosis were positive in seven of the eight cases identified by paleopathology, and negative in the assumed case of hip TB. However, the molecular results are consistent with highly fragmented DNA, which limited further analysis. Based on the present study and previously published cases, osteotuberculosis was found in Transdanubia mainly during the 9th-13th centuries. However, there are no signs of TB in many other 9th-13th century sites, even in those that lie geographically close to those where osteotuberculous cases were found. This may be due to a true absence of TB caused by the different living conditions, way of life, or origin of these populations. An alternative explanation is that TB was present in some individuals with no typical paleopathology, but that death occurred before skeletal morphological features could develop.


Subject(s)
Tuberculosis, Osteoarticular/history , Base Sequence , DNA Primers/genetics , DNA, Bacterial/genetics , DNA, Bacterial/history , DNA, Bacterial/isolation & purification , Fossils , History, 15th Century , History, 16th Century , History, 17th Century , History, 18th Century , History, Ancient , History, Medieval , Humans , Hungary , Molecular Sequence Data , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Paleopathology , Tuberculosis, Osteoarticular/microbiology , Tuberculosis, Osteoarticular/pathology , Tuberculosis, Spinal/history , Tuberculosis, Spinal/microbiology , Tuberculosis, Spinal/pathology
19.
Protein Cell ; 1(1): 14-21, 2010 Jan.
Article in English | MEDLINE | ID: mdl-21203994

ABSTRACT

Here we tell a 20-year long story. It began with an easily overlooked DNA degradation (Dnd) phenomenon during electrophoresis and eventually led to the discovery of an unprecedented DNA sulfur modification governed by five dnd genes. This unusual DNA modification, called phosphorothioation, is the first physiological modification identified on the DNA backbone, in which the nonbridging oxygen is replaced by sulfur in a sequence selective and stereo-specific manner. Homologous dnd gene clusters have been identified in diverse and distantly related bacteria and thus have drawn immediate attention of the entire microbial scientific community. Here, we summarize the progress in chemical, genetic, enzymatic, bioinformatical and analytical aspects of this novel postreplicative DNA modification. We also discuss perspectives on the physiological functions of the DNA phosphorothioate modification in bacteria and their implications.


Subject(s)
Bacteria/metabolism , DNA, Bacterial/metabolism , Sulfur/metabolism , Bacteria/genetics , DNA, Bacterial/chemistry , DNA, Bacterial/history , Genes, Bacterial , History, 20th Century , History, 21st Century , Multigene Family , Streptomyces lividans/genetics , Streptomyces lividans/metabolism , Sulfur/chemistry , Sulfur/history
20.
Adv Exp Med Biol ; 603: 327-38, 2007.
Article in English | MEDLINE | ID: mdl-17966429

ABSTRACT

The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR analysis can provide a very powerful typing tool, adapted to the systematic, large-scale genotyping of Y. pestis isolates, and the creation of international typing databases. In addition, CRISPRs do constitute a very promising new tool and genetic target to investigate ancient DNA. The corresponding genetic targets are small (<70bp), present in multiple copies (usually more than 10), highly conserved and specific. In addition, the assay can be run in any laboratory. Interpretation of the data is not dependent on accurate sequence data.


Subject(s)
DNA, Bacterial/genetics , DNA, Bacterial/history , Plague/history , Yersinia pestis/genetics , Base Sequence , Disease Outbreaks/history , Evolution, Molecular , Genes, Bacterial , History, Ancient , Humans , Interspersed Repetitive Sequences , Molecular Sequence Data , Phylogeny , Plague/epidemiology , Plague/microbiology , Species Specificity , Yersinia pestis/classification , Yersinia pestis/pathogenicity , Yersinia pseudotuberculosis/classification , Yersinia pseudotuberculosis/genetics
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